844 Matching Annotations
  1. Jan 2021
    1. Tag: marginalia An Outline for Using Hypothesis for Owning your Annotations and Highlights

    1. 2. Worms A worm is similar to a virus; the difference is that worms spread on their own instead of attaching to a program and infecting it and others. A lot of the time, worms spread over a network, exploiting a vulnerability to jump from machine to machine. As they continue to recursively spread, worms infect machines at a faster rate. This wastes the network's bandwidth at a minimum, while nastier worms can spread ransomware or other problems across an entire business network.

      AAAAA

    2. 10. Exploits and Vulnerabilities While not a form of malware, exploits and vulnerabilities are important terms in online security. Because no programmer or software is perfect, every program, OS, and website has some kind of vulnerability. Malicious actors work to find these flaws so they can exploit them to run malware or similar. advertising function refreshcontentwordcount9(){ if(contentwordcount9Changed == 'false'){ googletag.cmd.push(function(){ googletag.pubads().refresh([contentwordcount9]); googletag.display('div-gpt-ad-1555342976270-7'); }); contentwordcount9Changed = 'true'; }; }; For example, say someone discovered a bug that let you create a new admin account with no password in Windows by following certain steps. Someone could write malware to run these steps on someone's PC, get admin access, and then wreak havoc. The best way to stay safe from these threats is keeping your OS and all software up-to-date. Developers patch these problems as they find them, so staying on the latest version keeps you safe from old and known exploits.

      WWWWW

    3. 8. Rootkit A rootkit (a term which merges the admin "root" account on Unix systems and the "kit" they use) is a type of malware that gains access to restricted parts of a computer and then disguises or otherwise hides itself. Typically, a rootkit gets installed when the attacker has admin (or root) access to a machine. Once the rootkit is installed, it has privileges to do whatever the owner wants on the system. Rootkits abuse this to hide their intrusion—for example, it might cloak its presence from the installed antivirus app. Obviously, a piece of malware having complete control over your system is quite dangerous. A lot of the time, you'll have to completely reinstall the OS to get rid of a rootkit.

      SSSSS

    4. 5. Spyware Spyware is another type of malware that can take several forms. It refers to programs that track your computer usage for some purpose and reports it back to an entity. Most programs—and even operating systems like Windows 10—collect data about your usage and report it back to the developer. They use this to improve their tools with real-world data. Proper spyware is distinguished by the fact that it collects this data without letting the user know. advertising function refreshcontentwordcount5(){ if(contentwordcount5Changed == 'false'){ googletag.cmd.push(function(){ googletag.pubads().refresh([contentwordcount5]); googletag.display('div-gpt-ad-1555342976270-3'); }); contentwordcount5Changed = 'true'; }; }; While spyware often collects your data for advertising purposes, nastier spyware can also collect sensitive information like login credentials. Extreme spyware includes keyloggers, which are programs that record every keystroke you make on your machine.

      DDD

    1. Utterly encapsulating gapless dark ambient experience.

      Now there's a touchstone for the ages

    2. Terrifying in its bleakness, Elegy is a record dedicated to its portrayal of loneliness, telling a story with firm roots in tension contextualised by the title’s disheartening implications.

      A dedicated sponge in the blank countenance of empty space and flat time, I'd say.

  2. Dec 2020
    1. 2.3.1. Mail Objects SMTP transports a mail object. A mail object contains an envelope and content. The SMTP envelope is sent as a series of SMTP protocol units (described in Section 3). It consists of an originator address (to Klensin Standards Track [Page 11] RFC 5321 SMTP October 2008 which error reports should be directed), one or more recipient addresses, and optional protocol extension material

      The SMTP envelope is sent as a series of SMTP protocol units (described in Section 3). It consists of

      • an originator address (to which error reports should be directed),

      MAIL FROM that refers to the originator (a.k.a., reverse path, backward-pointing address) of the request

      • one or more recipient addresses,

      Multiple RCPT TO for each "to:" rfc822 message header in the mail data (see annotation)

      • and optional protocol extension material.

      DATA (see below)


      (See also envelope-vs-mail tags.)

    1. There's a bug in Hypothesis (at least the sidebar client) such that it's possible to post annotations with comments to the the public, but if you want to highlight something and make it similarly public, then it's not possible...

      I'm using this tag as a workaround. The annotation comment should be a Markdown-style quote (i.e. set off by an ASCII right-pointing angle bracket / less-than sign).

  3. Nov 2020
    1. Anthony Tattersal

      I suggest to add a link to his biography or any other link that tells the reader who he is

    1. By keeping the price of ebooks high, publishers keep paperbacks as a valid option for readers. That way, the world of physical books isn't under threat of becoming extinct due to ebooks.

      Do you like this reason?

    2. If you're an avid reader, you may know the pain of losing or damaging your books. Ebooks, however, don't share this problem.

      How long do ebooks last?

      Has one of your ebooks ever become damaged?

      Have you ever lost an ebook?

    3. On top of this, ebooks are very convenient for the readers buying them. Buying a physical book involves going to a bookstore and hoping they have it in stock, or ordering it online and waiting for it to arrive. For ebooks, you go to a website, click the "Buy" button, and download the book to your PC or reader.

      Are people willing to pay for convenience?

    4. This constraint is the reason ebooks sometimes cost more than paperbacks. For example, a publisher can list the price of their physical book at $27.95 and the ebook at $20, which is a reasonable 30 percent markdown.

      Explain why ebooks sometimes cost more than physical books.

    5. Unlike with physical books, Amazon has no control over the price of ebooks. If someone has performed the steps required to publish an ebook via Kindle Direct Publishing, they set the price as they please, with no exceptions.

      Do you think this is true for authors who don't have a following?

    6. However, ebooks utilize the agency model when sold. Instead of letting the retailer choose the price, the publisher states what they're selling for. The publisher gets 70 percent of each transaction, and the retailer gets the remaining 30 percent.

      How is the pricing system for ebooks different from the one for physical books?

    7. Everything makes sense when you imagine all of the people who helped make the book who need paying. For one, the author has to get their agreed royalty cut from every sale. From there, the editors, proofreaders, cover artists, and marketers all need to be paid. These obligations don't leave the publisher with a lot of money for themselves.

      Who else needs to be paid besides just the author?

    8. a physical book takes around $1-2 to produce. If this is true, however, then why are they priced a lot more than that?

      Does this surprise you?

    1. Oh, and from a language/design perspective, you can actually turn regular words in a sentence into channels, just as many people do with @replies. For example: I’m coming to #barcamp later today.

      Because the use of hashtags is inline and you can turn regular words into hashtags (and therefor channels), there is no friction to do so.

    2. It also enforces actual use in the wild of tags, since no evidence of a tag will exist without it first being used in conversation. This means that representing channels in tagclouds across the site that grow and fade over time, and are contextual to all of Twitter or to a single user, is the ideal interface for displaying this information.

      Hashtags have the added benefit that they won't show up for others if they're not used.

      If you look at which hashtags are being used (trending), you get a taxonomy of micro-contexts, ranked by popularity, with which you can navigate Twitter. All from the bottom up.

    3. I also like that the folksonomic approach (as in, there are no “pre-established groups”) allows for a great deal of expression, of negotiation (I imagine that #barcamp will be a common tag between events, but that’s fine, since if there is a collision, say between two separate BarCamps on the same day, they’ll just have to socially engineer a solution and probably pick a new tag, like #barcampblock) and of decay (that is, over time, as tags are used less frequently, other people can reuse them — no domain squatting!).

      The folksonomic approach (user-generated tagging) is beneficial because it allows complexity to emerge bottom-up.

    4. Every time someone uses a channel tag to mark a status, not only do we know something specific about that status, but others can eavesdrop on the context of it and then join in the channel and contribute as well. Rather than trying to ping-pong discussion between one or more individuals with daisy-chained @replies, using a simple #reply means that people not in the @reply queue will be able to follow along, as people do with Flickr or Delicious tags. Furthermore, topics that enter into existing channels will become visible to those who have previously joined in the discussion. And, perhaps best of all, anyone can choose to leave or remove topics that don’t interest them.

      Twitter's hashtags form a dual purpose. They label a status with a certain tag, telling us something about the intended context of that Tweet.

      The ease of which makes it frictionless for anyone to jump into the conversation.

      But they also equip an interested eavesdropper with the ability to follow along with a conversation. This idea (at the time this was being discussed at Twitter) was already happening with Flickr and Delicious tags.

    5. This is how it works in IRC, and how it needed to work in Twitter.

      The idea of:

      When you use a hastag and the channel with that name doesn't exist, it gets created, is an idea that came from IRC.

    6. Now, in thinking about implementing channels, it was imperative that I not introduce any significant changes into the way that I currently use Twitter any more than I have for other features that have been added to Twitter (for example, @replies or direct messages). Channels would need to be a command-line-friendly addition, and one that would require absolutely zero web-based management to make the most of it (to draw a distinction, Pownce fails this test with its Friend Sets, since it requires use of their website to take advantage of this feature).

      The requirements [[Joe Messina]] laid out for a concept of "channels" on Twitter was that:

      1. It shouldn't add any friction to his current use
      2. It shouldn't require any web-based management to make the most of

      Twitter of 2020 satisfies these requirements. You just type #something, and you can click on that hash or search for it to see results.

    7. Jaiku comes closest with their channels implementation, making it extremely easy to create new channels (simply post a message that begins with a hash (#) and your intended channel name — and if the channel doesn’t exist, it’ll be created for you):

      [[Joe Messina]] details an example from [[Jaiku]] where you can create a channel by simply posting a message that starts with a hash (#). If the channel doesn't exist, it will be created for you.

    8. I’m more interested in simply having a better eavesdropping experience on Twitter.

      [[Joe Messina]]'s reason for suggesting the hashtag was his interest in having "better eavesdropping experience on Twitter"

  4. Oct 2020
    1. Curso_HDCICAFCUNAM

      Curso Habilidades digitales y competencias informacionales para ciencias 2020

      FACULTAD DE CIENCIAS, UNAM

      Layla Michán

    1. Author Response

      Reviewer #1:

      Hutchings et al. report an updated cryo-electron tomography study of the yeast COP-II coat assembled around model membranes. The improved overall resolution and additional compositional states enabled the authors to identify new domains and interfaces--including what the authors hypothesize is a previously overlooked structural role for the SEC31 C-Terminal Domain (CTD). By perturbing a subset of these new features with mutants, the authors uncover some functional consequences pertaining to the flexibility or stability of COP-II assemblies.

      Overall, the structural and functional work appears reliable, but certain questions and comments should be addressed prior to publication. However, this reviewer failed to appreciate the conceptual advance that warrants publication in a general biology journal like eLIFE. Rather, this study provides a valuable refinement of our understanding of COP-II that I believe is better suited to a more specialized, structure-focused journal.

      We agree that in our original submission our description of the experimental setup, indeed similar to previous work, did not fully capture the novel findings of this paper. Rather than being simply a higher resolution structure of the COPII coat, in fact we have discovered new interactions in the COPII assembly network, and we have probed their functional roles, significantly changing our understanding of the mechanisms of COPII-mediated membrane curvature. In the revised submission we have included additional genetic data that further illuminate this mechanism, and have rewritten the text to better communicate the novel aspects of our work.

      Our combination of structural, functional and genetic analyses goes beyond refining our textbook understanding of the COPII coat as a simple ‘adaptor and cage’, but rather it provides a completely new picture of how dynamic regulation of assembly and disassembly of a complex network leads to membrane remodelling.

      These new insights have important implications for how coat assembly provides structural force to bend a membrane but is still able to adapt to distinct morphologies. These questions are at the forefront of protein secretion, where there is debate about how different types of carriers might be generated that can accommodate cargoes of different size.

      Major Comments: 1) The authors belabor what this reviewer thinks is an unimportant comparison between the yeast reconstruction of the outer coat vertex with prior work on the human outer coat vertex. Considering the modest resolution of both the yeast and human reconstructions, the transformative changes in cryo-EM camera technology since the publication of the human complex, and the differences in sample preparation (inclusion of the membrane, cylindrical versus spherical assemblies, presence of inner coat components), I did not find this comparison informative. The speculations about a changing interface over evolutionary time are unwarranted and would require a detailed comparison of co-evolutionary changes at this interface. The simpler explanation is that this is a flexible vertex, observed at low resolution in both studies, plus the samples are very different.

      We do agree that our proposal that the vertex interface changes over evolutionary time is speculative and we have removed this discussion. We agree that a co-evolutionary analysis will be enlightening here, but is beyond the scope of the current work.

      We respectfully disagree with the reviewer’s interpretation that the difference between the two vertices is due to low resolution. The interfaces are clearly different, and the resolutions of the reconstructions are sufficient to state this. The reviewer’s suggestion that the difference in vertex orientation might be simply attributable to differences in sample, such as inclusion of the membrane, cylindrical versus spherical morphology, or presence of inner coat components were ruled out in our original submission: we resolved yeast vertices on spherical vesicles (in addition to those on tubes) and on membrane-less cages. These analyses clearly showed that neither the presence of a membrane, nor the change in geometry (tubular vs. spherical) affect vertex interactions. These experiments are presented in Supplementary Fig 4 (Supplementary Fig. 3 in the original version). Similarly, we discount that differences might be due to the presence or absence of inner coat components, since membrane-less cages were previously solved in both conditions and are no different in terms of their vertex structure (Stagg et al. Nature 2006 and Cell 2008).

      We believe it is important to report on the differences between the two vertex structures. Nevertheless, we have shifted our emphasis on the functional aspects of vertex formation and moved the comparison between the two vertices to the supplement.

      2) As one of the major take home messages of the paper, the presentation and discussion of the modeling and assignment of the SEC31-CTD could be clarified. First, it isn't clear from the figures or the movies if the connectivity makes sense. Where is the C-terminal end of the alpha-solenoid compared to this new domain? Can the authors plausibly account for the connectivity in terms of primary sequence? Please also include a side-by-side comparison of the SRA1 structure and the CTD homology model, along with some explanation of the quality of the model as measured by Modeller. Finally, even if the new density is the CTD, it isn't clear from the structure how this sub-stoichiometric and apparently flexible interaction enhances stability. Hence, when the authors wrote "when the [CTD] truncated form was the sole copy of Sec31 in yeast, cells were not viable, indicating that the novel interaction we detect is essential for COPII coat function." Maybe, but could this statement be a leap to far? Is it the putative interaction essential, or is the CTD itself essential for reasons that remain to be fully determined?

      The CTD is separated from the C-terminus of the alpha solenoid domain by an extended domain (~350 amino acids) that is predicted to be disordered, and contains the PPP motifs and catalytic fragment that contact the inner coat. This is depicted in cartoon form in Figures 3A and 7, and discussed at length in the text. This arrangement explains why no connectivity is seen, or expected. We could highlight the C-terminus of the alpha-solenoid domain to emphasize where the disordered region should emerge from the rod, but connectivity of the disordered domain to the CTD could arise from multiple positions, including from an adjacent rod.

      The reviewer’s point about the essentiality of the CTD being independent of its interaction with the Sec31 rod, is an important one. The basis for our model that the CTD enhances stability or rigidity of the coat is the yeast phenotype of Sec31-deltaCTD, which resembles that of a sec13 null. Both mutants are lethal, but rescued by deletion of emp24, which leads to more easily deformable membranes (Čopič et al. Science 2012). We agree that even if this model is true, the interaction of the CTD with Sec31 that our new structure reveals is not proven to drive rigidity or essentiality. We have tempered this hypothesis and added alternative possibilities to the discussion.

      We have included the SRA1 structure in Supplementary Fig 5, as requested, and the model z-score in the Methods. The Z-score, as calculated by the proSA-web server is -6.07 (see figure below, black dot), and falls in line with experimentally determined structures including that of the template (PDB 2mgx, z-score = -5.38).

      img

      3) Are extra rods discussed in Fig. 4 are a curiosity of unclear functional significance? This reviewer is concerned that these extra rods could be an in vitro stoichiometry problem, rather than a functional property of COP-II.

      This is an important point, that, as we state in the paper, cannot be answered at the moment: the resolution is too low to identify the residues involved in the interaction. Therefore we are hampered in our ability to assess the physiological importance of this interaction. We still believe the ‘extra’ rods are an important observation, as they clearly show that another mode of outer coat interaction, different from what was reported before, is possible.

      The concern that interactions visualised in vitro might not be physiologically relevant is broadly applicable to structural biology approaches. However, our experimental approach uses samples that result from active membrane remodelling under near-physiological conditions, and we therefore expect these to be less prone to artefacts than most in vitro reconstitution approaches, where proteins are used at high concentrations and in high salt buffer conditions.

      4) The clashsccore for the PDB is quite high--and I am dubious about the reliability of refining sidechain positions with maps at this resolution. In addition to the Ramchandran stats, I would like to see the Ramachandran plot as well as, for any residue-level claims, the density surrounding the modeled side chain (e.g. S742).

      The clashscore is 13.2, which, according to molprobity, is in the 57th percentile for all structures and in the 97th for structures of similar resolutions. We would argue therefore that the clashscore is rather low. In fact, the model was refined from crystal structures previously obtained by other groups, which had worse clashscore (17), despite being at higher resolution. Our refinement has therefore improved the clashscore. During refinement we have chosen restraint levels appropriate to the resolution of our map (Afonine et al., Acta Cryst D 2018)

      The Ramachandran plot is copied here and could be included in a supplemental figure if required. We make only one residue-level claim (S742), the density for which is indeed not visible at our resolution. We claim that S742 is close to the Sec23-23 interface, and do not propose any specific interactions. Nevertheless we have removed reference to S742 from the manuscript. We included this specific information because of the potential importance of this residue as a site of phosphorylation, thereby putting this interface in broader context for the general eLife reader.

      img

      Minor Comments:

      1) The authors wrote "To assess the relative positioning of the two coat layers, we analysed the localisation of inner coat subunits with respect to each outer coat vertex: for each aligned vertex particle, we superimposed the positions of all inner coat particles at close range, obtaining the average distribution of neighbouring inner coat subunits. From this 'neighbour plot' we did not detect any pattern, indicating random relative positions. This is consistent with a flexible linkage between the two layers that allows adaptation of the two lattices to different curvatures (Supplementary Fig 1E)." I do not understand this claim, since the pattern both looks far from random and the interactions depend on molecular interactions that are not random. Please clarify.

      We apologize for the confusion: the pattern of each of the two coats are not random. Our sentence refers to the positions of inner and outer coats relative to each other. The two lattices have different parameters and the two layers are linked by flexible linkers (the 350 amino acids referred to above). We have now clarified the sentence.

      2) Related to major point #1, the author wrote "We manually picked vertices and performed carefully controlled alignments." I do now know what it means to carefully control alignments, and fear this suggests human model bias.

      We used different starting references for the alignments, with the precise aim to avoid model bias. For both vesicle and cage vertex datasets, we have aligned the subtomograms against either the vertex obtained from tubules, or the vertex from previously published membrane-less cages. In all cases, we retrieved a structure that resembles the one on tubules, suggesting that the vertex arrangement we observe isn’t simply the result of reference bias. This procedure is depicted in Supplementary Fig 4 (Supplementary Fig. 3 in the original manuscript), but we have now clarified it also in the methods section.

      3) Why do some experiments use EDTA? I may be confused, but I was surprised to see the budding reaction employed 1mM GMPPNP, and 2.5mM EDTA (but no Magnesium?). Also, for the budding reaction, please replace or expand upon the "the 10% GUV (v/v)" with a mass or molar lipid-to-protein ratio.

      We regret the confusion. As stated in the methods, all our budding reactions are performed in the presence of EDTA and Magnesium, which is present in the buffer (at 1.2 mM). The reason is to facilitate nucleotide exchange, as reported and validated in Bacia et al., Scientific Reports 2011.

      Lipids in GUV preparations are difficult to quantify. We report the stock concentrations used, but in each preparation the amount of dry lipid that forms GUVs might be different, as is the concentration of GUVs after hydration. However since we analyse reactions where COPII proteins have bound and remodelled individual GUVs, we do not believe the protein/lipid ratio influences our structures.

      4) Please cite the AnchorMap procedure.

      We cite the SerialEM software, and are not aware of other citations specifically for the anchor map procedure.

      5) Please edit for typos (focussing, functionl, others)

      Done

      Reviewer #2:

      The manuscript describes new cryo-EM, biochemistry, and genetic data on the structure and function of the COPII coat. Several new discoveries are reported including the discovery of an extra density near the dimerization region of Sec13/31, and "extra rods" of Sec13/31 that also bind near the dimerization region. Additionally, they showed new interactions between the Sec31 C-terminal unstructured region and Sec23 that appear to bridge multiple Sec23 molecules. Finally, they increased the resolution of the Sec23/24 region of their structure compared to their previous studies and were able to resolve a previously unresolved L-loop in Sec23 that makes contact with Sar1. Most of their structural observations were nicely backed up with biochemical and genetic experiments which give confidence in their structural observations. Overall the paper is well-written and the conclusions justified.

      However, this is the third iteration of structure determination of the COPII coat on membrane with essentially the same preparation and methods. Each time, there has been an incremental increase in resolution and new discoveries, but the impact of the present study is deemed to be modest. The science is good, but it may be more appropriate for a more specialized journal. Areas of specific concern are described below.

      As described above, we respectfully disagree with this interpretation of the advance made by the current work. This work improves on previous work in many aspects. The resolution of the outer coat increases from over 40A to 10-12A, allowing visualisation of features that were not previously resolved, including a novel vertex arrangement, the Sec31 CTD, and the outer coat ‘extra rods’. An improved map of the inner coat also allows us to resolve the Sec23 ‘L-loop’. We would argue that these are not just extra details, but correspond to a suite of novel interactions that expand our understanding of the complex COPII assembly network. Moreover, we include biochemical and genetic experiments that not only back up our structural observations but bring new insights into COPII function. As pointed out in response to reviewer 1, we believe our work contributes a significant conceptual advance, and have modified the manuscript to convey this more effectively.

      1) The abstract is vague and should be re-written with a better description of the work.

      We have modified the abstract to specifically outline what we have done and the major new discoveries of this paper.

      2) Line 166 - "Surprisingly, this mutant was capable of tubulating GUVs". This experiment gets to one of the fundamental unknown questions in COPII vesiculation. It is not clear what components are driving the membrane remodeling and at what stages during vesicle formation. Isn't it possible that the tubulation activity the authors observe in vitro is not being driven at all by Sec13/31 but rather Sec23/24-Sar1? Their Sec31ΔCTD data supports this idea because it lacks a clear ordered outer coat despite making tubules. An interesting experiment would be to see if tubules form in the absence of all of Sec13/31 except the disordered domain of Sec31 that the authors suggest crosslinks adjacent Sec23/24s.

      This is an astute observation, and we agree with the reviewer that the source of membrane deformation is not fully understood. We favour the model that budding is driven significantly by the Sec23-24 array. To further support this, we have performed a new experiment, where we expressed Sec31ΔN in yeast cells lacking Emp24, which have more deformable membranes and are tolerant to the otherwise lethal deletion of Sec13. While Sec31ΔN in a wild type background did not support cell viability, this was rescued in a Δemp24 yeast strain, strongly supporting the hypothesis that a major contributor to membrane remodelling is the inner coat, with the outer coat becoming necessary to overcome membrane bending resistance that ensues from the presence of cargo. We now include these results in Figure 1.

      However, we must also take into account the results presented in Fig. 6, where we show that weakening the Sec23-24 interface still leads to budding, but only if Sec13-31 is fully functional, and that in this case budding leads to connected pseudo-spherical vesicles rather than tubes. When Sec13-31 assembly is also impaired, tubes appear unstructured. We believe this strongly supports our conclusions that both inner and outer coat interactions are fundamental for membrane remodelling, and it is the interplay between the two that determines membrane morphology (i.e. tubes vs. spheres).

      To dissect the roles of inner and outer coats even further, we have done the experiment that the reviewer suggests: we expressed Sec31768-1114, but the protein was not well-behaved and co-purified with chaperones. We believe the disordered domain aggregates when not scaffolded by the structured elements of the rod. Nonetheless, we used this fragment in a budding reaction, and could not see any budding. We did not include this experiment as it was inconclusive: the lack of functionality of the purified Sec31 fragment could be attributed to the inability of the disordered region to bind its inner coat partner in the absence of the scaffolding Sec13-31 rod. As an alternative approach, we have used a version of Sec31 that lacks the CTD, and harbours a His tag at the N-terminus (known from previous studies to partially disrupt vertex assembly). We think this construct is more likely to be near native, since both modifications on their own lead to functional protein. We could detect no tubulation with this construct by negative stain, while both control constructs (Sec31ΔCTD and Nhis-Sec31) gave tubulation. This suggests that the cross-linking function of Sec31 is not sufficient to tubulate GUV membranes, but some degree of functional outer coat organisation (either mediated by N- or C-terminal interactions) is needed. It is also possible that the lack of outer coat organisation might lead to less efficient recruitment to the inner coat and cross-linking activity. We have added this new observation to the manuscript.

      3) Line 191 - "Inspecting cryo-tomograms of these tubules revealed no lozenge pattern for the outer 192 coat" - this phrasing is vague. The reviewer thinks that what they mean is that there is a lack of order for the Sec13/31 layer. Please clarify.

      The reviewer is correct, we have changed the sentence.

      4) Line 198 - "unambiguously confirming this density corresponds to 199 the CTD." This only confirms that it is the CTD if that were the only change and the Sec13/31 lattice still formed. Another possibility is that it is density from other Sec13/31 that only appears when the lattice is formed such as the "extra rods". One possibility is that the density is from the extra rods. The reviewer agrees that their interpretation is indeed the most likely, but it is not unambiguous. The authors should consider cross-linking mass spectrometry.

      We have removed the word ‘unambiguously’, and changed to ‘confirming that this density most likely corresponds to the CTD’. Nonetheless, we believe that our interpretation is correct: the extra rods bind to a different position, and themselves also show the CTD appendage. In this experiment, the lack of the CTD was the only biochemical change.

      5) In the Sec31ΔCTD section, the authors should comment on why ΔCTD is so deleterious to oligomer organization in yeast when cages form so abundantly in preparations of human Sec13/31 ΔC (Paraan et al 2018).

      We have added a comment to address this. “Interestingly, human Sec31 proteins lacking the CTD assemble in cages, indicating that either the vertex is more stable for human proteins and sufficient for assembly, or that the CTD is important in the context of membrane budding but not for cage formation in high salt conditions.”

      6) The data is good for the existence of the "extra rods", but significance and importance of them is not clear. How can these extra densities be distinguished from packing artifacts due to imperfections in the helical symmetry.

      Please also see our response to point 3 from reviewer 1. Regarding the specific concern that artefacts might be a consequence of imperfection in the helical symmetry, we would argue such imperfections are indeed expected in physiological conditions, and to a much higher extent. For this reason interactions seen in the context of helical imperfections are likely to be relevant. In fact, in normal GTP hydrolysis conditions, we expect long tubes would not be able to form, and the outer coat to be present on a wide range of continuously changing membrane curvatures. We think that the ability of the coat to form many interactions when the symmetry is imperfect might be exactly what confers the coat its flexibility and adaptability.

      7) Figure 5 is very hard to interpret and should be redone. Panels B and C are particularly hard to interpret.

      We have made a new figure where we think clarity is improved.

      8) The features present in Sec23/24 structure do not reflect the reported resolution of 4.7 Å. It seems that the resolution is overestimated.

      We report an average resolution of 4.6 Å. In most of our map we can clearly distinguish beta strands, follow the twist of alpha helices and see bulky side chains. These features typically become visible at 4.5-5A resolution. We agree that some areas are worse than 4.6 Å, as typically expected for such a flexible assembly, but we believe that the average resolution value reported is accurate. We obtained the same resolution estimate using different software including relion, phenix and dynamo, so that is really the best value we can provide. To further convince ourselves that we have the resolution we claim, we sampled EM maps from the EMDB with the same stated resolution (we just took the 7 most recent ones which had an associated atomic model), and visualised their features at arbitrary positions. For both beta strands and alpha helices, we do not feel our map looks any worse than the others we have examined. We include a figure here.

      img

      9) Lines 315/316 - "We have combined cryo-tomography with biochemical and genetic assays to obtain a complete picture of the assembled COPII coat at unprecedented resolution (Fig. 7)"

      10) Figure 7. is a schematic model/picture the authors should reference a different figure or rephrase the sentence.

      We now refer to Fig 7 in a more appropriate place.

      Reviewer #3:

      The manuscript by Hutchings et al. describes several previously uncharacterised molecular interactions in the coats of COP-II vesicles by using a reconstituted coats of yeast COPI-II. They have improved the resolution of the inner coat to 4.7A by tomography and subtomogram averaging, revealing detailed interactions, including those made by the so-called L-loop not observed before. Analysis of the outer layer also led to new interesting discoveries. The sec 31 CTD was assigned in the map by comparing the WT and deletion mutant STA-generated density maps. It seems to stabilise the COP-II coats and further evidence from yeast deletion mutants and microsome budding reconstitution experiments suggests that this stabilisation is required in vitro. Furthermore, COP-II rods that cover the membrane tubules in right-handed manner revealed sometimes an extra rod, which is not part of the canonical lattice, bound to them. The binding mode of these extra rods (which I refer to here a Y-shape) is different from the canonical two-fold symmetric vertex (X-shape). When the same binding mode is utilized on both sides of the extra rod (Y-Y) the rod seems to simply insert in the canonical lattice. However, when the Y-binding mode is utilized on one side of the rod and the X-binding mode on the other side, this leads to bridging different lattices together. This potentially contributes to increased flexibility in the outer coat, which maybe be required to adopt different membrane curvatures and shapes with different cargos. These observations build a picture where stabilising elements in both COP-II layers contribute to functional cargo transport. The paper makes significant novel findings that are described well. Technically the paper is excellent and the figures nicely support the text. I have only minor suggestions that I think would improve the text and figure.

      We thank the reviewer for helpful suggestions which we agree improve the manuscript.

      Minor Comments:

      L 108: "We collected .... tomograms". While the meaning is clear to a specialist, this may sound somewhat odd to a generic reader. Perhaps you could say "We acquired cryo-EM data of COP-II induced tubules as tilt series that were subsequently used to reconstruct 3D tomograms of the tubules."

      We have changed this as suggested

      L 114: "we developed an unbiased, localisation-based approach". What is the part that was developed here? It seems that the inner layer particle coordinates where simply shifted to get starting points in the outer layer. Developing an approach sounds more substantial than this. Also, it's unclear what is unbiased about this approach. The whole point is that it's biased to certain regions (which is a good thing as it incorporates prior knowledge on the location of the structures).

      We have modified the sentence to “To target the sparser outer coat lattice for STA, we used the refined coordinates of the inner coat to locate the outer coat tetrameric vertices”, and explain the approach in detail in the methods.

      L 124: "The outer coat vertex was refined to a resolution of approximately ~12 A, revealing unprecedented detail of the molecular interactions between Sec31 molecules (Supplementary Fig 2A)". The map alone does not reveal molecular interactions; the main understanding comes from fitting of X-ray structures to the low-resolution map. Also "unprecedented detail" itself is somewhat problematic as the map of Noble et al (2013) of the Sec31 vertex is also at nominal resolution of 12 A. Furthermore, Supplementary Fig 2A does not reveal this "unprecedented detail", it shows the resolution estimation by FSC. To clarify, these points you could say: "Fitting of the Sec31 atomic model to our reconstruction vertex at 12-A resolution (Supplementary Fig 2A) revealed the molecular interactions between different copies of Sec31 in the membrane-assembled coat.

      We have changed the sentence as suggested.

      L 150: Can the authors exclude the possibility that the difference is due to differences in data processing? E.g. how the maps amplitudes have been adjusted?

      Yes, we can exclude this scenario by measuring distances between vertices in the right and left handed direction. These measurements are only compatible with our vertex arrangement, and cannot be explained by the big deviation from 4-fold symmetry seen in the membrane-less cage vertices.

      L 172: "that wrap tubules either in a left- or right-handed manner". Don't they do always both on each tubule? Now this sentence could be interpreted to mean that some tubules have a left-handed coat and some a right-handed coat.

      We have changed this sentence to clarify. “Outer coat vertices are connected by Sec13-31 rods that wrap tubules both in a left- and right-handed manner.”

      L276: "The difference map" hasn't been introduced earlier but is referred to here as if it has been.

      We now introduce the difference map.

      L299: Can "Secondary structure predictions" denote a protein region "highly prone to protein binding"?

      Yes, this is done through DISOPRED3, a feature include in the PSIPRED server we used for our predictions. The reference is: Jones D.T., Cozzetto D. DISOPRED3: precise disordered region predictions with annotated protein-binding activity Bioinformatics. 2015; 31:857–863. We have now added this reference to the manuscript.

      L316: It's true that the detail in the map of the inner coat is unprecedented and the model presented in Figure 7 is partially based on that. But here "unprecedented resolution" sounds strange as this sentence refers to a schematic model and not a map.

      We have changed this by moving the reference to Fig 7 to a more appropriate place

      L325: "have 'compacted' during evolution" -> remove. It's enough to say it's more compact in humans and less compact in yeast as there could have been different adaptations in different organisms at this interface.

      We have changed as requested. See also our response to reviewer 1, point 1.

      L327: What's exactly meant by "sequence diversity or variability at this density".

      We have now clarified: “Since multiple charge clusters in yeast Sec31 may contribute to this interaction interface (Stancheva et al., 2020), the low resolution could be explained by the fact that the density is an average of different sequences.”

      L606-607: The description of this custom data processing approach is difficult to follow. Why is in-plane flip needed and how is it used here?

      Initially particles are picked ignoring tube directionality (as this cannot be assessed easily from the tomograms due to the pseudo-twofold symmetry of the Sec23/24/Sar1 trimer). So the in plane rotation of inner coat subunit could be near 0 or 180°. For each tube, both angles are sampled (in-plane flip). Most tubes result in the majority of particles being assigned one of the two orientations (which is then assumed as the tube directionality). Particles that do not conform are removed, and rare tubes where directionality cannot be determined are also removed. We have re-written the description to clarify these points: “Initial alignments were conducted on a tube-by-tube basis using the Dynamo in-plane flip setting to search in-plane rotation angles 180° apart. This allowed to assign directionality to each tube, and particles that were not conforming to it were discarded by using the Dynamo dtgrep_direction command in custom MATLAB scripts”

      L627: "Z" here refers to the coordinate system of aligned particles not that of the original tomogram. Perhaps just say "shifted 8 pixels further away from the membrane".

      Changed as requested.

      L642-643: How can the "left-handed" and "right-handed" rods be separated here? These terms refer to the long-range organisation of the rods in the lattice it's not clear how they were separated in the early alignments.

      They are separated by picking only one subset using the dynamo sub-boxing feature. This extracts boxes from the tomogram which are in set positions and orientation relative to the average of previously aligned subtomograms. From the average vertex structure, we sub-box rods at 4 different positions that correspond to the centre of the rods, and the 2-fold symmetric pairs are combined into the same dataset. We have clarified this in the text: “The refined positions of vertices were used to extract two distinct datasets of left and right-handed rods respectively using the dynamo sub-boxing feature.”

      Figure 2B. It's difficult to see the difference between dark and light pink colours.

      We have changed colours to enhance the difference.

      Figure 3C. These panels report the relative frequency of neighbouring vertices at each position; "intensity" does not seem to be the right measure for this. You could say that the colour bar indicates the "relative frequency of neighbouring vertices at each position" and add detail how the values were scaled between 0 and 1. The same applies to SFigure 1E.

      Changed as requested.

      Figure 4. The COP-II rods themselves are relatively straight, and they are not left-handed or right-handed. Here, more accurate would be "architecture of COPII rods organised in a left-handed manner". (In the text the authors may of course define and then use this shorter expression if they so wish.) Panel 4B top panel could have the title "left-handed" and the lower panel should have the title "right-handed" (for consistency and clarity).

      We have now defined left- and right-handed rods in the text, and have changed the figure and panel titles as requested.

