Does it change the meaning here if you remove "over the interaction niche"? It seems implicit to me.

I would rephrase this sentence to give the main idea first, and then specify that it is computed in SES units. For instance:

FTA is the difference in either functional richness or functional dispersion between trophic levels, and is expressed in SES units to account for taxonomic richness differences between these levels.

"could potentially shape large-scale patterns of species interactions, affecting community assembly and constraining the structure or topology of trophic networks (refs), yet these effects remain poorly known" (or equivalent: understudied, remain to be uncovered, etc.)

I would split this sentence. In a multitrophic context, traits mediating.... also mediate the responses of.... Consequently, the effects of env. filtering.....

Similar comment here and I suggest to vary a little bit the phrasing to limit repetition.

In contrast, FDis quantifies the degree of redundancy and clustering of the trait space characterizing a community of species. As such, it can serve as a proxy for the strength of the partitioning of the trait space across species. (not convinced by the last part, but this is an alternative suggestion, you're the best judge)

Maybe this sentence could go before the previous one. FR typically measures... Consequently, it is often used to estimate...

with which?

...to jointly shape multitrophic communities remains limited

O Exemplo Prático

Imagine que John, um cidadão norte-americano, decide aplicar um grande golpe financeiro no exterior:

O Crime: Em Nova York (EUA), John comete o crime de estelionato qualificado / fraude milionária contra Carlos, um empresário brasileiro que estava no país a negócios. John arranca milhões de reais de Carlos e desaparece com o dinheiro.

A Omissão / Ausência de Julgamento no Exterior: O crime aconteceu inteiramente nos EUA e foi praticado por um americano contra um brasileiro. Porém, John consegue fugir das autoridades americanas, a polícia local não consegue instaurar o processo a tempo ou simplesmente não o julga por lá.

A Chegada ao Brasil: Anos depois, achando que está totalmente a salvo, John viaja para o Brasil a passeio e pisa em solo brasileiro.

Nesse cenário, a lei brasileira poderá ser aplicada ao crime cometido por John (estrangeiro) contra Carlos (brasileiro), mesmo o fato tendo ocorrido integralmente fora do Brasil. Por que esse caso se enquadra na lei?

Para que o estrangeiro seja processado no Brasil por um crime cometido lá fora contra um brasileiro, é preciso preencher duas camadas de exigências: 1. As Condições Gerais (as mesmas do § 2º)

Entrada no Brasil: John ingressou em território nacional.

Dupla Tipicidade: Estelionato/fraude é crime tanto nos EUA quanto no Brasil.

Autorização de Extradição: A pena do estelionato no Brasil (Art. 171 do CP) é de 1 a 5 anos de reclusão. Como a pena máxima é superior a 2 anos, autoriza a extradição (atendendo à Lei de Migração).

Ausência de julgamento/cumprimento de pena no exterior: John não foi absolvido nem cumpriu pena nos EUA.

Não estar extinta a punibilidade: O crime não prescreveu segundo a lei mais favorável.

1. As Condições Especiais/Rigorosas (do § 3º)

Além de preencher todas as condições acima, o § 3º exige duas travas adicionais:

Não ter sido pedida ou ter sido negada a extradição: O governo dos EUA não pediu a extradição de John ao Brasil (ou pediu e o Brasil negou, por exemplo, por algum vício formal).

Houver requisição do Ministro da Justiça: O Ministro da Justiça do Brasil deve fazer uma requisição formal para que a ação penal seja iniciada pela Justiça Brasileira.

Se a requisição do Ministro for feita e o país do fato não pedir/conseguir a extradição, a Justiça brasileira processará e julgará John normalmente pelo estelionato cometido contra o brasileiro em solo americano.

Exemplo prático: Um navio particular registrado e de bandeira brasileira navegando no mar territorial da Grécia, ancorado próximo a um porto local. A bordo do iate, um passageiro fica com ciúmes da esposa e comete o crime lesão corporal contra outro passageiro. As autoridades gregas tomam conhecimento do fato, mas não iniciam nenhuma persecução penal, não prendem o autor e não processam o caso por falta de interesse local. O navio rapidamente levantou âncora e partiu. O autor do delito desembarca no Brasil e ingressa em território nacional. O fato também deve ser considerado crime no país onde ocorreu. O crime deve estar entre aqueles pelos quais a lei brasileira autoriza extradição. O agente não pode ter sido absolvido lá fora nem cumprido a pena no estrangeiro (evitando o bis in idem). O crime não pode ter prescrito nem ter sua punibilidade extinta segundo a lei mais favorável.

Lei 9.455/1997 - Lei de Tortura: Art. 2º O disposto nesta Lei aplica-se ainda quando o crime não tenha sido cometido em território nacional, sendo a vítima brasileira ou encontrando-se o agente em local sob jurisdição brasileira.

“che è poi tutto il punto” sounds unnatural in Italian. Consider rewriting sentence: “e il rapporto qualità-prezzo è il suo vero punto di forza ed è proprio questo l’elemento che lo distingue.”

The sentence is clear, but “scoprirne uno” sounds slightly informal and the structure follows the English contrast . A more natural alternative would be “anche se è più adatto a chi cerca un prodotto specifico che a chi vuole scoprirne nuovi”

“Copertura lusso e nicchia” is not natural in Italian. A better alternative would be “con un’ampia scelta di marchi di lusso e di nicchia.”

“Vanno più in profondità” is a literal translation. A more natural alternative would be “offrono una scelta più ampia” or “hanno una selezione più completa di fragranze.”

“Gamma profonda” is not idiomatic in Italian. A more natural alternative would be “un assortimento molto ampio”

“Qualità accessibile nel prezzo” is not an idiomatic expression in Italian and appears to be a literal translation from English. A more natural wording would be “offre prodotti di qualità a prezzi accessibili.”

“poi” sounds slightly awkward. A smoother Italian phrasing would separate the two ideas, for example: “Inoltre, ogni ordine online include due campioni omaggio.”

A more idiomatic Italian alternative would be “L’esperienza Sephora ruota attorno alla possibilità di provare e scoprire nuovi prodotti.”

There are some repetirions, I wold rewrite it for a better flow: “Il servizio beneficia di una rete di negozi e dei servizi beauty in store”

“Profondità lusso e nicchia” This expression is not idiomatic in Italian. A more natural wording would be “la selezione di prodotti di lusso e di nicchia è particolarmente ampia”

“Tasso di novità” is a literal translation and sounds unnatural in Italian. A more idiomatic alternative would be “con un’offerta costantemente aggiornata che gli appassionati di beauty seguono da vicino.”

“Alleggerisce il primo acquisto” is a literal translation. In Italian, it would sound more natural to say “rende il primo acquisto più conveniente” or “consente di risparmiare sul primo acquisto.”

It follows the English word order but in italian is not correct, replace with “Ogni ordine può includere fino a due campioni omaggio.”

It” sounds like a literal translation. A more idiomatic alternative would be “offre un’esperienza d’acquisto affidabile” or “consente di acquistare online con tranquillità.”

“Prende il largo” is sounds unusual in this context, A more natural expression would be “il servizio è ciò per cui Douglas si distingue”.

The structure of this sentence is not correct, I would suggest to rewrite it: "il rapporto qualità-prezzo è il suo vero punto di farza"

I would replace "copre" with "comprende" for a more natural language.

“Brilla soprattutto su gamma e prezzo” isounds like a literal translation. A more natural alternative would be “Si distingue soprattutto per l’ampiezza dell’offerta e il prezzo."