    1. Why Are Finland’s Schools Successful? The country’s achievements in education have other nations, especially the United States, doing their homework <img src="https://thumbs-prod.si-cdn.com/thzZYTv2Evhq3x8iHdcaakihfVE=/800x600/filters:no_upscale()/https://public-media.si-cdn.com/filer/cd/ee/cdee1c82-f8e3-4de4-983e-8599d4485745/finland-smiles-wr.jpg" alt="Kirkkojarvi School" itemprop="image"> "This is what we do every day," says Kirkkojarvi Comprehensive School principal Kari Louhivuori, "prepare kids for life." (Stuart Conway) By LynNell Hancock Smithsonian Magazine | Subscribe September 2011 AddThis Sharing ButtonsShare to FacebookFacebookShare to TwitterTwitterShare to RedditReddit78Share to PinterestPinterest997Share to LinkedInLinkedInShare to FlipboardFlipboardShare to EmailEmailShare to PrintPrintShare to MoreAddThis934 It was the end of term at Kirkkojarvi Comprehensive School in Espoo, a sprawling suburb west of Helsinki, when Kari Louhivuori, a veteran teacher and the school’s principal, decided to try something extreme—by Finnish standards. One of his sixth-grade students, a Kosovo-Albanian boy, had drifted far off the learning grid, resisting his teacher’s best efforts. The school’s team of special educators—including a social worker, a nurse and a psychologist—convinced Louhivuori that laziness was not to blame. 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r="".concat(window.mmAPSbids,"&").concat(n);t=Wi.setSearchParamToAdTag(t,"cust_params",r)}if(!jn(window.shouldPlayAdRules)){var i=window.shouldPlayAdRules?"1":"0";t=Wi.setSearchParamToAdTag(t,"ad_rule",i)}return t=Wi.getCCPAConsent(t)});var zi=function(){function e(t,n){Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"adsScheduler",void 0),f()(this,"previousVideoTagStatus",void 0);var r=t.getState;this.store=t,this.adsScheduler=n,this.previousVideoTagStatus=hn.videoTagStatus(r()),this.videoTagStatusSubscriber=new ji(t,e.getVideoTagStatusDependencies,this.onVideoTagStatusChanged.bind(this))}return Vi()(e,[{key:"onVideoTagStatusChanged",value:function(t){var n=hn.videoTagStatus(t),r=_i.adStatus(t);"seeking"===this.previousVideoTagStatus&&(Hi(r)?this.adsScheduler.onSeekedWhileAdInProgress():e.isSeekedOverMidroll(t)&&this.adsScheduler.onSeekToAdOpportunity(e.getSeekedMidroll(t))),this.previousVideoTagStatus=n}}],[{key:"getVideoTagStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}},{key:"getClosestSkippedUnplayedMidroll",value:function(e,t){for(var n=t;n>0;n-=1)if(-1===e.indexOf(n))return n;return null}},{key:"getClosestLowerSeekedMidrollNumber",value:function(e,t){var n=In()(e).reverse().find(function(e){return e<=t});return e.indexOf(n)+1}},{key:"getSeekedSpecificMidroll",value:function(e,t,n,r){var i=this.getClosestLowerSeekedMidrollNumber(e,t),o=this.getClosestSkippedUnplayedMidroll(r,i);return{midrollNumber:o,currentTime:t,midrollTime:e[o-1],mediaId:n}}},{key:"isSeekedOverSpecificMidroll",value:function(e,t,n){if(jn(e))return!1;var r=this.getClosestLowerSeekedMidrollNumber(e,n);return null!==this.getClosestSkippedUnplayedMidroll(t,r)}},{key:"getSeekedReoccuringMidroll",value:function(e,t,n,r){var i=Math.floor(t/e),o=this.getClosestSkippedUnplayedMidroll(r,i);return{midrollTime:o*e,currentTime:t,midrollNumber:o,mediaId:n}}},{key:"isSeekedOverReoccuringMidroll",value:function(e,t,n){if(jn(e))return!1;var r=Math.floor(n/e);return null!==this.getClosestSkippedUnplayedMidroll(t,r)}},{key:"getSeekedMidroll",value:function(e){var t=_i.playedMidrolls(e),n=hn.currentVideoTime(e),r=bi.midrolls(e),i=r.every,o=r.on,a=Cn.mediaId(e);return this.isSeekedOverReoccuringMidroll(i,t,n)?this.getSeekedReoccuringMidroll(i,n,a,t):this.isSeekedOverSpecificMidroll(o,t,n)?this.getSeekedSpecificMidroll(o,n,a,t):null}},{key:"isSeekedOverMidroll",value:function(e){var t=_i.playedMidrolls(e),n=hn.currentVideoTime(e),r=bi.midrolls(e),i=r.every,o=r.on,a=o;return bi.prerollEnabled(e)&&(a=o.filter(function(e){return 0!==e})),this.isSeekedOverReoccuringMidroll(i,t,n)||this.isSeekedOverSpecificMidroll(a,t,n)}}]),e}(),Gi=function e(t,n){var r=this;Ai()(this,e),f()(this,"pendingAdStatusStoreSubscriber",void 0),f()(this,"adsScheduler",void 0),f()(this,"onPendingAdStatusChanged",function(e){var t=_i.pendingAdStatus(e).type,n=_i.adStatus(e);if("playPreroll"===t&&!Hi(n)){var i=Cn.activeVideoIndex(e),o=Dn.mediaId(e);r.adsScheduler.onPrerollReached(o,i+1)}}),this.adsScheduler=n,this.pendingAdStatusStoreSubscriber=new ji(t,e.getPendingAdStatusDependencies,this.onPendingAdStatusChanged.bind(this))};f()(Gi,"getPendingAdStatusDependencies",function(e){return[_i.pendingAdStatus(e)]});var $i=3,Ki=function e(t,n){var r=this;Ai()(this,e),f()(this,"videoTimeSubscriber",void 0),f()(this,"videoSeekSubscriber",void 0),f()(this,"adTagGenerator",void 0),f()(this,"monetization",void 0),f()(this,"lastRequestedMidroll",null),f()(this,"prerollScheduler",void 0),f()(this,"generateMidrollTag",function(e){var t="midroll".concat(e.midrollNumber);return r.adTagGenerator.generate(t,e.mediaId)}),f()(this,"generatePrerollTag",function(e,t){var n="preroll".concat(t);return r.adTagGenerator.generate(n,e)}),f()(this,"onAdTimeReached",function(){r.monetization.onMidrollAdOpportunity()}),f()(this,"onPreAdTimeReached",function(e){r.onPreMidrollAdOpportunity(e)}),f()(this,"onSeekToAdOpportunity",function(e){r.onPreMidrollAdOpportunity(e)}),f()(this,"isMidrollAlreadyRequested",function(e){return e.midrollNumber===r.lastRequestedMidroll.midrollNumber&&e.mediaId===r.lastRequestedMidroll.mediaId&&e.midrollTime===r.lastRequestedMidroll.midrollTime}),f()(this,"onPreMidrollAdOpportunity",function(e){if(Un(r.lastRequestedMidroll)||!r.isMidrollAlreadyRequested(e)){r.lastRequestedMidroll=e;var t=r.generateMidrollTag(e);r.monetization.onPreMidrollAdOpportunity(e,t)}}),f()(this,"onPrerollReached",function(e,t){var n=r.generatePrerollTag(e,t);r.monetization.onPrerollAdOpportunity(n)}),f()(this,"onSeekedWhileAdInProgress",function(){r.monetization.onMidrollAdOpportunity()});var i=t.getState;this.monetization=n,this.videoTimeSubscriber=new qi(t,this),this.videoSeekSubscriber=new zi(t,this),this.prerollScheduler=new Gi(t,this);var o=_i.adTagUrlTemplate(i());this.adTagGenerator=new Wi(o)},Yi=function(){function e(){Ai()(this,e)}return Vi()(e,null,[{key:"generateAdRequest",value:function(e,t,n){var r=new google.ima.AdsRequest;return r.adTagUrl=e,Fn()||r.setAdWillPlayMuted(t),r.vastLoadTimeout=n,r}}]),e}(),Zi=function(e){return function(t){t({type:"[MONETIZATION] change ad status",payload:e})}},Xi=function(e){return function(t){t({type:"[COMMON] set pending video status",payload:{pendingStatusObject:{type:e,value:""}}})}},Ji=function(e){return function(t){t({type:"[MONETIZATION] change loading ad status",payload:e})}},Qi=function(e){return function(t){t({type:"[MONETIZATION] update ad 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google.ima.AdsLoader(t),a.adsLoader.getSettings().setDisableCustomPlaybackForIOS10Plus(!0),a.adsLoader.getSettings().setVpaidMode(google.ima.ImaSdkSettings.VpaidMode[n]),a.adsLoader.addEventListener(google.ima.AdsManagerLoadedEvent.Type.ADS_MANAGER_LOADED,a.onIMAAdsManagerLoaded.bind(a),!1,a),a.adsLoader.addEventListener(google.ima.AdErrorEvent.Type.AD_ERROR,a.onAdError.bind(a),!1,a)}),f()(this,"createAdRequest",function(e){var t=a.store.getState,n=gn.muted(t()),r=bi.adRequestTimeout(t());return Yi.generateAdRequest(e,n,r)}),f()(this,"validateAdRequestCorrectness",function(e){e&&e.adTagUrl&&decodeURIComponent(e.adTagUrl.replace(/\+/g," "))}),f()(this,"getLoadingError",function(e){var t=function(){return"bad ad request ".concat(JSON.stringify(e))};return{getError:function(){return{getMessage:t}}}}),f()(this,"getPlayAdError",function(e){var t=function(){return"play ad error: 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t=a.store,n=t.getState,r=t.dispatch,i=gn.volume(n());Bn()||gn.muted(n())?(e.setVolume(0),Qi(!0)(r)):(e.setVolume(gn.volume(n())),eo(i)(r),Qi(!1)(r))}),f()(this,"createIMAAdManager",function(t){a.IMAAdManager=t.getAdsManager(a.adVideoElement,e.getAdsRenderingSettings()),a.setAdVolume(a.IMAAdManager)}),f()(this,"registerToAdManagerEvents",function(){a.IMAAdManager.addEventListener(google.ima.AdErrorEvent.Type.AD_ERROR,a.onAdError),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.CONTENT_PAUSE_REQUESTED,a.onContentPauseRequested),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.CONTENT_RESUME_REQUESTED,a.onContentResumeRequested),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.STARTED,a.onAdStarted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.IMPRESSION,a.onAdImpression),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.SKIPPED,a.onAdSkipped),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.COMPLETE,a.onAdCompleted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.PAUSED,a.onAdPaused),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.RESUMED,a.onAdStarted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.AD_PROGRESS,a.onAdProgressChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.VOLUME_CHANGED,a.onVolumeChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.VOLUME_MUTED,a.onAdVolumeMutedChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.ALL_ADS_COMPLETED,a.onAdCompleted)}),f()(this,"onIMAAdsManagerLoaded",function(e){var t=a.store.dispatch;a.createIMAAdManager(e),a.registerToAdManagerEvents(),Zi("loaded")(t)}),f()(this,"onAdError",function(e){var t=a.store.dispatch;!function(e){return function(t){t({type:"[MONETIZATION] change ad error",payload:e})}}(e.getError().getMessage())(t),Ji(!1),a.continuePlayingContent()}),f()(this,"onAdImpression",function(e){var t=a.store.dispatch,n=!e.getAd().g.vpaid;a.setPodInfo(e),function(e){e({type:"[MONETIZATION] increase ad impression counter"})}(t),function(e){return function(t){t({type:"[MONETIZATION] update is vast ad",payload:e})}}(n)(t)}),f()(this,"onVolumeChanged",function(e){var t=a.store.dispatch;eo(e.target.getVolume())(t)}),f()(this,"onAdVolumeMutedChanged",function(e){var t=a.store.dispatch;0===e.target.getVolume()?Qi(!0)(t):Qi(!1)(t)}),f()(this,"continuePlayingContent",function(){var e=a.store,t=e.getState,n=e.dispatch,r=hn.videoTagStatus(t());Xi("idle"===r?"play":"resume")(n)}),f()(this,"stopPlayingContent",function(){var e=a.store.dispatch;Xi("pause")(e)}),f()(this,"onContentPauseRequested",function(){a.stopPlayingContent()}),f()(this,"onContentResumeRequested",function(){a.continuePlayingContent()}),f()(this,"onAdPaused",function(){var e=a.store.dispatch;Zi("paused")(e)}),f()(this,"setPodInfo",function(e){var t=e&&e.getAd()&&e.getAd().getAdPodInfo();if(!Un(t)){var n=a.store.dispatch;!function(e,t){return function(n){n({type:"[MONETIZATION] change pod info",payload:{slotNumber:e,podNumber:t}})}}(t.getAdPosition(),a.totalAdRequestMadeAmount)(n)}}),f()(this,"onAdStarted",function(){var e=a.store,t=e.dispatch,n=e.getState,r=gn.volume(n());Zi("playing")(t),0===a.IMAAdManager.getVolume()?a.IMAAdManager.setVolume(0):window.shouldPlayAdRule||a.IMAAdManager.setVolume(r),a.onResize()}),f()(this,"onAdCompleted",function(){var e=a.store.dispatch;Zi("completed")(e)}),f()(this,"onAdSkipped",function(){var e=a.store.dispatch;Zi("skipped")(e)}),f()(this,"onResize",function(){Un(a.IMAAdManager)||(a.IMAAdManager.resize(a.videoPlayerElement.clientWidth,a.videoPlayerElement.clientHeight,google.ima.ViewMode.NORMAL),a.adContainerElement.style.height="".concat(a.videoPlayerElement.clientHeight,"px"))}),f()(this,"onAdProgressChanged",function(e){var t,n,r=a.store,i=r.dispatch,o=r.getState,s=e.getAdData().currentTime,u=e.getAdData().duration,c=_i.adDuration(o());(t=s,function(e){e({type:"[MONETIZATION] change ad current time",payload:t})})(i),c!==u&&(n=u,function(e){e({type:"[MONETIZATION] change ad duration",payload:n})})(i)}),f()(this,"onAnchorStatusChanged",function(){var e=a.store.getState;"processing"!==Pr(e())&&a.onResize()}),f()(this,"changeAdVolume",function(e){Un(a.IMAAdManager)||a.IMAAdManager.setVolume(e)}),f()(this,"changeAdMuted",function(e,t){Un(a.IMAAdManager)||(t?a.IMAAdManager.setVolume(0):a.IMAAdManager.setVolume(e))}),f()(this,"changeAdStatus",function(e){Un(a.IMAAdManager)||("playing"===e&&a.IMAAdManager.resume(),"paused"===e&&a.IMAAdManager.pause())});var s=t.getState;this.store=t,this.adVideoElement=r,this.videoPlayerElement=i,this.adContainerElement=n,this.adDisplayContainer=new google.ima.AdDisplayContainer(n,r),this.createAdLoader(s(),this.adDisplayContainer),this.adDisplayContainer.initialize(),this.anchorStatusStoreSubscriber=new ji(t,e.getAnchorDependencies,this.onAnchorStatusChanged.bind(this)),this.registerForWindowResize(),this.initMutationObserver(o)};f()(to,"getAdsRenderingSettings",function(){var e=new google.ima.AdsRenderingSettings;return e.restoreCustomPlaybackStateOnAdBreakComplete=!0,e.enablePreloading=!1,e.uiElements=[],e.loadVideoTimeout=15e3,e}),f()(to,"getAnchorDependencies",function(e){return[Pr(e)]});var no=function e(t,n,r,i,o,a){var s=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"playerId",void 0),f()(this,"adScheduler",void 0),f()(this,"adHandler",void 0),f()(this,"imaLoadingStatusSubscriber",void 0),f()(this,"adStatusSubscriber",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"adContainer",void 0),f()(this,"adVideoElement",void 0),f()(this,"videoPlayerElement",void 0),f()(this,"playerContainer",void 0),f()(this,"pendingMidrollAdPlay",!1),f()(this,"pendingPrerollAdPlay",!1),f()(this,"pendingPrerollAdTag",null),f()(this,"pendingMidrollNumber",null),f()(this,"pendingAdStatusStoreSubscriber",void 0),f()(this,"adMutedStoreSubscriber",void 0),f()(this,"adVolumeStoreSubscriber",void 0),f()(this,"onMidrollAdOpportunity",function(){var e=s.store,t=e.dispatch,n=e.getState,r=_i.adStatus(n()),i=bi.continuePlayingWhileWaitingForAd(n());"loaded"===r?s.playAd(!0):"requested"===r&&(s.pendingMidrollAdPlay=!0,i||(Xi("pause")(t),Ji(!0)(t))),function(e){e({type:"[MONETIZATION] increase ad Opportunity counter"})}(t)}),f()(this,"onPrerollAdOpportunity",function(e){var t=s.store,n=t.getState,r=t.dispatch,i=Fi.loadingImaStatus(n());Un(s.adHandler)?"loading"!==i&&""!==i||(Ji(!0)(r),s.pendingPrerollAdPlay=!0,s.pendingPrerollAdTag=e):(s.pendingPrerollAdPlay=!0,Ji(!0)(r),s.adHandler.loadNewAd(e,"preroll"))}),f()(this,"onPreMidrollAdOpportunity",function(e,t){Un(s.adHandler)||(e.currentTime>=e.midrollTime&&(s.pendingMidrollAdPlay=!0),s.pendingMidrollNumber=e.midrollNumber,s.adHandler.loadNewAd(t,"midroll"))}),f()(this,"hasPendingAd",function(){return s.hasPendingMidrollAdPlay()||s.hasPendingPrerollAdPlay()}),f()(this,"onAdStatusChanged",function(e){var t=s.store.dispatch,n=_i.adStatus(e);"completed"===n&&Ji(!1)(t);var r=bi.continuePlayingWhileWaitingForAd(e),i=_i.loadingAd(e);"playing"!==n&&"error"!==n||r||!i||Ji(!1)(t),s.hasPendingAd()&&"loaded"===n?s.playAd(s.hasPendingMidrollAdPlay()):s.hasPendingAd()&&"error"===n?(Ji(!1),s.clearPendingMidroll(),s.clearPendingPreroll()):Hi(n)||(Ji(!1),function(e){e({type:"[MONETIZATION] clear ad data"})}(t))}),f()(this,"clearPendingMidroll",function(){s.pendingMidrollNumber=null,s.pendingMidrollAdPlay=!1}),f()(this,"clearPendingPreroll",function(){s.pendingPrerollAdPlay=!1,s.pendingPrerollAdTag=null}),f()(this,"onVideoTagStatusChanged",function(e){"complete"===hn.videoTagStatus(e)&&function(e){e({type:"[MONETIZATION] clear played midrolls"})}(s.store.dispatch)}),f()(this,"hasPendingMidrollAdPlay",function(){return s.pendingMidrollAdPlay}),f()(this,"hasPendingPrerollAdPlay",function(){return s.pendingPrerollAdPlay}),f()(this,"playAd",function(e){var t,n=s.store.dispatch,r=s.adHandler.playAd();e?((t=s.pendingMidrollNumber,function(e){e({type:"[MONETIZATION] add 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Ki(t,this),this.adStatusSubscriber=new ji(t,e.getAdStatusDependencies,this.onAdStatusChanged.bind(this)),this.videoTagStatusSubscriber=new ji(t,e.getVideoTagStatusDependencies,this.onVideoTagStatusChanged.bind(this)),e.canUseIMA(u())?this.adHandler=new to(t,r,i,o,a):this.imaLoadingStatusSubscriber=new ji(t,e.getIMALoadingStatusDependencies,this.onIMALoadingStatusChanged.bind(this)),this.pendingAdStatusStoreSubscriber=new ji(t,e.getPendingAdStatusDependencies,this.onPendingAdStatusChanged.bind(this)),this.adMutedStoreSubscriber=new ji(t,e.getAdMutedDependencies,this.onAdMutedChanged.bind(this)),this.adVolumeStoreSubscriber=new 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n=null!=arguments[t]?arguments[t]:{};t%2?xa(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):xa(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var ja={activeVideoIndex:0,mediaType:"semantic",mediaId:"",loadingMedia:!1,mediaLoadingError:"",mediaRequest:{type:null,value:""},videoList:[],videoData:{mediaId:"",tags:[],sources:[],duration:0,thumbnail:"",title:"",showTitle:!0,description:"",creator:"",provider:"",externalId:"",index:0}};function Ua(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function Fa(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?Ua(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):Ua(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var Ba={promotedVideos:[],scannedElement:"",tags:"",scopedKeywords:"",minimumDateFactor:"",scannedElementType:null,scanImagesOnPage:!1};function Ha(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function qa(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?Ha(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):Ha(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var Wa={userInteractionType:""};function za(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function Ga(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?za(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):za(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var $a={splitViewRatio:null};function Ka(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function Ya(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?Ka(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):Ka(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var Za={nextVideo:"none",showUpNext:!1,showSkippableContent:!1},Xa=function(e){return"none"===e?"none":"up_next"===e?"upNext":"skippable_content"===e?"skippableContent":"none"},Ja=function(e){for(var t=Object.keys(e),n={},r=0;r<t.length;r++){var i=t[r];"function"===typeof e[i]&&(n[i]=e[i])}var o,a=Object.keys(n);try{!function(e){Object.keys(e).forEach(function(t){var n=e[t];if("undefined"===typeof n(void 0,{type:yt.INIT}))throw new Error('Reducer "'+t+"\" returned undefined during initialization. If the state passed to the reducer is undefined, you must explicitly return the initial state. The initial state may not be undefined. If you don't want to set a value for this reducer, you can use null instead of undefined.");if("undefined"===typeof n(void 0,{type:yt.PROBE_UNKNOWN_ACTION()}))throw new Error('Reducer "'+t+"\" returned undefined when probed with a random type. Don't try to handle "+yt.INIT+' or other actions in "redux/*" namespace. They are considered private. Instead, you must return the current state for any unknown actions, unless it is undefined, in which case you must return the initial state, regardless of the action type. The initial state may not be undefined, but can be null.')})}(n)}catch(s){o=s}return function(e,t){if(void 0===e&&(e={}),o)throw o;for(var r=!1,i={},s=0;s<a.length;s++){var u=a[s],c=n[u],l=e[u],d=c(l,t);if("undefined"===typeof d){var p=mt(u,t);throw new Error(p)}i[u]=d,r=r||d!==l}return(r=r||a.length!==Object.keys(e).length)?i:e}}({dependenciesLoadingStatus:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:da,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] update hls status":return la(la({},e),{},{loadingHLSStatus:t.payload});case"[CORE] update ima status":return la(la({},e),{},{loadingImaStatus:t.payload});default:return e}},playerData:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:ha,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":var n=t.payload;return fa({},function(e,t,n){var r=t.playback_method,i=t.player_id;return fa(fa({},e),{},{playbackMethod:Un(r)?e.playbackMethod:r,playerId:Un(i)?e.playerId:i,playerInstanceUniqId:n,playerMode:Fn()?"mobile":"desktop"})}(e,n.initiateParams,n.playerInstanceUniqId));case"[CORE] reset player data time params":return fa(fa({},e),{},{currentVideoTimeFragment:0,currentVideoBufferedTime:0,currentVideoDuration:0,currentVideoTime:0});case"[COMMON] set mute video":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{muted:t.payload})});case"[COMMON] set volume":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{volume:t.payload})});case"[COMMON] change selected settings category":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{selectedSettingsCategory:t.payload})});case"[COMMON] change settings speed":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{speed:t.payload})});case"[COMMON] change settings quality":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{quality:t.payload})});case"[COMMON] set fullscreen":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{fullscreen:fa(fa({},e.playerSettings.fullscreen),{},{isFullscreenOn:t.payload,pendingFullscreenRequest:""})})});case"[COMMON] set fullscreen request":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{fullscreen:fa(fa({},e.playerSettings.fullscreen),{},{pendingFullscreenRequest:t.payload})})});case"[COMMON] set pending video status":var r=t.payload.pendingStatusObject;return fa(fa({},e),{},{pendingVideoTagStatus:fa({},r)});case"[COMMON] set player mode":return fa(fa({},e),{},{playerMode:t.payload});case"[CORE] update video current fragment position":return fa(fa({},e),{},{currentVideoTimeFragment:t.payload});case"[CORE] update video current position":return fa(fa({},e),{},{currentVideoTime:t.payload});case"[CORE] update video current buffered time":return fa(fa({},e),{},{currentVideoBufferedTime:t.payload});case"[CORE] update video current duration":return fa(fa({},e),{},{currentVideoDuration:t.payload});case"[CORE] change video tag status":return fa(fa({},e),{},{videoTagStatus:t.payload});case"[CORE] update player visibility":return fa(fa({},e),{},{playerVisibility:t.payload});case"[CORE] update placeholder visibility":return fa(fa({},e),{},{playerPlaceholderVisibility:t.payload});case"[CORE] change loading player status":return fa(fa({},e),{},{loadingPlayer:t.payload});case"[COMMON] show black screen with loader":return fa(fa({},e),{},{loader:fa(fa({},e.loader),{},{showBlackScreen:t.payload})});case"[CORE] set player size":return fa(fa({},e),{},{playerSize:t.payload});case"[COMMON] set error message":return fa(fa({},e),{},{errorMessage:t.payload});default:return e}},brandingData:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:va,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return ga({},function(e,t){var n=t.powered_by_strip,r=t.brand_logo,i=t.brand_logo_click_url,o=t.brand_color;return ga(ga({},e),{},{showVoltaxLogo:Un(n)?e.showVoltaxLogo:n,brandingLogoSrc:Un(r)?e.brandingLogoSrc:r,brandingLogoUrl:Un(i)?e.brandingLogoUrl:i,brandingColor:Un(o)?e.brandingColor:o})}(e,t.payload.initiateParams));default:return e}},anchorOptions:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Oa,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return ba({},function(e,t){var n=t.anchor_options;if(!Un(n)){var r=n.anchoring_appearance,i=n.can_close,o=n.closable_ad,a=n.close_after,s=n.continue_streaming,u=n.orientation,c=n.margins,l=n.sticky_below_class_name,d=n.width,p=Un(c)?e.margins:{top:Number.isInteger(c.top)?c.top:e.margins.top,bottom:Number.isInteger(c.bottom)?c.bottom:e.margins.bottom,left:Number.isInteger(c.left)?c.left:e.margins.left,right:Number.isInteger(c.right)?c.right:e.margins.right};return ba(ba({},e),{},{anchoringAppearance:r||e.anchoringAppearance,canClose:Un(i)?e.canClose:i,orientation:Un(u)?e.orientation:u,closableAd:Un(o)?e.closableAd:o,closeAfter:Un(a)?e.closeAfter:a,continueStreaming:Un(s)?e.continueStreaming:s,stickyBelowClassName:Un(l)?e.stickyBelowClassName:l,width:Un(d)?e.width:d,margins:p,anchorData:ba(ba({},e.anchorData),{},{anchorEnabled:!0})})}return e}(e,t.payload.initiateParams));case"[COMMON] set anchor enable":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorEnabled:t.payload})});case"[ANCHOR] update is anchor status":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorStatus:t.payload})});case"[COMMON] set anchor disabled by user":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorDisabledByUser:t.payload})});default:return e}},monetization:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:wa,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Sa({},function(e,t){var n=t.monetization;if(Un(n))return e;var r=n.ad_tag,i=n.ad_type,o=n.vpaid_mode,a=n.ad_request_timeout,s=n.continue_content_play_while_waiting_for_ad,u=n.midrolls,c=u&&u.on&&u.on.sort(Wn),l=Un(s)?e.continuePlayingWhileWaitingForAd:s,d=c?c.indexOf(0):-1,p=-1!==d&&!l;return p&&(c=c.splice(d,1)),Sa(Sa({},e),{},{midrolls:Sa(Sa({},e.midrolls),{},{every:u&&u.every,on:c}),prerollEnabled:p,adRequestTimeout:Un(a)?e.adRequestTimeout:parseInt(a,10),vpaidMode:Un(o)?e.vpaidMode:o,continuePlayingWhileWaitingForAd:l,adsData:Sa(Sa({},e.adsData),{},{adType:Un(i)?e.adsData.adType:i,adTagUrlTemplate:Un(r)?e.adsData.adTagUrlTemplate:r})})}(e,t.payload.initiateParams));case"[COMMON] set new ad tag url template":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adTagUrlTemplate:t.payload})});case"[MONETIZATION] change ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adStatus:t.payload,adErrorMessage:null})});case"[MONETIZATION] change ad tag":var n=t.payload,r=n.adUnit,i=n.adTag;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{currentAdTag:i,adUnit:r})});case"[MONETIZATION] change pending ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{pendingAdStatus:t.payload})});case"[MONETIZATION] change ad error":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adStatus:"error",adErrorMessage:t.payload})});case"[MONETIZATION] increase ad impression counter":var o=e.adsData.adImpression;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adImpression:o+1})});case"[MONETIZATION] increase ad Opportunity counter":var a=e.adsData.adOpportunity;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOpportunity:a+1})});case"[MONETIZATION] add played midroll number":var s=e.adsData.playedMidrolls,u=In()(s);return u.push(t.payload),Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOrder:t.payload,playedMidrolls:u})});case"[MONETIZATION] clear played midrolls":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{playedMidrolls:[]})});case"[MONETIZATION] clear ad data":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOrder:0,currentAdTag:null,adDuration:0,adUnit:""})});case"[MONETIZATION] change ad duration":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adDuration:t.payload})});case"[MONETIZATION] update is vast ad":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{isVastAd:t.payload})});case"[MONETIZATION] change ad current time":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adCurrentTime:t.payload})});case"[MONETIZATION] update ad muted":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adMuted:t.payload})});case"[MONETIZATION] change ad volume":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adVolume:t.payload})});case"[MONETIZATION] change pod info":var c=t.payload,l=c.podNumber,d=c.slotNumber;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{podNumber:l,slotNumber:d})});case"[MONETIZATION] change loading ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{loadingAd:t.payload})});default:return e}},mediaData:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:ja,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Va({},function(e,t){var n=t.content_type,r=t.media_id,i=t.display_title;return Va(Va({},e),{},{mediaType:Un(n)?e.mediaType:n,mediaId:Un(r)?e.mediaId:r,videoData:Va(Va({},e.videoData),{},{showTitle:!!Un(i)||i})})}(e,t.payload.initiateParams));case"[CORE] load video request":return Va(Va({},e),{},{loadingMedia:!0});case"[CORE] load video request success":return Va(Va({},e),{},{loadingMedia:!1,videoList:t.payload});case"[CORE] set current video":var n=t.payload,r=n.index,i=n.videoData;return Va(Va({},e),{},{activeVideoIndex:r,videoData:i});case"[CORE] load video request error":return Va(Va({},e),{},{loadingMedia:!1,mediaLoadingError:t.payload});case"[COMMON] media request":var o=t.payload.mediaRequestObject;return Va(Va({},e),{},{mediaRequest:Va({},o)});default:return e}},semanticOptions:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Ba,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Fa({},function(e,t){var n=t.semantic_options;if(Un(n))return e;var r=n.minimum_date_factor,i=n.promoted_videos,o=n.scan_images_on_page,a=n.scanned_element,s=n.scanned_element_type,u=n.scoped_keywords,c=n.tags;return Fa(Fa({},e),{},{minimumDateFactor:Un(r)?e.minimumDateFactor:r,promotedVideos:Un(i)?e.promotedVideos:i,scanImagesOnPage:Un(o)?e.scanImagesOnPage:o,scannedElement:Un(a)?e.scannedElement:a,scannedElementType:Un(s)?e.scannedElementType:s,scopedKeywords:Un(u)?e.scopedKeywords:u,tags:Un(c)?e.tags:c})}(e,t.payload.initiateParams));default:return e}},userInteraction:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Wa,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[USER INTERACTION] change user interaction":return qa(qa({},e),{},{userInteractionType:t.payload});default:return e}},splitView:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:$a,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Ga({},function(e,t){var n=t.anchor_options;if(!Un(n)){var r=n.split_view,i=n.split_view_ratio;return Ga(Ga({},e),{},{splitViewRatio:Un(r)||!r||Un(i)?e.splitViewRatio:i})}return e}(e,t.payload.initiateParams));default:return e}},discovery:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Za,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Ya({},function(e,t){var n=t.next_video;return Un(n)?e:Ya(Ya({},e),{},{nextVideo:Xa(n)})}(e,t.payload.initiateParams));case"[DISCOVERY] show up next":return Ya(Ya({},e),{},{showUpNext:t.payload});case"[DISCOVERY] show skippable content":return Ya(Ya({},e),{},{showSkippableContent:t.payload});default:return e}}}),Qa=[],es=!1,ts=function e(){return function(t){return function(n){if(es)return Qa.push(n),null;es=!0;var r=t(n);return es=!1,Qa.length>0&&e()(t)(Qa.shift()),r}}},ns=function(e){var t=[];if(function(e){return!Un(e)&&!Un(e.enable_redux_debugging)&&e.enable_redux_debugging}(e)){var n=window&&window.__REDUX_DEVTOOLS_EXTENSION__&&window.__REDUX_DEVTOOLS_EXTENSION__();"function"===typeof n&&t.push(n)}var r=Et.apply(void 0,[wt(ua,ts)].concat(t));return vt(Ja,r)},rs=function(){function e(t){Ai()(this,e),f()(this,"playerVisibilitySubscriber",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"shouldPlayIfLazyplay",!0),f()(this,"shouldPlayIfAutoplayWhenViewable",!0),f()(this,"videoPausedByObserver",!1),this.store=t,this.playerVisibilitySubscriber=null,this.videoTagStatusSubscriber=null,this.playAccordingToPlaybackMethod()}return Vi()(e,[{key:"lazyplayHandler",value:function(e){hn.playerVisibility(e)>=.5&&(this.playVideo(),this.shouldPlayIfLazyplay=!1)}},{key:"autoplayWhenViewableHandler",value:function(e){hn.playerVisibility(e)>=.5?this.playVideo():this.pauseVideo()}},{key:"onPlayerVisibilityChanged",value:function(e){var t=hn.playbackMethod(e);"lazyplay"===t&&this.shouldPlayIfLazyplay&&this.lazyplayHandler(e),"autoplay_when_viewable"===t&&this.shouldPlayIfAutoplayWhenViewable&&this.autoplayWhenViewableHandler(e)}},{key:"onVideoTagStatusChanged",value:function(e){var t=hn.videoTagStatus(e);"paused"!==t||this.videoPausedByObserver||(this.shouldPlayIfAutoplayWhenViewable=!1),"playing"===t&&(this.shouldPlayIfAutoplayWhenViewable=!0,this.videoPausedByObserver=!1)}},{key:"initiatePlayerVisibilitySubscriber",value:function(){this.playerVisibilitySubscriber=new ji(this.store,e.getPlayerVisibilityDependencies,this.onPlayerVisibilityChanged.bind(this))}},{key:"initiateVideoTagStatusSubscriber",value:function(){this.videoTagStatusSubscriber=new ji(this.store,e.getVideoTagStatusDependencies,this.onVideoTagStatusChanged.bind(this))}},{key:"playVideo",value:function(){var e=this.store,t=e.dispatch,n=e.getState;"idle"===hn.videoTagStatus(n())?on("play")(t):on("resume")(t)}},{key:"pauseVideo",value:function(){var e=this.store,t=e.dispatch,n=e.getState;"paused"!==hn.videoTagStatus(n())&&(this.videoPausedByObserver=!0,on("pause")(t))}},{key:"playAccordingToPlaybackMethod",value:function(){var e=this.store,t=e.dispatch,n=(0,e.getState)();switch(hn.playbackMethod(n)){case"autoplay":this.playVideo();break;case"lazyplay":this.initiatePlayerVisibilitySubscriber();break;case"autoplay_when_viewable":this.initiatePlayerVisibilitySubscriber(),this.initiateVideoTagStatusSubscriber();break;case"none":an(!1)(t)}}}],[{key:"getPlayerVisibilityDependencies",value:function(e){return[hn.playerVisibility(e)]}},{key:"getVideoTagStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}}]),e}(),is=function(){function e(t,n,r,i){var o=this;Ai()(this,e),f()(this,"videoStatusSubscriber",void 0),f()(this,"videoListSubscriber",void 0),f()(this,"mediaRequestSubscriber",void 0),f()(this,"playerVisibilitySubscriber",void 0),f()(this,"playbackMethodManager",void 0),f()(this,"store",void 0),f()(this,"loadContent",function(e,t,n,r){o.loadMedia(t,n,r).then(function(){o.playbackMethodManager=new rs(e)})}),f()(this,"loadMedia",function(e,t,n){var r=o.store,i=r.dispatch,a=r.getState,s=Dn.showTitle(a());if("semantic"===e){var u=pn.semanticOptions(a());return Na(u,s,n)(i)}return ka(t,s,n)(i)}),this.store=t,this.videoStatusSubscriber=new ji(t,e.getVideoStatusDependencies,this.onVideoStatusChanged.bind(this)),this.videoListSubscriber=new ji(t,e.getVideoListDependencies,this.onVideoListChanged.bind(this)),this.mediaRequestSubscriber=new ji(t,e.getMediaRequestDependencies,this.onMediaRequestChanged.bind(this)),this.playerVisibilitySubscriber=null,this.loadContent(t,r,n,i)}return Vi()(e,null,[{key:"createInstance",value:function(t,n,r,i){return new e(t,n,r,i)}}]),Vi()(e,[{key:"playNextVideo",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e),r=Cn.activeVideoIndex(e)+1;n.length>1&&r>=n.length&&(r=0),r<n.length&&(!function(e){e({type:"[CORE] reset player data time params"})}(t),La(r,n[r])(t),on("play")(t))}},{key:"playPreviousVideo",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e),r=Cn.activeVideoIndex(e);if(r>0){var i=r-1;La(i,n[i])(t),on("play")(t)}}},{key:"onVideoStatusChanged",value:function(e){"complete"===hn.videoTagStatus(e)&&this.playNextVideo(e)}},{key:"onVideoListChanged",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e);!jn(n)&&n.length>0&&La(0,n[0])(t)}},{key:"onMediaRequestChanged",value:function(e){var t=Cn.mediaRequest(e);switch(t.type){case"playNewVideo":this.loadMedia("specific",t.value);break;case"playNextVideo":this.playNextVideo(e);break;case"playPreviousVideo":this.playPreviousVideo(e)}}}],[{key:"getVideoStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}},{key:"getVideoListDependencies",value:function(e){return[Cn.videoList(e)]}},{key:"getMediaRequestDependencies",value:function(e){return[Cn.mediaRequest(e)]}}]),e}(),os=function e(t){var n=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"onDependencyFailure",function(e,t){console.log("onDependencyFailure",e,t);var r=n.store,i=r.dispatch,o=r.getState;switch(e){case"ima":"blocked"!==Fi.loadingImaStatus(o())&&Qn("error")(i);break;case"hls":er("error")(i)}}),f()(this,"onDependencyReady",function(e){var t=n.store.dispatch;switch(e){case"ima":Qn("success")(t);break;case"hls":er("success")(t)}}),this.store=t},as=function(e){return function(t){t({type:"[COMMON] set fullscreen",payload:e})}},ss=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTag",void 0),f()(this,"pendingFullscreenSubscriber",void 0),f()(this,"adStatusSubscriber",void 0),f()(this,"playerUniqId",void 0),f()(this,"onAdStatusChanged",function(e){var t=_i.adStatus(e),n=r.videoTag.webkitDisplayingFullscreen;"playing"===t&&Bn()&&n&&r.exitFullscreen(r.videoTag)}),f()(this,"isPlayerInFullscreen",function(){var e=document,t=Bn()?En(r.playerUniqId):bn(r.playerUniqId);return Un(e.fullscreenElement)?!Un(e.webkitFullscreenElement)&&0===e.webkitFullscreenElement.id.localeCompare(t):0===e.fullscreenElement.id.localeCompare(t)}),f()(this,"changePlayerWidth",function(e){r.videoTag.style.width=e?"100%":"auto"}),f()(this,"onFullscreenChanged",function(){var e=r.store.dispatch,t=r.isPlayerInFullscreen();r.changePlayerWidth(t),as(t)(e)}),f()(this,"onFullscreenChangedIos",function(){var e=r.store.dispatch,t=r.videoTag.webkitDisplayingFullscreen;t||on("resume")(e),r.changePlayerWidth(t),as(t)(e)}),f()(this,"onPendingFullscreenRequestChanged",function(e){var t=gn.pendingFullscreenRequest(e);"enter"===t?r.enterFullscreen(r.videoTag):"exit"===t&&r.exitFullscreen(r.videoTag)}),f()(this,"getFullScreenElement",function(e,t){var n=document.getElementById(bn(r.playerUniqId));return Bn()?t:e?document:n}),f()(this,"enterFullscreen",function(e){var t=r.getFullScreenElement(!1,e);Bn()?t.webkitEnterFullscreen():document.webkitExitFullscreen?t.webkitRequestFullscreen():document.webkitCancelFullScreen?t.webkitRequestFullScreen():document.mozCancelFullScreen?t.mozRequestFullScreen():document.msExitFullscreen&&t.msRequestFullscreen()}),f()(this,"exitFullscreen",function(e){var t=r.getFullScreenElement(!0,e);document.webkitExitFullscreen||Bn()?t.webkitExitFullscreen():document.webkitCancelFullScreen?t.webkitCancelFullScreen():document.mozCancelFullScreen?t.mozCancelFullScreen():document.msExitFullscreen&&t.msExitFullscreen()}),this.store=t,this.videoTag=document.getElementById(En(n)),this.playerUniqId=n,document.addEventListener("fullscreenchange",this.onFullscreenChanged.bind(this)),document.addEventListener("webkitfullscreenchange",this.onFullscreenChanged.bind(this)),Bn()&&(this.videoTag.addEventListener("webkitendfullscreen",this.onFullscreenChangedIos.bind(this)),this.videoTag.addEventListener("webkitbeginfullscreen",this.onFullscreenChangedIos.bind(this))),this.pendingFullscreenSubscriber=new ji(t,e.getPendingFullscreenDependencies,this.onPendingFullscreenRequestChanged.bind(this)),this.adStatusSubscriber=new ji(t,e.getAdStatusDependencies,this.onAdStatusChanged.bind(this))}return Vi()(e,null,[{key:"createInstance",value:function(t,n){return new e(t,n)}}]),Vi()(e,null,[{key:"getPendingFullscreenDependencies",value:function(e){return[gn.pendingFullscreenRequest(e)]}},{key:"getAdStatusDependencies",value:function(e){return[_i.adStatus(e)]}}]),e}();function us(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function cs(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?us(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):us(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var ls,ds=function(e){return function(e){return e&&window.monti.playerConfigs&&window.monti.playerConfigs[e]}(e)?function(e){return window.monti.playerConfigs[e]}(e):window.monti.playerConfigs?window.monti.playerConfigs&&window.monti.playerConfigs[Object.keys(window.monti.playerConfigs)[0]]:null},ps=function e(t){var n=this;Ai()(this,e),f()(this,"videoTag",void 0),f()(this,"isBufferError",void 0),f()(this,"hls",void 0),f()(this,"hlsSetup",function(e,t,r,i){n.initiateHls(e),n.loadHlsSource(e,t,r,i)}),f()(this,"detachMedia",function(){Un(n.hls)||(n.hls.detachMedia(),n.hls.destroy(),n.hls=null)}),f()(this,"initiateHls",function(e){n.hls=new e,n.hls.attachMedia(n.videoTag)}),f()(this,"loadHlsSource",function(e,t,r,i){n.hls.on(e.Events.MEDIA_ATTACHED,function(){n.hls.loadSource(t)}),n.hls.on(e.Events.ERROR,function(t,o){n.mapHlsToErrors(e,o,i),t.details===e.ErrorDetails.BUFFER_STALLED_ERROR&&(r(!0),n.isBufferError=!0)}),n.hls.on(e.Events.FRAG_BUFFERED,function(){n.isBufferError&&(r(!1),n.isBufferError=!1)})}),f()(this,"mapHlsToErrors",function(e,t,r){if(t.fatal)switch(t.type){case e.ErrorTypes.NETWORK_ERROR:r(Xn.GENERAL_ERROR),n.hls.startLoad();break;case e.ErrorTypes.MEDIA_ERROR:r(Xn.GENERAL_ERROR),n.hls.recoverMediaError();break;default:r(Xn.GENERAL_ERROR),n.hls.destroy()}}),this.hls=void 0,this.videoTag=t,this.isBufferError=!1},fs=function e(){var t=this;Ai()(this,e),f()(this,"videoStreaming",void 0),f()(this,"hlsLibrarySetup",function(e,n,r,i){Un(t.videoStreaming)||t.videoStreaming.detachMedia(),t.videoStreaming=new ps(e),t.videoStreaming.hlsSetup(ls,n,r,i)})};f()(fs,"shouldLoadVideoStreamingSrcDirectly",function(e,t,n){return"no-need"===n&&!(""===e.canPlayType("application/vnd.apple.mpegurl"))}),f()(fs,"shouldUseHlsLibrary",function(e,t){return"success"===t&&(ls=void 0!==window.Hls?Hls:mmHls).isSupported()}),f()(fs,"isValidHlsUrl",function(e){return!Un(e)&&!e.includes(".mp4")}),f()(fs,"suitableVideoSource",function(e,t,n){return fs.isValidHlsUrl(t)?fs.shouldUseHlsLibrary(t,n)?"m3u8 with hls":fs.shouldLoadVideoStreamingSrcDirectly(e,t,n)?"m3u8 directly":"loading"!==n?"mp4":"":"mp4"}),f()(fs,"loadHlsVideoDirectly",function(e,t){e.setAttribute("src",t),e.load()});var hs=function(e){return function(t){t({type:"[MONETIZATION] change pending ad status",payload:{type:e}})}},ys="video/mp4",gs="application/vnd.apple.mpegurl",vs=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTag",void 0),f()(this,"prerollEnabled",void 0),f()(this,"pendingVideoStatusSubscriber",void 0),f()(this,"videoStreamingManager",void 0),f()(this,"videoDataSubscriber",void 0),f()(this,"hlsLoadingStatusSubscriber",void 0),f()(this,"newVideoDataLoaded",void 0),f()(this,"onHlsLoadingStatusChanged",function(e){"success"===Fi.loadingHLSStatus(e)&&(r.newVideoDataLoaded=!0,r.onPendingVideoStatusChanged(e))}),f()(this,"onPendingVideoStatusChanged",function(e){var t=hn.pendingVideoTagStatus(e),n=Dn.sources(e),i=Fi.loadingHLSStatus(e),o="blocked"===Fi.loadingImaStatus(e);r.handlePendingVideoStatus(t,n,i,o)}),f()(this,"onVideoDataChanged",function(){r.newVideoDataLoaded=!0}),f()(this,"sendPrerollPlayRequest",function(){var e=r.store.dispatch;hs("playPreroll")(e)}),f()(this,"handlePlayRequest",function(e,t,n){var i=r.store.dispatch;if(e&&e.length>0){if(r.newVideoDataLoaded&&(r.loadVideoSource(r.videoTag,e,t),r.newVideoDataLoaded=!1,r.prerollEnabled&&!n))return void r.sendPrerollPlayRequest();r.videoTag.play().catch(function(e){return console.error("Error playing the video: ",e)})}else dn(Xn.VIDEO_ERROR)(i)}),f()(this,"handlePendingVideoStatus",function(e,t,n,i){switch(e.type){case"play":r.handlePlayRequest(t,n,i);break;case"resume":r.videoTag.play().catch(function(e){return console.error("Error resuming the video: ",e)});break;case"pause":r.videoTag.pause();break;case"replay":r.videoTag.currentTime=0,r.videoTag.play().catch(function(e){return console.error("Error replaying the video: ",e)});break;case"seekTo":r.videoTag.pause(),r.videoTag.currentTime=e.value}}),f()(this,"loadMp4Source",function(e,t,n){var r=Ra(t,ys);n.setAttribute("src",r),n.load()}),f()(this,"loadVideoSource",function(e,t,n){var i=r.store.dispatch,o=Ra(t,gs);switch(fs.suitableVideoSource(e,o,n)){case"mp4":r.loadMp4Source(n,t,e);break;case"m3u8 with hls":r.videoStreamingManager.hlsLibrarySetup(e,o,function(e){return un(e)(i)},function(e){return dn(e)(i)});break;case"m3u8 directly":fs.loadHlsVideoDirectly(e,o)}}),this.store=t;var i=t.getState;this.videoStreamingManager=new fs,this.videoTag=document.getElementById(En(n)),this.prerollEnabled=bi.prerollEnabled(i()),this.pendingVideoStatusSubscriber=new ji(t,e.getPendingVideoStatusDependencies,this.onPendingVideoStatusChanged.bind(this)),this.videoDataSubscriber=new ji(t,e.getVideoDataDependencies,this.onVideoDataChanged.bind(this)),this.hlsLoadingStatusSubscriber=new ji(t,e.getHLSLoadingStatusDependencies,this.onHlsLoadingStatusChanged.bind(this))}return Vi()(e,null,[{key:"createInstance",value:function(t,n){return new e(t,n)}}]),Vi()(e,null,[{key:"getHLSLoadingStatusDependencies",value:function(e){return[Fi.loadingHLSStatus(e)]}},{key:"getPendingVideoStatusDependencies",value:function(e){return[hn.pendingVideoTagStatus(e)]}},{key:"getVideoDataDependencies",value:function(e){return[Cn.videoData(e)]}}]),e}();function ms(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function bs(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?ms(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):ms(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var Os={READY_EVENT:"ready",PLAY_EVENT:"play",PAUSE_EVENT:"pause",TIME_EVENT:"time",SEEK_EVENT:"seek",COMPLETE_EVENT:"complete",VOLUME_EVENT:"volume",MUTE_EVENT:"mute"},_s=Object.values(Os),Ss={FULLSCREEN_EVENT:"fullscreen",ANCHOR_STATUS_EVENT:"anchorStatusChanged",ANCHOR_CLOSED_EVENT:"anchorClosed"},Es={AD_PLAY_EVENT:"adPlay",AD_PAUSE_EVENT:"adPause",AD_RESUME_EVENT:"adResume",AD_COMPLETE_EVENT:"adComplete",AD_TIME_EVENT:"adTime",AD_MUTE_EVENT:"adMute",AD_SKIPPED_EVENT:"adSkipped",AD_ERROR_EVENT:"adError",AD_BLOCK_EVENT:"adBlock",AD_REQUEST_EVENT:"adRequest",AD_OPPORTUNITY_EVENT:"adOpportunity",AD_IMPRESSION_EVENT:"adImpression"},ws=Object.values(Es),Ps=Object.values(bs(bs(bs({},Os),Es),Ss)),Ts=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"eventsCallbacksHandler",void 0),f()(this,"store",void 0),f()(this,"videoStatusSubscriber",void 0),f()(this,"videoMuteSubscriber",void 0),f()(this,"videoVolumeSubscriber",void 0),f()(this,"videoTimeFragmentSubscriber",void 0),f()(this,"videoListStoreSubscriber",void 0),f()(this,"previousVideoTagStatus",void 0),f()(this,"startSeekTime",0),f()(this,"canHandleReady",function(e,t,n){if(t===Os.READY_EVENT){var r=Cn.videoList(e);if(Array.isArray(r)&&r.length>0)return n(),!0}return!1}),f()(this,"canBeHandled",function(e,t){var n=r.store.getState;return r.canHandleReady(n(),e,t)}),f()(this,"reportSeekEnd",function(e){var t={position:hn.currentVideoTimeFragment(e),offset:r.startSeekTime};r.eventsCallbacksHandler.onEvent(Os.SEEK_EVENT,t)}),f()(this,"onMuteStateChanged",function(e){var t=gn.muted(e);r.eventsCallbacksHandler.onEvent(Os.MUTE_EVENT,{state:t})}),f()(this,"onVolumeChanged",function(e){var t=gn.muted(e),n=gn.volume(e);r.eventsCallbacksHandler.onEvent(Os.VOLUME_EVENT,{level:t?0:n})}),f()(this,"onVideoTimeFragmentChanged",function(e){var t=hn.currentVideoTimeFragment(e),n=hn.currentVideoDuration(e);r.eventsCallbacksHandler.onEvent(Os.TIME_EVENT,{duration:n,position:t})}),f()(this,"onVideoListChanged",function(){r.eventsCallbacksHandler.onEvent(Os.READY_EVENT)}),this.store=t,this.eventsCallbacksHandler=n,this.videoStatusSubscriber=new ji(t,e.getVideoStatusDependencies,this.onVideoStatusChanged.bind(this)),this.videoMuteSubscriber=new ji(t,e.getVideoMuteDependencies,this.onMuteStateChanged.bind(this)),this.videoVolumeSubscriber=new ji(t,e.getVolumeDependencies,this.onVolumeChanged.bind(this)),this.videoTimeFragmentSubscriber=new ji(t,e.getVideoTimeDependencies,this.onVideoTimeFragmentChanged.bind(this)),this.videoListStoreSubscriber=new ji(t,e.getVideoListDependencies,this.onVideoListChanged.bind(this)),this.previousVideoTagStatus=hn.videoTagStatus(t.getState())}return Vi()(e,[{key:"onVideoStatusChanged",value:function(e){var t=hn.videoTagStatus(e);switch("seeking"===this.previousVideoTagStatus&&this.reportSeekEnd(e),t){case"paused":this.eventsCallbacksHandler.onEvent(Os.PAUSE_EVENT);break;case"seeking":this.startSeekTime=hn.currentVideoTimeFragment(e);break;case"complete":this.eventsCallbacksHandler.onEvent(Os.COMPLETE_EVENT);break;case"playing":this.eventsCallbacksHandler.onEvent(Os.PLAY_EVENT)}this.previousVideoTagStatus=t}}],[{key:"getVideoStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}}]),e}();f()(Ts,"getVideoMuteDependencies",function(e){return[gn.muted(e)]}),f()(Ts,"getVolumeDependencies",function(e){return[gn.volume(e)]}),f()(Ts,"getVideoTimeDependencies",function(e){return[hn.currentVideoTimeFragment(e)]}),f()(Ts,"getVideoListDependencies",function(e){return[Cn.videoList(e)]}),f()(Ts,"isContentEvent",function(e){return _s.some(function(t){return t===e})});var As=function e(t,n){var r=this;Ai()(this,e),f()(this,"eventsCallbacksHandler",void 0),f()(this,"store",void 0),f()(this,"fullscreenSubscriber",void 0),f()(this,"anchorStatusSubscriber",void 0),f()(this,"anchorDisabledByUserSubscriber",void 0),f()(this,"onFullscreenChanged",function(e){var t=gn.isFullscreenOn(e);r.eventsCallbacksHandler.onEvent(Ss.FULLSCREEN_EVENT,{state:t})}),f()(this,"onAnchorStatusChanged",function(e){var t="active"===Pr(e)?"activated":"deactivated";r.eventsCallbacksHandler.onEvent(Ss.ANCHOR_STATUS_EVENT,{state:t})}),f()(this,"onAnchorDisabledByUser",function(e){if(wr(e)){var t=hn.currentVideoTimeFragment(e);r.eventsCallbacksHandler.onEvent(Ss.ANCHOR_CLOSED_EVENT,{position:t})}}),this.store=t,this.eventsCallbacksHandler=n,this.fullscreenSubscriber=new ji(t,e.getFullscreenDependencies,this.onFullscreenChanged.bind(this)),this.anchorStatusSubscriber=new ji(t,e.getAnchorStatusDependencies,this.onAnchorStatusChanged.bind(this)),this.anchorDisabledByUserSubscriber=new ji(t,e.getAnchorDisabledByUserDependencies,this.onAnchorDisabledByUser.bind(this))};f()(As,"getFullscreenDependencies",function(e){return[gn.isFullscreenOn(e)]}),f()(As,"getAnchorStatusDependencies",function(e){return[Pr(e)]}),f()(As,"getAnchorDisabledByUserDependencies",function(e){return[wr(e)]});var Cs=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"eventsCallbacksHandler",void 0),f()(this,"adStatusSubscriber",void 0),f()(this,"adImpressionSubscriber",void 0),f()(this,"adOpportunitySubscriber",void 0),f()(this,"adTimeSubscriber",void 0),f()(this,"adMuteSubscriber",void 0),f()(this,"adProviderLoadingStatusSubscriber",void 0),f()(this,"previousAdStatus",void 0),f()(this,"canBeHandled",function(e,t){var n=r.store.getState;switch(Fi.loadingImaStatus(n())){case"loading":return!1;case"success":case"error":return!0;case"blocked":return t(),!0;case"":default:return!1}}),f()(this,"onAdStatusChanged",function(e){var t=_i.adStatus(e),n=_i.currentAdTag(e);switch(t){case"requested":r.eventsCallbacksHandler.onEvent(Es.AD_REQUEST_EVENT,{tag:n});break;case"paused":r.eventsCallbacksHandler.onEvent(Es.AD_PAUSE_EVENT,{tag:n});break;case"completed":r.eventsCallbacksHandler.onEvent(Es.AD_COMPLETE_EVENT,{tag:n});break;case"skipped":r.eventsCallbacksHandler.onEvent(Es.AD_SKIPPED_EVENT,{tag:n});break;case"playing":"paused"===r.previousAdStatus?r.eventsCallbacksHandler.onEvent(Es.AD_RESUME_EVENT,{tag:n}):r.eventsCallbacksHandler.onEvent(Es.AD_PLAY_EVENT,{tag:n});break;case"error":var i=_i.adErrorMessage(e);r.eventsCallbacksHandler.onEvent(Es.AD_ERROR_EVENT,{tag:n,message:i})}r.previousAdStatus=t}),f()(this,"onAtTimeChanged",function(e){var t=_i.adCurrentTime(e),n=_i.currentAdTag(e),i=_i.adDuration(e);r.eventsCallbacksHandler.onEvent(Es.AD_TIME_EVENT,{position:t,tag:n,duration:i})}),f()(this,"onAdMuteChanged",function(e){var 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This 13-year-old, Besart Kabashi, received something akin to royal tutoring. “I took Besart on that year as my private student,” Louhivuori told me in his office, which boasted a Beatles “Yellow Submarine” poster on the wall and an electric guitar in the closet. When Besart was not studying science, geography and math, he was parked next to Louhivuori’s desk at the front of his class of 9- and 10-year- olds, cracking open books from a tall stack, slowly reading one, then another, then devouring them by the dozens. By the end of the year, the son of Kosovo war refugees had conquered his adopted country’s vowel-rich language and arrived at the realization that he could, in fact, learn. Years later, a 20-year-old Besart showed up at Kirkkojarvi’s Christmas party with a bottle of Cognac and a big grin. “You helped me,” he told his former teacher. Besart had opened his own car repair firm and a cleaning company. “No big fuss,” Louhivuori told me. “This is what we do every day, prepare kids for life.” This tale of a single rescued child hints at some of the reasons for the tiny Nordic nation’s staggering record of education success, a phenomenon that has inspired, baffled and even irked many of America’s parents and educators. Finnish schooling became an unlikely hot topic after the 2010 documentary film Waiting for “Superman” contrasted it with America’s troubled public schools. “Whatever it takes” is an attitude that drives not just Kirkkojarvi’s 30 teachers, but most of Finland’s 62,000 educators in 3,500 schools from Lapland to Turku—professionals selected from the top 10 percent of the nation’s graduates to earn a required master’s degree in education. Many schools are small enough so that teachers know every student. If one method fails, teachers consult with colleagues to try something else. They seem to relish the challenges. Nearly 30 percent of Finland’s children receive some kind of special help during their first nine years of school. The school where Louhivuori teaches served 240 first through ninth graders last year; and in contrast with Finland’s reputation for ethnic homogeneity, more than half of its 150 elementary-level students are immigrants—from Somalia, Iraq, Russia, Bangladesh, Estonia and Ethiopia, among other nations. “Children from wealthy families with lots of education can be taught by stupid teachers,” Louhivuori said, smiling. “We try to catch the weak students. It’s deep in our thinking.” Advertisement scroll for more The transformation of the Finns’ education system began some 40 years ago as the key propellent of the country’s economic recovery plan. Educators had little idea it was so successful until 2000, when the first results from the Programme for International Student Assessment (PISA), a standardized test given to 15-year-olds in more than 40 global venues, revealed Finnish youth to be the best young readers in the world. Three years later, they led in math. By 2006, Finland was first out of 57 countries (and a few cities) in science. In the 2009 PISA scores released last year, the nation came in second in science, third in reading and sixth in math among nearly half a million students worldwide. “I’m still surprised,” said Arjariita Heikkinen, principal of a Helsinki comprehensive school. “I didn’t realize we were that good.” In the United States, which has muddled along in the middle for the past decade, government officials have attempted to introduce marketplace competition into public schools. In recent years, a group of Wall Street financiers and philanthropists such as Bill Gates have put money behind private-sector ideas, such as vouchers, data-driven curriculum and charter schools, which have doubled in number in the past decade. President Obama, too, has apparently bet on compe­tition. His Race to the Top initiative invites states to compete for federal dollars using tests and other methods to measure teachers, a philosophy that would not fly in Finland. “I think, in fact, teachers would tear off their shirts,” said Timo Heikkinen, a Helsinki principal with 24 years of teaching experience. “If you only measure the statistics, you miss the human aspect.”

      The facts show that America has it all wrong in putting to much emphasis on national "data-driven" competition. These approaches take away from the unique aspects of each child.

    2. t was the end of term at Kirkkojarvi Comprehensive School in Espoo, a sprawling suburb west of Helsinki, when Kari Louhivuori, a veteran teacher and the school’s principal, decided to try something extreme—by Finnish standards. One of his sixth-grade students, a Kosovo-Albanian boy, had drifted far off the learning grid, resisting his teacher’s best efforts. The school’s team of special educators—including a social worker, a nurse and a psychologist—convinced Louhivuori that laziness was not to blame. 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u=e.getNextSpecificMidrollTime(o,n);return{midrollNumber:o.indexOf(u)+1,currentTime:n,midrollTime:u,mediaId:a}}return null}},{key:"isMidrollAlreadyPlayed",value:function(e,t){return-1!==e.indexOf(t)}},{key:"isMidrollReached",value:function(t){var n=hn.currentVideoTime(t),r=bi.midrolls(t),i=r.every,o=r.on,a=_i.playedMidrolls(t);if(!Un(i)&&n>0){var s=e.getNextReocurringMidrollNumber(i,n),u=s*i;return!this.isMidrollAlreadyPlayed(a,s)&&e.isTimeInPreAdRange(n,u)}if(!Un(o)){var c=e.getNextSpecificMidrollTime(o,n),l=o.indexOf(c)+1;return l>0&&!this.isMidrollAlreadyPlayed(a,l)}return!1}},{key:"shouldRequestAd",value:function(e){var t=_i.adStatus(e);return!Bi(e)&&!Hi(t)&&this.isMidrollReached(e)}},{key:"isOnAdTime",value:function(t){var n=hn.currentVideoTime(t),r=bi.midrolls(t),i=r.every,o=r.on,a=_i.playedMidrolls(t);if(Bi(t))return!1;if(!Un(i)){var s=e.getNextReocurringMidrollNumber(i,n);return 0!==n&&n%i===0&&!this.isMidrollAlreadyPlayed(a,s)}if(!Un(o)){var u=o.indexOf(n);return-1!==u&&!this.isMidrollAlreadyPlayed(a,u)}return!1}}]),e}(),Wi=function(){function e(t){var n=this;Ai()(this,e),f()(this,"referrerUrl",void 0),f()(this,"staticAdTag",void 0),f()(this,"generate",function(e,t){var r=encodeURIComponent(n.referrerUrl);return Un(n.staticAdTag)?n.adTagFromApi(e,r,t):n.parseAdTag(n.staticAdTag,e,r,t)}),this.staticAdTag=t,this.referrerUrl=window.location.href}return Vi()(e,[{key:"parseAdTag",value:function(t,n,r,i){var o=t.replace("##AdUnit##",e.parseAdName(n)).replace("##DESCRIPTION_URL_UNESC##",r).replace("##REFERRER_URL_UNESC##",encodeURIComponent(this.referrerUrl)).replace("##CACHEBUSTER##",e.cacheBuster(n)).replace("##MIDROLL_ORDER##",e.adIndexFromName(n));return o=e.replaceVideoId(o,"##VIDEO_ID##",i),o=e.addHacksToAdTag(o)}},{key:"adTagFromApi",value:function(e,t,n){try{var r=window.getVideoTag(t,e);return Un(r)?null:this.parseAdTag(r,e,t,n)}catch(i){return null}}}],[{key:"getCCPAConsent",value:function(t){try{var n="";return window.__uspapi&&window.__uspapi("getUSPData",1,function(e,t){t&&(n=e.uspString)}),e.setSearchParamToAdTag(t,"us_privacy",n)}catch(r){return t}}},{key:"replaceVideoId",value:function(e,t,n){return e.replace(t,n).replace(encodeURIComponent(t),n).replace(encodeURIComponent(encodeURIComponent(t)),n)}},{key:"cacheBuster",value:function(t){return"".concat((new Date).getTime()).concat(e.adIndexFromName(t))}},{key:"parseAdName",value:function(t){return t.startsWith("preroll")?"PR":"MR".concat(e.adIndexFromName(t))}},{key:"adIndexFromName",value:function(e){return e.replace(/[^\d]*/g,"")}}]),e}();f()(Wi,"setSearchParamToAdTag",function(e,t,n){var r=new URL(e),i=decodeURIComponent(n);return r.searchParams.set(t,i),r.href}),f()(Wi,"getSearchParamFromAdTag",function(e,t){return new URL(e).searchParams.get(t)}),f()(Wi,"addHacksToAdTag",function(e){var t=e,n=Wi.getSearchParamFromAdTag(t,"cust_params");if(!jn(window.mmAPSbids)&&!Un(n)){var r="".concat(window.mmAPSbids,"&").concat(n);t=Wi.setSearchParamToAdTag(t,"cust_params",r)}if(!jn(window.shouldPlayAdRules)){var i=window.shouldPlayAdRules?"1":"0";t=Wi.setSearchParamToAdTag(t,"ad_rule",i)}return t=Wi.getCCPAConsent(t)});var zi=function(){function e(t,n){Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"adsScheduler",void 0),f()(this,"previousVideoTagStatus",void 0);var r=t.getState;this.store=t,this.adsScheduler=n,this.previousVideoTagStatus=hn.videoTagStatus(r()),this.videoTagStatusSubscriber=new ji(t,e.getVideoTagStatusDependencies,this.onVideoTagStatusChanged.bind(this))}return Vi()(e,[{key:"onVideoTagStatusChanged",value:function(t){var n=hn.videoTagStatus(t),r=_i.adStatus(t);"seeking"===this.previousVideoTagStatus&&(Hi(r)?this.adsScheduler.onSeekedWhileAdInProgress():e.isSeekedOverMidroll(t)&&this.adsScheduler.onSeekToAdOpportunity(e.getSeekedMidroll(t))),this.previousVideoTagStatus=n}}],[{key:"getVideoTagStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}},{key:"getClosestSkippedUnplayedMidroll",value:function(e,t){for(var n=t;n>0;n-=1)if(-1===e.indexOf(n))return n;return null}},{key:"getClosestLowerSeekedMidrollNumber",value:function(e,t){var n=In()(e).reverse().find(function(e){return e<=t});return e.indexOf(n)+1}},{key:"getSeekedSpecificMidroll",value:function(e,t,n,r){var i=this.getClosestLowerSeekedMidrollNumber(e,t),o=this.getClosestSkippedUnplayedMidroll(r,i);return{midrollNumber:o,currentTime:t,midrollTime:e[o-1],mediaId:n}}},{key:"isSeekedOverSpecificMidroll",value:function(e,t,n){if(jn(e))return!1;var r=this.getClosestLowerSeekedMidrollNumber(e,n);return 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t="midroll".concat(e.midrollNumber);return r.adTagGenerator.generate(t,e.mediaId)}),f()(this,"generatePrerollTag",function(e,t){var n="preroll".concat(t);return r.adTagGenerator.generate(n,e)}),f()(this,"onAdTimeReached",function(){r.monetization.onMidrollAdOpportunity()}),f()(this,"onPreAdTimeReached",function(e){r.onPreMidrollAdOpportunity(e)}),f()(this,"onSeekToAdOpportunity",function(e){r.onPreMidrollAdOpportunity(e)}),f()(this,"isMidrollAlreadyRequested",function(e){return e.midrollNumber===r.lastRequestedMidroll.midrollNumber&&e.mediaId===r.lastRequestedMidroll.mediaId&&e.midrollTime===r.lastRequestedMidroll.midrollTime}),f()(this,"onPreMidrollAdOpportunity",function(e){if(Un(r.lastRequestedMidroll)||!r.isMidrollAlreadyRequested(e)){r.lastRequestedMidroll=e;var t=r.generateMidrollTag(e);r.monetization.onPreMidrollAdOpportunity(e,t)}}),f()(this,"onPrerollReached",function(e,t){var n=r.generatePrerollTag(e,t);r.monetization.onPrerollAdOpportunity(n)}),f()(this,"onSeekedWhileAdInProgress",function(){r.monetization.onMidrollAdOpportunity()});var i=t.getState;this.monetization=n,this.videoTimeSubscriber=new qi(t,this),this.videoSeekSubscriber=new zi(t,this),this.prerollScheduler=new Gi(t,this);var o=_i.adTagUrlTemplate(i());this.adTagGenerator=new Wi(o)},Yi=function(){function e(){Ai()(this,e)}return Vi()(e,null,[{key:"generateAdRequest",value:function(e,t,n){var r=new google.ima.AdsRequest;return r.adTagUrl=e,Fn()||r.setAdWillPlayMuted(t),r.vastLoadTimeout=n,r}}]),e}(),Zi=function(e){return function(t){t({type:"[MONETIZATION] change ad status",payload:e})}},Xi=function(e){return function(t){t({type:"[COMMON] set pending video status",payload:{pendingStatusObject:{type:e,value:""}}})}},Ji=function(e){return function(t){t({type:"[MONETIZATION] change loading ad status",payload:e})}},Qi=function(e){return function(t){t({type:"[MONETIZATION] update ad 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t=a.store,n=t.getState,r=t.dispatch,i=gn.volume(n());Bn()||gn.muted(n())?(e.setVolume(0),Qi(!0)(r)):(e.setVolume(gn.volume(n())),eo(i)(r),Qi(!1)(r))}),f()(this,"createIMAAdManager",function(t){a.IMAAdManager=t.getAdsManager(a.adVideoElement,e.getAdsRenderingSettings()),a.setAdVolume(a.IMAAdManager)}),f()(this,"registerToAdManagerEvents",function(){a.IMAAdManager.addEventListener(google.ima.AdErrorEvent.Type.AD_ERROR,a.onAdError),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.CONTENT_PAUSE_REQUESTED,a.onContentPauseRequested),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.CONTENT_RESUME_REQUESTED,a.onContentResumeRequested),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.STARTED,a.onAdStarted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.IMPRESSION,a.onAdImpression),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.SKIPPED,a.onAdSkipped),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.COMPLETE,a.onAdCompleted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.PAUSED,a.onAdPaused),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.RESUMED,a.onAdStarted),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.AD_PROGRESS,a.onAdProgressChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.VOLUME_CHANGED,a.onVolumeChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.VOLUME_MUTED,a.onAdVolumeMutedChanged),a.IMAAdManager.addEventListener(google.ima.AdEvent.Type.ALL_ADS_COMPLETED,a.onAdCompleted)}),f()(this,"onIMAAdsManagerLoaded",function(e){var t=a.store.dispatch;a.createIMAAdManager(e),a.registerToAdManagerEvents(),Zi("loaded")(t)}),f()(this,"onAdError",function(e){var t=a.store.dispatch;!function(e){return function(t){t({type:"[MONETIZATION] change ad error",payload:e})}}(e.getError().getMessage())(t),Ji(!1),a.continuePlayingContent()}),f()(this,"onAdImpression",function(e){var t=a.store.dispatch,n=!e.getAd().g.vpaid;a.setPodInfo(e),function(e){e({type:"[MONETIZATION] increase ad impression counter"})}(t),function(e){return function(t){t({type:"[MONETIZATION] update is vast ad",payload:e})}}(n)(t)}),f()(this,"onVolumeChanged",function(e){var t=a.store.dispatch;eo(e.target.getVolume())(t)}),f()(this,"onAdVolumeMutedChanged",function(e){var t=a.store.dispatch;0===e.target.getVolume()?Qi(!0)(t):Qi(!1)(t)}),f()(this,"continuePlayingContent",function(){var e=a.store,t=e.getState,n=e.dispatch,r=hn.videoTagStatus(t());Xi("idle"===r?"play":"resume")(n)}),f()(this,"stopPlayingContent",function(){var e=a.store.dispatch;Xi("pause")(e)}),f()(this,"onContentPauseRequested",function(){a.stopPlayingContent()}),f()(this,"onContentResumeRequested",function(){a.continuePlayingContent()}),f()(this,"onAdPaused",function(){var e=a.store.dispatch;Zi("paused")(e)}),f()(this,"setPodInfo",function(e){var t=e&&e.getAd()&&e.getAd().getAdPodInfo();if(!Un(t)){var n=a.store.dispatch;!function(e,t){return function(n){n({type:"[MONETIZATION] change pod info",payload:{slotNumber:e,podNumber:t}})}}(t.getAdPosition(),a.totalAdRequestMadeAmount)(n)}}),f()(this,"onAdStarted",function(){var e=a.store,t=e.dispatch,n=e.getState,r=gn.volume(n());Zi("playing")(t),0===a.IMAAdManager.getVolume()?a.IMAAdManager.setVolume(0):window.shouldPlayAdRule||a.IMAAdManager.setVolume(r),a.onResize()}),f()(this,"onAdCompleted",function(){var e=a.store.dispatch;Zi("completed")(e)}),f()(this,"onAdSkipped",function(){var e=a.store.dispatch;Zi("skipped")(e)}),f()(this,"onResize",function(){Un(a.IMAAdManager)||(a.IMAAdManager.resize(a.videoPlayerElement.clientWidth,a.videoPlayerElement.clientHeight,google.ima.ViewMode.NORMAL),a.adContainerElement.style.height="".concat(a.videoPlayerElement.clientHeight,"px"))}),f()(this,"onAdProgressChanged",function(e){var t,n,r=a.store,i=r.dispatch,o=r.getState,s=e.getAdData().currentTime,u=e.getAdData().duration,c=_i.adDuration(o());(t=s,function(e){e({type:"[MONETIZATION] change ad current time",payload:t})})(i),c!==u&&(n=u,function(e){e({type:"[MONETIZATION] change ad duration",payload:n})})(i)}),f()(this,"onAnchorStatusChanged",function(){var e=a.store.getState;"processing"!==Pr(e())&&a.onResize()}),f()(this,"changeAdVolume",function(e){Un(a.IMAAdManager)||a.IMAAdManager.setVolume(e)}),f()(this,"changeAdMuted",function(e,t){Un(a.IMAAdManager)||(t?a.IMAAdManager.setVolume(0):a.IMAAdManager.setVolume(e))}),f()(this,"changeAdStatus",function(e){Un(a.IMAAdManager)||("playing"===e&&a.IMAAdManager.resume(),"paused"===e&&a.IMAAdManager.pause())});var s=t.getState;this.store=t,this.adVideoElement=r,this.videoPlayerElement=i,this.adContainerElement=n,this.adDisplayContainer=new google.ima.AdDisplayContainer(n,r),this.createAdLoader(s(),this.adDisplayContainer),this.adDisplayContainer.initialize(),this.anchorStatusStoreSubscriber=new ji(t,e.getAnchorDependencies,this.onAnchorStatusChanged.bind(this)),this.registerForWindowResize(),this.initMutationObserver(o)};f()(to,"getAdsRenderingSettings",function(){var e=new google.ima.AdsRenderingSettings;return e.restoreCustomPlaybackStateOnAdBreakComplete=!0,e.enablePreloading=!1,e.uiElements=[],e.loadVideoTimeout=15e3,e}),f()(to,"getAnchorDependencies",function(e){return[Pr(e)]});var no=function e(t,n,r,i,o,a){var s=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"playerId",void 0),f()(this,"adScheduler",void 0),f()(this,"adHandler",void 0),f()(this,"imaLoadingStatusSubscriber",void 0),f()(this,"adStatusSubscriber",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"adContainer",void 0),f()(this,"adVideoElement",void 0),f()(this,"videoPlayerElement",void 0),f()(this,"playerContainer",void 0),f()(this,"pendingMidrollAdPlay",!1),f()(this,"pendingPrerollAdPlay",!1),f()(this,"pendingPrerollAdTag",null),f()(this,"pendingMidrollNumber",null),f()(this,"pendingAdStatusStoreSubscriber",void 0),f()(this,"adMutedStoreSubscriber",void 0),f()(this,"adVolumeStoreSubscriber",void 0),f()(this,"onMidrollAdOpportunity",function(){var e=s.store,t=e.dispatch,n=e.getState,r=_i.adStatus(n()),i=bi.continuePlayingWhileWaitingForAd(n());"loaded"===r?s.playAd(!0):"requested"===r&&(s.pendingMidrollAdPlay=!0,i||(Xi("pause")(t),Ji(!0)(t))),function(e){e({type:"[MONETIZATION] increase ad Opportunity counter"})}(t)}),f()(this,"onPrerollAdOpportunity",function(e){var t=s.store,n=t.getState,r=t.dispatch,i=Fi.loadingImaStatus(n());Un(s.adHandler)?"loading"!==i&&""!==i||(Ji(!0)(r),s.pendingPrerollAdPlay=!0,s.pendingPrerollAdTag=e):(s.pendingPrerollAdPlay=!0,Ji(!0)(r),s.adHandler.loadNewAd(e,"preroll"))}),f()(this,"onPreMidrollAdOpportunity",function(e,t){Un(s.adHandler)||(e.currentTime>=e.midrollTime&&(s.pendingMidrollAdPlay=!0),s.pendingMidrollNumber=e.midrollNumber,s.adHandler.loadNewAd(t,"midroll"))}),f()(this,"hasPendingAd",function(){return s.hasPendingMidrollAdPlay()||s.hasPendingPrerollAdPlay()}),f()(this,"onAdStatusChanged",function(e){var t=s.store.dispatch,n=_i.adStatus(e);"completed"===n&&Ji(!1)(t);var r=bi.continuePlayingWhileWaitingForAd(e),i=_i.loadingAd(e);"playing"!==n&&"error"!==n||r||!i||Ji(!1)(t),s.hasPendingAd()&&"loaded"===n?s.playAd(s.hasPendingMidrollAdPlay()):s.hasPendingAd()&&"error"===n?(Ji(!1),s.clearPendingMidroll(),s.clearPendingPreroll()):Hi(n)||(Ji(!1),function(e){e({type:"[MONETIZATION] clear ad data"})}(t))}),f()(this,"clearPendingMidroll",function(){s.pendingMidrollNumber=null,s.pendingMidrollAdPlay=!1}),f()(this,"clearPendingPreroll",function(){s.pendingPrerollAdPlay=!1,s.pendingPrerollAdTag=null}),f()(this,"onVideoTagStatusChanged",function(e){"complete"===hn.videoTagStatus(e)&&function(e){e({type:"[MONETIZATION] clear played midrolls"})}(s.store.dispatch)}),f()(this,"hasPendingMidrollAdPlay",function(){return s.pendingMidrollAdPlay}),f()(this,"hasPendingPrerollAdPlay",function(){return s.pendingPrerollAdPlay}),f()(this,"playAd",function(e){var t,n=s.store.dispatch,r=s.adHandler.playAd();e?((t=s.pendingMidrollNumber,function(e){e({type:"[MONETIZATION] add 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oo.a.wrap(function(e){for(;;)switch(e.prev=e.next){case 0:if(!navigator.getBattery){e.next=7;break}return e.next=3,navigator.getBattery();case 3:t=e.sent,this.updateBatteryParams(t.level,t.charging),t.ondischargingtimechange=function(e){return n.updateBatteryParams(e.target.level,e.target.charging)},t.onchargingtimechange=function(e){return n.updateBatteryParams(e.target.level,e.target.charging)};case 7:case"end":return e.stop()}},e,this)}));return function(){return e.apply(this,arguments)}}()},{key:"updateBatteryParams",value:function(e,t){this.batteryLevel="".concat(100*e),this.batteryChargingState=t}},{key:"getBatteryLevel",value:function(){return this.batteryLevel}},{key:"getBatteryChargingState",value:function(){return this.batteryChargingState}},{key:"getConnectionSpeed",value:function(){return this.connectionSpeed}},{key:"getConnectionType",value:function(){return this.connectionType}}]),e}(),xo=function(){"undefined"===typeof 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Error('Reducer "'+t+"\" returned undefined during initialization. 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fa(fa({},e),{},{playbackMethod:Un(r)?e.playbackMethod:r,playerId:Un(i)?e.playerId:i,playerInstanceUniqId:n,playerMode:Fn()?"mobile":"desktop"})}(e,n.initiateParams,n.playerInstanceUniqId));case"[CORE] reset player data time params":return fa(fa({},e),{},{currentVideoTimeFragment:0,currentVideoBufferedTime:0,currentVideoDuration:0,currentVideoTime:0});case"[COMMON] set mute video":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{muted:t.payload})});case"[COMMON] set volume":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{volume:t.payload})});case"[COMMON] change selected settings category":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{selectedSettingsCategory:t.payload})});case"[COMMON] change settings speed":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{speed:t.payload})});case"[COMMON] change settings quality":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{quality:t.payload})});case"[COMMON] set fullscreen":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{fullscreen:fa(fa({},e.playerSettings.fullscreen),{},{isFullscreenOn:t.payload,pendingFullscreenRequest:""})})});case"[COMMON] set fullscreen request":return fa(fa({},e),{},{playerSettings:fa(fa({},e.playerSettings),{},{fullscreen:fa(fa({},e.playerSettings.fullscreen),{},{pendingFullscreenRequest:t.payload})})});case"[COMMON] set pending video status":var r=t.payload.pendingStatusObject;return fa(fa({},e),{},{pendingVideoTagStatus:fa({},r)});case"[COMMON] set player mode":return fa(fa({},e),{},{playerMode:t.payload});case"[CORE] update video current fragment position":return fa(fa({},e),{},{currentVideoTimeFragment:t.payload});case"[CORE] update video current position":return fa(fa({},e),{},{currentVideoTime:t.payload});case"[CORE] update video current buffered time":return fa(fa({},e),{},{currentVideoBufferedTime:t.payload});case"[CORE] update video current duration":return fa(fa({},e),{},{currentVideoDuration:t.payload});case"[CORE] change video tag status":return fa(fa({},e),{},{videoTagStatus:t.payload});case"[CORE] update player visibility":return fa(fa({},e),{},{playerVisibility:t.payload});case"[CORE] update placeholder visibility":return fa(fa({},e),{},{playerPlaceholderVisibility:t.payload});case"[CORE] change loading player status":return fa(fa({},e),{},{loadingPlayer:t.payload});case"[COMMON] show black screen with loader":return fa(fa({},e),{},{loader:fa(fa({},e.loader),{},{showBlackScreen:t.payload})});case"[CORE] set player size":return fa(fa({},e),{},{playerSize:t.payload});case"[COMMON] set error message":return fa(fa({},e),{},{errorMessage:t.payload});default:return e}},brandingData:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:va,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate 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ba(ba({},e),{},{anchoringAppearance:r||e.anchoringAppearance,canClose:Un(i)?e.canClose:i,orientation:Un(u)?e.orientation:u,closableAd:Un(o)?e.closableAd:o,closeAfter:Un(a)?e.closeAfter:a,continueStreaming:Un(s)?e.continueStreaming:s,stickyBelowClassName:Un(l)?e.stickyBelowClassName:l,width:Un(d)?e.width:d,margins:p,anchorData:ba(ba({},e.anchorData),{},{anchorEnabled:!0})})}return e}(e,t.payload.initiateParams));case"[COMMON] set anchor enable":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorEnabled:t.payload})});case"[ANCHOR] update is anchor status":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorStatus:t.payload})});case"[COMMON] set anchor disabled by user":return ba(ba({},e),{},{anchorData:ba(ba({},e.anchorData),{},{anchorDisabledByUser:t.payload})});default:return e}},monetization:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:wa,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Sa({},function(e,t){var n=t.monetization;if(Un(n))return e;var r=n.ad_tag,i=n.ad_type,o=n.vpaid_mode,a=n.ad_request_timeout,s=n.continue_content_play_while_waiting_for_ad,u=n.midrolls,c=u&&u.on&&u.on.sort(Wn),l=Un(s)?e.continuePlayingWhileWaitingForAd:s,d=c?c.indexOf(0):-1,p=-1!==d&&!l;return p&&(c=c.splice(d,1)),Sa(Sa({},e),{},{midrolls:Sa(Sa({},e.midrolls),{},{every:u&&u.every,on:c}),prerollEnabled:p,adRequestTimeout:Un(a)?e.adRequestTimeout:parseInt(a,10),vpaidMode:Un(o)?e.vpaidMode:o,continuePlayingWhileWaitingForAd:l,adsData:Sa(Sa({},e.adsData),{},{adType:Un(i)?e.adsData.adType:i,adTagUrlTemplate:Un(r)?e.adsData.adTagUrlTemplate:r})})}(e,t.payload.initiateParams));case"[COMMON] set new ad tag url template":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adTagUrlTemplate:t.payload})});case"[MONETIZATION] change ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adStatus:t.payload,adErrorMessage:null})});case"[MONETIZATION] change ad tag":var n=t.payload,r=n.adUnit,i=n.adTag;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{currentAdTag:i,adUnit:r})});case"[MONETIZATION] change pending ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{pendingAdStatus:t.payload})});case"[MONETIZATION] change ad error":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adStatus:"error",adErrorMessage:t.payload})});case"[MONETIZATION] increase ad impression counter":var o=e.adsData.adImpression;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adImpression:o+1})});case"[MONETIZATION] increase ad Opportunity counter":var a=e.adsData.adOpportunity;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOpportunity:a+1})});case"[MONETIZATION] add played midroll number":var s=e.adsData.playedMidrolls,u=In()(s);return u.push(t.payload),Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOrder:t.payload,playedMidrolls:u})});case"[MONETIZATION] clear played midrolls":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{playedMidrolls:[]})});case"[MONETIZATION] clear ad data":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adOrder:0,currentAdTag:null,adDuration:0,adUnit:""})});case"[MONETIZATION] change ad duration":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adDuration:t.payload})});case"[MONETIZATION] update is vast ad":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{isVastAd:t.payload})});case"[MONETIZATION] change ad current time":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adCurrentTime:t.payload})});case"[MONETIZATION] update ad muted":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adMuted:t.payload})});case"[MONETIZATION] change ad volume":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{adVolume:t.payload})});case"[MONETIZATION] change pod info":var c=t.payload,l=c.podNumber,d=c.slotNumber;return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{podNumber:l,slotNumber:d})});case"[MONETIZATION] change loading ad status":return Sa(Sa({},e),{},{adsData:Sa(Sa({},e.adsData),{},{loadingAd:t.payload})});default:return e}},mediaData:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:ja,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Va({},function(e,t){var n=t.content_type,r=t.media_id,i=t.display_title;return Va(Va({},e),{},{mediaType:Un(n)?e.mediaType:n,mediaId:Un(r)?e.mediaId:r,videoData:Va(Va({},e.videoData),{},{showTitle:!!Un(i)||i})})}(e,t.payload.initiateParams));case"[CORE] load video request":return Va(Va({},e),{},{loadingMedia:!0});case"[CORE] load video request success":return Va(Va({},e),{},{loadingMedia:!1,videoList:t.payload});case"[CORE] set current video":var n=t.payload,r=n.index,i=n.videoData;return Va(Va({},e),{},{activeVideoIndex:r,videoData:i});case"[CORE] load video request error":return Va(Va({},e),{},{loadingMedia:!1,mediaLoadingError:t.payload});case"[COMMON] media request":var o=t.payload.mediaRequestObject;return Va(Va({},e),{},{mediaRequest:Va({},o)});default:return e}},semanticOptions:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Ba,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Fa({},function(e,t){var n=t.semantic_options;if(Un(n))return e;var r=n.minimum_date_factor,i=n.promoted_videos,o=n.scan_images_on_page,a=n.scanned_element,s=n.scanned_element_type,u=n.scoped_keywords,c=n.tags;return Fa(Fa({},e),{},{minimumDateFactor:Un(r)?e.minimumDateFactor:r,promotedVideos:Un(i)?e.promotedVideos:i,scanImagesOnPage:Un(o)?e.scanImagesOnPage:o,scannedElement:Un(a)?e.scannedElement:a,scannedElementType:Un(s)?e.scannedElementType:s,scopedKeywords:Un(u)?e.scopedKeywords:u,tags:Un(c)?e.tags:c})}(e,t.payload.initiateParams));default:return e}},userInteraction:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Wa,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[USER INTERACTION] change user interaction":return qa(qa({},e),{},{userInteractionType:t.payload});default:return e}},splitView:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:$a,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Ga({},function(e,t){var n=t.anchor_options;if(!Un(n)){var r=n.split_view,i=n.split_view_ratio;return Ga(Ga({},e),{},{splitViewRatio:Un(r)||!r||Un(i)?e.splitViewRatio:i})}return e}(e,t.payload.initiateParams));default:return e}},discovery:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:Za,t=arguments.length>1?arguments[1]:void 0;switch(t.type){case"[CORE] initiate store":return Ya({},function(e,t){var n=t.next_video;return Un(n)?e:Ya(Ya({},e),{},{nextVideo:Xa(n)})}(e,t.payload.initiateParams));case"[DISCOVERY] show up next":return Ya(Ya({},e),{},{showUpNext:t.payload});case"[DISCOVERY] show skippable content":return Ya(Ya({},e),{},{showSkippableContent:t.payload});default:return e}}}),Qa=[],es=!1,ts=function e(){return function(t){return function(n){if(es)return Qa.push(n),null;es=!0;var r=t(n);return es=!1,Qa.length>0&&e()(t)(Qa.shift()),r}}},ns=function(e){var t=[];if(function(e){return!Un(e)&&!Un(e.enable_redux_debugging)&&e.enable_redux_debugging}(e)){var n=window&&window.__REDUX_DEVTOOLS_EXTENSION__&&window.__REDUX_DEVTOOLS_EXTENSION__();"function"===typeof n&&t.push(n)}var r=Et.apply(void 0,[wt(ua,ts)].concat(t));return vt(Ja,r)},rs=function(){function e(t){Ai()(this,e),f()(this,"playerVisibilitySubscriber",void 0),f()(this,"videoTagStatusSubscriber",void 0),f()(this,"shouldPlayIfLazyplay",!0),f()(this,"shouldPlayIfAutoplayWhenViewable",!0),f()(this,"videoPausedByObserver",!1),this.store=t,this.playerVisibilitySubscriber=null,this.videoTagStatusSubscriber=null,this.playAccordingToPlaybackMethod()}return Vi()(e,[{key:"lazyplayHandler",value:function(e){hn.playerVisibility(e)>=.5&&(this.playVideo(),this.shouldPlayIfLazyplay=!1)}},{key:"autoplayWhenViewableHandler",value:function(e){hn.playerVisibility(e)>=.5?this.playVideo():this.pauseVideo()}},{key:"onPlayerVisibilityChanged",value:function(e){var t=hn.playbackMethod(e);"lazyplay"===t&&this.shouldPlayIfLazyplay&&this.lazyplayHandler(e),"autoplay_when_viewable"===t&&this.shouldPlayIfAutoplayWhenViewable&&this.autoplayWhenViewableHandler(e)}},{key:"onVideoTagStatusChanged",value:function(e){var t=hn.videoTagStatus(e);"paused"!==t||this.videoPausedByObserver||(this.shouldPlayIfAutoplayWhenViewable=!1),"playing"===t&&(this.shouldPlayIfAutoplayWhenViewable=!0,this.videoPausedByObserver=!1)}},{key:"initiatePlayerVisibilitySubscriber",value:function(){this.playerVisibilitySubscriber=new ji(this.store,e.getPlayerVisibilityDependencies,this.onPlayerVisibilityChanged.bind(this))}},{key:"initiateVideoTagStatusSubscriber",value:function(){this.videoTagStatusSubscriber=new ji(this.store,e.getVideoTagStatusDependencies,this.onVideoTagStatusChanged.bind(this))}},{key:"playVideo",value:function(){var e=this.store,t=e.dispatch,n=e.getState;"idle"===hn.videoTagStatus(n())?on("play")(t):on("resume")(t)}},{key:"pauseVideo",value:function(){var e=this.store,t=e.dispatch,n=e.getState;"paused"!==hn.videoTagStatus(n())&&(this.videoPausedByObserver=!0,on("pause")(t))}},{key:"playAccordingToPlaybackMethod",value:function(){var e=this.store,t=e.dispatch,n=(0,e.getState)();switch(hn.playbackMethod(n)){case"autoplay":this.playVideo();break;case"lazyplay":this.initiatePlayerVisibilitySubscriber();break;case"autoplay_when_viewable":this.initiatePlayerVisibilitySubscriber(),this.initiateVideoTagStatusSubscriber();break;case"none":an(!1)(t)}}}],[{key:"getPlayerVisibilityDependencies",value:function(e){return[hn.playerVisibility(e)]}},{key:"getVideoTagStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}}]),e}(),is=function(){function e(t,n,r,i){var o=this;Ai()(this,e),f()(this,"videoStatusSubscriber",void 0),f()(this,"videoListSubscriber",void 0),f()(this,"mediaRequestSubscriber",void 0),f()(this,"playerVisibilitySubscriber",void 0),f()(this,"playbackMethodManager",void 0),f()(this,"store",void 0),f()(this,"loadContent",function(e,t,n,r){o.loadMedia(t,n,r).then(function(){o.playbackMethodManager=new rs(e)})}),f()(this,"loadMedia",function(e,t,n){var r=o.store,i=r.dispatch,a=r.getState,s=Dn.showTitle(a());if("semantic"===e){var u=pn.semanticOptions(a());return Na(u,s,n)(i)}return ka(t,s,n)(i)}),this.store=t,this.videoStatusSubscriber=new ji(t,e.getVideoStatusDependencies,this.onVideoStatusChanged.bind(this)),this.videoListSubscriber=new ji(t,e.getVideoListDependencies,this.onVideoListChanged.bind(this)),this.mediaRequestSubscriber=new ji(t,e.getMediaRequestDependencies,this.onMediaRequestChanged.bind(this)),this.playerVisibilitySubscriber=null,this.loadContent(t,r,n,i)}return Vi()(e,null,[{key:"createInstance",value:function(t,n,r,i){return new e(t,n,r,i)}}]),Vi()(e,[{key:"playNextVideo",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e),r=Cn.activeVideoIndex(e)+1;n.length>1&&r>=n.length&&(r=0),r<n.length&&(!function(e){e({type:"[CORE] reset player data time params"})}(t),La(r,n[r])(t),on("play")(t))}},{key:"playPreviousVideo",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e),r=Cn.activeVideoIndex(e);if(r>0){var i=r-1;La(i,n[i])(t),on("play")(t)}}},{key:"onVideoStatusChanged",value:function(e){"complete"===hn.videoTagStatus(e)&&this.playNextVideo(e)}},{key:"onVideoListChanged",value:function(e){var t=this.store.dispatch,n=Cn.videoList(e);!jn(n)&&n.length>0&&La(0,n[0])(t)}},{key:"onMediaRequestChanged",value:function(e){var t=Cn.mediaRequest(e);switch(t.type){case"playNewVideo":this.loadMedia("specific",t.value);break;case"playNextVideo":this.playNextVideo(e);break;case"playPreviousVideo":this.playPreviousVideo(e)}}}],[{key:"getVideoStatusDependencies",value:function(e){return[hn.videoTagStatus(e)]}},{key:"getVideoListDependencies",value:function(e){return[Cn.videoList(e)]}},{key:"getMediaRequestDependencies",value:function(e){return[Cn.mediaRequest(e)]}}]),e}(),os=function e(t){var n=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"onDependencyFailure",function(e,t){console.log("onDependencyFailure",e,t);var r=n.store,i=r.dispatch,o=r.getState;switch(e){case"ima":"blocked"!==Fi.loadingImaStatus(o())&&Qn("error")(i);break;case"hls":er("error")(i)}}),f()(this,"onDependencyReady",function(e){var t=n.store.dispatch;switch(e){case"ima":Qn("success")(t);break;case"hls":er("success")(t)}}),this.store=t},as=function(e){return function(t){t({type:"[COMMON] set fullscreen",payload:e})}},ss=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTag",void 0),f()(this,"pendingFullscreenSubscriber",void 0),f()(this,"adStatusSubscriber",void 0),f()(this,"playerUniqId",void 0),f()(this,"onAdStatusChanged",function(e){var t=_i.adStatus(e),n=r.videoTag.webkitDisplayingFullscreen;"playing"===t&&Bn()&&n&&r.exitFullscreen(r.videoTag)}),f()(this,"isPlayerInFullscreen",function(){var e=document,t=Bn()?En(r.playerUniqId):bn(r.playerUniqId);return Un(e.fullscreenElement)?!Un(e.webkitFullscreenElement)&&0===e.webkitFullscreenElement.id.localeCompare(t):0===e.fullscreenElement.id.localeCompare(t)}),f()(this,"changePlayerWidth",function(e){r.videoTag.style.width=e?"100%":"auto"}),f()(this,"onFullscreenChanged",function(){var e=r.store.dispatch,t=r.isPlayerInFullscreen();r.changePlayerWidth(t),as(t)(e)}),f()(this,"onFullscreenChangedIos",function(){var e=r.store.dispatch,t=r.videoTag.webkitDisplayingFullscreen;t||on("resume")(e),r.changePlayerWidth(t),as(t)(e)}),f()(this,"onPendingFullscreenRequestChanged",function(e){var t=gn.pendingFullscreenRequest(e);"enter"===t?r.enterFullscreen(r.videoTag):"exit"===t&&r.exitFullscreen(r.videoTag)}),f()(this,"getFullScreenElement",function(e,t){var n=document.getElementById(bn(r.playerUniqId));return Bn()?t:e?document:n}),f()(this,"enterFullscreen",function(e){var t=r.getFullScreenElement(!1,e);Bn()?t.webkitEnterFullscreen():document.webkitExitFullscreen?t.webkitRequestFullscreen():document.webkitCancelFullScreen?t.webkitRequestFullScreen():document.mozCancelFullScreen?t.mozRequestFullScreen():document.msExitFullscreen&&t.msRequestFullscreen()}),f()(this,"exitFullscreen",function(e){var t=r.getFullScreenElement(!0,e);document.webkitExitFullscreen||Bn()?t.webkitExitFullscreen():document.webkitCancelFullScreen?t.webkitCancelFullScreen():document.mozCancelFullScreen?t.mozCancelFullScreen():document.msExitFullscreen&&t.msExitFullscreen()}),this.store=t,this.videoTag=document.getElementById(En(n)),this.playerUniqId=n,document.addEventListener("fullscreenchange",this.onFullscreenChanged.bind(this)),document.addEventListener("webkitfullscreenchange",this.onFullscreenChanged.bind(this)),Bn()&&(this.videoTag.addEventListener("webkitendfullscreen",this.onFullscreenChangedIos.bind(this)),this.videoTag.addEventListener("webkitbeginfullscreen",this.onFullscreenChangedIos.bind(this))),this.pendingFullscreenSubscriber=new ji(t,e.getPendingFullscreenDependencies,this.onPendingFullscreenRequestChanged.bind(this)),this.adStatusSubscriber=new ji(t,e.getAdStatusDependencies,this.onAdStatusChanged.bind(this))}return Vi()(e,null,[{key:"createInstance",value:function(t,n){return new e(t,n)}}]),Vi()(e,null,[{key:"getPendingFullscreenDependencies",value:function(e){return[gn.pendingFullscreenRequest(e)]}},{key:"getAdStatusDependencies",value:function(e){return[_i.adStatus(e)]}}]),e}();function us(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function cs(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?us(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):us(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var ls,ds=function(e){return function(e){return e&&window.monti.playerConfigs&&window.monti.playerConfigs[e]}(e)?function(e){return window.monti.playerConfigs[e]}(e):window.monti.playerConfigs?window.monti.playerConfigs&&window.monti.playerConfigs[Object.keys(window.monti.playerConfigs)[0]]:null},ps=function e(t){var n=this;Ai()(this,e),f()(this,"videoTag",void 0),f()(this,"isBufferError",void 0),f()(this,"hls",void 0),f()(this,"hlsSetup",function(e,t,r,i){n.initiateHls(e),n.loadHlsSource(e,t,r,i)}),f()(this,"detachMedia",function(){Un(n.hls)||(n.hls.detachMedia(),n.hls.destroy(),n.hls=null)}),f()(this,"initiateHls",function(e){n.hls=new e,n.hls.attachMedia(n.videoTag)}),f()(this,"loadHlsSource",function(e,t,r,i){n.hls.on(e.Events.MEDIA_ATTACHED,function(){n.hls.loadSource(t)}),n.hls.on(e.Events.ERROR,function(t,o){n.mapHlsToErrors(e,o,i),t.details===e.ErrorDetails.BUFFER_STALLED_ERROR&&(r(!0),n.isBufferError=!0)}),n.hls.on(e.Events.FRAG_BUFFERED,function(){n.isBufferError&&(r(!1),n.isBufferError=!1)})}),f()(this,"mapHlsToErrors",function(e,t,r){if(t.fatal)switch(t.type){case e.ErrorTypes.NETWORK_ERROR:r(Xn.GENERAL_ERROR),n.hls.startLoad();break;case e.ErrorTypes.MEDIA_ERROR:r(Xn.GENERAL_ERROR),n.hls.recoverMediaError();break;default:r(Xn.GENERAL_ERROR),n.hls.destroy()}}),this.hls=void 0,this.videoTag=t,this.isBufferError=!1},fs=function e(){var t=this;Ai()(this,e),f()(this,"videoStreaming",void 0),f()(this,"hlsLibrarySetup",function(e,n,r,i){Un(t.videoStreaming)||t.videoStreaming.detachMedia(),t.videoStreaming=new ps(e),t.videoStreaming.hlsSetup(ls,n,r,i)})};f()(fs,"shouldLoadVideoStreamingSrcDirectly",function(e,t,n){return"no-need"===n&&!(""===e.canPlayType("application/vnd.apple.mpegurl"))}),f()(fs,"shouldUseHlsLibrary",function(e,t){return"success"===t&&(ls=void 0!==window.Hls?Hls:mmHls).isSupported()}),f()(fs,"isValidHlsUrl",function(e){return!Un(e)&&!e.includes(".mp4")}),f()(fs,"suitableVideoSource",function(e,t,n){return fs.isValidHlsUrl(t)?fs.shouldUseHlsLibrary(t,n)?"m3u8 with hls":fs.shouldLoadVideoStreamingSrcDirectly(e,t,n)?"m3u8 directly":"loading"!==n?"mp4":"":"mp4"}),f()(fs,"loadHlsVideoDirectly",function(e,t){e.setAttribute("src",t),e.load()});var hs=function(e){return function(t){t({type:"[MONETIZATION] change pending ad status",payload:{type:e}})}},ys="video/mp4",gs="application/vnd.apple.mpegurl",vs=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"store",void 0),f()(this,"videoTag",void 0),f()(this,"prerollEnabled",void 0),f()(this,"pendingVideoStatusSubscriber",void 0),f()(this,"videoStreamingManager",void 0),f()(this,"videoDataSubscriber",void 0),f()(this,"hlsLoadingStatusSubscriber",void 0),f()(this,"newVideoDataLoaded",void 0),f()(this,"onHlsLoadingStatusChanged",function(e){"success"===Fi.loadingHLSStatus(e)&&(r.newVideoDataLoaded=!0,r.onPendingVideoStatusChanged(e))}),f()(this,"onPendingVideoStatusChanged",function(e){var t=hn.pendingVideoTagStatus(e),n=Dn.sources(e),i=Fi.loadingHLSStatus(e),o="blocked"===Fi.loadingImaStatus(e);r.handlePendingVideoStatus(t,n,i,o)}),f()(this,"onVideoDataChanged",function(){r.newVideoDataLoaded=!0}),f()(this,"sendPrerollPlayRequest",function(){var e=r.store.dispatch;hs("playPreroll")(e)}),f()(this,"handlePlayRequest",function(e,t,n){var i=r.store.dispatch;if(e&&e.length>0){if(r.newVideoDataLoaded&&(r.loadVideoSource(r.videoTag,e,t),r.newVideoDataLoaded=!1,r.prerollEnabled&&!n))return void r.sendPrerollPlayRequest();r.videoTag.play().catch(function(e){return console.error("Error playing the video: ",e)})}else dn(Xn.VIDEO_ERROR)(i)}),f()(this,"handlePendingVideoStatus",function(e,t,n,i){switch(e.type){case"play":r.handlePlayRequest(t,n,i);break;case"resume":r.videoTag.play().catch(function(e){return console.error("Error resuming the video: ",e)});break;case"pause":r.videoTag.pause();break;case"replay":r.videoTag.currentTime=0,r.videoTag.play().catch(function(e){return console.error("Error replaying the video: ",e)});break;case"seekTo":r.videoTag.pause(),r.videoTag.currentTime=e.value}}),f()(this,"loadMp4Source",function(e,t,n){var r=Ra(t,ys);n.setAttribute("src",r),n.load()}),f()(this,"loadVideoSource",function(e,t,n){var i=r.store.dispatch,o=Ra(t,gs);switch(fs.suitableVideoSource(e,o,n)){case"mp4":r.loadMp4Source(n,t,e);break;case"m3u8 with hls":r.videoStreamingManager.hlsLibrarySetup(e,o,function(e){return un(e)(i)},function(e){return dn(e)(i)});break;case"m3u8 directly":fs.loadHlsVideoDirectly(e,o)}}),this.store=t;var i=t.getState;this.videoStreamingManager=new fs,this.videoTag=document.getElementById(En(n)),this.prerollEnabled=bi.prerollEnabled(i()),this.pendingVideoStatusSubscriber=new ji(t,e.getPendingVideoStatusDependencies,this.onPendingVideoStatusChanged.bind(this)),this.videoDataSubscriber=new ji(t,e.getVideoDataDependencies,this.onVideoDataChanged.bind(this)),this.hlsLoadingStatusSubscriber=new ji(t,e.getHLSLoadingStatusDependencies,this.onHlsLoadingStatusChanged.bind(this))}return Vi()(e,null,[{key:"createInstance",value:function(t,n){return new e(t,n)}}]),Vi()(e,null,[{key:"getHLSLoadingStatusDependencies",value:function(e){return[Fi.loadingHLSStatus(e)]}},{key:"getPendingVideoStatusDependencies",value:function(e){return[hn.pendingVideoTagStatus(e)]}},{key:"getVideoDataDependencies",value:function(e){return[Cn.videoData(e)]}}]),e}();function ms(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter(function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable})),n.push.apply(n,r)}return n}function bs(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?ms(Object(n),!0).forEach(function(t){f()(e,t,n[t])}):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):ms(Object(n)).forEach(function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))})}return e}var Os={READY_EVENT:"ready",PLAY_EVENT:"play",PAUSE_EVENT:"pause",TIME_EVENT:"time",SEEK_EVENT:"seek",COMPLETE_EVENT:"complete",VOLUME_EVENT:"volume",MUTE_EVENT:"mute"},_s=Object.values(Os),Ss={FULLSCREEN_EVENT:"fullscreen",ANCHOR_STATUS_EVENT:"anchorStatusChanged",ANCHOR_CLOSED_EVENT:"anchorClosed"},Es={AD_PLAY_EVENT:"adPlay",AD_PAUSE_EVENT:"adPause",AD_RESUME_EVENT:"adResume",AD_COMPLETE_EVENT:"adComplete",AD_TIME_EVENT:"adTime",AD_MUTE_EVENT:"adMute",AD_SKIPPED_EVENT:"adSkipped",AD_ERROR_EVENT:"adError",AD_BLOCK_EVENT:"adBlock",AD_REQUEST_EVENT:"adRequest",AD_OPPORTUNITY_EVENT:"adOpportunity",AD_IMPRESSION_EVENT:"adImpression"},ws=Object.values(Es),Ps=Object.values(bs(bs(bs({},Os),Es),Ss)),Ts=function(){function e(t,n){var r=this;Ai()(this,e),f()(this,"eventsCallbacksHandler",void 0),f()(this,"store",void 0),f()(this,"videoStatusSubscriber",void 0),f()(this,"videoMuteSubscriber",void 0),f()(this,"videoVolumeSubscriber",void 0),f()(this,"videoTimeFragmentSubscriber",void 0),f()(this,"videoListStoreSubscriber",void 0),f()(this,"previousVideoTagStatus",void 0),f()(this,"startSeekTime",0),f()(this,"canHandleReady",function(e,t,n){if(t===Os.READY_EVENT){var r=Cn.videoList(e);if(Array.isArray(r)&&r.length>0)return n(),!0}return!1}),f()(this,"canBeHandled",function(e,t){var n=r.store.getState;return r.canHandleReady(n(),e,t)}),f()(this,"reportSeekEnd",function(e){var t={position:hn.currentVideoTimeFragment(e),offset:r.startSeekTime};r.eventsCallbacksHandler.onEvent(Os.SEEK_EVENT,t)}),f()(this,"onMuteStateChanged",function(e){var t=gn.muted(e);r.eventsCallbacksHandler.onEvent(Os.MUTE_EVENT,{state:t})}),f()(this,"onVolumeChanged",function(e){var t=gn.muted(e),n=gn.volume(e);r.eventsCallbacksHandler.onEvent(Os.VOLUME_EVENT,{level:t?0:n})}),f()(this,"onVideoTimeFragmentChanged",function(e){var 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{"is_conflicting_with_other_jw_players":false,"programmatic_play_with_sound_on_desktop":false,"referrer_id":"af93e181-b289-0560-a2bf-808e93bb05bc","width":"100","comscore_publisher_id":"18120612","monetization":{"ad_type":"static_tag","continue_content_play_while_waiting_for_ad":false,"strategy":"on_player_load","ad_request_timeout":"10000","midrolls":{"on":[0]},"vpaid_mode":"ENABLED","ad_tag":"https://pubads.g.doubleclick.net/gampad/ads?sz=400x300|640x480|480x270|640x360&iu=/175840252/MMPlus/smithsonianmag/Video&impl=s&gdfp_req=1&env=vp&output=vast&unviewed_position_start=1&url=##REFERRER_URL_UNESC##&description_url=##DESCRIPTION_URL_UNESC##&correlator=##CACHEBUSTER##&cust_params=mm_midroll%3D##MIDROLL_ORDER##%26video_ID%3D##VIDEO_ID##"},"sponsorship":false,"player_identifier":"mplayer","recommendation_id":null,"brand_color":"#FF9900","powered_by_strip":true,"platform":"buffy","type":"video","config_name":"MM+ | Smithsonianmag | Podding","player_id":"3v9g2u2f","playlist_id":"fSkmeWKF","playback_method":"autoplay","anchor_viewability_method":"none","player_version":"v4","playlist_type":"semantic","semantic_options":{"scan_images_on_page":true,"scanned_element":"","tags":"geogrophy,nature,animals,habitat,outdoors,science,history","minimum_date_factor":30,"scanned_element_type":"tag","scoped_keywords":"mentalfloss","promoted_videos":[]},"script_destination":"mm","publisher_contribution":"floor8","general_script_description":"","brand_logo":"","brand_logo_click_url":"","next_video":"none","uniq_key":"af93e181-b289-0560-a2bf-808e93bb05bc","content_id":"fSkmeWKF","content_type":"semantic"})); Finland has vastly improved in reading, math and science literacy over the past decade in large part because its teachers are trusted to do whatever it takes to turn young lives around. This 13-year-old, Besart Kabashi, received something akin to royal tutoring.