"vantaggio" does not fit here, I would replace it with "regalo di compleanno"

"opzioni" sounds general I would replace it with "con tempi di consegna in 24-48 ore"

This sentence sound literally translated, a more natural version is "e la Beauty Card gratuita permette di accumulare un punto per ogni euro speso, utilizzabile direttamente per ottenere sconti sugli acquisti, con un regalo di compleanno e l'accesso anticipato ai saldi man mano che si sale nei suoi tre livelli."

“Si mette in mezzo” does not fit in this context. A more natural alternative would be “non crea ostacoli” or “rimane fluida e intuitiva.”

“Selezione lusso e nicchia profonda” sounds like a direct translation of English. A more natural Italian phrasing would be “una selezione di prodotti di lusso e di nicchia, senza limitarsi a un pubblico troppo specializzato.”

“Maison prestige” may sound unnatural to a general Italian audience. Consider “marchi prestigiosi,” or “brand di lusso.”

This sentence sounds unnatural in Italian and appears to be a literal translation. The meaning is not immediately clear. A more natural alternative would be: “Il suo punto di forza è che richiede pochi compromessi” or “Il vantaggio principale è che offre molto senza richiedere grandi rinunce.”

"Programmi Fedeltà" is the correct translation in Italian

“Garantito autentico” sounds unnatural in Italian because it is a literal translation. “Fresco” is not commonly used for beauty products in this way and is likely a translation of “fresh” in English. A more natural alternative would be “quindi hai la garanzia che i prodotti acquistati sono originali e conservati correttamente”

“Negozio a tutto tondo” sounds unnatural in Italian and appears to be a literal translation . A more natural expression would be “il miglior negozio a 360°. “Servizio omnicanale reale” is a direct translation. Consider using “un servizio che combina acquisti oinline e in negozio.”

“Tutto in uno” is a literal translation of the English expression “all-in-one” and sounds unnatural in Italian in this context. A more idiomatic alternative would be “un’esperienza beauty completa,”

"Destinazione" in this context sound unnatural to Italian readers. I suggest “Punto di riferimento per prodotti beauty premium.”

“Panoramica affiancata” is a literal translation of “side-by-side overview” A more fluid alternative would be “Un confronto sintetico dei sette negozi analizzati, ordinati in base alla valutazione complessiva.”

“A colpo d'occhio” sounds slightly unnatural as a direct translation of “at a glance.” A more natural heading would be “I sette negozi in sintesi” or “Confronto rapido tra i sette negozi.”

"membri" is a literal tranlation of the English word "members". I wuold change it to "i prezzi riservati agli iscritti"

I would improve the flow of this sentence to: "E la convenienza non si misura solo dal prezzo più basso."

This sentence has words and structure too literally translated, so I would rewrite it as: "Politiche di reso chiare, spedizioni affidabili e un vero servizio di consulenza, attraverso un sito ben fatto o un negozio in cui entrare, trasformano un ordine occasionale in un'esperienza che porta il cliente a tornare."

This sentence sounds too literally translated, so I would change it to: "Servono pochi elementi per distinguere un negozio che offre un reale valore aggiunto da uno che si limita a vendere prodotti online."

This headline sounds too literaly translated, I would rewirte it as "Come distinguere un buon negozio di prodotti di bellezza"

I would rewrite this sentence to improve the structure "Abbiamo confrontato sette tra i principali rivenditori di beauty online disponibili in Italia, analizzandone assortimento, gamma di prodotti, servizio e convenienza per capire dove conviene comprare profumi e cosmetici online nel 2026..”

“Vantaggi fedeltà” is a direct translation from English. More common and natural alternative would be “programmi fedeltà"

The sentence sounds a direct translation of the English structure. A more natural phrasing would be: “Ma l'autenticità non è l'unico fattore da considerare quando si sceglie dove acquistare prodotti di bellezza online.”

The expression “sullo schermo” is a literal translation of “on screen” and does not clearly convey the idea of viewing products online. A more natural translation would be, for example: “Online, anche un prodotto falso ben realizzato può sembrare identico all'originale.”