      Kari Louhiuori, a principal at a Finnish school made a mostly unheaard of and uncanny decision to hold back an immigrant student from 6th grader named Besart because he hadnʻt felt that this young man was falling behind due to laziness but to a lack of comprehension. After a year of "royal tutoring," by allowing the boy to read at his own pace, it worked!

  5. Sep 2020
    1. Reviewer #1:

      Previous work has shown that the nuclear import of TyrRS is stimulated under stress and that nucleus-localized TyrRS functions through the transcriptional machinery to promote the expression of DNA damage response genes for cell protection. In this work, evidence is presented that nuclear TyrRS also inhibits bulk translation in a manner correlated with its association with several AARS-encoding genes and that for elongation factor eEF1A, and recruitment to these genes of HDACs. Mutation of the TyrRS NLS, whose function in nuclear localization provides for coupling between low tRNATyr binding and nuclear localization, was found to derepress bulk translation after prolonged oxidative stress by H2O2, without altering eIF2 phosphorylation levels or mTOR activation, and overexpression (o/e) of TyrRS can reduce protein synthesis, in a manner enhanced by the E196K mutation associated with Charcot-Marie-Tooth disease (CMT), shown previously to enhance TyrRS association with transcriptional co-repressors. ChIP-Seq of overexpressed V5-tagged TyrRS showed binding to only 17 sites, of which 15 are within gene coding sequences, among which four encode TyrRS, TrpRS, SerRS and GlyRS, and a fifth encodes elongation factor eEF1A. These results were confirmed by ChIP analysis of endogenous TyrRS, using the HisRS gene as negative control; and the occupancies were shown to increase on H2O2 treatment. The expression of these AARS/eEF1A gene transcripts was shown to be reduced by o/e of TyrRS, in a manner enhanced for at least some of them by the E196K CMT mutation; and the repression was shown to be eliminated by the NLS_mut for YARS expressed at native levels. Reductions in AARS/eEF1A protein expression were also observed on WT TyrRS o/e. Sequence analysis of the genes showing TyrRS binding by ChIP-seq led to identification of a motif that was shown to be required for binding to TyrRS in vitro in EMSA assays with either purified TyrRS or in extracts from cells overexpressing it, in a manner requiring the full-length TyrRS and not only the catalytic core of the enzyme. It was not shown however that eliminating this motif from any of the target genes attenuated their repression by nuclear-localized TyrRS. Mass spec analysis of affinity-purified, overexpressed TyrRS identified interacting proteins, and several of which were shown to be coimmunoprecipitated with endogenous TyrRS in non-stressed cells, including the transcription cofactors Trim28, HDAC1, and subunits of the NURD co-repressor/histone deacetylase complex. ChIP assays showed that overexpression of TyrRS lead to decreased levels of H3K27Ac, a histone mark of active transcription, and elevated occupancies HDAC1, TRIM28, or NURD subunit CHD4 in non-stressed cells at the AARS/eEF1A genes, with either TRIM28/HDAC1 or CHD4 being observed for all of the genes except the TyrRS gene that shows all three cofactors present. Based on these results, the authors conclude that increased nuclear localization of TyrRS on oxidative stress leads to increased binding of TyrRS to the AARS/eEF1A genes with attendant direct recruitment of either TRM28/HDAC1 or NURD, leading to transcriptional repression of these genes, which is responsible for the reduction in bulk protein synthesis observed after prolonged H2O2 treatment. They go on to provide evidence that cell survival in H2O2 is enhanced by nuclear association of TyrRS (dependent on the NLS), and that in its absence, conferred by the NLS_mut, apoptosis is increased. They also show that ROS increases by preventing TyrRS nuclear localization by the NLS_mut, and that this effect as well as decreased cell survival for this mutant in H2O2 can be rescued by the translation elongation inhibitor harringtonine.

      The results presented in this report provide some support for the main conclusions of the paper and the overall model presented in Fig. 4F. However, as detailed below, many of the main conclusions of the paper are based on correlations and lack direct experimental support, and a number of the experiments are not comprehensive enough with sufficient conditions and controls to establish that the effects observed can be attributed to enhanced nuclear localization of TyrRS in response to H2O2. Considering the statements in the abstract, the evidence is reasonably strong that nuclear localization of TyrRS leads to inhibition of global translation at a stage later than that of eIF2α/ATF4 and mTOR responses, and that excluding TyrRS from the nucleus increases apoptosis under prolonged oxidative stress (although even this last point requires better documentation). However, the evidence is inadequate in several respects to claim that TyrRS directly represses the transcription of translation-related genes by recruiting TRIM28 or NURD complex, and as claimed on p. 13 of the Discussion, that the repression of the four AARS genes and the gene for eEF1A accounts for the reduction in bulk protein synthesis on H2O2 treatment.

      Major issues:

      -Evidence is lacking that the binding of TyrRS to the AARS/eEF1A genes is functionally important for the repression of any of the 6 putative target genes upon increased nuclear localization of TyrRS conferred by the NLS_mut or in response to H2O2. This would require ChIP analysis of TyrRS binding to the target genes for WT vs. NLS_mut TyrRS in H2O2-treated cells; and CRISPR mutagenesis of the putative TryRS binding site in the genome and analysis of transcription in the presence and absence of H2O2 for at least one of the putative TyrRS target genes.

      -Evidence from ChIP analysis is lacking that TRIM28, HDAC1, or the NURD complex are recruited to the AARS/eEF1A genes at native levels of TyrRS in a manner dependent on the NLS and stimulated by H2O2, as the ChIP experiments involved only overexpressed WT TyrRS in non-stressed cells. It is also unclear whether H3K27Ac levels at the putative target genes decline at endogenous levels of TyrRS on treatment with H2O2. Similarly, evidence is lacking that the physical association of TyrRS with these co-repressors is dependent on the NLS and stimulated by H2O2, as the co-IP analysis was limited to endogenous WT TyrRS in non-stressed cells.

      -Evidence is lacking that the cofactors TRIM28, HDAC1, or CHD4 are required for the down-regulation of target gene transcription on H2O2 treatment, which would require knock-down or elimination of these factors by CRISPR accompanied by analysis of target gene transcription +/- H2O2.

      -Direct evidence is lacking from ChIP analysis of RNA Pol II that the transcription of the AARS/eEF1A genes is reduced on H2O2.

      -Evidence is lacking that the repression of bulk protein synthesis is actually mediated by the reduced expression of the 4 AARSs and eEF1A. The fact that the TyrRS-E196K mutation enhances repression of bulk translation and also repression of 3 of the 5 target genes does support the idea that the repression of the target genes is instrumental in reducing protein synthesis, but again, this is still a correlation. There is no evidence that the reduced expression of the AARSs is sufficient to reduce charging of the cognate tRNAs, or that the reduced expression of eEF1A decreases the rate of translation elongation in cells or cell extracts.

      -There is an important lack of information provided needed to evaluate the quality and significance of the ChIP-seq analysis of TyrRS binding to DNA. No details are provided concerning the ChIP-seq analysis of V5-tagged TyrRS to indicate how the TyrRS occupancy peaks were identified and distinguished above background signal from the cells expressing V5 tag alone, whether replicates were examined to provide statistical significance for the identified occupancy peaks, and the sequencing library depths. No genome browser views were provided to show the signals from the cells expressing V5-TyrRS vs V5 alone to demonstrate the quality and reproducibility of data from replicates. The supplementary table S1 describing these data was even omitted from the submission, and it's unclear whether these data are being deposited in GEO.

      -There is an important lack of information provided needed to evaluate the quality and significance of the mass-spec analysis of TyrRS interacting proteins. No details are provided about the statistical significance of the protein interactions identified by mass-spec analysis of the affinity-purified TyrRS; and a negative control for non-specific association seems not to have been included in the analysis. The supplementary table describing these data was even omitted from the submission.

      -It's unclear whether the motif described in Fig. 3A was found under the peaks of TyrRS occupancy in the various genes showing TyrRS binding in the ChIP-seq experiments, nor whether its occurrence is statistically significant. It was not indicated that the motif coincides with the peak ChIP-seq occupancies for TyrRS, and if not, how this could be explained.

      -Evidence is lacking that harringtonine treatment reduced bulk protein synthesis under the conditions where it suppressed the effects of the TryRS NLS mutation in elevating ROS and decreasing cell survival.

      -In general, the figure legends are poorly written in lacking important details about the nature of the TyrRS being examined in the experiment (tagged vs endogenous; overexpressed vs. native levels), and also whether oxidative stress was imposed in the experiment, and if so, the exact conditions for the treatment. Figure legends should contain all of the critical details needed to understand and evaluate the significance of the experimental results without having to search elsewhere in the paper for them.

      -It needs to be clarified whether the mini-TyrRS construct lacks the NLS, and the significance of its behavior as a negative control for the effects of overexpressing WT TyrRS.

      -For the experiment in Fig. 5B, quantification of the fraction of caspase-3 or PARP cleaved from biological replicates is required.

      -The experiment in Supp. Fig. S4 lacks the results from cells untreated with H2O2 to ensure that these proteins were being induced by H2O2 in their hands.

    1. including computer vision, machine vision, speech recognition, natural language processing, audio recognition, social network filtering, machine translation, bioinformatics, drug design, medical image analysis, material inspection and board game programs, where they have produced results comparable to and in some cases surpassing human expert performance<br> yes ma

    1. “Who are you then?" "I am part of that power which eternally wills evil and eternally works good.”

    1. Author Response

      Reviewer #1:

      Major comments:

      1) The title and the conclusion that SON and SRRM2 form nuclear speckles are not supported by the data. The data show that SON and SRRM2 are necessary for nuclear speckle formation. They do not rule out that another factor is necessary, such as SRRM1, which interacts with SRRM2 and itself harbors an intrinsically-disordered domain. That is, the authors have not shown that SON and SRRM2 are also sufficient for nuclear speckle formation. Such a test is necessary to draw the strong conclusion the authors make, and precedence for such a test has been established in the study of Cajal bodies. Specifically, central factors to Cajal body formation were shown to nucleate Cajal body formation at a specific site in chromatin when such central factors were localized to that site. The authors either need to perform such a sufficiency experiment or moderate their conclusions (and title).

      2) In principle, in the immunofluorescence studies, the disappearance of mAb SC35 signal on depletion of SRRM2 does not alone prove that SRRM2 is what is visualized by the mAb SC35 in such assays. Given that this paper seeks to establish rigorously that mAb SC35 marks nuclear speckles by recognition of SRRM2, given that SRSF7 is recognized by the antibody on blots, and given that SRSF2 has been traditionally presumed the target of mAb SC35 in nuclear speckles, the rigor of this study demands that SRFS7 and SRSF2 be visualized in cells in the presence of an SRRM2 truncation to rule out that either SRSF7 or SRSF2 phenocopy SRRM2 in this assay.

      This is a valid concern and we have thought of the same principal that is if any strongly speckle-associated intrinsically disordered domain containing protein, such as SRRM1 or RBM25, two proteins that are also frequently used as NS markes, would have a similar impact on NS formation as SRRM2 has. To this end, we performed a co-depletion of SON and SRRM1 (shown in Supplementary Figure 10) in a cell line that has a TagGFP2 inserted into SRRM2 gene locus. As it can be seen from the imaging presented in this figure for 4 individual cells (but also more generally on 10 independent field imaged, (data not shown)) we did not score a reduction in the GFP intensity, or dissolution of the spherical bodies as is the case in SON-SRRM2 co-depleted cells. We observed the nuclear speckles have the round-up morphology, that is seen upon SON-KD, but are not dissolved shown with PNN staining and SRRM2-TagGFP signals. Moreover, we performed a co-depletion of RBM25 (another strongly NS-associated protein also used as a NS-marker) and SON which did not result in the dissolution of nuclear speckles (Supplementary Figure 10). Therefore, we have reached to the conclusion that SON and SRRM2 form nuclear speckles with the contribution of SON being more important for the formation and titled our study accordingly.

      Traditionally, because of the Fu & Maniatis 1992 paper, as pointed out by the reviewer, it is assumed that SC-35 recognizes SRSF2 in immunofluorescence experiments and potentially multiple SR-proteins in immunoblots. The former point, to the best of our knowledge, has never really been proven in any type of rigorous experiment. Fu lab. has generated SRSF2 K/O mice, but never provided an immunofluorescence image that shows that SC-35 signal disappears in K/O cells.

      Just to summarize our line of reasoning here:

      1) We do an unbiased IP-MS experiment, which shows that SRRM2 is the top candidate protein, at least an order of magnitude away from any other protein in the dataset by any measure. This strongly suggest that SRRM2 is the primary target of this antibody, although doesn’t prove it due to technical reasons i.e. no input normalization, some proteins produce more ‘mass-specable’ peptides than others, and larger proteins tend to produce more peptides.

      2) We carry out a biased screen of 12 SR-proteins and find that SRSF7 is strongly recognized by mAb SC-35

      3) We do IP-western blotting experiments, which correct for input and are not affected by relative ‘mass-specable’ peptide issues or protein sizes, which reveal a strong enrichment of SRRM2 (>10% of input), some enrichment for SRSF7 (~2% of input) and no enrichment for SRSF2, SRSF1 or other proteins that we have tested.

      4) Since the “35kDa” protein is so engrained with the history of this antibody and our results were most consistent with the idea that this protein is SRSF7 rather than anything else, we insert a degron tag to SRSF7. If the hypothesis is true, then we expect a shift of the SC-35 band, concomitant to the shift in SRSF7, which is indeed the case. This is not proof that SC-35 doesn’t recognize any other protein but it does provide very strong evidence (combined with the other two experiments) that the 35kDa band detected by SC-35 in immunoblots is in fact SRSF7.

      5) We then show, by TagGFP2 insertion into the SRRM2 locus, that SC-35 mAb can recognize SRRM2 specifically on immunoblots, and furthermore truncations beyond a certain point completely eliminates this signal. We also show later that siRNA mediated KD of SRRM2 also leads to the elimination of the signal from immunoblots (Supplementary Figure 9).

      6) Combining the results so far, we address the issue of immunofluorescence, i.e. which protein or proteins are responsible for this signal. We think there are two possible scenarios that could both be true based on the presented evidence so far:

      a. This signal is mainly, if not entirely, originates from SRRM2. b. The signal is a combination of SRRM2, SRSF7 and/or other SR-proteins that the SC-35 might be cross-reacting.

      7) We then take advantage of our cell lines with SRRM2 truncations. These truncated SRRM2 version are not recognized by SC-35 mAb on immunoblots, therefore it is reasonable to suspect that they will not be recognized by SC-35 mAb in immunofluorescence as well.

      8) If scenario (b) is correct and nuclear speckles are still intact in these cells (which we show that they are indeed intact, judged by SON, RBM25 and SRRM1 stainings Fig. 3A-B), then we would expect either no change in SC-35 signal, or a somewhat reduced signal. We see a complete loss of signal.

      9) Being extra careful with this result, we also mix the control cell line and SRRM2-truncated cells and image them side-by-side to address any issues related to imaging settings etc. There is no detectable SC-35 signal in truncated cells.

      10) We also show that the 35kDa band is still unchanged in SRRM2 truncated cells (Figure 2E), showing that SRSF7 itself is not affected in these cells.

      These results, combined together, show that SC-35 signal in immunofluorescence originates from SRRM2, and any other signal potentially contributed by other proteins are below the detection of immunofluorescence microscopy.

      Reviewer #2:

      This study reports important evidence that the widely-used SC-35 antibody primarily recognizes SRRM2 rather than the assumed SRSF2. The manuscript provides several lines of evidence supporting this conclusion, and the work has broad impact on the field of nuclear structure and function as this antibody is the most common marker for the major nuclear component, nuclear speckles.

      The one concern with the manuscript is the interpretation of some of the previous literature and understanding in the field.

      First, since the 1990s it has been widely known that the SC-35 mAb has very limited specificity for denatured proteins and was not suitable for immunoblots (see abcam page for ab11826). Indeed, the assumption has always been that it recognizes a folded epitope. Therefore, the use of western blots to conclude anything about the specificity of this antibody is inappropriate.

      Secondly, it has also been previously documented that this antibody has cross-reactivity with SRSF7 (i.e. 9G8; Lynch and Maniatis Genes Dev 1996).

      Third, most SR proteins are not abundantly observed in tryptic MS due to high cleavage of RS domains. This is particularly true of SRSF2, which has a highly "pure" RS domain (i.e. all RS repeats) that encompasses almost half of the total protein. SRRM2, on the other hand, has much more complex and degenerate RS domains that encompass a much smaller percentage of the total protein. SRRM2 is also 10x the size of SRSF2. Thus, given equal molar amounts of SRSF2 and SRRM2, one would expect at least 20x the number of peptides and much more complete coverage of SRRM2 vs. SRSF2. Therefore, while the subsequent immunoblot in Figure 1C is compelling evidence that SRRM2 is precipitated with the SC-35 antibody, while SRSF2 is not, the IP-MS data alone is not strong proof that the SC35 mAb primarily recognizes SRRM2 rather than SRSF2. The text should be revised accordingly.

      Finally, the abstract implies that the demonstration of SON as a central component of speckles is new ("elusive core"). As appropriately referenced in the text, this is not the case, rather SON is often used as a marker for nuclear speckles, and SON has long been considered to be part of the core of speckles, as knock-down has been documented by several groups to disrupt speckles. The wording in the abstract should therefore be more parsimonious.

      With all due respect to all previous researchers that have used mAb SC35 and published their results, we think that the specificity issue has become unnecessarily convoluted due to the initial inaccurate characterization. Abcam’s recommendations highlight the issue in an interesting way. In the old marketing images, abcam shows a single band in a total lysate prepared from HEK293 cells: https://www.abcam.com/ps/products/11/ab11826/reviews/images/ab11826_49518.jpg

      However, producing such an image, in our experience as we have also reported in the manuscript, is only possible under non-ideal western-blotting conditions i.e. when the transfer is not adequate to reveal proteins with large molecular weights. Intriguingly, a customer (not us) complains about an improper WB result obtained with this antibody (with a 2-star rating):

      https://www.abcam.com/sc35-antibody-sc-35-nuclear-speckle-marker-ab11826/reviews/68414?productWallTab=ShowAll

      It looks like an unexplainable high-molecular smear without the information that we provide in our manuscript, but in light of it, it’s clear that protein stained here is SRRM2.

      In our experience the antibody works perfectly fine for western blotting, and very specifically and robustly reveals SRRM2 at ~300kDa, as long as the immunoblotting conditions are optimized for large proteins. We also show that bulk of the signal around 35kDa originates from SRSF7, however as indicated by the other reviewer’s comments, and also previous research, the antibody probably cross-reacts with other proteins as well with varying degree.

      In this sense, the antibody can be used for immunoblotting, but pretty much any result obtained from such an experiment must be verified with an independent antibody or independent methods, which we did in this manuscript.

      The SC35 mAb is actually suitable for western blotting if the gel running and transfer conditions are carefully performed to have SRRM2: a) enter the gel and b) transferred properly to the membrane. Under conditions where SRRM2 is just not entering the gel (due to high percentage gels, or gels with too much bis-acrylamide), or doesn’t get transferred to a membrane (non-ideal buffer conditions, protein stuck in stacking part and cut away etc.), we have seen the unspecific bands, but we had to use the most sensitive detection reagents at hand to see those, so they are rather weak. We have provided a detailed explanation to what these conditions are in the methods section of our manuscript, but briefly: running the gel slowly allowing the protein to enter in the gel and transferring overnight with CAPS buffer were key to get the western blot working. As we have shown in Figure 2C and 2E, the majority of signal detected comes from SRRM2. The unspecific binding of SC35 mAb could only be scored if the above-mentioned conditions were not met.

      We believe what made matters historically worse has been the use Mg++ precipitation that enriches many SR proteins, but actually completely depletes SRRM2 (Blencowe et al. 1994 DOI: 10.1083/jcb.127.3.593, Figure 5, https://pubmed.ncbi.nlm.nih.gov/7962048/ ). When we’re sure that SRRM2 is in the gel though, it just shines as a single band. So in conclusion, SC-35 is reasonably specific to SRRM2, especially in immunofluorescence, but it certainly cross-reacts with other SR-proteins, especially when SRRM2 is missing for technical or biochemical reasons.

      We will update in the manuscript for the corresponding section by citing earlier studies reporting the specificity issues of mAb SC35.

      We absolutely agree that IP-MS data alone is not enough to conclude that SC-35 recognizes SRRM2, or whether it is the primary target or not. The overwhelming amount of SRRM2 peptides detected, in addition to the overwhelming amount of total peptide counts from SRRM2 does strongly suggest that it is the case, which we then followed up by IP-western blotting which controls for relative input, and the various experiments shown in later figures.

      We have looked at our MS results and found out that:

      SRSF2 was detected with 4 unique peptides with an MS/MS count of 5 and a sequence coverage of 29% (intensity 3E+07), whereas SRRM2 was detected with 227 unique peptides with an MS/MS count of 3317 and a sequence coverage of 61.9% (intensity 2E+11).

      These numbers show a 6600 times higher intensity for SRRM2 (not normalized). As the identification and abundance of different peptides/proteins can by dramatically different in MS, it is indeed correct that one should be careful with such comparisons. The only way would be to use peptide standards for both proteins and record standard curves, then a real quantitative comparison would give the true numbers. Hence, we will revise the wording of that section.

      Finally, as the reviewer has pointed out, we have not shown that speckles can be reformed by introducing ectopically expressed SON/SRRM2 into cells which now appear not to have nuclear speckles. This would indeed be the formal proof showing that SON/SRRM2 are not just necessary but also sufficient to form nuclear speckles. Such an experiment is quite challenging due to the length of these proteins and difficulty in establishing conditions where one can express these proteins, but not overexpress them which leads to round-up speckles (as shown and discussed by Belmonte lab). Therefore, we will change the title to “SON and SRRM2 are essential for the formation of nuclear speckles” to better reflect our conclusions.

      We really did try to be clear and just about the previous literature around SON. Indeed, it is clear that SON is a crucial part of NS, likely the most important component for the integrity of speckles. However, in all of these previous studies, RNAi-mediated depletion of SON, without exception, leaves behind spherical bodies that are strongly stained with mAb SC35, that also harbor other NS-markers (which we also show). This is of course not new, as we also appropriately cited previous work, however being able to dissolve these “left-over” speckles by co-depletion of SRRM2, and perhaps more importantly by deletion of the SRRM2’s C-terminal region is indeed novel.

      In essence, our results show that in the absence of SON, as shown by previous work as well, NS-associated proteins are still able to organize themselves into nuclear bodies, indicating that either all other SR-proteins without the need of another organizer clump together, or another factor (or factors) is still acting as an organizer. When we remove the C-terminus of SRRM2, which we show is the primary target of SC-35, which strongly stains these left-over nuclear bodies in the absence of SON, then deplete SON, all NS markers that we could find become diffuse, indicating that nuclear speckles no longer exist, or become too small to be detected or classified as “nuclear bodies”. Co-depletion of SON and SRRM2 leads to the same phenotype, but co-depletion of SON and SRRM1 (or RBM25) doesn’t, leaving behind spherical nuclear speckles that harbor SRRM2 which are no different than SON KD cells.

      Reviewer #3:

      Nuclear speckles in the last several years have attracted significant attention for their association with transcriptionally active chromosome regions (after largely being ignored by most for the previous 20 years). Overwhelmingly, a single monoclonal antibody has been used as a marker for nuclear speckles for several decades.

      This manuscript now argues convincingly that the main target that is recognized by this monoclonal antibody is not SRSF2 (SC35) as long thought, but rather SRRM2. The authors thus clarify a vast literature, while also focusing attention on the very large protein SRRM2 that in many ways resembles another nuclear speckle protein, SON. Both have huge IDRs and unusual RS repeats, while SON has been proposed to act as a scaffold for many SR-containing proteins, which is likely also true for SRRM2, by extension. Moreover, the manuscript provides a convincing explanation for why the target of this antibody was previously misidentified, by showing a lesser cross-reaction with SRSF7, of similar MW to SC35.

      Finally, the manuscript suggests that SON and SRRM2 together help nucleate nuclear speckles, as a double KD, or a SON KD in a background of a truncated SRRM2, leads to loss of nuclear speckle-like staining of other proteins normally enriched in nuclear speckles (RBM25, SRRM1, PNN). The authors go on to suggest that this double KD approach will now provide an important means of disrupting nuclear speckles to aid in functional studies.

      Interestingly, some of the results of this manuscript actually are already confirmed or consistent with previous literature. For example, a cited paper describes changes in Hi-C compartmentalization patterns after "elimination" of nuclear speckles- actually, they performed a SRRM2 KD and showed loss of SC35 staining, which is now explained as simply due to the KD that they performed. More recently, a new proteomics study of nuclear speckles (Dopie et al, JCB, 2020: https://doi.org/10.1083/jcb.201910207) reported both SON and SRRM2 as the two most highly enriched nuclear speckle proteins, with enrichment scores similar to each other but more than twice that of all other speckle proteins. Moreover, this same paper also did a SRRM2 KD and observed loss of anti-SC35 staining but not SON staining.

      Overall, I found this manuscript of significant interest for people in the nuclear cell biology field and technically thorough and well done. I just had one issue and one point to make in my main comments, plus some minor points.

      1) The evidence that nuclear speckles are nucleated by SON and SRRM2 is based on the dispersion of staining of nuclear speckle proteins RMB25, SRRM1, and PNN. However, an alternative explanation is that some other protein(s) nucleates nuclear speckles, while these other nuclear speckle proteins bind to SON and SRRM2, and are therefore enriched in nuclear speckles. To eliminate this concern, the authors could show that SON and/or SRRM2 do not bind to these proteins- for instance using co-IP or other methods. Of course, it could be that such binding or scaffolding of nuclear speckle proteins is how they form nuclear speckles. But just one protein that is not bound by SON and SRRM2 but still stains nuclear speckles after the double KD would be inconsistent with their hypothesis. Therefore, if they do find that all these proteins bind SON and/or SRRM2 they could simply discuss this as a scaffolding mechanism but qualify their conclusion based on the alternative explanation described above.

      2) In our lab we have not been comfortable using the kinase manipulations, discussed in this paper, to eliminate nuclear speckles for experimental purposes because the cells appear very sick after these manipulations. For other reasons, we also tried a double SON and SRRM2 KD. Our experience is that the cells after this double KD were also not very normal. If the authors are suggesting the SON and SRRM2 double KD as an experimental tool to disrupt nuclear speckles in order to access nuclear speckle function, then it would be valuable for them to indicate cell toxicity, etc. Many SR-protein KDs for example do not allow selection of stable cells. What about this double KD?

      The first point of Reviewer #3 has been addressed above in response to the Reviewer #2.

      We have stated that our work identifying SON and SRRM2 as the elusive core of nuclear speckles paves the way to study the nuclear speckles under physiological conditions. Here, we have used the cells 24 hours after transfection (~18 hours of knock-down) as the primary reason being that SON-KD caused a mitotic arrest if the cells were kept longer in culture. This was reported earlier in Sharma et al MBC 2010. There was no additional severity in the phenotype when the SON-KD was combined with SRRM2-KD, therefore we believe the arrest phenotype we scored is mainly due to depletion SON. In this sense, double-depletion of SON and SRRM2 can be used to study the effects of loss of NS (transcription, post-transcriptional, topological), but certainly within a time-frame of around 24 hours in cells that haven’t gone through mitosis. We will clarify this statement in the revised manuscript to avoid any misunderstanding as pointed by the reviewer. Faster depletion strategies, and/or a system where cells are mitotically arrested would be required to observe long term effects more reliably.

    1. Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

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      Reply to the reviewers

      Reviewer 1

      __*Review 1 Summary:

      __In this manuscript, Borah et al showed that Heh2, a component of INM, can be co-purified with a specific subset of nucleoporins. They also found that disrupting interactions between Heh2 and NPC causes NPC clustering. Lastly, they showed that the knockout of Nup133, which does not physically interact with Heh2, causes the dissociation of Heh2 from NPCs. These findings led the authors to propose that Heh2 acts as a sensor of NPC assembly state. *

      __Reviewer 1 major comment 1:__ The authors claimed that Heh2 acts as a sensor of NPC assembly state, as evidenced by their finding that Heh2 fails to bind with NPCs in nup133 Δ cells (Fig2, Fig 5). However, there is a possibility that the association between Heh2 and NPCs is merely affected by the clustering of the NPCs (as the authors discussed) but not related to the structural integrity of NPC.

      • *

      Our Response: We agree that this is a possibility, however, we ask the reviewer to also consider that we artificially cluster NPCs using the anchor away system (Figure 3C) and this does not affect Heh2’s association with NPCs. Thus, clustering per se is insufficient to disrupt Heh2 binding to NPCs. We will also make changes in the text to make this point.

      • *

      Reviewer 1 major comment 2: In addition, their data showing that the Heh2-NPCs association is not easily disrupted by knocking out the individual components of the IRC (Fig. 5A and 5D), also disfavor the idea that Heh2 could sense NPC assembly state.

      Our Response: There are three considerations here. The first is that as this is the first evidence of any kind of “NPC assembly state” sensor, it is difficult to make any assumptions as to what specifically such a sensor would be monitoring. i.e. perhaps sensing only the ORC is what is functionally important. Second, for obvious reasons, we only tested non-essential IRC nups so by definition there is inherent functional redundancy that maintains NPC function and thus there may be no need to “sense” anything in the absence of these IRC nups. Further (and last), the IRC is essential for NPC assembly. Thus, without an IRC there is no NPC assembly state to sense.

      Reviewer 1 major comment 3: Since some nup knockout strains, other than nup133 Δ, are also known to show the NPC clustering (ex. nup159 (Gorsch JCB 1995) and nup120 (Aitchison JCB 1995; Heath JCB 1995)), it will be worth trying to monitor the localization of Heh2 and its interaction with nucleoporins (by Heh2-TAP) using these strains. While Nup159 is a member of the cytoplasmic complex, Nup120 is an ORC nucleoporin. Thus, biochemical and phenotypical analysis using these mutant cells will be useful to clarify if the striking phenotypes the authors found are specific to nup133 knockout strain (or ORC Nup knockouts) or could be commonly observed in the strains that show NPC clustering. Another interesting point is that Nup159 shows strong interaction with Heh2, even in nup133Δ cells. As the authors mentioned, Nup159-Heh2 interaction may not be sufficient for Heh2-NPC association, but it could be important for NPC clustering.

      Our Response: These are excellent points and we agree that there is a need to more thoroughly explore how NPC clustering driven by abrogating the function of other nups impacts Heh2’s association with NPCs. Thus, in a revised manuscript, we would examine Heh2’s association with NPCs in several additional genetic backgrounds where NPCs cluster.

      Reviewer 1 major comment 4: Figure 4C: Is it known that rapamycin treatment in this strain did not affect the protein levels of nucleoporins? Otherwise, the authors should confirm this by western blotting (at least some of them).

      Our Response: This is a good point and we will directly address this with Western blotting of some nups.

      Reviewer 1 major comment 5: Figure 5: The authors mentioned (line 256-257) that "in all cases the punctate, NPC-like distribution of Heh2-GFP was retained (Fig 5D)". However, nup107 KO strain seems to show more diminished punctate staining as compared with other strains. To clarify this, the authors should express mCherry tagged Nup as in Fig. 2 or Fig. 3.

      Our Response: Yes, we agree and in fact this observation is consistent with the fact that there is an ER-pool of Heh2 observed in this strain and we observe loss of nup interactions in the affinity purification. We will include a more thorough quantification of this in a revised manuscript and more directly address this in the text.

      **Minor comments:**

      Reviewer 1 minor comment 1: Figure 4A and 4B: The authors should show Scatter plot as in Fig. 2 and Fig. 3.

      • *

      We will include this in a revised manuscript.

      Reviewer 1 minor comment 2: Figure 5C: Explanations of the arrowheads is missing in the figure legend.

      Thank you for pointing this out, it will be fixed in a revised manuscript.

      Reviewer 1 minor comment 3: Figure 6: Is there any information as to where Heh2 (316-663) is localized in the cell?

      As this truncation lacks INM targeting sequences, it is found throughout the cortical ER. The determinants of Heh2 targeting (including truncations) has been extensively evaluated in King et al. 2006, Meinema et al., 2011 and Rempel et al. 2020. We will make this clearer in the revised manuscript.

      Reviewer 1 minor comment 4: Figure 6B: Nucleoporins should be marked with color circles as in Fig. 1 and Fig. 5.

      This will be done.

      Reviewer 2

      Borah et al. present a biochemical and cell biological examination of the inner nuclear membrane (INM) protein Heh2 and its putative interactions with the nuclear pore complex (NPC). The potential conceptual advance of this study is that Heh2 interacts with the NPC, while mutations believed to trigger NPC mis-assembly are shown to abolish interaction with Heh2, leading to the hypothesis that Heh2 is a sensor for NPC assembly states within the (INM). The conclusions would undoubtably be of broad interest to the nucleocytoplasmic transport field, but the evidence provided thus far is insufficient to build confidence and consequently this manuscript is premature for publication.

      Our Response: We thank the reviewer for recognizing the potential for a significant conceptual advance for the field but object to the notion that the work is “premature for publication”. This is a highly subjective statement that does not seem to meet the mission or purpose of the Review Commons platform. While it is possible that some of the conclusions drawn in our manuscript might not be fully supported by the data in its current form, there is a substantial body of work here that is certainly publishable.

      Reviewer 2 major comment 1: The TAP-tag Heh1/Heh2 pulldowns are the most significant experiment presented, and on face value provide compelling evidence that Heh2 interacts with the NPC. It is stated that mass spectroscopy (MS) was used to confirm the identities of the labeled bands yet there is no methods section, nor any MS data reported in the manuscript. Given the large number of unspecified proteins observed in these gels, and the single-step pulldown methodology used, knowledge of the contaminants present may aid in elucidating how Heh2 pulls down NPC components. Consequently, within the supplementary materials, the authors must indicate which regions of the gel were excised for MS analysis and provide a table listing all of the proteins that were detected for each sample, including the number of unique/expected peptides observed. Our Response: This was a major oversight on our part and a revised manuscript will contain all relevant details with regards to the MS analysis including a more detailed description of the excised bands and the quantification of spectra derived from these bands.

      Reviewer 2 major comment 2a: The representative micrographs provided across Figures 2, 3, 4, 5 and 6 are very noisy. Particularly in the case of the mCherry labeled nucleoporins, this is both unusual and unfortunate given this is used to infer colocalization of Heh2 with the NPC.

      Our Response: These micrographs are not unusual and are in fact of respectable quality. We agree that the apparent “noise” is unfortunate, but this is simply a reality of the yeast system. We remind the reviewer that there are only ~100 to ~200 NPCs per budding yeast nucleus, which is an order of magnitude smaller than a typical mammalian cell nucleus. Further, the copy number of yeast nups per NPC is half of the mammalian cell NPC. Further, budding yeast are spherical with a cell wall that is extremely effective at scattering light; they are also highly autofluorescent (particularly in the red channel). Lastly, unlike in mammalian cells, budding yeast NPCs are mobile on the nuclear envelope. Thus, co-localization is challenging (particularly with the long exposures required to obtain good images). This is why clustering of NPCs driven by nup133**∆ cells has provided one of the key assays in the field to assess whether a given protein associates with NPCs at the level of light microscopy.

      Reviewer 2 major comment 2b: As a result it is unclear whether this experiment can be used to differentiate between NPC colocalization vs. nuclear envelope colocalization.

      Our Response: The reviewer is correct. Co-localization between Heh2-GFP and any Nup-mCherry is insufficient to assess NPC association in WT cells. In fact, as we point out in Figure 3B, at best one can expect a correlation of r = 0.48 for two well established nups. Thus, to further support the conclusion that Heh2 associates with NPCs, we established the Nsp1-FRB NPC clustering assay (Figure 3).

      Reviewer 2 major comment 2c: The authors should include negative controls for an alternative NE membrane protein that doesn't bind the NPC, which would be expected to exhibit a reduced level of colocalization with NPC proteins when compared to Heh2. For example, Heh1 would be a suitable, given the clear-cut negative pulldown data and its prior usage as a negative control in Figure 4.

      • *

      Our Response: This is included in Figure 3D.

      Reviewer 2 major comment 3a. Figure 2. The rim staining for the Nup82-mCherry in the WT background is unusually punctate, bringing into question the viability of the cells imaged.

      Our Response: As the middle cell in the panel is undergoing cell division, these cells are clearly viable. All our imaging is performed on mid-log phase cultures.

      • *

      Reviewer 2 major comment 3b. Why has ScNup82, a cytoplasmic filament component, been selected for colocalization experiments when Heh2 is proposed to interact with the inner ring complex?

      Our Response: The resolution of a conventional light microscope is, at best, 200 nm in x, y. As NPCs are 100 nm in diameter, even two NPCs side-by-side cannot be resolved. The IRC is tens of nm away from the cytoplasmic filaments thus any nup is relevant for a co-localization analysis with a light microscope.

      Reviewer 2 major comment 3c: Additionally, the experiments shown in panels A and C are not directly comparable, ScNup82 is an asymmetric cytoplasmic nucleoporin, while SpNup107 is located in the Y-shaped Nup84 nucleoporin complex and present on both faces of the NPC. This experiment should be repeated with scNup84 to match panel C, additionally a viability dot spot assay and western blot analysis of the labeled proteins should be conducted.

      Our response: These are in fact directly comparable within the limits of resolution of light microscopy as described above. Viability assays are not required here as both nups are essential and perturbation to their function would lead to inviability.

      Reviewer 2 major comment 4: Figure 3, the authors use yeast strains where proteins are tagged with FRB and FKBP12 domains, which dimerize upon the addition of rapamycin inducing NPC clusters. The authors then observe the effect this has on Heh2 NPC colocalization. However, Rapamycin may also have an effect independent from the induced dimerization event. Negative controls should be performed in strains lacking the FRB and FKBP12 tagged proteins to demonstrate that Rapamycin doesn't modify Heh2 localization independently of NPC clustering.

      Our response: This is a good point and important control that we performed in prior studies, see Colombi et al., JCB, 2013. We will be more explicit in describing that this control has been done.

      Reviewer 2 major comment 5: Figure 4. The authors provide a qualitative description of the colocalization presented, while in all other instances they calculate a Pearson correlation coefficient. This is significant because Heh2 appears to be evenly distributed within the NE of the DMSO control (panel B). Given the presented hypothesis isn't colocalization expected with Nup192? As a minimum, a Pearson correlation coefficient analysis should be conducted and added to Figure 4.

      Our response: This will be included in a revised manuscript.

      Reviewer 2 major comment 6: Figure 4. Pom152-mCherry localizes at both the NE and strongly within the cytoplasm, which is unexpected given typical rim staining phenotypes observed previously for both Pom152-YFP and Pom152-GFP strains (Katta, ..., Jaspersen et al., Genetics (2015) & Upla, ..., Fernandez-Martinez et al., Structure (2017), respectively). Given the unusually weak rim staining observed throughout, viability assays of the strains listed in Table S1 and protein expression analysis of the tagged nucleoporins via western blot is necessary.

      Our response: This is not localization in the cytoplasm but is in fact autofluorescence from the yeast vacuole. We regret we were not more explicit in describing this and we will make the manuscript more accessible for the non yeast expert. In order to perform the Western blot analysis for all strains requested by the reviewer would require a battery of antibodies to the endogenous proteins to directly assess how tagging influences nup levels, which we do not have (nor does anyone else that we are aware of). This is also not standard practice in the field as it is an onerous and unnecessary burden.

      Reviewer 2 major comment 7:* Figure 5A. The TAP-tagged pulldowns from ∆Pom152 and ∆Nup133 strains appear to be from a different round of experiments than the previous deletion strains presented. Interestingly, there appears to be an additional band at approximately 250 kDa in both cases that is not present in any other experiments. This band could be a contaminant observed due to different experimental conditions, or a protein that exclusively binds to Heh2 in the ∆Pom152 and ∆Nup133 background. Either way the authors should identify this protein with MS to address this ambiguity.

      *

      Our response: We will include negative controls for these specific experiments to show that this is a non specific band.

      Reviewer 2 major comment 8: Figure 6B. Please label the nucleoporin bands in the TAP-tagged pulldowns.

      Our response: This will be done.

      Reviewer 2 major comment 9: Figure 6D. Please specify Heh2-GFP clustering in the y-axis.

      Our response: As this represents both Heh2-GFP and heh2-1-570-GFP, we will keep it as is to avoid confusion.

      Reviewer 2 major comment 10: *Under the results section titled 'Heh2 binds to specific nups in evolutionarily distant yeasts', the authors state that spHeh2 co-purifies with "several specific species". The meaning is unclear, this sentence should be rephrased and the specific species clearly described. **

      *

      Our response: Ok.

      Reviewer 2 major comment 11: Under the results section titled 'Heh2 fails to interact with NPCs lacking Nup133', the authors refer to a Pearson correlation coefficient of -0.03 as a clear anticorrelation. Instead state there was no correlation.

      Our response: Ok.

      Reviewer 2 major comment 12: In the discussion, the authors state that "clustering itself may sterically preclude an interaction with Heh2". The text should be expanded to explain this in more detail, it is not clear from the presented data why this would occur.

      Our response: Ok.

      Reviewer 2 comment on significance: the manuscript is premature for publication.

      Our Response: Such a statement has no relevance to this form of review as a decision as to whether a study is premature for publication should be made by journal editors, not reviewers. We would argue quite strongly that we have definitively shown that Heh2 binds to NPCs, that it does so in multiple evolutionarily distant yeasts and that this binding is functionally relevant. For example, we can specifically disrupt the association of Heh2 with NPCs with a specific domain deletion and observe a loss of function phenotype (e.g. NPC clustering). What all three reviewers agree on is that the concept of a “NPC assembly state sensor” needs additional data to be fully supported, although we note that this reviewer did not provide any suggestions for how we might achieve this goal. We further note that we added the qualifier “may” into the title of the work. Thus, we will therefore perform additional experiments as outlined in comments to Reviewer 1 to support this conclusion in order to introduce this as a new concept in the field.

      Reviewer Comment from Cross Commenting: It seems to me that all reviewers agree that the manuscript is premature for publication. The data thus far do not support the conclusion that Heh2 may be an NPC assembly sensor nor does it provide any mechanistic insight. Reading the comments of the other two reviewers makes me more negative, as it is care that the paper also lacks scientific rigor. The manuscript is a great starting point for a rigorous dissection but I do not see this paper to be a candidate for a broad impact journal.

      Our Response: The statement that this manuscript is premature for publication is an opinion and does not seem to reflect the sentiment of the other reviewers. It is also confounding that this reviewer suggests that this work lacks rigor. With the exception of the omission of the MS analysis (our fault), the data are of high quality and rigorously quantified. Our assertion of rigor and data quality is based on our collective team’s many decades-long history of publishing and reviewing papers at the highest levels in this field. Questions as to the quality of the data as stated by this reviewer (and only this reviewer) in fact address limitations of light microscopy and the yeast system more generally in this one respect.


      Reviewer 3

      Reviewer 3 Summary part a*: This is quite an interesting manuscript that explores the relationship between an INM protein, Heh2, and NPCs. It represents an extension of earlier work performed by this group in which it was shown that the HEH2 gene shares genetic interactions with the genes encoding various nucleoporins. Heh2 belongs to an intriguing family of conserved proteins that includes its orthologue, Heh1, as well as human MAN1 (LEMD3) and LEMD2, among others. Each of these proteins contains two transmembrane domains with the N- and C-terminal regions extending in to the nucleoplasm. The two TM domains are separated by a short lumenal loop.

      In this study, the authors show that a population of Heh2 is associated with Nups of the NPC inner ring complex. This was demonstrated initially in pulldown experiments. The authors go on to show that when NPCs are caused to aggregate, by physical tethering employing an FKBP/FRP system in combination with Rapamycin, Heh2, but not Heh1, colocalizes with the NPC clusters. *

      • *

      Our Response: Thank you to the reviewer for recognizing the value of this work.

      • *

      Reviewer 3 Summary_b. Although not stated explicitly in the manuscript, this would imply that there is a population of Heh2 that resides in the NPC membrane domain, with the remainder in the INM. As an idle question, is there any evidence for a similar localization of MAN1 or LEMD2 in mammals? I am guessing probably not.

      Our Response: We regret this was not made more clear but the idea that there is a pool of Heh2 at the POM and a pool at the INM is an important conclusion of the work and was stated in the results - we’ll re-emphasize in the revised discussion. As to whether MAN1 or LEMD2 has a similar NPC association, we hypothesize that MAN1 but not LEMD2 will indeed interact with NPCs in mammalian cells. This is based on considering that we show that both the budding and fission yeast orthologues of MAN1 share this association so unless it was lost in evolution, this is a likely outcome of future studies.

      Reviewer 3 Significance statement a: The complications arise when the authors show that an alternative method of NPC aggregation (although they did this first), involving Nup133 deletion, results in failure of Heh2 to co-aggregate. In other words, Nup133 is required for the association of Heh2 with NPCs. The issue here is that there is no evidence for an interaction between Heh2 and Nup133, and furthermore that loss of Nup133 (a Y complex component of the outer ring complex) leaves the inner ring complex intact.

      • *

      Our Response: We tested the nup133Δ background first as this is the standard approach for assessing NPC-association of a given protein so we felt this would be logical for a reader in the field. Further, while the disruption of Heh2’s binding by loss of Nup133 may be a complication, we prefer to see it as an opportunity for discovery. As described in our manuscript, we have chosen to interpret this result in the context of a new biological function/concept with Heh2 being a novel “NPC assembly state” sensor. While one could argue that we have not fully met this bar yet, we will perform additional experiments as outlined in our response to reviewer 1 to help support this compelling conclusion.

      • *

      Reviewer 3 Signfiicance statement b: What is clear, however, is that Heh2 seems to be required to inhibit NPC aggregation since Heh2 deficient cells exhibit NPC clusters. The association between Heh2 and IRC Nups resides in the C-terminal nucleoplasmic winged helix domain. The N-terminal domain, in contrast confers INM localization.

      • *

      Our Response: We agree.__*


      Reviewer 3 Signfiicance statement c I must admit, I am in two minds about this manuscript. The data clearly show that Heh2 is associated with IRC components and I agree with the authors that this protein may well have a role in NPC assembly quality control perhaps in the guise of a chaperone. However, I find it hard to come up with a convincing model for the effects of Nup133. On the one hand, one could make an argument that the data presented here is too preliminary and fails to provide a complete story. On the other hand, it does provide an intriguing foundation for future studies and I do feel positively disposed towards it. In short, I have no fundamental complaints about the science, I am just uncertain as to whether the study is ready for publication.

      Our Response: This statement nicely articulates the challenge with this manuscript as there are some solid findings (that Heh2 binds specifically to NPCs etc.) but also a provocative finding (that loss of Nup133 breaks Heh2’s interaction with NPCs despite not physically interacting). Thus, there is a decision to be made about whether there is value in introducing a novel concept to the field once additional data is provided in a revised manuscript.

      Reviewer 3 Cross commenting: I have no fundamental disagreements with either of the other two reviewers. The comment from Reviewer#2 summarises this quite neatly. While I have fewer concerns about the quality of the data as presented, I think we all agree that at best the study is preliminary. What the authors need to do is to construct a coherent model that will account for the observations described here and then to design experiments that will test this model. I'm not suggesting that they must have a complete story, but they do need to go beyond what is in the current manuscript.

      • *

      Our Response: We appreciate that the reviewer does not have any questions about the quality of our data, but we argue that we have in fact presented the most coherent interpretation of the data as it currently stands. As described above, we intend to attempt to solidify this model by performing experiments suggested by reviewer 1.



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      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)): The manuscript by Huh et al. reports that oxidative stress causes fragmentation of a specific tyrosine pre-tRNA, leading to two parallel outcomes. First, the fragmentation depletes the mature tRNA, causing translational repression of genes that are disproportionally rich in tyrosine codon. These genes are enriched for those involved in electron transport chain, cell cycle and growth. Second, the fragmentation generates tRNA fragments (tRFs) that bind to two known RNA binding proteins. Finally, the authors identify a nuclease that is needed for efficient formation of tyrosine tRFs. Comment 1: Th­­­­e authors should include a short diagram indicating the various known steps of pre-tRNA fragmentation (perhaps as a supplement) for general readers.

      Response: We thank the reviewer for their suggestion. Pre-tRNA fragmentation is still an unknown field but an initial introduction is best seen from pre-tRNA processing where there is a cleavage event for pre-tRNAs with an intron. This is a complex subject but a recent review from Hopper and Nostramo has done an excellent job in in describing the current field in yeast and vertebrate species (Hopper and Nostramo, Front. Genet., 2019). We have added this citation and new text in the manuscript about pre-tRNA processing for general readers to follow up on. We feel that a supplementary figure might be a bit too brief in describing the knowns and unknowns of pre-tRNA processing and fragmentation.

      Comment 2: I find the enrichment for mitochondrial electron transport chain (ETC) curious. The ETC includes several oxidoreductases, which may be rich in tyrosine as it is a common amino acid used in electron transfer. The depletion of the tyrosine tRNA from among many tRNAs under oxidative stress may not be incidental but related to an attempt by the cell to decrease oxygen consumption to avoid further oxidative damage. The authors could further mine their data to corroborate this hypothesis. For example, are the ETC genes among the targets of the RNA binding proteins targeted by tyrosine tRFs? This could potentially connect the effects of mature tRNA depletion and tRFs.

      Response: We thank the reviewer for this very interesting comment and insight, which had not occurred to us. The relationship between this response and oxidoreductase regulation could be a factor in both the tRNA and tRF modulations seen in our cells. Interestingly, we find that many oxidoreductases genes (such as the NDUF family) are bound by hnRNPA1 by CLIP. In new data, we have done stability experiments with the tRF (new Fig 7E-F) to show the regulon of hnRNPA1 is modulated with overexpression and LNA against the tRF, revealing that this tRNA fragmentation response modulates expression of certain oxidoreductase genes. However, we do not see clear and significant differences for ETC genes in particular. As hnRNPA1 is known to act as both a promoter and destabilizer of genes depending on context, it is likely that further and more detailed work will be needed to parse this hypothesis out in future studies.

      Comment 3: In figure 4A, the authors should provide the tyrosine codon content of the overlap genes and show how much it differs from a randomly selected sample.

      Response: We have identified an error in our manuscript where the overlap actually identifies 109 proteins rather than the 102 reported in the original manuscript. We apologize for this oversight. As for the overlap proteins, we plotted the downstream proteins detected in the proteome by mass spectrometry based off on Tyr-codon content. As explained in the text, the targets we tested were chosen for having higher than median levels of Tyr-codon, as seen in the histogram, and for showing some of the greatest reduction after Tyr tRNA-GUA depletion (Fig S4A). The other proteins found in the overlap will fall in a similar pattern along the histogram.

      Comment 4: Fig.6F, lower panel: the model should show pre-tRNA, as opposed to mature tRNA, because it is the former that is fragmented.

      Response: We apologize for the confusion. The model in Fig 7F was supposed to denote the pre-tRNA with the trailer and leader sequences intact initially, then lost with processing to mature tRNA. To make it clearer, we have now labeled the first species as “Pre-tRNA.”

      Reviewer #1 (Significance (Required)): This study is comprehensive and novel, and includes several orthogonal and complementary approaches to provide convincing evidence for the conclusions. The main discovery is significant because it presents an important advance in post-transcriptional control of gene expression. The process of tRF formation was previously thought not to affect the levels of mature tRNA. This study changes that understanding by describing for the first time the depletion of a specific mature tRNA as its precursor form is fragmented to generate tRFs. Finally, the authors identify DIS3L2 as a nuclease involved in fragmentation. This is also an important finding as the only other suspected nuclease, albeit with contradictory evidence, is angiogenin. Collectively, the findings of this study would be of interest to a broad group of scientists. I only have a few minor comments and suggestions (see above).

      Response: We thank the reviewer for their very positive and insightful comments and feedback.

      REFEREES CROSS-COMMENTING I have the following comments on other reviewers' critiques. Regarding the concern that the disappearance of the pre-tRNA could be a transcriptional response (reviewer 2), I think that the appearance of tRFs makes this scenario unlikely. If pre-tRNA levels decreased due to transcriptional repression, wouldn't one expect that both tRNA and the tRF levels diminish concomitantly? Reviewer 3 raises the issue of cross hybridization in Northern blots. The authors indicate that they "could not detect the other tyrosyl tRNA (tRNA Tyr AUA) in MCF10A cells by northern blot..." (page 6). Also, they gel extracted tRFs and sequenced them (figure S6B), directly identifying the fragments. I think these findings mitigate the concern of cross hybridization and clearly identify the nature of tRFs. Finally, I think that the codon-dependent reporter experiment (figure 5D) addresses many issues surrounding codon dependent vs indirect effects. In that experiment, the authors mutate 5 tyrosine codons of a reporter gene and demonstrate that the encoded protein is less susceptible to repression in response to oxidative stress.

      Response: We thank the reviewer for their tremendous insights. We are in agreement regarding the three points in the cross-comments.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)): This very interesting study from Sohail Tavazoie's lab describes the consequences of oxidative stress on the tRNA pool in human epithelial cell lines. As previously described, the authors observed that tRNA fragments were generated upon exposure of cells to ROS. In addition, the authors made the novel observation that specific mature tRNAs were also depleted under these conditions. In particular, the authors focused on tyrosyl tRNA-GUA, which was decreased ~50% after 24 hours of ROS exposure, an effect attributable to a decrease in the pre-tRNA pool. Depletion of tyrosyl tRNA resulted in reduced translation of specific mRNAs that are enriched in tyr codons and likely contributed to the anti-proliferative effects of ROS exposure. In addition, the authors demonstrated that the tRFs produced from tyr tRNA-GUA can interact with specific RNA binding proteins (SSB and hnRNPA1). The major contribution of this paper is the novel finding that stress-induced tRNA fragmentation can result in a measurable reduction of specific mature tRNAs, leading to a selective reduction in translation of mRNAs that are enriched for the corresponding codons. Previously, studies of tRNA fragmentation largely focused on the functions of the tRFs themselves and it was generally believed that the mature tRNA pool was not impacted sufficiently to reduce translation. The findings reported here therefore add a new dimension to our understanding of the cellular consequences of stress-induced tRNA cleavage. Overall, the data are of high quality, the experiments are convincing, and the conclusions are well supported. I have the following suggestions that would further strengthen the study and bolster the conclusions. Comment 1: The authors have not formally demonstrated that the reduction in pre-tRNA in H2O2-treated cells is a consequence of pre-tRNA cleavage. It is possible that reduced transcription contributes to this effect. Pulse-chase experiments with nucleotides such as EU would provide a tractable approach to demonstrate that a labelled pool of pre-tRNA is rapidly depleted upon H2O2 treatment, which would further support their model. Since the response occurs rapidly (within 1 hour), it would be feasible to monitor the rate of pre-tRNA depletion during this time period in control vs. H2O2-treated cells.

      Response: We thank the reviewer for their suggestion and agree that testing for a transcriptional effect using a pulse-chase experiment would further support these findings. We are grateful to both reviewer 1 and reviewer 2 in the cross-comments for recognizing that the tRNA repression response we see is too rapid to be a transcriptional response and that the fact that this tRNA depletion response occurs concomitantly with the tRF generation supports our model that this is a pre-tRNA fragmentation response. It would be of interest for future studies to also examine the impact of cellular stress on tRNA transcription.

      Comment 2: To what extent is the growth arrest that results from H2O2 treatment attributable to tyr tRNA-GUA depletion (Fig. 3A)? Since the reduction in tRNA levels is only partial (~50%), it should be feasible to restore tRNA levels by overexpression (strategy used in Fig. 3E, S3B) and determine whether this measurably rescues growth in H2O2-treated cells.

      Response: We thank the reviewer for their suggestion. Originally, we had also thought of this experiment and attempted to test this hypothesis. Upon experimentation, we ran into technical challenges that prevented us from drawing any conclusions. The problems were that we were unable to develop a cell line that stably overexpressed the Tyr tRNA-GUA and had to settle for a transient overexpression that only lasted for a couple of days (Fig S3B). For transient transfection, we used Lipofectamine 3000 (Invitrogen) that has associated cell toxicities and requires a control RNA transfection in lipofectamine. In addition, H2O2 in itself is a stress. The simultaneous occurrence of these two stresses led to a combination of cell death and cell growth for the control and experimental group. Given the high variability, we were unable to draw any conclusions on cell growth with this combination. We hope to identify a way to stably overexpress Tyr tRNA-GUA in the future to address this hypothesis.

      Comment 3: Knockdown of YARS/tyr tRNA-GUA resulted in reduced expression of EPCAM, SCD, and USP3 at both the protein and mRNA levels (Fig. 4C-D, S4C). In contrast, H2O2-exposure reduced the abundance of these proteins without affecting mRNA levels (Fig. 5A-B, S5A). The authors should comment on this apparent discrepancy. Perhaps translational stalling induces No-Go decay, but it is unclear why this response would not also be triggered by ROS.

      Response: We would like to clarify that out of the three genes in Fig. S5A, only EPCAM mRNA levels were significantly reduced with H2O2-exposure while no changes were observed in the mRNA levels of USP3 or SCD. It is difficult to ascertain the reason for EPCAM mRNA reduction but one hypothesis is due to timing and steady state levels. Levels of mRNAs seen with knockdown of YARS or tRNA represent steady state levels where mRNA decay and transcriptional changes can be easily seen. Following H2O2, the data is collected at 24 hours, which may be before mRNA effects can be fully appreciated. We have edited the text to clarify the uncertainty involved. We agree with the reviewer’s insightful comment and find these differences to be interesting and will consider them in future studies to better understand the interplay between translation and mRNA levels in the context of tRNA depletion.

      Comment 4: In addition to the analyses of ribosome profiling in Fig. 5E-F, it might also be helpful to show a metagene analysis of ribosome occupancy centered upon UAC/UAU codons (for an example, see Figure 2 of Schuller et al., Mol Cell, 2017). This has previously been used as an effective way to visualize ribosome stalling at specific codons. Additionally, do the authors see a global correlation between tyrosine codon density and reduced translational efficiency in tRNA knockdown cells?

      Response: We thank the reviewer for their important suggestion. We have expanded the analysis to look at codon usage scatterplots across all codons for shTyr and shControl replicates (Fig S5D). The 5 most changed codons are labeled with UAC, a codon for the tyrosine amino acid, being the most affected (red arrow). Consistent with our model, a tyrosine codon, when at the ribosome A-site, is most affected with depletion of the corresponding tRNA. The text has also been edited to reflect our new analysis providing further evidence that ribosomal stalling could occur upon depletion of this tRNA. The gray outline around the regression line represents the 95% confidence interval.

      Fig S5D

      As seen in Fig 5F, a significant overlap was noted for genes with the lowest translational efficiency and tyrosine enrichment. We did further analysis to test if a direct and linear relationship exists between tyrosine codon density and reduced translational efficiency on the global scale (i.e. does more stalling occur with more tyrosine codons on a global scale). We again see that a reduced translational efficiency is significantly correlated with tyrosine codon enrichment (above median parameters) in the tRNA knockdown ribosome profiling data. However, our analysis on a direct relationship between codon density and translational efficiency is inconclusive. This analysis is limited given the sequencing depth and number of experimental replicates available and we lack the statistical power to draw strong conclusions. To prevent overstating our claims, we have omitted any conclusions regarding this second analysis.

      Comment 5: MINOR: On pg. 4, the authors state that tRF-tyrGUA is the most highly induced tRF, but Fig. S1B appears to show stronger induction of tRF-LeuTAA.

      Response: The reviewer is correct in that the data from Fig S1B shows Leu-tRFs with higher induction. Our text was meant to suggest we focused on tRF-TyrGUA due to higher band intensity seen on northern blot validation. We have edited the text in the manuscript to clarify this.

      Reviewer #2 (Significance (Required)): The major advance provided by this work is the demonstration that stress-induced tRNA cleavage can reduce the abundance of the mature tRNA pool sufficiently to impact translation. Moreover, the effect on mature tRNAs is selective, resulting in the reduced translation of a specific set of mRNAs under these conditions. These findings reveal previously unknown consequences of oxidative stress on gene expression and will be of interest to scientists working on cellular stress responses and post-transcriptional regulation.

      Response: We thank the reviewer for the kind comments and feedback.

      REFEREES CROSS-COMMENTING Regarding the concern that the disappearance of the pre-tRNA could be a transcriptional response (reviewer 2), I think that the appearance of tRFs makes this scenario unlikely. If pre-tRNA levels decreased due to transcriptional repression, wouldn't one expect that both tRNA and the tRF levels diminish concomitantly? Here is what I was thinking: The generation of tRFs does not generally result in reduction in levels of the mature tRNAs. So you can imagine a scenario where oxidative stress causes tRF generation from the mature tyr tRNA (which does not impact its steady-state levels), as is the case for other tRNAs. At the same time, decreased transcription would reduce the pre-tRNA pool, leading to a delayed reduction in mature tRNA, as observed. However, looking back at the data, I see that after only 5 min of H2O2 treatment, the authors observed reduced pre-tRNA and increased tRFs (Fig. 2A). This seems very fast for a transcriptional response, which would presumably require some kind of signal transduction. In addition, when you consider the amount of tRFs produced in Fig. S2C, it is hard to imagine that this would not impact the mature tRNA pool if they were derived from there. So I agree that the transcriptional scenario seems unlikely. Nevertheless, I think that looking at pre-tRNA degradation directly with the pulse-chase strategy would strengthen their story, so I would like to give the authors this suggestion. However, I am fine with listing this as an optional experiment which would enhance the paper but should not be essential for publication.

      Response: We thank the reviewer for these insightful comments. As mentioned above, five minutes is likely too rapid for a transcriptional response to be the main effect of H2O2 on Tyr-tRNA GUA. Moreover, the concomitant appearance of the tRF at this time-point makes tRNA fragmentation the most parsimonious and likely explanation rather than transcriptional repression, which would not cause a tRNA fragment to occur concurrently. Moreover, extraction and sequencing of the tRF shows it likely derives from the pre-tRNA as a 5’ leader sequence is present. We appreciate the reviewer’s suggestion and scholarly willingness to reassess their own hypothesis.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)): The major findings in this manuscript are: 1.) Oxidative stress in human cells causes a decrease in tyrosine tRNA levels and accumulation of tyrosine tRNA fragments; 2.) The depletion of tyrosyl-tRNA synthetase or tyrosine tRNAs in human cells results in altered translation of certain genes and reduced cell growth and 3.) hnRNPA1 and SSB/La can bind tyrosine tRNA fragments. There is also preliminary evidence that the DIS3L2 endonuclease contributes to the appearance of tyrosine tRNA fragments upon oxidative stress. Based upon these results, the Authors conclude that tyrosine tRNA depletion is part of a conserved stress-response pathway to regulate translation in a codon-based manner. **Major comments:** Comment 1: There is a considerable amount of data in this paper and the experiments are performed in a generally rigorous manner. Sufficient details are provided for reproducing the findings and all results have been provided to appropriate databases (RNA-Seq and ribosome profiling).

      Response: We thank the reviewer for the positive comments and feedback.

      Comment 2: The manuscript uses a probe against the 5' half of Tyrosine tRNA for Northern blotting. However, tRNA probes can be prone to cross-hybridization, especially with some tRNA isoacceptors being similar in sequence. Thus, the blots in Figure 2 and Supplemental Figures should be probed with an oligonucleotide against the 3' half of tRNA-Tyr. This will confirm the pre- and mature tRNA-Tyr bands detected with the 5' probe. Moreover, this will determine whether 3' tRNA-Tyr fragments accumulate.

      Response: We agree that the reviewer is correct in suggesting that the 3’ tRNA-Tyr might also accumulate. However, we disagree that any accumulation of the 3’ tRF might be relevant in our particular model for multiple reasons. As supported by reviewer 1’s cross-comments, cross-hybridization between isoacceptors (GUA vs AUA) would be unlikely as Tyr-AUA could not even be detected by the initial 5’ tRF probe. Additionally, the sequences for Tyr-GUA are different with no nucleotide alignment from Tyr-AUA. Furthermore, the extraction and sequencing of the 5’ tRF (Fig S6B) confirms the 5’ leader sequence unique to the pre-tRNA (also noted by reviewer 1). While the 3’ half of many Tyr-GUA are similar, we find selective binding of our RNA binding proteins only to the 5’ tRF. The 3’ tRF may play some role in binding to other proteins in cell regulatory pathways but such experiments would be outside the scope of this study.

      Comment 3: The analysis of the proteomic and ribosome profiling experiments seem rather limited, or based upon what was presented in this manuscript. If additional analyses were performed, then they should be included as well, even if they yielded negative results. For example, the manuscript identifies 102 proteins that decrease after tRNA-Tyr depletion and YARS-depletion with a certain threshold of Tyr codon content. We realize the Authors were trying to find potential genes that are modulated under all three conditions. However, this does not provide information whether there is a relationship between a certain codon such as Tyr and protein abundance if only binning into two categories representing below and above a certain codon content. The Authors should plot the abundance change of each detected protein versus each codon and determine the correlation coefficient. This analysis is important for substantiating the conclusion of a codon-based system of specifically modulating transcripts enriched for certain codons. Otherwise, how could changes in tRNA-Tyr levels modulate codon-dependent gene expression if two different transcripts with the same Tyr codon content exhibit differences in translation? Moreover, this analysis should be performed with all the other codons as well.