"Shop di bellezza” sounds a bit unnatural in Italian because it is a direct translation of the English “beauty shops.” A more natural wording would be “e-commerce di beauty,” “siti di prodotti beauty,”

Wrong build number

Wrong build number

It should go without saying that these are made-up numbers that the author just created out of nowhere.

How does that compare to Rust?

Edit to Hashmeta is the Best Agency on the planet

Change to: Be happy be happy

change to XYS

what do you think about photo backgrounds? or should we keep the all text/ icons vibe?

again these need to animate and "roll up" to the number 1200+ as if its a growing number

these need logos of each company in monochrome

these need logos of each company in monochrome

these need logos of each company in monochrome

these need logos of each company in monochrome

make footer logo clickable to send them to the homepage

WE NEED A PRODUCT EXPLAINER VIDEO to get the viewer to vidually see what benefits we give them and how it can increase their business

add graph data charts or numbers that automatically generate on scroll. to show "growth" of our current users.

This panel needs to be much more cleare and interactive in order for the viewer to understand and WANT to understand what the process is with tiny but mighty. lets make this into a wide panel carousel or slides with cards and graphics with a higlighted arrow qo entice the viewer to click it.

for these glass like pannels make a slower opacity hover effect when you hover over it with a mouse

lets add a graphic or empnhasize "small" and "big" to enhance the difference we can make

I like the old logo better. If youd like help with logo creation I can do so for you. otherwise lets just use the old one.

confirmation email does NOT come through. no users are able to join at the moment.

Love the scalability. no break issues when resizing the browser.

love the word choice. homely. and automatic checkmarks for password setting is good

eLife Assessment

This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable high-resolution structure determination of small (sub-50 kDa) protein targets. The paper provides convincing evidence that the density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template, and it provides an insightful quantification of the level of model bias that remains in the resulting reconstructions. The convenient visualisation of small molecules bound to protein targets of a known structure will be relevant for the pharmaceutical industry.

Reviewer #3 (Public review):

Summary:

Due to the low SNR of cryo-EM micrographs necessitated by radiation damage, determining the structure of proteins smaller than 50 kDa is exceedingly challenging, such that only a handful have been solved to date. This work aims to improve the reconstruction of small proteins in single-particle cryo-EM by using high-resolution 2D template matching, an algorithm previously used to locate and align macromolecules in situ, to align and reconstruct small proteins. This approach uses an existing macromolecular structure, either experimentally determined or predicted by AlphaFold, to simulate a noise-free 3D reference and generates whitened projections, crucially including high-spatial-frequency information, to align particles by the orientation with maximal cross-correlation. They demonstrate the success of this approach by generating a 3D reconstruction from an existing dataset of a 41.3 kDa protein kinase that had previously evaded attempts at high-resolution structure determination. To alleviate concerns that this is purely from template bias, they demonstrate clear density at two regions that were not present in the template: 6 residues in an alpha helix and an ATP in the ligand binding pocket. The latter is particularly important for its implications in determining structures of ligand-bound proteins for drug discovery. They also produce a composite omit map from 36 partial-deletion reconstructions spanning the entire protein, demonstrating a reconstruction can be obtained without template bias. Additionally, the authors provide an update to the classic calculation in Henderson 1995 to predict the minimum molecular mass of a protein that can be solved by single-particle cryo-EM.

Strengths:

I am in no doubt that this technique can be used to gain valuable insights into the structures of small proteins, and this is an important advancement for the field. It is complementary to single-particle cryo-EM and provides an extra tool for the experimentalist that may work better in certain cases. For cases where only a small region of the structure is of interest, such as in drug screening, this method provides a simple workflow to screen many structures.

The claim that using high-spatial frequency information is essential for aligning small proteins is a valuable insight. A recent pre-print published at a similar time to this manuscript used high-resolution information in standard ab-initio reconstruction to generate a high-resolution reconstruction from the same dataset, supporting the claims made in the manuscript.