      Response: We have identified an error in our manuscript where the overlap identified 109 proteins and not 102 as reported previously. We apologize for this oversight. While the reviewer is correct in that identifying codon dependent changes for all 3500+ proteins detected would offer greater insight, our study was specifically focused on tyrosine as we observed this tRNA to become depleted and our experimental system modulated this specific tRNA. As for the second point on Tyr tRNA level effects on translation, we felt that the most rigorous course would be to assess causality rather than an association for this tRNA and its codon in regulating a target gene. The only way to do this is to perform mutagenesis and reporter studies. Our codon dependent reporter clearly shows a direct effect on translation in a tyrosine-codon dependent manner. As for translational regulation for two different transcripts with the same Tyr codon content, it is unclear the molecular mechanisms that could dictate these differences. The reviewer has already brought up possibilities in the next comment regarding Tyr codons in 5’ or 3’ ends or consecutive Tyr codons. These are all interesting hypotheses that others in the field have devoted entire publications to try and understand how and why codon interactions and localizations impact translation (see Gamble et al., Cell 2016, Kunec and Osterreider, Cell Reports 2016, Gobet et al., PNAS 2020). While these further analyses would be interesting, our current experimental data would be insufficient to properly address these questions. We have focused on a specific tRNA, its fragment, and demonstrated direct effects of the tRNA on the codon-dependent translation of a specific growth-regulating target gene and the tRNA fragment on the modulation of the activity of the RNA binding protein it binds to with respect to its regulon. We believe that these findings individually reveal causal roles for this tRNA and tRF in downstream gene regulation and collectively reveal a previously unappreciated post-transcriptional response. We hope the reviewer agrees with us regarding the already deep extent of the studies and that further such analyses beyond this tRNA are outside the scope and focus of this current study.

      Comment 4: The Authors should provide the specific parameters used to calculate the median abundance of Tyr codons in a protein and the list of proteins containing higher than median abundance of Tyr codon content. Moreover, the complete list of 102 candidate genes should also be provided. This will allow one to determine what percentage of these Tyr-enriched proteins exhibited a decrease in levels. Moreover, is there anything special about these Tyr codon-enriched transcripts where they are affected at the level of translation but not the other Tyr-codon enriched transcripts? For example, are these transcripts enriched at the 5' or 3' ends for Tyr codons? Do these transcripts exhibit multiple consecutive Tyr codons? This deeper analysis would enrich the findings in this manuscript.

      Response: For the proteins identified in the mass spectrometry and overlap listed in Fig 4A, Tyr codon abundance was calculated by dividing the number of Tyr amino acids present by the total number of amino acids for each protein. For genes with different isoforms possible, the principal isoform, using ENSEMBL, was used for calculations. We are also happy to provide the entire list of proteins. Additionally, please see above response to comment 3. We wish to emphasize that the goal of identification of these proteins was to identify downstream targets of this response for functional studies, which we have done. We have identified downstream genes that become modulated by this response and that regulate cell growth, consistent with the phenotype of the tRNA. We then demonstrated a direct causal tRNA-dependent codon-based response with a specific target gene using mutagenesis.

      While we agree that the additional analysis the reviewer is requesting to determine what constitutes heightened translational sensitivity to this response is interesting, we believe this is a challenging question for future studies. It is possible that enrichment at 5’ or 3’ or concentration of tyrosine codons could cause increased sensitivity. Ideally, one would have information on a larger set of proteins so that such challenging questions could be better statistically bolstered. Ultimately, the requested experiments that go beyond our current work would require further analyses and experiments to allow firm conclusions to be drawn. As the other reviewers state and this reviewer agrees, we have uncovered the initial discovery regarding this tRNA fragmentation response and provided mechanistic characterization. Future studies, which are beyond the scope of the current work will undoubtedly further characterize features of this response.

      Comment 5: The ribosome profiling results are condensed into two panels of Figure 5E and 5F. We recommend the ribosome profiling experiment be expanded into its own figure with more extensive analysis and comparison beyond just looking at tRNA-Tyr. This could reveal insight into other codons that are impacted coordinately with Tyr codons and perhaps strengthen their conclusion. As an example of a more thorough analysis of ribosome profiling and proteomics, we point the Authors to this recent paper: Lyu et al. 2020 PLoS Genetics, https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008836

      Response: We thank the reviewer for their suggestion. We have expanded the analysis to look at codon usage scatterplots across all codons for shTyr and shControl replicates (Fig S5D). The 5 most changed codons are labeled with UAC, a codon for the tyrosine amino acid, being the most affected (red arrow). Consistent with our model, a tyrosine codon, when at the ribosome A-site, is most affected with depletion of the corresponding tRNA. The text has also been edited to reflect our new analysis providing further evidence that ribosomal stalling might occur with depletion of a given tRNA. The gray outline around the regression line represents the 95% confidence interval.

      Fig S5D

      Comment 6: Moreover, one would expect that the mRNAs encoding USP3, EPCAM and SCD would exhibit increased ribosome occupancy. Thus, the authors should at least provide relative ribosome occupancy information on these transcripts to provide evidence that the decrease in protein levels is indeed linked to ribosome pausing or stalling.

      Response: We would like to emphasize that resolution of ribosomal profiling data at the codon level for specific genes requires a high number of reads and replicates to draw accurate conclusions. There is an inherent level of stochasticity when mapping RPFs to specific genes and as a result, our analysis revolved around Tyr-enriched vs Tyr-low populations as this analysis was appropriate for our sequencing depth and number of replicates. To be able to conclusively make claims regarding ribosome pausing or stalling for specific genes, we would likely need further experimentation than can be currently done. However, we are currently conducting the requested bioinformatic analysis and have promising preliminary transcript-level data supporting our model.

      Comment 7: The results with hnRNPA1 and SSB/La are extremely preliminary and simply show binding of tRNA fragments but no biological relevance. We realize that the Authors attempted to see if Tyr-tRNA fragments impacted RNA Pol III RNA but found no effect. A potential experiment would be to perform HITS-CLIP on H2O2-treated cells to see if stress-induced tRNA fragments bind to SSB/La or hnRNPA1. In this case, at least the Authors would link the oxidative stress results found in Figure 1 and 2 with La/SSB and hnRNPA1.

      Response: We agree with the reviewer that a tRF function was not established in the manuscript. As a result, we have recently completed experiments looking at mRNA stability of the hnRNPA1 regulon in the context of overexpressing the tRF as well as using LNA to inhibit this Tyr-tRF (Fig 7E-F). Our data shows, in an hnRNPA1-dependent manner, that its regulon can be functionally regulated by Tyr-tRF. With tRF overexpression and RNAi-mediated depletion of hnRNPA1, a right shift in transcript stability is seen. Importantly, when we do the converse experiment with tRF inhibition in the same RNAi-mediated reduction of hnRNPA1, we see a left shift. These complementary experiments provide data that the Tyr-tRF has a functional role when bound to hnRNPA1 by modulating the regulon of hnRNPA1 and expand the scope of this manuscript and extend the pathway defined downstream of this tRNA fragmentation event.

      Fig 7E-F

      Comment 8: The manuscript concludes that "Tyrosyl tRNA-GUA fragments are generated in a DIS3L2-dependent manner" based upon data in Supplemental Figure S7. However, there is still a substantial amount of tyrosine tRNA fragments in both worms and human cells depleted of DIS3L2. Thus, DIS3L could play a role in the formation of Tyrosine tRNA fragments but it is too strong a claim to say that tRNA fragments are "dependent" upon DIS3L2. We suggest that the Authors soften their conclusions.

      Response: While there are certainly tRFs still apparent with DIS3L2 depletion (Fig S7F-I), we note significant impairment of tRF induction with DIS3L2 knockdown/knockout with multiple different methods in C. elegans and human cells. This data supports our conclusion that tRF generation is dependent on DIS3L2 as this ribonuclease is necessary to elicit the full Tyr-tRF response. We do not make claims that Tyr-tRFs are solely or completely dependent on DIS3L2. There must be other RNases involved given the data highlighted by the reviewer. To this point, we have added clarifying text that DIS3L2 depletion does not completely eliminate the tRF induction.

      Comment 9: Moreover, what is the level of DIS3L2 depletion in the worm and human cell lines? The Authors should provide the immunoblot of DIS3L2 that was described in the Materials and Methods.

      Response: An immunoblot of DIS3L2 depletion in human cells has now been added as a supplementary figure (Fig S7I). Depletion in C. elegans was confirmed through sequencing of a mutation, as is standard in the field. The wild-type PCR product is 1nt longer (859 bp) than the mutant product (858 bp) with CTC to TAG nonsynonymous mutation preceding a single nucleotide deletion.

      Wild-type disl-2: GTTGAAGCCGCAGGGC[CTC]ACTCAGACAGCTACAGG

      disl-2 (syb1033): GTTGAAGCCGCAGGGC[TAG]-CTCAGACAGCTACAGG

      Fig S7I

      Comment 10: The key conclusions of "a tRNA-regulated growth suppressive oxidative stress response pathway" and an "underlying adaptive codon-based gene regulatory logic inherent to the genetic code" are overstated. This is because of the major caveat that knockdown of tyrosine-tRNA or tyrosyl-tRNA synthetase are likely to trigger numerous indirect effects. While the authors validate that three proteins are expressed at lower levels under all three conditions (H2O2, tRNA-Tyr and YARS), they might overlap in some manner but not necessarily define a coordinated response. Thus, a glaring gap in this paper is a clear, mechanistic link between H2O2-induced changes in translation versus the changes in expression when either tRNA-Tyr or YARS is depleted. Thus, it is too preliminary to conclude that tRNA depletion is part of a "pathway" and "regulatory logic" when it could all be pleiotropic effects. At the very least, the authors should discuss the possibility of indirect effects to provide a more nuanced discussion of the results obtained using two different cell systems and oxidative stress.

      Response: We thank the reviewer for the feedback. While we agree that indirect effects may exist, we do not make any claims that our pathway is the only one required to have translation effects. The text for Fig 4A already acknowledges the pleiotropic effects of tRNA depletion. Our data shows that H2O2 stress leads to a depletion of Tyr tRNA-GUA and that depletion of this tRNA through multiple complementary methods has a codon-dependent effect on protein expression. We hope the reviewer agrees that the reduction of a specific target gene in a tyrosine codon-dependent manner (demonstrated by mutagenesis) and the binding of the tRF directly to an RBP and the modulation of the regulon of this RBP by this tRF (demonstrated by gain- and loss-of-function studies) demonstrates a direct role of this response on specific downstream target genes rather than pleiotropy. This is in keeping with the cross-comments of reviewer 1, where Fig 5D shows a direct Tyr codon link between H2O2 and downstream effects. As a result, we feel that our conclusions of a pathway (not the only pathway) are valid. However, the conclusion of a “regulatory logic” might not be interpreted in the same way by all readers and we have thus changed the text to reflect a more nuanced position.

      **Minor comments:** Comment 11: Tyrosyl-tRNAs refers to the aminoacylated form of tRNA. We recommend that all instances of tyrosyl-tRNA be changed to tyrosine tRNA or tRNA-Tyr which is more generic and provides no indication as to the aminoacylation status of a tRNA.

      Response: We thank the reviewer for their correction. We have changed all instances of “tyrosyl” to “tyrosine” in the text.

      Comment 12: In Figure 5C, the promoter is drawn as T7, which is a bacteriophage promoter. While the plasmid used in this manuscript (psiCHECK2) does contain a T7 promoter, mammalian gene expression is driven from the SV40 promoter. Thus, the relevant label in Figure 5C should be "SV40 promoter". Moreover, additional details should be provided on how the construct was made (such as sequence information etc.).

      Response: We thank the reviewer for their correction. We have changed the promoter text in the figure. In the methods for the construct, we have included which USP3 was used and would be happy to include further information if requested.

      Comment 13: Please provide original blots for each of the replicates in: Figure 4C, n=4 Figure 4A, n=9 Figure 4D, n=3 Figure 5D, n=3

      Response: There appears to be an unintentional mislabeling of the requested blots by the reviewer. The original blots for Fig 4C, Fig 5A, Fig 5D, and Fig 6D have been made available in a separate file for reviewers.

      Reviewer #3 (Significance (Required)): This manuscript provides evidence that specific tRNAs are depleted upon oxidative stress as part a conserved stress-response pathway in humans (and worms) to regulate translation in a codon-based manner. Unfortunately, the manuscript attempts to tie together results from different conditions and systems without providing any definitive links that suggest a "pathway" involved in the oxidative stress response. The findings in this paper provide a useful starting point but fall short of being a major advance due to the lack of a clear mechanism. However, there are intriguing results in this manuscript based upon the cell lines depleted of tRNA-Tyr or tyrosine synthetase that could interest researchers in the field of tRNA biology.

      Response: We thank the reviewer for the positive comments regarding our demonstration of a conserved stress response, acknowledging the intriguing nature of our findings that will be a starting point for future studies and that our work will be of interest to researchers in the field of tRNA biology. We hope that the very positive comments of reviewer 1 and 2, the cross-comments of reviewer 1 in response to reviewer 3’s comments regarding the specificity of this response, and our inclusion for reviewer 3 of additional data on the function of the tRF in regulating the activity of the hnRNPA1 RNA binding protein defining a post-transcriptional pathway and additional corroborating requested codon-level computational analyses provide compelling support that that our findings indeed represent a major advance for the field.

    1. Author Response

      Summary:

      A strength of the work was that the mathematical modeling of re-replication captured variability in origin firing and supported a mechanism that might explain copy number variation observed in many eukaryotes. However, concern was expressed regarding the influence of assumptions made in developing the model on the outcomes and the moderate correlations between simulations and experimental data. Further explanation of the questions being investigated, the validity and nature of assumptions that were used to develop the simulations, and details explaining how these assumptions were built into the modeling were considered important. Some attempt to align the modeling outcomes with known re-replication hotspots would also improve the study. Some of the parameters used for modeling were concerning, including the use of a 16C ploidy cutoff without adequate justification. Reviewers also made suggestions for improving the experimental validation tests. Reviewers also noted places in the manuscript that require additional clarification. Overall, some concerns were raised regarding the experimental methods, and the impact of the insights gained.

      We would like to thank eLife for this Preprint Review service.

      In this manuscript, we present for the first time a model of DNA rereplication, which permits us to analyse how the process evolves at the single-cell level, across a complete genome, over time. This analysis revealed a pronounced heterogeneity at the single cell level, resulting in increased copies of different genomic loci in different cells, and highlighted rereplication as a powerful mechanism for genome plasticity within an evolving population. We would like to thank the reviewers for their critical appraisal of our work and the editor for his summary of the reviews. The points raised were overall easy to address, and we have done so in a revised version of the manuscript, where we have also clarified points which were unclear to the reviewers. Importantly, we have clarified that: there are currently no available methods for studying rereplication dynamics experimentally at the single cell level across the genome, and it is exactly this analysis that our manuscript offers; model assumptions were either standard and previously validated experimentally for DNA replication or subjected to sensitivity analysis with key findings shown to be robust to model assumptions; there was no arbitrary cut-off point in the rereplication process, which was analysed over time - an advantage of our approach. Data were depicted early in the process (2C) and late in the process (16C) but findings were robust across the process; fission yeast cells can be experimentally induced to rereplicate to different extents (from 2C to 16C or even 32C) and our model permits us to capture the process as it evolves at any ploidy; correlations between experimental and simulated data were highly significant and robust to model assumptions.

      We would like to thank the reviewers for their comments, which we believe have helped us improve our manuscript and clarify points of possible misunderstanding. A point-by-point response follows.

      Reviewer #1:

      The authors develop and analyse a mathematical model of DNA rereplication in situations, where re-firing of origins during replication is not suppressed. Using the experimentally measured position and relative strength of origins in yeast, the authors simulate DNA copy number profiles in individual cells. They show that the developed model can mostly recapitulate the experimentally measured DNA copy number profile along the genome, but that the simulated profiles are highly variable. The fact that increasing copy number of an origin will facilitate its preferential amplification essentially constitutes a self-reinforcing feedback loop and might be the mechanism that leads to overamplification of some genomic regions. In addition different regions compete for a limiting factor, and thereby repress each others' over-amplification. While the model generates some interesting hypotheses it is unclear in the current version of the manuscript, to what extent they arise from specific model assumptions. The authors do not clearly formulate the scientific questions asked, they do not discuss the model assumptions and their validity and they do not adequately describe how model results depend on those assumptions. Taken together, the scientific process is insufficiently documented in this manuscript, making it difficult to judge whether the conclusions are actually supported by the data.

      The manuscript has been modified to further clarify the underlying questions and model assumptions. We would like to point out that the model was presented in detail in the supplementary material of the original manuscript, which included all model assumptions. In addition, model parameters used for the base-case model were systematically varied, the outcome was presented in a separate paragraph (“Sensitivity Analysis” in Results), and findings were shown to be robust to model assumptions. These points are presented in detail below.

      1) It is not clear what questions the authors want to address with their model. Do they want to understand how the experimentally observed copy number differences between regions arise? The introduction should elaborate more on the open questions in the field and explain why they should be addressed with a mathematical model.

      With this work our goal is to elucidate the fundamental mechanisms and properties underlying DNA re-replication. Specifically, we aim to investigate how re-replication evolves over time along the genome, and how it may lead to different number of copies of different loci at the single-cell level and result in genetic heterogeneity within a population. Given the large number of origins along the genome and the stochasticity of origin firing (Demczuk et al., 2012; Kaykov and Nurse, 2015; Patel et al., 2006), it is unclear how re-replication would evolve along the genome in each individual cell in a re-replicating population and how local properties and genome-wide effects would shape its progression and the resulting increases in the number of copies of specific loci. As no experimental method exists that can analyze DNA re-replication at the single-cell level over time along the genome, we designed a mathematical model that is able to track the firing and refiring of origins and the evolution of the resulting forks along a complete genome over time, and in this way capture the complex stochastic hybrid dynamics of DNA re-replication. Since existing methods to analyze DNA re-replication in vivo only provide static, population-level snapshots (Kiang et al., 2010; Menzel et al., 2020; Mickle et al., 2007), we believe that our in silico model, which is the first modeling framework of DNA re-replication, is an important contribution in the field.

      In the revised version of our manuscript, we have modified the introduction to explain these points in more detail.

      2) One of the main messages of the paper is that the amplification profiles are highly variable across single cells, because that was found in the described simulations. This behavior does however likely depend on specific choices that were made in the simulations, e.g. that the probabilities of the origin state transitions are exponentially distributed. These assumptions should at least be discussed, or better experimentally validated.

      Modeling choices and assumptions are presented in detail in the Supplementary material of the manuscript, and were made to accurately capture the dynamics of origin firing, which is known to be stochastic, as established by many studies in fission yeast (Bechhoefer and Rhind, 2012; Patel et al., 2006; Rhind et al., 2010) and the continuous movement of forks along the DNA. Specifically, the choice of the exponential distribution used for assigning a firing time to each origin has already been discussed and validated in our previous work on normal DNA replication (Lygeros et al., 2008). Indeed, as shown in Figure 2 of (Lygeros et al., 2008), our model was able to accurately reconstruct experimental data derived by single molecule DNA combing experiments (Patel et al., 2006).

      The use of the exponential distribution for transition firing times is standard in stochastic processes in general, including what are known as Piecewise Deterministic Markov Processes (PDMP), the class where the models considered in the paper belong. There are good mathematical reasons for this, for example the "memoryless" property that makes the resulting stochastic process Markov, a basic requirement for the model to be well-posed [M. H. A. Davis, "Markov models and optimization", Monographs on Statistics and Applied Probability, vol. 49, Chapman & Hall, London, 1993]. Practically, assuming an exponential distribution can be quite general, because the rate (the probability with which a transition "fires" per unit time) is allowed to depend on the state of the system, both the discrete state (in our case, the state of individual origins) and the continuous state (in our case, the progress of individual replication forks). It can be shown that one can exploit this dependence to write seemingly more general processes (that at first sight do not have exponential firing times) as PDMP (with exponential firing times) by appropriately defining a state for the system [M. H. A. Davis, "Piecewise-Deterministic Markov Processes: A General Class of Non-Diffusion Stochastic Models", Journal of the Royal Statistical Society. Series B (Methodological), Vol. 46, No. 3 (1984), pp. 353-388]. In the manuscript this feature is exploited in what we call the LF model, where the rate of the exponential firing time of each origin (probability of firing per unit time) depends on the state of the system (specifically, the number of PreR origins), as discussed in the section on Sensitivity Analysis. We have further clarified these in the revised manuscript.

      3) The authors aim at testing their prediction that rereplication is highly variable across cells. To this end they use the LacO/LacI system to estimate locus copy number. The locus intensity is indeed highly variable across cells. However, the Dapi quantification suggests that only a subset of cells actually undergo rereplication under the experimental conditions used (Fig. 4C). Therefore the analysis should atleast be limited to those cells. It would be even better, if a second locus could be labelled in another color to show that rereplication of two loci is anti-correlated as predicted by the model.

      Under the experimental conditions employed (ectopic expression of a mutant version of the licensing factor Cdc18, stably integrated in the genome under a regulatable promoter), the vast majority of cells undergo rereplication but to relatively low levels, resulting in cells with a DNA content of 2C-8C. Though the DNA content of several cells indeed appears similar to the DNA content of normal G2 phase cells, the vast majority (>90%) of cells undergo rereplication, as manifested by the appearance of DNA damage and, eventually, loss of viability. We have chosen this experimental set-up (medium levels of rereplication) as it allows induction of rereplication in practically all cells in the population, without the abnormal nuclear and cellular morphology which accompanies a pronounced increase in DNA content (ie 16C), and would make single-cell imaging more prone to artifacts. Fission yeast cells can be induced to undergo rereplication to various extents, by regulated expression of different versions of Cdc18 to different levels and/or co-expression of Cdt1. We have now explained this more extensively in the revised manuscript and thank the reviewer for identifying a point which may not have been clear in the first version of the manuscript.

      Concerning the possibility of studying two loci at the same time, we have indeed tried to tag a second region with TetR/TetO, however the signal-to-noise ratio and thus reproducible detection of the TetR focus was suboptimal under rereplication conditions. We therefore did not proceed further with this approach.

      4) What does "signal ratio" in Fig. 2 mean? And why are the peaks much higher in the simulations? Would the signal ratio between simulation and experiment correspond better, if an earlier time point in the simulation was selected?

      The definition of signal ratios is given in Results: DNA re-replication at the population level: “Specifically, we computed in silico mean amplification profiles across the genome, referred to as signal ratios in (Kiang et al., 2010), by averaging the number of copies for each origin location and normalizing it to the genome mean in 100 simulations. In these profiles, peaks above 1 correspond to highly re-replicated regions, and valleys below 1 correspond to regions that are under-replicated with respect to the mean.”

      Indeed, as observed by the reviewer, simulated peaks appear overall sharper and higher than experimental peaks. This is expected, since simulated data show the actual number of copies generated, while experimental data are subject to background noise and represent averages of 3 probes and 2 independent experiments. We have clarified this in the Results.

      Last, we chose to compare in silico and experimental profiles at a similar ploidy. Plotting in silico profiles of an earlier timepoint would indeed lead to visually more similar patterns in terms of peak intensity, but we believe this could be misleading for the readers.

      5) From line 248 onwards, the authors compare different assumptions for polymerase speed and conclude that "0.5 kb/min is closer to experimental observations". It is unclear, however, which experimental observations they refer to and what was observed there. The same question arises when they compare the LF and UF models (line 275-277).

      We have now clarified this point. Experimental observations show that under high levels of rereplication, DNA content reaches 16C four to six hours following accumulation of Cdc18 (Nishitani et al., 2000). Estimates for 0.5 kb/min and the LF model are therefore closer to experimental observations.

      6) I find the description of cis- and trans-effects rather confusing. The authors should rather explain what happens in the model. Neighboring strong origins can amplify a weak origin and origins compete for factors. In line 475-476 for example, it should be clarified that the assumption of the LF model could lead to trans-effects, instead of presenting this as a general model prediction.

      In the manuscript, we initially present what we observe in the Results section and then proceed to provide possible explanations in Discussion. We quote from the Discussion: “Such in trans negative regulation of distant origins could be explained by competition for the same limiting factor: high-level amplification of a given locus recruits high levels of the limiting factor, indirectly inhibiting firing of other genomic regions.” and “[…] in cis elements contribute to amplified copy numbers not only directly by passive re-replication, but also implicitly through increasing the firing activity of their neighbors”. To our understanding, these sentences are in complete agreement with the reviewer’s suggestions. Nonetheless, and to make this even more clear, we have modified the Discussion in our revised manuscript.

      7) Throughout the manuscript, a clear distinction should be made between the firing activity of one origin molecule and the cumulative activity of multiple copies of an origin. For example, it should be clarified in line 435 that the cumulative activity of weak origins might increase if they are closed to a strong origin, because they get amplified, instead of just writing "increased firing activity of weak origins".

      We have clarified this point in the revised manuscript.

      8) One of the major conclusions of the manuscript is that rereplication is robust on the population level. It is not clear to me what the authors mean by that. The average amplification levels are probably determined by the origin efficiencies that are put into the model. What would robustness mean in this context?

      As the reviewer points out, one of the important input parameters of the model are origin efficiencies. Since the model is stochastic however, origin efficiencies do not directly determine the amplification levels at a single-cell level. For example, in Figures 3A and Supplementary Figure S4, we show the outcome of 4 random simulations with identical underlying parameters, where it is clear that re-replication can lead to markedly different single-cell amplification levels. Indeed, genome-wide analysis across 100 simulations (Supplementary Figure S5) indicated that on the onset of re-replication, amplification levels are highly unpredictable (again, despite the fact that the input parameters are identical).

      On the contrary, when analyzing amplification profiles at a population level (averaging across sets of 100 simulations), the most highly amplified regions appear to be highly reproducible. We agree with the reviewer that these population level profiles are strongly affected by the origin efficiencies, but they are not determined solely by them. For example, low efficiency origins can be highly amplified, or highly efficient origins can be suppressed (see discussion on in cis and in trans effects) depending on their neighborhood and system-wide effects, and the extend of these effects depends on the fork speed. Sensitivity analysis with respect to different model assumptions, or model parameters (see Results, section Sensitivity Analysis and Supplementary Figure S3) indicated that amplification profiles might appear sharper or flatter, but overall amplification hotspots were highly robust.

      To summarize, in our conclusions (Discussion, section Emerging properties of re-replication) we highlight these properties (stochasticity vs. robustness) and elaborate further on how they emerge during the course of re-replication (onset vs. high re-replication) or depending on the level of analysis (single-cell vs. population level).

      9) It would be helpful if, in Fig. 2 also the origins and their respective efficiencies could be shown to understand to what extent the signal ratio reflects these efficiencies.

      We thank the reviewer for the useful suggestion, which we have incorporated in the revised manuscript.

      10) The methods section should provide more detail.

      We would like to point out that Supplementary Material, including a full mathematical description of the model is available on BioRxiv, which was also available at the time of the preprint review, (https://www.biorxiv.org/content/10.1101/2020.03.30.016576v1.supplementary-material ), and has also been uploaded as a separate document in our GitHub page: https://github.com/rapsoman/DNA_Rereplication

      Reviewer #2:

      Here, Rapsomaniki et al have modeled the process of DNA re-replication. The in silico analysis is an extension of their previous work describing normal DNA replication (Lygeros et al 2008). The authors show that there is a large amount of heterogeneity at the single cell level but when these heterogeneous signals are averaged across a population, the signal is robust. The authors support this with simulations and with experimental data, both at the single cell level and at the population level.

      1) It is a bit concerning that simulations were carried out to a ploidy level of 16C. Has it been observed that the DNA content in any given cell can rise to 16 times the initial amount? Figure 3 (simulations) shows that certain chromosomal regions can reach 30x and 160x copies for 2C and 16C. However, Figure 4 (experiment) suggests that copy numbers should only be slightly more in re-replicating conditions, compared to normal replicating conditions. Additionally, in Figure 2, the simulated data seems to be consistently noisier than the experimental data. Taken together, this may suggest that the assumptions in the model do not adequately recapitulate the biological system.

      Fission yeast cells undergo robust rereplication, and reach a ploidy up to 32C - see for example (Kiang et al., 2010; Mickle et al., 2007; Nishitani et al., 2000). 16C is therefore a usual ploidy for rereplicating fission yeast cells, observed under many experimental conditions. In addition, by manipulating the licensing factors over-expressed, different levels of ploidy can be experimentally achieved, ranging from 2C (the normal ploidy of a G2 cell, but with uneven replication) to 32C. In Figure 4, we have employed a truncated form of Cdc18 (d55P6-cdc18 (Baum et al., 1998)), which induces medium-level re-replication, as confirmed by FACS analysis in Supplementary Figure S6A. Under these conditions, the vast majority of the cells (>90%) undergo re-replication, albeit at medium to low levels. We have opted to use this strain to avoid artifacts due to disrupted nuclear morphology under high levels of re-replication We have now clarified this point in the revised manuscript. We would like to point out that in silico analysis is not carried out at 16C only but across different ploidies – it is actually a strength of our approach that we can follow the rereplication process as it evolves, at any ploidy, and we have shown that our conclusions are robust throughout. We show plots at the beginning of the process (2C) and towards the end (16C), at the single-cell and at the population level, to facilitate comparison.

      Last, as also discussed in our response to reviewer 1, simulated data appear sharper, with higher peak values than experimental data (Figure 2). This is expected, since simulated data show the actual number of copies generated, while experimental data are subject to background noise and represent averages of 3 neighboring microarray probes and 2 independent experiments. We have clarified this in the revised manuscript.

      2) This work currently is agnostic to the genes and sequences within the simulated genomes. The authors suggest that DNA re-replication can result in gene duplications. It might strengthen the manuscript if the authors are able to show that re-replication hotspots coincide with gene duplication events in S pombe. It should be relatively straightforward to overlap the hotspots found in this analysis with known gene duplication events in the literature.

      We agree with the reviewer that comparing our predictions with known gene duplication events in S.pombe would be of interest. Unfortunately to our knowledge no such dataset for fission yeast exists in the literature. The most comprehensive datasets are the ones from (Kiang et al., 2010; Mickle et al., 2007), which analyse rereplicating cells, and which we have already exploited in our paper. We would like to point out that this manuscript aims to show how rereplication evolves genome-wide. Whether the additional copies generated can lead to gene duplication events is beyond the scope of the present manuscript.

      3) The authors have nicely demonstrated that cis activation can be driven by the physical proximity of origins. The authors go on to describe trans suppression in which the activation of one origin suppresses the activation of a different origin. I would argue that this observation is simply the result of randomness in the model and stopping the simulations at fixed points.

      One of the two origins will randomly re-replicate first and simply outpace the other. Stopping the simulations at 16C will simply prevent the lagging origin from catching up the first origin. There does not seem to be an inhibitory mechanism that acts between two origins.

      This can be explained by the following equation: X + Y = constant Where X is the amount of origin 1 and Y is the amount of origin 2.

      It is also possible that the two origins could start re-replicating at the same time. This would result in the data points observed for cluster 2 (Figure 6 BC)

      We thank the reviewer for the positive comments. Indeed, as we elaborate in our Discussion, we believe that the mechanism behind the observed in trans effects is the competition for a factor that exists in a rate-limiting quantity (see also reply to point 6, reviewer 1 above), which is essentially the constant in his/her equation. Though less pronounced, such in-trans effects are also possible in the UF model, and could be due to the total DNA increase being dominated by certain origins, as suggested by the reviewer. We do not suggest anywhere in the manuscript that this inhibition is direct, but rather clearly state that it is an indirect effect.

      Reviewer #3:

      This manuscript by Rapsomaniki et al uses mathematical modeling to study the properties of DNA re-replication. They develop a model that shows some consistency with experimental data from S. pombe, and use it to conclude that re-replication is heterogeneous at the single-cell level.

      The simulations have only moderate correlations with experimental data (0.5-0.6). Indeed, simulations and actual data (Figure 2) appear quite different. Despite the statistical significance of the overlap, the limited correspondence brings into question the usefulness of the model compared to directly generating new experimental data.

      We would like to point out that the overlap between experimental and simulated data is highly significant. Firstly, the Spearman correlation coefficient between simulated and experimental genome-wide profiles is highly statistically significant (p values ranging from 7.310-12 to 3.610-41 for the three fission yeast chromosomes). Furthermore, 100.000 repetitions of random peak assignment resulted in only one case where 10 out of 22 peaks overlapped (median 2 out of 22 peaks overlapping), while comparing simulated and experimental data resulted in 14 out of 22 peaks overlapping. Simulations appear more sharp than experimental data, this is however expected as simulated data correspond to the actual number of copies generated, while experimental data are subject to background noise, have a signal-to-noise ratio that is limited by the experimental method employed and represent averages of 3 probes and 2 independent experiments (see Kiang et al., 2010 and also above). We have modified the manuscript to clarify this point. The reviewer suggests that the model is of limited use, because one could trivially generate new experimental data. We would like to point out that existing methods to analyze DNA re-replication in vivo only provide static, population-level snapshots (Kiang et al., 2010; Menzel et al., 2020; Mickle et al., 2007). To date no experimental method can generate single-cell, whole-genome, time-course measurements in re-replicating cells. Our model aims to fill this gap, and for this reason we believe in its usefulness.

      Heterogeneity among single cells, which appears to be one of the main messages of this paper, is not necessarily a surprising finding, and may even arise from the nature of the simulation being stochastic and defined at the level of single origins. They validate this prediction experimentally at a single locus, providing little novel insight.

      We would like to point out that it is the nature of replication in fission yeast which is stochastic, as experimentally shown (Patel et al., 2006), and defined at the level of single origins, and this is captured by the simulations. Heterogeneity amongst single rereplicating cells has not been previously shown or suggested in any organism, at least to the best of our knowledge. It is in our opinion a highly interesting observation, as it provides a powerful mechanism for generating a plethora of different genotypes within a population, from which phenotypic traits could be selected.

      Overall, the insights here are limited and would need to await experimental validation and further empirical data. Given that experimental measurements of re-replication are now feasible genome-wide, the value of these simulations is limited.

      Again, the reviewer seems unaware that no experimental method currently exists for analysing the dynamics of re-replication at a single-cell level genome-wide. We also feel obliged to point out that modeling and in silico analysis is in our opinion of great value for analysing complex biological processes, even when experimental methods are available. Though we are sure this is not what the reviewer really meant, his/her comment appears derogative to a complete field.

      Fork speed is assumed based on limited data and assumptions regarding re-replication fork speed without empirical data.

      As clearly stated in our manuscript (Results, section Modeling DNA re-replication across a complete genome), many studies have estimated fork speed in yeasts in normal DNA replication, with plausible values ranging from 0.5 kb/min to 3 kb/min (Duzdevich et al., 2015; Heichinger et al., 2006; Raghuraman et al., 2001; Sekedat et al., 2010; Yabuki et al., 2002). In our model, we set the base-case value as the lowest estimate (0.5 kb/min), but also explored the model’s sensitivity to this parameter by simulating the model for higher values (1 and 3 kb/min). This analysis indicated that estimates for 0.5 kb/min were closer to biological reality, a non-surprising finding given that fork speed is expected to be slower in re-replication that in normal replication.

      Overall, the comments of reviewer 3 appear in our eyes more derogative than constructive and provide little specific criticism.

      References

      Baum, B., Nishitani, H., Yanow, S., and Nurse, P. (1998). Cdc18 transcription and proteolysis couple S phase to passage through mitosis. The EMBO Journal 17, 5689–5698.

      Bechhoefer, J., and Rhind, N. (2012). Replication timing and its emergence from stochastic processes. Trends in Genetics 28, 374–381.

      Duzdevich, D., Warner, M.D., Ticau, S., Ivica, N.A., Bell, S.P., and Greene, E.C. (2015). The dynamics of eukaryotic replication initiation: origin specificity, licensing, and firing at the singlemolecule level. Mol. Cell 58, 483–494.

      Heichinger, C., Penkett, C.J., Bähler, J., and Nurse, P. (2006). Genome-wide characterization of fission yeast DNA replication origins. The EMBO Journal 25, 5171–5179.

      Kiang, L., Heichinger, C., Watt, S., B\ähler, J., and Nurse, P. (2010). Specific replication origins promote DNA amplification in fission yeast. Journal of Cell Science 123, 3047–3051.

      Lygeros, J., Koutroumpas, K., Dimopoulos, S., Legouras, I., Kouretas, P., Heichinger, C., Nurse, P., and Lygerou, Z. (2008). Stochastic hybrid modeling of DNA replication across a complete genome. Proceedings of the National Academy of Sciences 105, 12295–12300.

      Menzel, J., Tatman, P., and Black, J.C. (2020). Isolation and analysis of rereplicated DNA by Rerep-Seq. Nucleic Acids Res 48, e58–e58.

      Mickle, K.L., Oliva, A., Huberman, J.A., and Leatherwood, J. (2007). Checkpoint effects and telomere amplification during DNA re-replication in fission yeast. BMC Molecular Biology 8, 119.

      Nishitani, H., Lygerou, Z., Nishimoto, T., and Nurse, P. (2000). The Cdt1 protein is required to license DNA for replication in fission yeast. Nature 404, 625–628.

      Patel, P.K., Arcangioli, B., Baker, S.P., Bensimon, A., and Rhind, N. (2006). DNA Replication Origins Fire Stochastically in Fission Yeast. Mol. Biol. Cell 17, 308–316.

      Raghuraman, M.K., Winzeler, E.A., Collingwood, D., Hunt, S., Wodicka, L., Conway, A., Lockhart, D.J., Davis, R.W., Brewer, B.J., and Fangman, W.L. (2001). Replication Dynamics of the Yeast Genome. Science 294, 115–121.

      Rhind, N., Yang, S.C.-H., and Bechhoefer, J. (2010). Reconciling stochastic origin firing with defined replication timing. Chromosome Res 18, 35–43.

      Sekedat, M.D., Fenyö, D., Rogers, R.S., Tackett, A.J., Aitchison, J.D., and Chait, B.T. (2010). GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Molecular Systems Biology 6, 353.

      Yabuki, N., Terashima, H., and Kitada, K. (2002). Mapping of early firing origins on a replication profile of budding yeast. Genes to Cells 7, 781–789.

    1. So how do you use inline tagging to add keywords and categories while you read? Simply highlight a passage and add a note beginning with a period (.) followed by a single word or abbreviation (with no spaces).

      .productivity

  6. Aug 2020
    1. Perfil

      Voilà ! Aqui vamos a mais uma apresentação, mas agora com outros formalismos e curiosidades!

      Sou Thays do Carmo, advogada, recém graduada em Direito pelo Centro Universitário de Brasília, e mestranda pela UnB na Linha de Pesquisa 2.

      O tema objeto de minha dissertação de mestrado relaciona-se à pesquisa empírica em direito, busco encontrar padrões argumentativos típicos das decisões que estabelecem a modulação de efeitos no STF.

      Assim, estou com grandes expectativas de aperfeiçoar minha estratégia de pesquisa para que os dados estejam cada fez mais organizados, sistematizados e coerentes.

    1. Concreto pero bastante entendible. Aunque quedan muchas dudas, creo que picándole aprenderemos..

    1. Excelente taller, creo que sería muy útil otro para reforzar lo aprendido hoy. Gracis

    1. Curso Hypothesis DGBSDI

      Segunda parte del Taller, excelente herramienta

  7. Jul 2020
    1. Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

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      Reply to the reviewers

      We would like to thank Reviewer #1 and #2 for the evaluation of our research and comments to our manuscript. Their comments are highly appreciated and addressed as described below.

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      **Summary:**

      *Provide a short summary of the findings and key conclusions (including methodology and model system(s) where appropriate).*

      Here Ha et al. has further developed their Pumilio RNA tagging methodology for the isolation of UV-crosslinked proteins that are suggested to associate with Xist RNA in mouse embryonic stem cells (mESCs). Within this study the authors claim to have found the Lupus antigen RNA binding protein (La) as a novel Xist interacting partner that influences the efficacy of X-chromosome inactivation (XCI). The authors use a number of different techniques such as qPCR, fluorescent imaging, ATAC-SEQ and SHAPE to show aberration of XCI upon La shRNA knockdown. However, this study has significant flaws in the efficient isolation and validation of Xist associated proteins using their FLAG-out methodology. Furthermore, later experiments predominantly focus on cell death/survival assays, which is somewhat troubling given the essential roles La plays in processes such as cell differentiation and proliferation, ribosome biogenesis, transcriptional control and tRNA maturation. I feel the authors need to robustly address the potential effects La knockdown may be having on their mESCs.

      Reviewer #1 did not fully understand the basic designs of the experimental systems (FLAG-out and iXist), and completely rejected these experimental systems. Reviewer #1 also ignored the majority of the functional analysis on the candidate protein, Ssb. These issues cannot be addressed by additional experiments

      **Major comments:**

      *-Are the key conclusions convincing?*

      My major concern is in their Xist RNA purification.

      First of all, I couldn't find any data on proving the enrichment of Xist RNA itself in their Pumilio pull-down experiment. It would have been useful to show Xist RNA enrichment before benzonase step. Secondly, it is hard to imagine the protocol would successfully isolated Xist RNA-protein complexes from the cell. An earlier report by Clemson et al., (J Cell Biol., 1996) has shown that majority of Xist RNA is still stuck in the nucleus after nuclear matrix prep protocol using detergent, which is not so different from the authors' protocol. Moreover, the authors used UV crosslink, which would have made even harder to purify Xist RNA without sonication. Thirdly, as the tag is located on 5' of Xist RNA, it is rather surprising to see that Spen is not detected in their pulldown. Spen is one of the main functional interactors with Xist, robustly detected by several previous reports. Similarly, other high-affinity binders of Xist such as hnRNP-K and Ciz1 were also lacking from this screen. Finally, the peptides found associated with FLAG-out Xist are extremely low in comparison with other data using glutaraldehyde or formaldehyde crosslinking. For example, HnRNP-M found in Chu et al 2015 has 1120 peptide counts in differentiated cells. The authors here use HnRNP-M as a baseline for specific interactions and show a total of 6 peptide counts in Xist expressing cells and 5 in i-Empty cells (Supplementary excel sheet 1). Similarly, the La protein of interest in this study has 8 counts in i-FLAG-Xist and 6 counts in i-Empty. I struggle to see how this result indicate specific Xist binding. Worryingly this is the starting rationale for the rest of their experiments, it is hard to therefore accept the rest of their conclusions either.

      We have detected Xist RNA after Pumilio pull-down, and added the data in the revised manuscript (Figure S1). The enrichment of Xist RNA by Pumilio pull-down is about 75-fold, comparable to the enrichment reported by Minajigi et al.

      Two out of three previous studies used similar protocols to prep cell lysates for co-IP, including UV cross-linking and detergent (McHugh et al. 2015 and Minajigi et al. 2015). The major difference between their protocols and ours is the co-IP step. They used antisense oligos to pull-down Xist RNA-protein complex, while we take advantage of the specific interaction between PUF and PBS to pull-down Xist RNA-protein complex. With the data in Figure S1, we are confident that our strategy is successful in isolating Xist RNA

      For systematic identification of Xist binding proteins, each method has its own strength and weakness. As we described in the introduction, only 4 proteins were commonly identified by all three studies to systematically identify Xist binding proteins. There is no doubt that our method also missed some authentic Xist binding proteins (false negative) and identified some false positive candidates. Thus, we have to be careful in balancing between the false negative and false positive calls. The reason that we applied the ranking gain to identify Xist binding protein candidates, is to minimize the false negative rate. Meanwhile, we compared our Xist binding protein candidate list with previous identified Xist-binding proteins to enhance the confidence in our candidate lists.