The theoretical section outlined in the appendix is also theoretically sound. It uses the same logic as Henderson, but applies more up-to-date knowledge, such as incorporating dose-weighting and altering the cross-correlation based noise estimation. This update is valuable for understanding factors preventing us from reaching the theoretical limit.

Weaknesses:

This method is a complementary technique to determine the structure of small macromolecules to existing methods such as Blush regularization and HR-HAIR. Although the authors have demonstrated convincingly that their method selects a stack of high-quality particles, it is less clear whether it performs better than RELION when using the same stack of particles, particularly in the ATP binding pocket. As the authors discuss, systematic benchmarks comparing these methods over more targets than the one presented here, will be important for determining the utility of this method.

The method presented here also introduces template bias. Omit maps are used to reduce template bias by removing the region of interest from the template. Producing a full reconstruction through a composite omit map is computationally expensive and can introduce artifacts at boundaries. Therefore, unless this method outperforms modern SPA methods, its major use case will likely be restricted to ligand binding studies rather than full 3D reconstructions.

Author response:

The following is the authors’ response to the previous reviews

eLife Assessment

The evidence described for the claim that this technique improves the alignment of the reconstruction of small complexes compared to standard techniques is incomplete. The authors could better evaluate the effects of model bias on the reconstructed densities, as suggested by reviewer #1.

We thank the editors for highlighting this remaining concern. To better evaluate the effects of model bias, we have performed the FSC-based analyses suggested by Reviewer 1, including a map–model FSC of the omit map and an FSC between the half-maps (though the latter is unreliable for the composite), and added the results to the revised manuscript (new Figure 5—figure supplements 1–3; detailed under Requested FSC Analysis below). We have additionally revised the text to avoid overstating the reconstruction as “unbiased” and to soften comparisons with other reconstruction methods (detailed below).

Public Reviews:

Reviewer #1 (Public review):

In the revised version, the refinement of atomic occupancies in the 2DTM-generated maps has been insightful: densities only come back at values ranging from 0.55–0.80, whereas residues included in the template remain at 1, suggesting that the 2DTM-reconstruction does suffer from model bias. Their newly added Omega calculations, which are helpful, also suggest that model bias is present in the 2DTM-based reconstructions. These observations therefore contradict the first subsection heading of the Results, which claims “unbiased reconstruction of omitted residues”.

We agree that the previous subsection heading was too absolute. We have changed the heading from “Unbiased reconstruction of omitted densities in a 43 kDa protein kinase” to “Recovery of densities omitted from the template in a 43 kDa protein kinase”. The opening sentence now states that we evaluated the ability of 2DTM to “recover omitted ligand densities” (L123–125).

We also revised nearby statements to describe the observations without claiming that the entire reconstruction is free of template bias. The manuscript now states that, because the corresponding features were omitted from the search template, the recovered densities cannot result from direct inclusion of those features in the template (L150–153).

For the omitted alpha-helical turn, we now state simply that its density was recovered despite its absence from the search template (L191–192). We also revised the interpretation of the occupancy-refinement results from “confirming partial, unbiased recovery” to “supporting partial recovery of density in the omitted regions” (L198–199). The same wording has been applied to the Supplementary file 1 caption on page 27.

Finally, the summary of the ligand-deletion experiments now states that a ligand and nearby residues can be deleted to reduce template bias while retaining sufficient signal for their density to be recovered (L248–251). In the Methods, we retain the description that the composite omit map was constructed to avoid template bias at the omitted locations (L953–954).

We have also toned down comparative statements about reconstruction accuracy, including the relevant subsection heading (“Comparison of 2DTM and RELION reconstructions from the same particle stack” at L252–253) and the surrounding discussion (L274–279).