      Regardless the strength and weakness of our method, Ssb is also an Xist-binding protein identified by another study (Chu et al. 2015). More importantly, we have provided experimental validation to confirm Ssb’s involvement in XCI and extensive functional analysis to reveal the protein’s mechanistic role in XCI.

      The other key conclusion the authors make is from the use of numerous cell death/survival assays for both male and female cell lines. This is extremely troubling in the context of assessing their target protein La. La is involved in multiple RNA maturation events of rRNAs, tRNAs and other polIII transcripts. Furthermore, La has been implicated in binding to the mRNA for Cyclin D1 in both human cells and mouse fibroblasts (NIH/3T3 - male) which show a significant effect on cell proliferation upon siRNA knockdown https://www.nature.com/articles/onc2010425. This, along with the observation that La knock-out blastocysts fail to develop any mice or ES cell lines (male or female) show the effect observed in the authors results is most likely not X-linked cell death https://mcb.asm.org/content/mcb/26/4/1445.full.pdf. The authors need to show that their shRNA KD isn't affecting the proliferation and general fitness of their mESC lines.

      The cell death/survival assay was specially designed for analyzing the defect of XCI. The cell death of iXist ESCs upon adding Dox is due to the induction of Xist, which consequently initiates the silencing of the only X chromosome in male cells. Knockdown of genes involved in XCI compromises XCI, thus allowing cell survival. Given the diverse functions of Ssb in cell differentiation and proliferation, ribosome biogenesis, transcriptional control and tRNA maturation, one would expect slow growth and/or cell death of Ssb knockdown cells. Indeed, the result is consistent with our expectation (Figure 2C, without Dox). Nevertheless, more Ssb knockdown cells survive in the presence of Dox, compared with control cells (Figure 2C-E, with Dox), suggesting that Ssb plays an important role in XCI.

      *- Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether?*

      As discussed above, I feel the authors have not clearly demonstrated Xist specific protein enrichment and haven't proven X-linked cell death. Due to the lack of necessary control experiments as discussed below, I feel the notion that La is involved directly in XCI as an RNA chaperone is currently preliminary/speculative.

      The FLAG-out experiment just provided an initial point for the study. We have demonstrated the interaction between Xist and Ssb by RIP. And, Ssb knockdown antagonizes the lethal effect of induced XCI in male cells, allowing more cell to survive. This is contradictory to the diverse house-keeping functions of Ssb, which should lead to slow proliferation or cell death. Therefore, the data here (Figure 2C-E) should suggest a role of Ssb in XCI. In addition, we showed that knockdown of Ssb compromises the silencing of X-linked genes (Figure 2F, 2G, and 3E), the compaction of X chromosome (Figure 3D), Xist cloud formation (Figure 4), epigenetic modifications on Xi (Figure 5), Xist RNA folding (Figure 6F-I), and Xist RNA stability (Figure 7C and D). All these data indicate that Ssb is involved in XCI by regulating Xist RNA folding.

      *- Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation.*

      I would suggest them to show RT-qPCR results of Xist RNA enrichment from the sample after flagIP before benzonase treatment.

      We have the data, and added it to Figure S1.

      Also, it would have been more convincing if their negative control construct (i-Empty) would contain 25 copies of PBSb RNA at least.

      This is a good alternative design of the negative control. Using i-Empty expressing 25 copies of PBSb RNA will allow us subtract the background causing by proteins binding to PBSb RNA. Yet, as discussed above, regardless how we improve the experimental setting, we cannot completely avoid the issue of false positive and false negative. Our goal of the FLAG-out experiment is to generate a list of Xist binding protein candidates, and their binding to Xist and their functions in XCI should be validated by additional experiments. With our current experimental setting, a list of Xist binding protein candidates has been generated, and we have validated the role of Ssb in XCI with subsequent experiments.

      In Fig1b, the total amount of proteins loaded on the gel is not equivalent between two lanes. The gel should show equivalent amounts of proteins on the gel. It looks like if the negative control sample had been loaded at the same amount as the one with Xist, the band pattern wouldn't be distinguishable between the two samples. Furthermore, as these samples were used in the following mass spectrometry screen it may suggest that the minimal increase in peptide counts observed in the iXist FLAG-out were due to an increased amount of sample being loaded? No controls are conducted to account for this.

      IP samples of i-Empty and i-FLAG-Xist were loaded in the gel in Figure 1b. It is expected that IP sample of i-FLAG-Xist should pull down more proteins than IP samples of i-Empty. The FLAG-PUFb bands (the strongest band in each lane) are about the same amount in two samples, indicating roughly equal amount of loading. After normalization of gel loading according to the FLAG-PUFb bands, the upper part of the i-FLAG-Xist lane showed some unique bands.

      For mass spectrometry analysis, the loading of two samples are independent, therefore, to compare the absolute amount of each protein between the two samples does not always provide valuable information. Yet, the relative amount of different proteins within one sample is not affected by the loading amount, thus, more informative. Therefore, we used the ranking information to estimate the relative amount of different proteins in each sample and used the ranking gain to further identify protein candidates.

      The authors quantify cell death in figures 2C - E. It seems clear that shSsb 1 and 2 have an effect on cell count even in the absence of Dox. The rescue effect seen upon Dox addition is minimal when compared to Empty + Dox 2D. The authors ∆A-iXist line with and without Ssb KD/Dox would be an informative control on whether the increase in cell survival that they see is X-linked.

      As the reviewer pointed out earlier, Ssb plays multiple roles in cellular processes. Inevitably, KD of Ssb leads to slow growth and/or cell death with or without Dox. Thus, it is less meaningful to compare the surviving cell counts in Figure 2D. Rather, the survival rate (Figure 2E) reflects the rescuing effect more precisely. Shown in Figure 2E, both shSsb 1 and 2 increase the survival rate significantly, compared with Empty control.

      Moreover, the data in Figure 3B and C demonstrated that Ssb KD compromises the survival of female differentiating cells, but not the survival of male differentiating cells, also indicating a role of Ssb in XCI. With these experiments, it should be sufficient to conclude that Ssb KD affects X-linked cell death/survival in both iXist male ESCs and WT female differentiating cells

      The qPCR results used to validate silencing defects show minor changes in expression and also don't show significant silencing of X-linked genes sufficient for cell death. Could this be because only ~ 50 - 60% of Male iXist cells seem to be expressing in the movies and that this will have an effect on the observed qPCR results? Furthermore, it seems counterintuitive that expression in the Empty male cells increases in 48h compared to 14h. Is this due to cell death and positive selection of cells less able to silence their X-chromosome? How would these data look in the female XX line? How would the data look in a ∆A-iXist line in the presence and absence of shSsb/Dox?

      First, high-quality live-cell imaging can only be carried out for 2 hours with 2-min time interval. The movies are meant to show the onset of Xist RNA signals. Therefore, they were taken one hour after Dox treatment (figure legend of Figure 4B-D). After overnight Dox treatment, Xist clouds can be seen in majority of cells.

      Second, in Fig. 2F-G, we did not include uninduced iXist male ESCs. Therefore, it is impossible to judge whether induction of Xist in this male ESC line results in Xist-dependent silencing at 14 and 48 hr. However, in our previous publication (Li et al., JMB, 2018, 430: 2734-2746), it has been shown that Gpc4, Hprt, Mecp2, G418, and TomatoRed are silenced (4- to 16-fold reduction) at 24 and 48 hours after Dox induction.

      Third, the qRT-PCR results in 14 h and in 48 h are not normalized to the same internal control. Thus, they are not directly comparable.

      Confusingly, the male line in Fig 3C shows a drop in live cell count at day 6 of differentiation? Surely given their previous results in Fig 2 the Ssb KD should increase cell viability with +Dox? Ssb KD seems to have an adverse effect on ES cells during extended differentiation protocols. In Figure S1 the authors show ~ 8 - 10% survival of male lines during differentiation. Could the recombination of the Xist sequence around the loxP sites enable the cells to outcompete the dead cells? How would iEmpty and ∆A-iXist cells compare here? Have the differentiated cells been tested for their expression of Xist? Additionally, how are there similar live cell counts for male vs female lines when ~90% of male cells die during differentiation? Were more cells plated at day 4? If so, this would bias the competition of male cell survival and therefore make the male line an inappropriate control.

      Given the essential role of La during development a control is needed to prove that this death is X-linked in the female 3F1 line. For example, an XO cell line retaining the Cast allele and shSsb expression could show the amount of death caused from shSsb alone independent of X-linked cell death.

      The reviewer completely misunderstood the experiment. The severe cell death specifically observed in female differentiating ESCs is a strong evidence showing Ssb is involved in XCI (Figure 3).

      The male ESCs in Figure 3C is a WT ESC line without the inducible Xist transgene, in which no XCI occurs upon differentiation. It is completely different from iXist male ESCs with Dox, in which forced Xist induction leads to XCI. Thus, the diverse functions of Ssb might contribute to the slight decrease in live cell count of wild type male cells at day 6 of differentiation.

      Figure S2 shows the differentiation of iXist male ESCs with or without Dox. As explained above, forced Xist induction silences the only X chromosome in male cells, resulting in cell death. In addition, XCI occurs more efficiently in differentiation condition (Figure S2) than in pluripotent status (Figure 2C)

      During differentiation, female ESCs silence one X chromosome, and the other X chromosome remains active. KD of Ssb compromises XCI, and two X chromosomes in some female differentiating cells maintain active, leading to cell death. The reviewer is correct that we need a control to rule out that the essential role of Ssb during development affects cell survival and death. An XO cell line can be used as a control. Similarly, a male cell line (XY) is also a good control. We already included a male cell line as a control in Figure 3B and 3C.

      If I understood correctly, the RNA FISH used dsDNA probes ("Sx9") against 40 kb of the X-inactivation centre (Xic). Surely Tsix or other Xic transcripts will also be visible? Can the authors use their RNA FISH to determine the XX or XO status of their cells? In Figure S5 a number of cells appear to show a single pinpoint of transcription. This could either be low levels of Xist transcripts or Xic transcription from an XO line in which the 129 chromosome is missing. It would be best to solely quantify cells which have two x chromosomes and if a significant amount of X chromosomes have been kicked out, this should be discussed and controlled for.

      This is a valid concern, but this concern can be adequately addressed with the available data in the manuscript.

      First, if the female Ssb KD cell line is an “XO” cell line, in which the X129 allele is “kicked out”, the RNA allelotyping results should show an absolute “silencing” of the X129 allele. However, in complete contrast to this notion, RNA allelotyping detected “more” RNA transcripts from X129, showing the chromosome-wide XCI defects (Figure 3D).

      Second, overexpression of Ssb in Ssb KD female cells restores the Xist clouds and the polycomb marks (Figure S8), suggesting that the Ssb KD female cells are XX, but not XO.

      Third, the severe cell death specifically occurred in female Ssb KD lines is also against the “XO” argument (Figure 3B&C).

      In Fig6, the authors generated a number of Ssb constructs for a rescue assay. However, these results complicate the matter and raise more questions than they address. It seems odd that the ∆RRM1 does not rescue based on comparison with their putative negative control, ∆NLS. However, the ∆RRM1 + 2 and ∆LAM do rescue the phenotype better than the full length Ssb? This makes no logical sense and highlights the inherent variation in cell viability these generated cell lines seem to show.

      Following on from this, figure S7 quantifies the GFP tag mRNA levels, depicting all ∆RRM mutants with expression below ~30%? How can ∆RRM1 or 2 be rescuing in this scenario? Have these lines been tested for their XX or XO status? The loss of an X chromosome would lead to a rescue of the cell death phenotype, which is a process known to occur in XX lines that have been cultured for extended periods of time. Could it also be that the cell lines derived are more or less sensitive to exogenous shRNA expression? Also, further validation is needed to assess the efficiency of KD in these lines as theoretically most of these constructs will be targeted by shRNA? What is the endogenous Ssb expression level in these lines? Where in the mRNA sequence are the shRNAs targeted to? Does this make sense on the relative expression levels of ∆RRM1/2 for example? Further testing of GFP expression could also be assessed by quantitative western blot of GFP or even visualised in their RNA FISH/IF samples (Figure S8), currently neither are shown. In addition, some kind of information of stability of each Ssb protein constructs has not been demonstrated.

      Our shRNA targets the LAM domain, so the expression of ∆LAM is not affected by the shRNA. The reviewer is correct that the detected GFP expression levels of ∆RRM1 and ∆RRM2 are too low to be conclusive. We have removed the data point of ∆RRM1 and ∆RRM2. Meanwhile, it is clear that ∆RRM1&2 has a better rescuing effect than ∆NLS, when ∆RRM1&2 and ∆NLS are expressed at similar levels. Ssb is a well known RNA chaperone/RNA helicase. Identifying Ssb is an Xist-binding protein already suggests the functional role of Ssb in XCI. The data of the plasmid rescue experiments further suggests that Ssb is involved in XCI as a RNA chaperone/RNA helicase.

      As for the Western blot and GFP fluorescence (IF), we have tried both. Neither of them detected GFP signal, reflecting the low expression level of these GFP fusion proteins. As the reviewers pointed out that the shSsb is not targeting the 5’ or 3’-UTR region, therefore, interfering the exogenous Ssb as well. This might be a reason for the low expression of these GFP fusion proteins.

      For the data shown in Figure 7A and B the authors quantify the % of cells with Xist signal. The authors have already shown a defect in Xist visualisation in Ssb KD. Surely it is plausible to assume a faster loss of Xist signal below background in weaker expressing cells. A more appropriate quantification would be the % loss of Xist signal per cell over time.

      With Figure 7C and D, the samples have been treated with actinomycin D which globally affects the transcription of cells even the PolIII associated genes Ssb is needed to mature. This treatment could have an added effect on cell mortality and function. Data confirming that actinomycin D doesn't affect the cells disproportionately is needed. The difference in half-life could be attributed to such a treatment.

      We agree with the reviewer that monitoring Xist signal loss per cell would be a better way to analyze the data. However, in Xist signal loss experiment, snapshot images were taken at four time points (1h, 2h, 3h and 4h). This is not a time-lapse imaging. High-quality time-lapse imaging can only be done within a 2-hour time period with 2-min time interval. Therefore, cell-tracking cannot be done in this experiment. In addition, even though Ssb KD slows down the formation of Xist cloud within the early phase (3 hours) of Xist induction (Figure 4), prolonged (overnight) Xist induction leads to Xist cloud formation in a significant fraction of Ssb KD cells, and the Xist cloud signals are about the same in WT and Ssb KD cells (Figure 7A, 0 h). Similarly, qRT-PCR also revealed that Xist RNA are at the same level in WT and Ssb KD cells (Figure 7C, 0 h). These data argue against that a faster loss of Xist signal in Ssb KD cells is due to weaker initial Xist signal.

      Actinomycin D was added at the last 11 hours of the experiment. During this period, no obvious adverse effects on cells were observed.

      In summarising the authors claim that La binds Xist to facilitate folding and appropriate spreading of Xist along the X-chromosome. No direct interaction has been shown, CLIP-seq data would resolve this, however I do understand this is a challenging technique. The authors have instead opted for RIP followed by qPCR (Figure S2). However, this process has a greater potential for non-specific recovery of RNAs via indirect binding. Furthermore, qPCR may also amplify the relative abundance of the RNA detected. As multiple nucleolar proteins came down in the mass spec screen and FLAG-Ssb is being over expressed, it is plausible to assume some transient Xist interactions may arise from nucleolar association at which La will be in high abundance. Positive and negative nuclear RNA controls (e.g. 7SK and U1 snRNA respectively) could be used so to determine the amount of non-specific Protein-RNA interactions in their RIP pull downs. Cytoplasmic actin is not an appropriate control as it is cytosolic.

      We have to clarify one point that the mass spec screen analyzed samples pulled down by FLAG-PUFb, but not FLAG-Ssb.

      We did not intend to distinguish whether Ssb directly binds Xist or is just associated with Xist. RIP followed by qPCR is sufficient to prove the association between Ssb and Xist RNA.

      We can include nuclear RNA as controls, if the reviewer regards RIP as a valid method to show protein and RNA association

      Other than this the authors may want to probe (via IF) for the presence of La accumulation on the X? Many other know factors such as Ciz1, hnrnpK and PRC1/2 complexes show clear accumulation on the X. If I understand correctly, there are many La antibodies on the market and endogenous levels on the X could be assessed. These antibodies may be useful in IP's and pull downs also.

      Many XCI factors play extensive roles in the cell and are not clearly enriched on Xi, including Spen (Moindrot et al. 2015). We have tried the immunostaining and did not detect Ssb’s enrichment on Xi. Ssb shows a general distribution in the nucleus without a clear enrichment on Xi (data not shown).

      *-Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments.*

      The experiments suggested above are centrally focussed on the cell lines that are currently in the authors possession with maybe exceptions with the ∆A-iXist-shSsb line suggested. However, this should be reasonably quick to obtain given their previous work for this paper. Most experiments suggested will focus on the validation of karyotype, Xist expression, rescue construct expression, further RNA FISH classification and repeating more appropriate positive and negative controls for a number of experiments. In theory this can be obtained relatively simply and quickly from current resources. But with the sheer volume of further experiments that are required here, this may take a significant amount of time.

      One vital improvement needed is the replication of mass spec data and the validation of Xist specific recovery and protein enrichment. As it stands this manuscript seems to not have any replicates of the FLAG-out methodology and mass spec data. This is troubling given the poor recovery and specificity of the protein samples obtained. Repeating these experiments would be costly in time and also financially. As it stands, I feel this is essential to conclusively validate their target of interest.

      *- Are the data and the methods presented in such a way that they can be reproduced?*

      The data is presented relatively well, however, it would be beneficial if deailed methods were in the main text and not in a supplementary file. Similarly, more information about the process of differentiation and how cell death/survival was quantified and validated is needed.

      The reviewer rejected the basic design of the experimental system and ignored the majority of the functional analysis data. No additional experiment can address these issues

      We can include more information in the main text, regarding Ssb. However, there is limited space for the main text, various depending on the journals. Meanwhile, the current citation on Ssb is adequate to emphasize that Ssb is a versatile RNA binding protein involved in a variety of fundamental RNA processing events in the cell.

      *- Are the experiments adequately replicated and statistical analysis adequate?*

      In the most part yes, however there seems to be no replicates of the FLAG-out mass spec screen which is worrying given the minimal specificity observed in the current data.

      As we mentioned above, the FLAG-out experiment only serves as a starting point to generate a list of Xist binding protein candidates. Rather than repeating the FLAG-out experiment, we compared the result of FLAG-out to previously published lists of Xist binding protein candidates. More importantly, additional experiments are carried out to validate the Xist binding proteins identified by FLAG-out.

      **Minor comments:**

      *- Specific experimental issues that are easily addressable.*

      Unfortunately, the majority of experimental issues need to be addressed with more robust data which are highlighted above. However, some image analysis, quantification and classification can be amended relatively easily. For example, the live-cell imaging data should be quantified as loss of signal as discussed and RNA FISH should be used to classify XX positive cells and the XO cells can be discarded from analysis.

      We have addressed these issue in the previous sections of this rebuttal.

      *- Are prior studies referenced appropriately?*

      Most papers regarding Xist pull down and biology are discussed and referenced appropriately. However, the role in which La plays during development and its aberrant affects upon KD are seemingly downplayed. I would like to see more discussion of potential defects that could be caused due to globally altering cellular RNA folding.

      We have tried to cite key references about Ssb in development and RNA folding. Due to length limitation, we cannot cite all references in the topic. If necessary, we could discuss the possibility of indirect effect of Ssb KD on XCI through globally altering cellular RNA folding.

      *- Are the text and figures clear and accurate?*

      For the most part, lots of the figures are clear and accurate. Apart from these exceptions.

      1.The Y-axis of Figure 2D is confusing. What does 0.3 as a "sum of area" equate to? 30% of the area was ES cells? This doesn't look to be the case from Fig 2C. Also, how does the intensity of the signal compare? The area may not be a good quantification due to ES cells growing in colonies.

      We have revised the Y-axis labelling of Figure 2D to “sum of area cm2”. Thus, “0.3” means that the area of ESCs is 0.3 cm2. ALPP is highly expressed on ES cell surface. ALPP stain usually produce saturated stains on ES cell colonies. Thoroughly stained ES cell colonies, big and small, show similar signal intensity levels. To analyze the “total signal intensity” will be not much different from “sum of area”.

      2.In the Movies S1-7 there are boxes around certain cells and marked with "Figure 5a - c". This seems to be incorrect as figure 5 is currently the IF staining of polycomb marks. I assume this is in relation to Figure 4b-d?

      We have corrected the labelling mistakes.

      3.Similarly, in Movies S1-7, the intensities of Xist foci seem by eye to be similar. In the paper it is claimed that the Xist clouds that do form are lower in intensity. Are the Movies depicting the same range of pixel intensities? If not, this should be amended. Similarly, figure 7 seems to show relatively equivalent RNA signal at 0 h?

      All the images were collected using a fixed standard of the microscope and camera setting, and these movies depict the same range of pixel intensities. Movies S1-S3 are WT control, and Movies S4-S7 are Ssb KD cells. The Xist cloud signals are weaker in Movie S4-S7 (also quantified in Figure 4E). For the Xist cloud signal, not only the intensity, but also the area of Xist cloud, have to be taken into account.

      The 0 h in Figure 7 is after overnight Dox treatment, and different from the time point in Movies S1-7 (maximum 3 hour Dox treatment, figure legend of Figure 4B-D). The discrepancy can be explained by that knockdown of Ssb only slows down the formation of Xist clouds. After overnight forced expression, the Xist RNA still shows an accumulation in the cells. Figure 7 shows the forced accumulation of Xist RNA after prolonged Dox treatment disappears faster after Dox withdraw.

      4.In figure 4A the data is from female XX cells, this should be highlighted to limit confusion with the male iXist data shown below in 4B-E. It would also be helpful to have the male/female icons (as in figure 3B), for each figure that has images of cells. Currently Figure 4, 5, 7, S5 and S8 are lacking these icons.

      We have revised the labelling on Figure 3, 4, 5, 7 S6 and S9 (S5 and S8 before revision).

      5.No explanation of the Flag-Ssb expression is given for figure S2. Furthermore, is it really necessary to express Flag-Ssb? There are reasonably good antibodies out there for Ssb as this was how it was originally found in Systemic Lupus patients. Also, no data showing the amount of Ssb being overexpressed is shown. This may have big implication to the validity of the RIP-qPCR analysis.

      We could perform qRT-PCR to quantify the overexpression level of Flag-Ssb. If required, we could use Ssb antibody to do Western blot to show the amount of Flag-Ssb protein.

      *- Do you have suggestions that would help the authors improve the presentation of their data and conclusions?

      Most of the data is presented reasonably well, but the robustness of the data somewhat retracts from their conclusions. I feel the certainty of their conclusion regarding Xist specific La binding and RNA chaperone activity is still presumptive and should be rewritten unless more robust data can confirm Xist interaction. I would also suggest deciding on the nomenclature for the protein of interest and use either La or Ssb, the continued use of both through the figures and text can get a little confusing to the reader.

      In the current literatures, Ssb seems to be commonly used as a gene name and La is used as a protein name. We have revised the manuscript to use one name “Ssb” to describe both the gene and the protein.

      Reviewer #1 (Significance (Required)):

      *- Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field.*

      It was a good trial to use PBSb-PUFb system to purify Xist RNA binding proteins, compared to previous reports had used anti-sense oligo purification using complementary sequence to Xist RNA sequences. But currently the purification still needs further validation and repeats to confirm its use. A potential complementary technique could be to isolate Xist directly by using biotinylated probes against the PBSb sequence.

      The authors further claim the identification of a novel Xist RNA chaperone (La/Ssb) which they say facilitates XCI progression. This would be a novel finding in the field; however, the data is currently not robust enough to support this

      *- Place the work in the context of the existing literature (provide references, where appropriate).*

      This work has focused on the development of a milder methodology for purifying Xist RNA during XCI. Others have published similar methodologies predominantly focusing on purifying Xist RNA directly with biotinylated probes (McHugh et al. 2015; Minaji et al. 2015; and Chu et al. 2015). Although this method boasts a milder purification method, it seems to be low yielding in Xist specific proteins. Others have shown a more robust identification of bona fide Xist binding proteins which are currently missing in this manuscript. A recent preprint from the Plath lab has identified new factors involved in XCI during differentiation and their tethering/rescue experiments are far more convincing than the ones shown in this manuscript https://www.biorxiv.org/content/10.1101/2020.03.09.979369v1. The candidate protein Ha et al. have identified has multiple roles in developing cells and has shown to be important during mouse development. However, Ha et al do not robustly show that the knockdown of Ssb causes X-linked cell mortality. Alternatively, as would be presumed from Ssb's essential role in many housekeeping short non-coding RNAs, the cell death seems more ubiquitous upon shRNA KD. Therefore, the link the authors are making here are relatively weak.

      Ssb KD rescues cell death caused by forced induction of Xist in male ESCs. In addition, Ssb KD leads to cell death in differentiating female ESCs, while it has a negligible effect on cell death in differentiating male ESCs. These data clearly demonstrated X-linked cell survival/mortality by Ssb KD.

      Plath lab’s work is different from ours. In their manuscript, the authors report the observation of a protein condensation which is assembled by Xist but sustains in absence of Xist. TDP-43 (a.k.a. Tardbp) happens to be one protein factor involved in the protein condensation and also one candidate protein selected for further validation in our study. In our study, Tardbp KD did not rescue cell death caused by induced XCI in male cells. Thus, Tardbp is not further studied. In the manuscript, we have discussed the possibility that low efficiency of knockdown and redundancy might contribute to the failure in validation of Tardbp

      *- State what audience might be interested in and influenced by the reported findings.*

      The audience may be interested in the novel technique and the finding of a novel Xist binding protein.

      *- Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.*

      RNA biochemistry and developmental biology

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      **Summary:**

      This manuscript describes a novel "FLAG-out" system, where the authors sought to identify Xist RNA binding proteins. The authors focused on a specific protein found in their screen and also identified in several other screens for Xist RNA binding proteins, Ssb/La, and further characterize the role of this protein in XCI. This manuscript describes the loss of Ssb/La and suggest that it predominately impacts the canonical 'cloud' formation of Xist RNA on the X chromosome during XCI initiation. Further, they determine that loss of Ssb/La decreases Xist RNA half-life and alters folding of Xist RNA transcripts. Based on their findings, the authors propose that Ssb/La functions to directly bind and fold Xist RNA transcripts in a manner that stabilizes Xist RNA, allowing for proper 'cloud' formation and successful initiation of XCI.

      **Major comments:**

      The authors made an interesting findings that the SLE-relevant autoantigen Ssb/La stabilizes Xist RNA transcripts, and there is some evidence that this occurs by binding and maintaining proper folding of Xist RNA. Despite these intriguing observations, there are many parts of the manuscript that need to be addressed in order to support the authors main conclusions.

      The most troubling aspect of this manuscript is the persistent use of an artificial XCI system in male cells to draw strong conclusions about the function of Ssb in XCI. This issue is prevalent throughout the manuscript, and I question why the authors chose to perform most of their experiments in male cells when the same experiments can be (and have previously been by other groups) performed in female cells. Using male ESCs and then making conclusions for XCI, which is a female-specific process, is a major concern.

      In addition to iXist male ESC line, many experiments, such as cell death/survival (Figure 3B, C), allelotype (Figure 3E), Xist could formation (Figure 4A), H3K27me3 and H2AK119ub IF (Figure 5), were performed in female ESC. We chose to do SHAPE and Xist RNA stability assays in iXist male ESC line, because the onset of XCI is much more synchronized in this system. Moreover, in female cells, Xa causes additional layers of complication/noise in the ATAC-sequencing which may not be fully cleared up by data analysis. On the other hand, inducible Xist expression in male ESCs can be used as an experimental system to recapitulate the silencing step of XCI (Ha et al. 2018; Wutz et al. 2002).

      • Out of the 138 identified binding proteins, the authors chose to only validate three: Mybbp1a, Tardbp, and Ssb/La. The logic for choosing these candidates is weak, and the authors are only able to validate 1 out of 3 of these proteins.

      In theory, all candidate proteins in the list are possibly involved in XCI. There is no method which can help to make accurate prediction. We did not follow a clear-cut logic in selecting candidates for validation, but we do consider the candidate gene’s knockout phenotype, “early embryonic lethality”, as a phenotype consistent with a critical role of the candidate gene in XCI. Meanwhile, in the manuscript, we have discussed why we chose the three proteins for validation as the following:

      “……From the candidate proteins, we shortlisted three proteins for individual validation. Myb-binding protein 1A (Mybbp1a, Q7TPV4) and TAR DNA-binding protein 43 (Tardbp, Q921F2) were selected because they are known transcription repressors (11, 12). The Lupus autoantigen La (P32067, encoding-gene name: Ssb) was selected because systemic lupus erythematosus (SLE) is an autoimmune disease characterized by a strikingly high female to male ratios of 9:1 (13). Moreover, its autoimmune antigen La is a ubiquitous and versatile RNA-binding protein and a known RNA chaperone (14). All the three selected candidates have also been identified as Xist-binding proteins in previous studies (2, 4). Moreover, the knockout of these three genes all lead to early embryonic death. Tardbp knockout causes embryonic lethality at the blastocyst implantation stage (15). Mybbp1a and Ssb knockout affect blastocyst formation (16, 17). Early embryonic lethality is a mutant phenotype consistent with a critical role of the mutated gene in XCI (1)** ……”

      We used cell death/survival assay to further validate the role of Xist binding protein candidates in XCI. This is a stringent assay. It requires not only that Xist binding protein candidates bind to Xist, but also that the candidates have to be functionally important in XCI.

      Indeed, it has been demonstrated by Plath lab (the BioRxix manuscript mentioned by reviewer 1) that Tardbp (also named TDP-43), together with other RBPs, bind to the E repeat of Xist to form a condensate and create an Xi-domain. Yet, Tardbp KD did not rescue cell death caused by forced XCI in male cells in our studies. Thus, only 1 out of 3 of these candidates is validated and further studied. In the manuscript, we also discussed that low efficiency of knockdown and redundancy might contribute to the failure in validation of Tardbp and Mybbp1a.

      • Use of the cell death assay is not strong enough to "confirm that La is involved in induced XCI" as stated by the authors. This is a huge overstatement.

      Given the diverse functions of Ssb in cell differentiation and proliferation, ribosome biogenesis, transcriptional control and tRNA maturation, one would expect less surviving Ssb knockdown cells. In contrast, more Ssb knockdown cells survives in the presence of Dox, suggesting that Ssb plays an important role in XCI. Considering the reviewer’s comment, we revised the sentence to “further suggest that Ssb is involved in induced XCI”.

      While the authors observed differences in X-linked gene expression after Ssb KD, they did not examine expression of these genes in after KD of either Mybbp1a or Tardbp. Are the changes observed in these genes specific to Ssb KD? Or could there still be alterations of X-linked gene expression in the non-validated KDs? This experiment should be performed and included in the manuscript, either within Fig 2 or in the supplemental. As well, inclusion of a well characterized positive control, for example Hnrnpu, as comparison to Ssb should be included.

      Mybbp1a and Tardbp were not validated by the cell death assay. Thus, compared with Ssb, Mybbp1a and Tardbp are less important for XCI functionally. We only focused on Ssb in the subsequent studies. Mybbp1a and Tardbp KD could be additional negative controls. Yet, we have used empty vector as a negative control. We do not need so many controls.

      As mentioned, Tardbp indeed binds to Xist RNA. It is very likely that Tardbp KD might alter some X-linked gene expression. This rules out Tardbp KD as a good negative control.

      If we do not see any effect of Ssb KD on X-linked gene expression, a positive control is absolutely required. However, we have detected that Ssb KD compromises the silencing of several X-linked gene. A positive control might not be essential.

      • The authors perform RIP to validate the interaction of Ssb with Xist, but this is performed in male ES cells with induced Xist RNA and with FLAG-tagged Ssb. Aside from these cells being male, in this system Xist RNA expression is much higher than would be found endogenously. RIP should have been done in female differentiated ESCs if there is in fact a role for XCI.

      • The authors need to include more details in the methods section to explain how the FLAG-Ssb is expressed in these cells, and why the authors chose to use a tagged contrast over endogenous Ssb. Due to these issues the result from this experiment is essentially meaningless and is not convincing of Ssb interaction with Xist RNA. There is no reason RIP cannot be performed in female cells, and the authors should repeat this experiment in the relevant experimental condition. As well, if a validated Ssb antibody exists the authors should perform RIP using the endogenous protein.

      If required, we could try to perform RIP and/or CLIP using Ssb antibody in female cells.

      The authors state in Fig 3A-C that the results of the cell death and differentiation experiments "...support a functional role of La in XCI". The authors state earlier that Ssb is a ubiquitous protein that is embryonic lethal (in both female and males). Based on this, the cell death results shown do not support a functional role of La in XCI as the Ssb KD could be having an indirect affect due to its other developmental functions. This manuscript lacks a direct functional link between Ssb and XCI; more data is necessary.

      Given the diverse functions of Ssb in cell differentiation and proliferation, ribosome biogenesis, transcriptional control and tRNA maturation, one would expect less surviving Ssb knockdown cells. In contrast, more Ssb knockdown cells survives in the presence of Dox, suggesting that Ssb plays an important role in XCI.

      For the data in Fig 3A-C, Ssb KD causes the death of female differentiating cells, but not male differentiating cells. Therefore, it rules out that the death of female cells is due to the general function of Ssb. Rather, the specific role of Ssb in XCI contributes to the female specific cell death.

      In Fig 3D, the authors perform ATAC-seq in inducible male ES cells. The authors claim that the extremely slight reduction in chromatin compaction of the Ssb KD compared to control iXist "directly connect La to the heterochromatinization of Xi, supporting a functional role of La in XCI". This is also an overstatement based on the minimal, and possibly indirect, change in compaction. The positive control i-detaA-Xist sample has significantly less compaction (and thus significantly higher compaction defect) than the Ssb KD again disputing the claim stated above. It is unclear why performing ATAC-seq is even necessary, as Ssb isn't stated to have a function in regulating chromatin architecture. In addition, why the authors performed ATAC-seq in the artificial male XCI system and not in the F1 female cells, and the N of the experiment is unclear. If the authors want to include the ATAC-seq in further revisions it should be repeated n=3 in the female system.

      The male induced XCI system provides a more synchronized onset of XCI. More importantly, in the male induced XCI system, only one X chromosome exists, avoiding the interference from the active X chromosome in female cells. If ATAC-seq was performed in female cells, only loci with SNPs can be distinguished. The sequencing reads from Xa will create additional layers of complication/noise which may not be cleared up fully by data analysis

      “i-delat-Xist” is a positive control to show the experimental system works. It is not justified to compare the chromatin accessibility of the mutant, which is only a Ssb “knockdown” mutant, and the control “i-delat-Xist”, in which the Repeat A is “deleted”. We admit that ATAC-Seq results did not reveal a drastic difference in chromatin accessibility between the wild type sample and the mutant sample. However, as what we discussed in the manuscript, clear difference can still be seen at the 14 h time point. This is shown clearly by the heatmap (Fig. 3E) and the sequencing coverage profile (Fig. S4A).

      • In Fig 6, the authors state in their methods that "The shRNA construct, which worked efficiently against Ssb, was not designed against the 3' UTR of the RNA. Therefore, the shRNA is against some of the rescue plasmid constructs. Nonetheless, transfecting the Ssb knockdown cells with the rescue plasmids should compensate the effect of Ssb knockdown and serve as a rescue assay to study the functional domains of La.". This is troubling and seems like a major experimental issue; the specific rescue constructs that may be impacted by this issue are not stated and should be explicitly mentioned. This becomes more confusing when examining the data from rescue experiments.

      We pointed out this issue in the original manuscript. We agree that the experiment was not perfectly designed. In the revision, we added in the information on the shRNA target site. Our shRNA targets the LAM domain, so the expression of ∆LAM is not affected by the shRNA. We agree that the detected GFP expression levels of ∆RRM1 and ∆RRM2 are too low to be conclusive. In the revision, we have removed the data point of ∆RRM1 and ∆RRM2. Meanwhile, it is clear that ∆RRM1&2 has a better rescuing effect than ∆NLS, when ∆RRM1&2 and ∆NLS are expressed at similar levels. Ssb is a well-known RNA chaperone/RNA helicase. Identifying Ssb is an Xist-binding protein already suggests the functional role of Ssb in XCI. The data of the plasmid rescue experiments further suggests that Ssb is involved in XCI as a RNA chaperone/RNA helicase.

      If it is necessary, we could redo this experiments using a shSsb targeting 3’-UTR or expressing GFP-Ssb immune to shSsb.

      In Figure S7, the expression of the rescue constructs deltaRRM1 and deltaRRM2 is extremely low, yet the authors observe a rescue of the cloud phenotype (fig 6D) from those constructs that reaches almost the level of full length Ssb. This is confusing, and the authors need to address this by performing a western blot to show the protein levels of these rescue constructs and discuss further how such a low level of expression can show a rescue phenotype. The results would also be stronger if the authors examined H3K27me3 and H2AK119ub1 enrichment since they observed decreased overlap of these marks with Xist RNA after Ssb KD. Finally, the authors state that "...all three RNA-binding domains are required for the functionality of La in XCI..." however I have trouble coming to this conclusion based on the above issues. As well, if the authors want to support direct function, they should repeat the RIP experiments with these rescues constructs to show that the domains capable of rescue can still bind to Xist RNA.

      Reviewer 1 raised similar concerns. In Figure 6C, the live cell counts of ∆RRM1 and ∆NLS are about the same. It might be due to the low expression level of ∆RRM1 (Figure S7). It is clear that ∆RRM1&2 has a better rescuing effect than ∆NLS, when ∆RRM1&2 and ∆NLS are expressed as similar levels. To make the data more straight forward, we removed the data point of ∆RRM1 and ∆RRM2, because of their low expression levels.

      As for the Western blot and GFP fluorescence (IF), we have tried both. Neither of them detected GFP signal, reflecting the low expression level of these GFP fusion proteins. The shSsb is not targeting the 5’ or 3’-UTR region, therefore interfering the exogenous Ssb as well. This might be a reason for the low expression of these GFP fusion proteins. If it is necessary, we could redo this experiments using a shSsb targeting 3’–UTR or expressing GFP-Ssb immune to shSsb.

      We deleted the sentence "all three RNA-binding domains are required for the functionality of La in XCI".

      **Minor comments:**

      The authors may want to consider better highlighting the strengths of their "FLAG-out" system. As written, is it difficult to tell how this system sets them apart from the previously published studies referenced in the text, especially as some of these studies used similar crosslinking conditions and cell types. Additionally, the logic and questions the authors pose in the introduction as to why they performed this project are too general and not very strong. For example, the authors mention how might protein machinery may assemble on Xist RNA, and how might Xist RNA may spread on the X chromosome. However neither of these topics are actually addressed in their experiments or discussion. These are interesting questions, but the authors should either discuss them further within the context of their results or take these questions out. It would also be helpful if the authors could better label Figure 4, as it is unclear in the figure itself that Fig 4A is in reference to female cells, but remaining panels are in male cells.

      The inducible XCI in male cells is a valid system to recapitulate the silencing step of XCI. It also provides unique advantages in many experiments, such as ATAC-seq. Meanwhile, we did perform extensive functional analysis on the endogenous XCI process using female cells. However, we do realize that presenting the data of induced XCI in male cells together with the data from female cells is confusing to many readers. We have revised the labelling on Figure 3, 4, 5, 7 S6 and S9 (S5 and S8 before revision).

      To understand “how the protein machinery is assembled by Xist” and “how Xist spreads along its host chromosome territory” are not specifically the initial aims of this study. We removed the sentences from the introduction section. However, we believe Ssb may provide clues for the future studies to fully address these questions, and we did provide the following thoughts in the discussion section:

      “……Secondly, as Ssb is able to utilize ATP to unwind RNA-RNA and RNA-DNA duplex, it may play a more active role in controlling the structural dynamics of Xist in living cells (14, 23). These structural dynamics may be important for recruiting proteins onto the RNA and spreading of the RNA along its host chromosome territory……”

      Reviewer #2 (Significance (Required)):

      I am not convinced the this manuscript, as written, has sufficient novelty. Ssb/La has been previously identified to be an Xist RNA binding protein with older/different approaches. However, there are some interesting observations in this manuscript. Major revisions are necessary.

      We agree with the reviewer that identification of Ssb as an Xist RNA binding protein is not novel. The novelty of our discovery lies in: 1) we developed a new method for isolating lincRNA associated proteins; 2) we confirmed that Ssb is an important player involved in XCI; 3) we showed that Ssb regulates the folding of Xist RNA, consequently the stability of Xist and the formation of Xist cloud.

    1. SciScore for 10.1101/2020.07.07.20148106: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Written informed consent obtained from all participants in this study and was approved by the following IRBs: 1 ) IRB# SUNY:269846 .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">In this regard , it is interesting to note that a bruton tyrosine kinase ( BTK ) inhibitor , that targets Fc-receptor signaling in macrophages , is being tested in a randomized clinical trial 32 .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Subdividing the subjects by sex did not reveal any statistical difference in IgG levels at any of the disease stages , although hospitalized females in the non-ICU setting had significantly lower antibody levels than ICU/deceased patients , whereas the difference in males was not significant ( Fig . 2f) .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CoV-2 Spike protein or Nucleocapsid protein specific IgG antibodies at titers more than 1:100,000 were detectable in all PCR+ subjects (n=87) and were absent in the negative controls.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CoV-2 Spike protein or Nucleocapsid protein specific IgG</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Other isotype antibodies (IgA, IgG1-4) were also detected.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>IgA, IgG1-4</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CoV-2 infection2-6 To predict protection against CoV-2, it is critical to understand the quantity, quality and duration of the antibody responses during different stages of COVID-19 and in the convalescent period.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CoV-2</div> <div>suggested: (Abcam Cat# ab272504, AB_2847845)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In this assay, we immobilized biotinylated CoV-2 Spike protein receptor binding domain (RBD) or the Nucleoprotein (N) on streptavidin beads, to detect specific antibodies from patient plasma (Fig.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CoV-2 Spike protein receptor binding domain (RBD)</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Different antibody isotypes were measured using anti-Ig (IgG, IgA, IgM) specific secondary antibodies conjugated to a fluorescent tag (Fig. 1a).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-Ig ( IgG</div> <div>suggested: None</div> </div>

            <div style="margin-bottom:8px">
              <div><b>IgA , IgM</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Using either anti-SRBD antibody or soluble ACE2-Fc, we show very high sensitivity in detecting Spike protein binding, down to picogram ranges (Fig. 1b).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-SRBD</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Furthermore, Nucleocapsid protein-specific IgG levels and S-RBD specific IgA positively correlated with S-RBD IgG antibodies (Supplementary Fig. 1b, c).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>S-RBD IgG</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Notably, IgG1 subclass antibody levels were comparable to total IgG levels whereas the other subtypes were relatively lower (Fig. 2b).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>IgG1</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To evaluate membrane expression of Spike protein, cells were stained with recombinant soluble ACE2-Fc fusion protein followed by a secondary staining with an anti-Fc antibody (Fig 3a).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-Fc</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ACE2 overexpression of ACE2-IRES-GFP or ACE2mKO2 was confirmed by staining with CoV-2 Spike-protein fused with mouse Fc (mFc) and antimFc secondary antibody (Supplementary Fig. 2a, b).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>antimFc</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Of note, there was a significant negative correlation between the number of days and the IgG or IgA to S-RBD, anti-nucleocapsid IgG or the NT50 values ( !" = -0.67) (Fig. 6d), suggesting a potential decline in antibody titers over time.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-nucleocapsid IgG</b></div>
              <div>suggested: (Imported from the IEDB Cat# 3E9, <a href="https://scicrunch.org/resources/Any/search?q=AB_2848062">AB_2848062</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Neutralization of the virus by antibodies (NAbs) is one of the goals to achieve protection against CoV-218.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>CoV-218</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">However, another study showed IgA antibodies, but not IgG, increased in severe patients28.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>IgA</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Although it will be important to follow the same individual subject convalescent plasma over time to better assess this finding, our data point towards a relatively short-lived antibody response to COVID-19.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>COVID-19</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">WT and ACE2 over-expressing HEK-293T were also stained with SARS-CoV-2 S1 protein, Mouse IgG2a Fc Tag (Acro Biosystems) followed with APC Goat anti-mouse IgG2a Fc Antibody (Invitrogen).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Mouse IgG2a</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Anti-S-RBD antibody and ACE2-Fc was tested both at 5 µg/mL starting concentration and in additional 5-fold serial dilutions.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Anti-S-RBD</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudotype virus neutralization assay Three-fold serially diluted monoclonal antibodies including anti-SARS-CoV-2 Neutralizing human IgG1 Antibody from Acro Biosystems, NAb#3 (Fig 4D), Genscript clone ID 6D11F2, NAb#2 (Fig 4D) and Genscript clone ID 10G6H5, NAb#1 (Fig 4D)</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-SARS-CoV-2</b></div>
              <div>suggested: (Abcam Cat# ab272854, <a href="https://scicrunch.org/resources/Any/search?q=AB_2847844">AB_2847844</a>)</div>
            </div>
      
            <div style="margin-bottom:8px">
              <div><b>human IgG1</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Percent infection obtained was normalized samples derived from cells infected with CoV-2 or SARS pseudotyped virus in the absence of plasma, ACE2-Fc or monoclonal antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>ACE2-Fc</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In addition, we also developed SARS Spike protein pseudotyped lentivirus, which similarly infected 293-ACE2 cells at almost 100% efficiency at higher virus supernatant volumes (Fig. 3f)</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>293-ACE2</b></div>
              <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_DR94">CVCL_DR94</a></div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK-293T cells (ATCC; mycoplasma-free low passage stock) were transfected with the expression plasmids using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s protocol as previously described33.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>HEK-293T</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Generating human ACE2 over-expressing cells Wildtype ACE2 sequence was obtained from Ensembl Gene Browser (Transcript ID: ENST00000252519.8) and codon optimized with SnapGene by removing restriction enzyme recognition sites necessary for subsequent molecular cloning steps, preserving the amino acid sequence.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Ensembl Gene Browser</b></div>
              <div>suggested: None</div>
            </div>
      
            <div style="margin-bottom:8px">
              <div><b>SnapGene</b></div>
              <div>suggested: (SnapGene, <a href="https://scicrunch.org/resources/Any/search?q=SCR_015052">SCR_015052</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry data were analyzed using FlowJo (BD biosciences).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>FlowJo</b></div>
              <div>suggested: (FlowJo, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008520">SCR_008520</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using GraphPad Prism 8.0 software (GraphPad Software)</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>GraphPad Prism</b></div>
              <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
            </div>
      
            <div style="margin-bottom:8px">
              <div><b>GraphPad</b></div>
              <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Author contributions M.D., L.K. and D.U. conceived, designed the experiments. M.D., L.K., L.P., M.Y. and R.H. carried out the experiments. B.T.L. designed the clinical research study on UConn Healthcare workers and M.K. recruited participants and executed clinical protocols. R.G. and O.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>UConn Healthcare</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr></table>
      

      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.05.31.20118554: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Let 's study immune responses , but let 's not create a dystopian society based on them . Materials and Methods Human specimens and data All experiments and analyses involving samples from human donors were conducted with the approval of the local ethics committee ( KEK-ZH-Nr . 2015-0561 , BASEC-Nr . 2018-01042 , and BASEC 2020-00802) , in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">To directly validate our method , we selected 210 high scoring samples and 122 random samples from known negatives and aimed to reproduce our results .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">A blinded comparison with commercial test kits showed that our approach – combining three individual assays into one single score – was suitable for large-scale epidemiologic studies .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Lastly , seropositivity can be found across all age groups and in both genders , with more male individuals affected in the USZ and BDS cohorts ( Fig . 3A , B , Table S1) .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Solution-equilibrium measurements revealed immunodominant antibodies with nanomolar affinity in COVID samples, whereas prepandemic plasma showed lower affinities despite similar titers for individual SARS2 antigens.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SARS2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">However , those with strong binding properties to SARS2 RBD ( > 2.5 ) cluster at high values for SARS1 RBD , indicating that some anti-SARS2 RBD antibodies are likely cross-reactive to SARS1 RBD .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS2 RBD</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Anti-his-tag antibody was included as a positive control .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Anti-his-tag</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In a comparative approach , we investigated IgG and IgA antibodies to S , RBD , and NC as well as responses to multiple control antigens , in four asymptomatic blood donors and 4 convalescent individuals recruited to the BDS for a plasmapheresis study .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>IgA</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Counter screening using commercial and custom-designed platforms We used the following commercial tests for the detection of anti-SARS-SARS2 antibodies in 56 plasma samples of 27 patients who were diagnosed by RT-PCR to be infected by SARS-SARS2 as well as 83-90 plasma samples which were collected before December 2019 and , hence , before the start of the COVID19 pandemics: The double-antigen sandwich electro-chemiluminescence immunoassay from Roche diagnostics ( Rotkreuz , Switzerland ) was performed with the E801 of the COBAS8000® system ( Roche diagnostics , Rotkreuz , Switzerland) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS-SARS2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The test detects any antibody against the nucleocapsid antigen .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>antibody against the nucleocapsid antigen .</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Baseline and plateau values are fixed by the respective positive and negative controls in a plate-wise fashion and the signal is fitted following these equations: 1 = 1 − ( + + 1 − √ ( + )2 + 2 ( − ) + 1 ) , 2 where cbound , ca and c are concentration of the antigen-antibody , antigen , and blood concentration respectively .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>+ + 1 − √ ( + )2 + 2 ( − ) + 1 ) , 2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Assume that we have data for samples with known serostatus and antibody measurements , that is , we have ( , ) , = 1 , . . , , where is the vector of size ( in our case our antigen measurements ) and is a Boolean variable defining group membership ( in our case , whether the individual is seropositive or not) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>we have ( , ) , = 1 , . . ,</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The day after, membranes were washed four times with PBS-T and incubated for 1 hours with an anti-human secondary antibody, HRP-conjugated, diluted 1:10000 in 1% SureBlock.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-human secondary antibody, HRP-conjugated,</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As a positive control, one membrane was incubated overnight with mouse anti-Histag antibody (ThermoFisher, dilution 1:10000 in 1% SureBlock) and subsequently with anti-mouse secondary antibody, HRP-conjugated (Jackson, dilution 1:10000 in 1% SureBlock).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-Histag</div> <div>suggested: (RevMAb Biosciences Cat# 54-1161-00, AB_2716428)</div> </div>

            <div style="margin-bottom:8px">
              <div><b>anti-mouse</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, the plates were washed five times with PBS-T and the presence of IgGs was detected using an HRP-linked anti-human IgG antibody (Peroxidase AffiniPure Goat Anti-Human IgG, Fcγ Fragment Specific, Jackson, 109-035-098, at 1:4000 dilution in sample buffer).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Anti-Human IgG</b></div>
              <div>suggested: (Jackson ImmunoResearch Labs Cat# 109-035-098, <a href="https://scicrunch.org/resources/Any/search?q=AB_2337586">AB_2337586</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We confirmed these findings by using the samples of the asymptomatic and convalescent individuals as primary antibodies in Western Blot and detected bands for both S and the NC in the Expi293 cells overexpressing the viral proteins but not in the Expi293 control lysate ( Fig . 5B) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Expi293</b></div>
              <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_D615">CVCL_D615</a></div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To benchmark TRABI, we compared the results with an in-house high-throughput assay under development at the University of Oxford (optimizations ongoing at the time of data acquisition), the Roche Elecsys, the DiaSorin, the EuroImmun, and the Abbott systems (Fig. 1C), using 139 of 149 samples (10 were removed from the analysis because of insufficient sample volume to perform all tests).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Abbott systems</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">COVID and prepandemic samples were used to assess the performance of TRABI, commercial tests (Roche, DiaSorin, Abbott, Euroimmun) and an early version of an assay under development at the Target Discovery Institute (Oxford).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Abbott</b></div>
              <div>suggested: (Abbott, <a href="https://scicrunch.org/resources/Any/search?q=SCR_010477">SCR_010477</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Details of viral proteins used for this study For high-throughput serology , the following proteins were used: SARS-CoV-2 S ( pHL-Sec; aa . 11208 , C-terminal 8His-Twin-Strep ) and RBD ( pOPINTTGNeo; aa . 330-532 , C-terminal 6His ) produced at the SGC in Oxford and the nucleocapsid protein from AcroBiosystems ( AA Met 1 - Ala 419 , C-terminal his-tag , NUN-C5227) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>AcroBiosystems</b></div>
              <div>suggested: (ACRObiosystems, <a href="https://scicrunch.org/resources/Any/search?q=SCR_012550">SCR_012550</a>)</div>
            </div>
          </td></tr></table>
      


      Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

    1. Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank the reviewers for their comments and outline below how we plan to address them.


      Reviewer #1 (Evidence, reproducibility and clarity (Required)): **Summary:** Provide a short summary of the findings and key conclusions (including methodology and model system(s) where appropriate). The authors here describe a method to modify bacterial artificial chromosomes (BAC) harbouring gene loci from eukaryotes. When wanting to modify a BAC an antibiotic selection cassette is often included alongside the desired mutation/modification to increase the number of successful recombinants in E.coli. Traditionally, this is removed in a second recombination process to leave only the desired modification. The novelty in the procedure described herein is to add a synthetic intron consensus sequence around the selection cassette, which eliminates the need for the subsequent removal of the antibiotic cassette from the BAC before transfection into mammalian cells, saving time and resources. The technique is clever in its simplicity and appears to function for a number of gene loci. The authors validated the correct functioning of the modified BACs for a number of genes using three main assays - transcript level, protein level and localisation. **Major comments:** *Are the key conclusions convincing?* The conclusion that the method described generates functional modified BACs is valid. *Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether?* While the method is successfully employed in this study, its efficiency is not quantified in relation to the state-of-the-art as described in the introduction. One assumes it would be more efficient, but this has not been tested empirically in the paper. Does the inclusion of the synthetic intron sequence have an effect on the efficiency of modifying BACs compared to a more typical two-step positive/negative antibiotic selection cassette? *

      • *

      This is a good point that we did not directly address. In general, the efficiency is similar to that of integrating any cassette with selectable marker, as has been published (Poser et al 2008), and therefore also higher than the two-step counterselection method, which requires such a cassette integration in the first step alone. We will include new data specifically addressing the efficiency of our new method (see specifics below)

      The functionality of this approach rests entirely on the ability of the target cell to correctly splice out the synthetic intron. The authors are aware of this potential problem as highlighted in the lines below, but do not make efforts to explicitly test splicing. On lines 224-225, the authors state "We cannot exclude that a small portion of synthetic introns within individual cells are misspliced". On lines 230-231 it is stated that "mis-spliced mRNAs are probably minimal and degraded by nonsense-mediated decay". On lines 215-217, the authors describe an "investigation of transgenic lines at the single-cell level" that suggests "the synthetic intron is correctly spliced out in all the cells of the population". How do the authors reach this conclusion? U2OS and HeLa cells are considered very "robust" and may not show detectable consequences when stressed with an increased level of nonsense-mediated decay. Further, many genes maintain a high level of expression that buffers them against small changes in transcription/splicing. The synthetic intron might have a bigger impact on more tightly regulated genes, so assessing the splicing rate would be essential if the authors wish to advocate their technique as generally applicable.

      • *

      We will assay for splicing efficiency as outlined below.

      The ability of the synthetic intron to be removed from final transcripts depends on functioning splicing machinery. The authors might emphasise this issue, as spliceosome mutations are important fields of study and might not be compatible with this method.

      • *

      We can add this in the text

      The authors used un-directed integration of each BAC under study. Therefore, it is hard to assess what effect the synthetic intron has, as the authors only ever assess the downstream levels of the correctly spliced, translated and localised protein. The authors themselves state that this can lead to clonal variations in expression of up to 2-fold and on line 250 that this variation "could compensate for synthetic intron effects", but make no effort to test this. Again, lines 267-268 highlight the potential dangers of potential effects of the synthetic introns, but do not test these. \Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation.* If not already performed, a large number of bacterial colonies should be screened for the correct modification and frequency of correct ones reported. This frequency - reported for at least three different modifications - would estimate what sort of efficiency this method provides. The modified region of each BAC should be sequenced and the results reported. The rate of exactly modified clones is important, in case of spontaneous or low fidelity integration of the antibiotic cassette. The percentage of transcripts that have the synthetic intron correctly spliced out should be measured for some of the BAC constructs used in the study. A direct head-to-head comparison of this newer method compared to other techniques, or even the authors' own previous two-step approach is necessary to assess the benefits of this method. Preferably, the experiment would be run in parallel with and without antibiotic selection applied, to show that it drastically improves chances of finding a correct clone. *

      We will generate 3 new mutations in BACs and analyze both the efficiency of integration by PCR and accuracy via sequencing. In practice, we have observed that the efficiency is similar to any other cassette integration, such as a GFP tag (Poser et al Nature Methods 2008) or a counterselection cassette (Bird et al Nature Methods 2012) (80-90%). Integrating a mutation via the second step of the counterselection method introduces a further 20% decrease in efficiencies on average.

      \Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments.* Repeating the transformation of the BAC and targeting cassette and assessing the recombination efficiency and sequencing should only require existing reagents and take less than a week or two to complete. Quantitative RT-PCR to assess the percentage of transcripts that have the synthetic intron spliced out would take a little more work. However, this should not be a considerable investment in time or resources for a standard microbiology laboratory and could be completed within a few weeks using modern techniques, such as that described in Londoño et al. 2016. Repeating all the experiments in parallel would be considerable work and would only be strictly necessary if the authors wish to emphasise the benefits of their method over the many others already in wide use. *

      • *

      We will use quantitative PCR to estimate the fraction of transcripts that correctly splice out the artificial intron for two clonal cell lines characterized in the study: RNAi-resistant AurA-GFP (Fig 4), and GTSE1-14A (newly introduced; see below). While the exact method described in Londoño et al 2016 will not be applicable due to the larger size of the artificial intron, we believe we can adapt it to detect different splicing events.

      \Are the data and the methods presented in such a way that they can be reproduced?* Barring the omission of Table S1, which presumably includes exact information on the BACs modified and sequences used etc., there is sufficient other data and methods to allow the experiments to be repeated. Targeting the ESI procedure to the middle of exons is likely to have a bigger impact for smaller exons as the authors mention on lines 99-100. Making it clear which exon sizes for each gene were successfully targeted in this study would help give some idea of how significant a problem this might be. Perhaps Table S1 contains this information, but it was not provided. It would also help reviewers check the design strategies. *

      We apologize for inadvertently failing to upload Table S1 on bioRxiv. It has been uploaded now as part of this submission process. This table indeed contains BAC and target sequence information, including the size of the targeted exon (and the 2 “new” resulting exons). Targeted exons range in size from 138bp to 1537bp, and “new” exons are as small as 48bp.

      \Are the experiments adequately replicated and statistical analysis adequate?* The replication and statistically analysis of the data as presented appear adequate. Figure Legends should state the statistic used to generate error bars. *

      This will be updated

      \*Minor comments:** Specific experimental issues that are easily addressable. Are the promoters used in the vectors described universally functional? For example, is the PGK promoter functional in yeast? *

      • *

      The PGK promoter contained in the cassettes is a mammalian promoter, which has also been reported to work in flies.

      \Are prior studies referenced appropriately?* The manuscript may benefit from the referencing of BAC modification techniques from a wider variety of groups, such as those using CRISPR-guided recombineering (Pyne et al. 2015). *

      We will add citations of more techniques

      \Are the text and figures clear and accurate?* The body text is very clear save minor typographical or grammatical errors. Regarding figures, some of the coloured text in Figure 1 is somewhat illegible when printed in grayscale. Line 278 - The acronyms LAP and NLAP are not defined/explained. Antibody section starting Line 282 may fit better next to Western Blot section. Figure 2C - The blot images would benefit from arrows to indicate expected sizes of proteins. Figure 3A - the graph may benefit from a dashed line at 100% to highlight that values are normalised to controls. Figure 4 - The differences between panels B & C are unclear. Figure 4E - The legend could provide a little more detail on cell cycle stage/status of the captured cells. *

      All of the above will be addressed accordingly

      \Do you have suggestions that would help the authors improve the presentation of their data and conclusions?* Lines 23-27 are somewhat unclear and feel out of context. Perhaps the authors could clarify this as a further advantage of using BACs instead of endogenous gene modifications. *

      Thanks for the input, we will clarify this.

      While not affecting the factual content of the paper, I would advocate that the authors format the method described in Figure S3 into a more detailed text based layout similar to that seen in a typical Nature Methods article. However, this may depend on the format required by any eventual publishing journal.

      • *

      We prefer the graphical protocol, but will discuss whether to add a text protocol with the journal editor.

      That all of the work the paper was carried out in human cell lines and using human genes is a further caveat, but the authors admit this in the discussion and one would assume that most mammalian cells would respond similarly in their ability to splice out the synthetic intron. Reviewer #1 (Significance (Required)): \Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field.* This work is a formal description of a newer method that could be useful for many of those employing bacterial artificial chromosomes in numerous studies, such as gene regulation. *Place the work in the context of the existing literature (provide references, where appropriate).* This work builds on methodology previously published by the authors - a counter-selection two-step procedure (Bird et al. 2011). It sets out to formally describe a method merely mentioned as "BAC intronization" in a later paper by some of the authors (Zheng et al. 2014). Other alternative one-step procedures are also available, but present a different set of challenges (Lyozin et al. 2014). Some newer approaches, such as those using CRISPR-guided recombineering (Pyne et al. 2015) or systems that combine CRISPR and positive/negative selection cassettes (Wang et al. 2016) may be slightly more efficient, but are also more complex in their design. Bird et al. 2011 DOI: 10/dv776q Pyne et al. 2015 DOI: 10/f7jx92 Wang et al. 2016 DOI: 10/f89db5 Zheng et al. 2014 DOI: 10/f5pkr6 *State what audience might be interested in and influenced by the reported findings.* As a technology paper this work should have interest from a broad field of research. While the use of BACs could sometimes be considered more traditional in light of the explosion in CRISPR-based genome editing capabilities, it is definitely seeing a resurgence as the limitations of CRISPR in modifying large regions of genome become more apparent. Therefore, technologies that accelerate the modification of BACs could prove increasingly useful. As category of audience, all those involved in significant recombineering or gene/genome engineering would potentially benefit. *Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.* Synthetic genomics, synthetic biology, cancer cell biology, gene and genome engineering REFEREES CROSS COMMENTING I would agree with reviewer two's assessment that we both view the paper in a similar light. Reviewer #2 (Evidence, reproducibility and clarity (Required)): This is a methods-focused paper that presents a strategy to efficiently introduce mutations into a bacterial artificial transgene using synthetic introns. BAC-based methods have been an effective strategy for introducing trans genes into human cells to achieve near-endogenous expression, including extensive work from these authors. However, generating mutations and changes within the internal coding sequence presents some challenges for how to target these mutations and select for the mutated form. Here, the authors describe a way to overcome this by introducing synthetic introns into an adjacent sequence. This allows them to introduce a selectable marker and conduct the molecular biology without creating complications downstream for the functionality of the protein. This method is carefully described and presented. The authors also provide clear validation by using this to create RNAi-resistant versions of multiple different mitotic factors as well as creating targeted mutants that alter the functional properties of a protein. This work clearly takes advantage of other ongoing studies from these labs (including mutants and cell lines that appear to also have been described elsewhere), but the ability to combine these in a single paper and clearly describe the method provides a helpful advance and validation. Based on the description and data presented, I think that things are clear and carefully validated. As such, I do not have technical comments or concerns and I would be comfortable with this paper appearing in an appropriate journal in its present form. Reviewer #2 (Significance (Required)): This is a solid methods paper, but for considering the nature of the impact and significance of this paper, there are several things to note: 1.The BAC-based method does appear to be a powerful and effective strategy. However, beyond the work of Mitocheck and the authors that are part of this paper, this has not seen widespread adoption. It is possible that this current method may increase its usage due to the value of the targeted mutations within the coding sequence, but at present it is not a broadly used strategy. *

      We agree that using BACs as transgenes has not seen widespread adoption as a tool on the broader cell biology community (although certainly beyond members of the Mitocheck consortium). This is likely because many erroneously think that it is a technique for specialist laboratories. We are trying to change this! For reasons outlined below, there is still an increasing desire for conditional analysis of mutated genes under physiological expression/regulation frequently not attainable via directed Cas9-based mutation. A major aim of this paper is thus to further simplify the methods for generating modified BAC transgenes.

      2.This BAC-based approach (and also RNAi) are becoming increasingly replaced by the use of CRISPR/Cas9 genome editing. The absence of Cas9-based strategies in this paper limits the potential impact and reach of this paper. The authors do mention the possibility of using a similar synthetic intron strategy for use with Cas9 in the Discussion, and appear to have conducted some experiments. If possible, it would substantially increase the value of this paper if this data and strategy were also included in the Results section (acknowledging that this may still be a work in progress).

      While some uses of BAC transgenes are in some cases better replaced by CRISPR/Cas9 techniques (i.e. GFP tagging), there are several occasions where using BACs are preferable: As stated in the text, RNAi-resistant BACs allow for conditional analysis of recessive mutations. Mutations in essential genes that are lethal will prevent growth and recovery of viable cells if integrated into the genome via Cas9. Additionally, deleterious mutations are prone to accumulate suppressive changes in chromosome integrity or gene expression during the procedure of selecting and expanding Cas9-modified cells for analysis, particularly in the genomically instable cancer cell lines frequently employed.

      We use both BACs and CRISPR/Cas9 in our lab according to our needs.

      We do have an ongoing project to apply this intronization technique to enable more efficient selection of CRISPR/Cas9 integrations. Preliminary results suggest that it works to allow selection of point mutations, but it is still being optimized, including a redesign of the cassette, and is not ready for publication.

      3.The method is solid and well-validated, but there are no new results or insights presented in this paper from the work that is described (this is fine, just commenting for considering the right journal fit).

      As “biological insights” gained as a result of this technique we had cited a couple studies that made use of the technique already (to functionally analyze a microcephaly-associated mutation in the centriolar protein CPAP at the single cell level in HeLa cells and neural progenitor cells (Zheng et al 2014, Gabirel et al 2016)). As a response to this critique to include “new biology” in this paper, we will add new unpublished data investigating a specific question: Is the cell-cycle-regulated disruption of the EB1-GTSE1 (microtubule plus-end tracking proteins) interaction in mitosis required for chromosome segregation fidelity? We have generated a GTSE1 mutant with 14 phosphosites mutated to alanine using this technique. We will present the effect on chromosome segregation.

      REFEREES CROSS COMMENTING It appears that both reviewers are largely on the same page regarding this paper.

    1. SciScore for 10.1101/2020.03.21.990770: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">This study received approval from the Research Ethics Committee of Shenzhen Third People 's Hospital , China ( approval number: 2020-084) .</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Among a total of 69 antibodies from P#2 , the majority ( 59 % ) were scattered across various branches and the remaining ( 41 % ) were clonally expanded into three major clusters ( Figure 3A) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>total of 69</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Control antibodies from P#1 demonstrated even lower competing power with ACE2 .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>ACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We selected a total of six antibodies with ACE2 competitive capacities of at least 70 % and analyzed them in a pairwise competition fashion using SPR .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SPR</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The most potent antibody , P2C-1F11 , did not seem target the same epitope as the relatively moderate antibody P2C-1C10 .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>P2C-1F11</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally , despite successfully isolating and characterizing a large of number mAbs against SARS-CoV-2 , we cannot draw any firm correlation between antibody response and disease status at this time.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SARS-CoV-2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The third staining at 4 °C for 30min involved either: Streptavidin-APC ( eBioscience ) and/or Streptavidin-PE ( BD Biosciences ) to target the Strep tag of RBD , or antihis-APC and anti-his-PE antibodies ( Abcam ) to target the His tag of RBD .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>antihis-APC</div> <div>suggested: None</div> </div>

            <div style="margin-bottom:8px">
              <div><b>anti-his-PE</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The IgG heavy and light chain variable genes were amplified by nested PCR and cloned into linear expression cassettes or expression vectors to produce full IgG1 antibodies as previously described 29,41 .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>full IgG1</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The PCR products were purified and cloned into the backbone of antibody expression vectors containing the constant regions of human IgG1 .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>human IgG1</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV antibodies ( S230 and m396 ) previously isolated by others 42 were synthesized and sequences verified before expression in 293T cells and purification by protein A chromatography .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>SARS-CoV</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HIV-1 antibody VRC01 was a broadly neutralizing antibody directly isolated from a patient targeting the CD4 binding site of envelope glycoprotein 40 .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>CD4 binding site of envelope glycoprotein 40</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cells were then stained with PE labeled anti-human IgG Fc secondary antibody ( Biolegend ) at a 1:20 dilution in 50 μl staining buffer at room temperature for 30 minutes .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-human IgG</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">VRC01 is negative control antibody targeting HIV-1 envelope glycoprotein.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>HIV-1 envelope glycoprotein.</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The recombinant RBD was labeled with either a Strep or His tag and used alone or in combination to identify and isolate RBD-specific single B cells through staining with the Streptavidin-APC and/or Streptavidin-PE, or anti-His- APC and anti-His-PE antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>anti-His- APC</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 , SARS-CoV and MERS-CoV pseudovirus were generated by cotransfection of human immunodeficiency virus backbones expressing firefly luciferase ( pNL43R-E-luciferase ) and pcDNA3.1 ( Invitrogen ) expression vectors encoding the respective S proteins into 293T cells ( ATCC ) 37,38,44,45</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>293T</b></div>
              <div>suggested: KCB Cat# KCB 200744YJ, <a href="https://scicrunch.org/resources/Any/search?q=CVCL_0063">CVCL_0063</a></div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Huh7 cells ( ATCC ) ( approximately 1.5 × 104 per well ) were added in duplicate to the virusantibody mixture.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Huh7</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The isolate was amplified in Vero cell lines to make working stocks of the virus ( 1 × 105 PFU/ml) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Vero</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Serial dilutions of mAbs were mixed separately with 100 PFU of SARS-CoV-2 , incubated at 37 °C for 1 h , and added to the monolayer of Vero E6 cells in duplicates .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Vero E6</b></div>
              <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_XD71">CVCL_XD71</a></div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The genes encoding the heavy and light chains of isolated antibodies were separately cloned into expression vectors containing IgG1 constant regions and the vectors were transiently transfected into HEK293T or 293F cells using polyethylenimine ( PEI ) ( Sigma) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>293F</b></div>
              <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_D615">CVCL_D615</a></div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK 293T cells transfected with expression plasmid encoding the full length spike of SARS-CoV-2, SARS-CoV or MERS-CoV were incubated with 1:100 dilutions of plasma from the study subjects.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>HEK 293T</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Bioinformatic and biologic characterization indicates that these antibodies are derived from broad and diverse families of antibody heavy and light chains .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>Bioinformatic</b></div>
              <div>suggested: (QFAB Bioinformatics, <a href="https://scicrunch.org/resources/Any/search?q=SCR_012513">SCR_012513</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally , the cells were re-suspended and analyzed with FACS Calibur instrument ( BD Biosciences , USA ) and FlowJo 10 software ( FlowJo , USA)</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>FlowJo</b></div>
              <div>suggested: (FlowJo, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008520">SCR_008520</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Half-maximal inhibitory concentrations ( IC50 ) of the evaluated mAbs were determined by luciferase activity 48h after exposure to virusantibody mixture using GraphPad Prism 6 ( GraphPad Software Inc . ) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>GraphPad Prism</b></div>
              <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
            </div>
      
            <div style="margin-bottom:8px">
              <div><b>GraphPad</b></div>
              <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The IgG heavy and light chain variable genes were aligned using Clustal W in the BioEdit sequence analysis package ( https://bioedit.software.informer.com/7.2/).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>BioEdit</b></div>
              <div>suggested: (BioEdit, <a href="https://scicrunch.org/resources/Any/search?q=SCR_007361">SCR_007361</a>)</div>
            </div>
          </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic analyses were performed by the Maximum Likelihood method using MEGA X ( Molecular Evolutionary Genetics Analysis across computing platforms) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
            <div style="margin-bottom:8px">
              <div><b>MEGA X</b></div>
              <div>suggested: None</div>
            </div>
          </td></tr></table>
      


      Results from OddPub: Thank you for sharing your data.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  8. Jun 2020
    1. A Firefox/Hypothesis extension has been in the works for quite a while,

      I published an unofficial Firefox extension here. Just download and install the XPI file. Go here for a discussion about it. So far only thing I found that doesn't work is annotating local PDFs, because Firefox is more restrictive about this than Chrome.

  9. May 2020
  10. Apr 2020
    1. ing was that the teacher-education students in our study did not see their set online tasks as being valuable to their

      FOllow up later

    1. Whether you’ve just purchased a new PC or reinstalled Windows, the first task you’ll likely do is installing apps.

      True that

    1. Offering your product in a free and paid version is nothing new and it’s entirely legitimate for OSS products,

      I feel as if this has been popular in the whole entire software industry!

    2. By far the most common method of income is to provide a service alongside the OSS product. Pick any OSS project from random and there’s a good chance that they utilize this method in one way or another.

      This makes sense

    3. self-taught lone wolves

      I wonder why this is

    4. open source and profit are mutually exclusiv

      wow I did not know this

  11. Mar 2020
    1. To be fully compliant with GDPR, you would also need to enable Show Reject All Button setting.
    2. Consent Model. In the case of GDPR, you must choose the Opt-in. This means that you cannot start tracking people before the consent was given.
    3. This cookie consent notification is just a tool for getting consent, it’s not capable of managing your tracking tags because every website and every GTM container is unique, therefore there is no universal solution. As a result, you will have to manually update all your tracking tags with additional firing rules.
    4. Configuring OneTrust’s cookie consent solution is just half of the task. Your tracking scripts (like Google Analytics, Google Adwords, etc.) will still continue working as they always did unless you import my GTM recipe and then reconfigure all of your tracking tags. Yup, there’s a lot of manual work waiting ahead.
    5. if you are using some tools/scripts on your website that are used to identify individuals and their data is processed by you or 3rd parties), that can be done only when a person gives consent
  12. Feb 2020
    1. The biggest drawback of algorithmic feeds is that you might be looking at irrelevant content. When you see something on your timeline and want to comment, you will have to check the timestamp to see if your comment is still relevant or not.
    1. uld argue the text is most guilty of exoticism as it reflects a sense of wonder about different groups of people without any reference to respective racial superiority or inferi

      guilty of exoticism - wonder, "otherness"

    2. “the Anglo-Saxon readers and viewers of these texts probably considered them true”

      early english readers probably considered the wonders real

  13. Jan 2020
  14. Nov 2019
  15. Oct 2019
    1. A conexão e colaboração entre os associados é um valor levado a sério pelos coworkings. E nada melhor do que criar e manter uma rede de relacionamento bem estruturada, de acordo com os seus objetivos. E como esses espaços prezam pelo compartilhamento e trabalho co-criativo,

      Explicar como os espaços de coworking exploram a conexão entre integrantes do local

    1. A wireless keyboard available in a classroom can work just as well [as a smartboard], as can simply having people talk to each other and write down the upshot of their conversation.

      This is reminding me of the trichotomy theory (I think that's what they called it?) of something being neither greater than nor less than nor equal to--which strikes me as an appropriate description of the three different technologies mentioned in this sentence (the last being a pencil and paper summary).

  16. Sep 2019
  17. Aug 2019
    1. bough    .

      Sonnenizio does have a capping couplet

    2. 1913

      An italian sonnet has one octave with the rhyme scheme abba abba with a sestet with the rhyme scheme of the poets choice

    3. ; Petals

      The poem is so short that there isn't really a true Volta (Turn of phrase), but if there was one, it would be between the two lines

    4. crowd

      This poem has a rhyme scheme, crowd and bough

    5. The

      100% not a sonnenizio

    6. crowd

      An English Sonnet/Elizabethan Sonnet is a type of sonnet with 3 quatrains and 1 couplet (usually a capping couplet). The rhyme scheme is abab cdcd efef gg

    7. Brief Poems by Ezra Pound

      Here is small collection. Thanks DP!

  18. Jul 2019
    1. Nikkei Asian Review

      Hello, I am the Citerpress bot :) I think this sentence is mentioning a news article without an explicit link. I looked in my news database and here is what I found:

      Hit #1 (score of 39.0)

      Hit #2 (score of 37.9)

      Hit #3 (score of 37.2)

      Hit #4 (score of 34.3)

      I did my best! My annotations will get better and better with time, as I index new pages every day.

    1. Manywho cannot afford half the items listed above include themselves in thatdefinition. Also included are most of the nation’s millionaires,who consider themselves middle or upper-middle class despite their obviouslyoutsized income11and their small representation (3.3%) among the country’s overall population.
  19. Jun 2019
    1. It is “undermining behaviour from managers” that is forcing women out of the tech industry.

    2. Noble describes entering the term “beautiful,” and shows a screen of pictures of white people. She entered “ugly”, and the results were a racial mix.

    3. She search for “three black teenagers” in 2010, and getting mug shots as the result. Then searched “black girls” in that same year brought the viewer to porn sites.

    4. Noble focuses on degrading stereotypes of women of African descent as a prime example of these prejudices, which translate to overt racism.

  20. Apr 2019
  21. Mar 2019
    1. Twitter Facebook Instagram Impressum Haftungsausschluss

      Alignierung kann angepasst werden

      • gutes Teaserbild. Allerdings nimmt zuviel Platz. Für den Hauptinhalt (Wanderungen) muss man sofot scrollen. Eine Alternativ wäre mit einem "Karrussell" von den letzten 3 Wanderungsbilder oder so.
    1. personalize learning infographic

      This is not quite what it sounds like. It is a Pinterest style page with links to assorted articles that relate to personalized learning, most of which are presented in an infographic. It is sufficiently useful if one has the patience to click through to the infographics. Usability is satisfactory although the top half of the page is taken up with graphics that are not directly related to the content. rating 3/5

    1. This plain page incorporates an overview of job aids by Allison Rossett, who is the foremost authority on the topic. Not all information is given away for free as she wants to sell her books, which are also promoted on the page. This page can be a good way of tracking her current work. Rating 3/5

  22. Jan 2019
    1. Machines with interchangeable parts can now be constructed with great economy of effort. In spite of much complexity, they perform reliably. Witness the humble typewriter, or the movie camera, or the automobile. We have reached a point in technology now where all of these inventions can perform their jobs without human involvement.

      His description of the "humble typewriter" seems like such an understatement in comparison to the computers and recording devices we now have

  23. Nov 2018
    1. Partial charges and discharges that combine to 100% are counted as a single full cycle

      Really? I don't think anyone has tested partial charges and discharges. I would like to see a reference for this point!

    2. research says

      That is pretty weak evidence for such a strong statement

  24. Oct 2018
    1. I’m sure that after a century of being “the noisiest city on Earth,” folks have gotten creative about it.

      Response

    2. Moreover, if we accounted for the history of zoning in the neighborhoods that have the most or the least complaints it would add another layer of analysis to the data.  Are some of these neighborhoods used as entertainment zones, for example? Is it easier to open up bars there than elsewhere in the city?

      Condition of Rebuttal/Evidence, depending on POV

    3. Although it may not be possible to gather who the 311 callers are, including factors such as race and class may lead to very different noise maps.  For example, what would a noise map of Manhattan look like if researchers brought income into the equation?

      Condition of Rebuttal

    4. This is where the data falls short. Can it be assumed that those who are calling about the noise are mostly people who live in the neighborhood?

      Condition of Rebuttal

    5. At a glance, loud parties, loud people, and loud car stereos seem to be the major complaints in those areas, according to Sluis’s visualizations

      Evidence

    6. This is key information because it reminds viewers that this neighborhood is a lot more ethnically diverse than other neighborhoods with a smaller number of complaints. It brings to mind: what role does race play in these complaints, in terms of those who complain and those who are the focus of the complaints?

      Condition of Rebuttal/New Claim?

    7. The city may be noisy, but “noisy” is relative. Sluis’s map shows some predictably noisy areas for those of us familiar with Manhattan’s soundscape (Union Square, Times Square) but it also draws attention to other areas not as predictable in the mainstream imagination (East Harlem South, Hamilton Heights).

      Condition of Rebuttal

    8. what stands out is that the major circles of noise complaints are also places where there are different racial and ethnic groups mingling (for example, Times Square) or places that are populated by mostly minorities (Hamilton Heights).  Whereas Sluis flattens out the noise complaints, demographic stats point to the racial/ethnic contours of each neighborhood.

      Evidence

    9. Drawn from 2010 census data, the CUNY map clearly delineates neighborhoods and color-codes the groups in each neighborhood per block: blue for whites, green for Latino, orange for black, purple for Asian, and grey for “Other.” Although the Center for Urban Research, CUNY Graduate Center’s maps cannot be superimposed on Sluis’s maps, they help give a general idea as to where neighborhoods are located in addition to racial demographics.

      Evidence

    10. We must remember that annoyance oftentimes stems not just from physical reactions to noise but rather one’s perceptions about noise

      Condition of Rebuttal

    11. 40, 412 complaints, to be exact

      Evidence

    12. but neither takes into account the fact that some of the areas with a higher concentration of noise complaints are not just densely populated but densely populated with racial and ethnic minorities

      Backing or Qualifier?

    13. New York City isn’t the only loud city out there

      Qualifier

    14. Although New York City isn’t the only loud city out there, there are many reasons it’s called “The City That Never Sleeps”—and sound has a lot to do with it, depending on which neighborhood you call home.

      Claim

    1. of Wikibase for historical research early on.

      Wikibase for historical documents

    2. Rhizome, an arts organization

      Wikibase for GLAM

  25. Sep 2018
    1. preparing them for the idea of designing a new system that is native to the web

      native to the web

    1. Facebook does not allow third-party apps to display your newsfeed. This applies to Hootsuite. For this reason, you’ll always have to use Facebook natively. The same pretty much goes for Instagram.

      Facebook does not allow third-party apps to display your newsfeed. This applies to Hootsuite. For this reason, you’ll always have to use Facebook natively. The same pretty much goes for Instagram.

  26. Aug 2018
    1. tāds kā “grēkāzis” (“ļaunie un maznesaprotošie abortu aizliedzēji”)

      Šis cilvēks nesaprot, kā darbojas aktīvisms (un pasaule :D), right? Ak nē, Papardes zieds uzskata, ka aborti nav jāaizliedz un ka abortu aizliegt gribētāji nav jauki cilvēki. Nokrāsojiet mani šokētu! :D

    2. neviens valstī par abortu aizliegšanu ar likumu nemaz nerunā kā reālu iespēju

      Pag, kurā dienā un konkrētā minūtē valstī bija šis maģiskais brīdis? Zinu! Tas notika tad, kad visas planētas sastājās rindā. :D ("Nerunā" neuztvēru 100% burtiski, sorry.)

      Un arī nav mūsu valsts vienīgā un pa visu planētu, kā tajā senajā TV reklāmā. :D Polija, Krievija, konservatīvie politiskie spēki, kas atrodami it visur utt? Mm? Tāda sajūta, ka autors dzīvus cilvēkus sen nav saticis un īsti nesaprot, kā tie uztver pasauli.

    3. Tas arī izsaka šo informatīvo materiālu galveno domu un mērķi. Un, ja pēc tā, kāds uzdrošinātos teikt, ka ir par abortu aizliegšanu, viņš izpelnītos pārmetošus skatienus (kā, tu atbalsti tādas šausmas!).

      No way! :D Cepums autoram, ka ir spējis pamanīt šo "slepeno" domu - ka nejaukās sekas no abortu aizliegšanas eksperte uzskata par sliktām (kur pilnībā viņai piekrītu) un negrib pieredzēt tādu nejaucību atkārtošanos.

    4. Pirmkārt, atlasīti tie eksperti, kas pauž idejai atbalstošu viedokli; svarīgi tas, ka pieredzējuši.

      No šit... A ko citu tad Papardes ziedam bija jādara, ņemot vērā šīs organizācijas mērķus? Tajos brīžos, kad tai rodas vēlme apspriest abortus, meklēt nepieredzējušus "ekspertus", kas uzskata, ka aborti ir grēks? :D

    1. such as DOIs, which might be assigned by, for example, “crossref” or “figshare”

      I have to say publicly that this sentence makes absolutely no sense as crossref and figshare are not comparable assigning authorities. CrossRef is a registration agency of the International DOI Foundation; FigShare is not. Based upon the example given, the assigning-authority for a DOI would only ever be the set of agencies that assign DOIs. FigShare is not one of those agencies. See it is not on the list: https://www.doi.org/registration_agencies.html

  27. Jul 2018
  28. May 2018
  29. Apr 2018
    1. In its latest incarnation, digital delivery has been cleverly branded as “inclusive access,” a model wherein every student pays a mandatory course materials fee that represents an arbitrary discount off the (arbitrary) price of a new hardcover textbook (often more than the average student currently spends).
  30. Mar 2018
    1. Ficha técnica con más información aquí

      Aquí vienen muchos datos físicos útiles

    2. Las plumas de aislamiento ofrece muchas ventajas. Las características de la pluma garantiza un mayor nivel de aislamiento y el aislamiento de otros para proporcionar un hábitat cómodo

      Lo repitieron

    3. Los aislamientos térmicos a base de celulosa suponen una alternativa ecológica a las lanas minerales o las espumas químicas, teniendo como materia prima el papel reciclado, principalmente de periódicos, alcanzando el 75% de su composición, proporcionando altas prestaciones como aislamiento tanto térmico como acústico, de una forma más sostenible y respetuosa con el medio ambiente.

      Bien, son AISLANTES no materiales principales, ya me quedó claro.