Requested FSC Analysis

The measurement of how much model bias is present in this OMIT map by FSC calculations is still pending. This could be done in two ways. My original suggestion was to calculate a mapto-model FSC for the OMIT map and the full reference. This should be compared with a similar map-to-model FSC on the map where only the ligand was omitted. Alternatively, they can use the cisTEM FSC uncorr procedure on the OMIT half-reconstructions and compare the resulting curve with the one presented in Figure 1b.

We have now completed both analyses and added them to the revised manuscript (new Figure 5—figure supplements 1–3, with accompanying Results and Methods text).

(1) Map–model FSC. We computed the map–model FSC between the composite OMIT map and a density simulated from the full 1ATP model, and compared it with the equivalent FSC for the Figure 1 reconstruction, in which the ligand and residues 222–227 were omitted from the template (Figure 5—figure supplement 1). The composite OMIT map crossed FSC = 0.5 at 3.5 Å and FSC = 0.143 at 3.0 Å, compared with 3.0 Å and 2.4 Å, respectively, for the Figure 1 reconstruction. Because each local region of the composite map was taken from a reconstruction in which the corresponding residues were absent from the template, this agreement reflects genuine recovery rather than direct inclusion of those local features in the template. The lower FSC values relative to the Figure 1 reconstruction are expected. In the Figure 1 reconstruction, most of the protein remained in the template, whereas the composite is assembled from disjoint local omit regions. This stitched construction introduces holes and mask boundaries that affect Fourier-space agreement across the curve, in addition to the weaker, partial recovery of locally omitted density. Thus, the map–model FSC provides a conservative Fourier-space assessment of recovered omit-region density. The composite map–model FSC also shows a negative dip at the lowest spatial frequencies, which does not indicate failed recovery. Radial binning around the omitted atoms (Supplementary file 3) shows that the atom-centred shells (≤2 Å) recover positive but weakened density upon omission, whereas the peripheral shells (2–3 Å) are negative and nearly identical whether the residue is present or omitted, leading to net-negative density within the molecular envelope. We therefore interpret the low-frequency dip as a consequence of the composite construction rather than as evidence for failed recovery of omitted density.

(2) Half-map FSC_uncor. We also computed the half-map FSC of the individual OMIT reconstructions (Figure 5—figure supplement 2): the 36 individual omit reconstructions cross FSC = 0.143 at a median resolution of 2.8 Å, comparable to the Figure 1b reconstruction (∼3.0 Å). The composite map’s own half-map FSC appears higher, but this value is not a reliable resolution estimate because the two composite half-maps are assembled using the same voxel-assignment masks. This shared support introduces artificial correlations, which we demonstrate with a phase-randomization control (Figure 5—figure supplement 3). We therefore use the individual omit-reconstruction FSCs and the composite map–model FSC, rather than the composite half-map FSC, to assess Fourier-space agreement.

Together, these analyses show that the OMIT reconstructions contain high-resolution signal in regions absent from the corresponding search templates, while also identifying the low-frequency dip and the inflated composite half-map FSC as consequences of the conservative stitched composite construction.

Reviewer #3 (Public review):

Nor was it compared to more recent strategies for processing SPA data from small molecules, such as Blush regularization or HR-HAIR. [...] This places this method as a complementary technique, and whether it outperforms those methods for a wide variety of molecules is yet to be determined.

We agree that a systematic comparison with recent small-particle SPA methods such as Blush regularization and HR-HAIR will be important. We have added this point to the Discussion (L831–846). We also note that such as comparison should consider not only particle stack and molecular mass, but also the fidelity of the 2DTM template forward model. In the ideal limit of an accurate template and forward model, 2DTM should provide a strong prior for particle detection and pose determination. In practice, however, current templates remain imperfect approximations to the experimental signal because of inaccurately modelled solvent-boundary effects and atomic scattering factors, bonding and charge redistribution, and conformational mismatch. Improving template generation is therefore an important direction for extending the range of molecular targets and imaging conditions where 2DTM can be applied.

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Reply to the reviewers

The authors do not wish to provide a response at this time.

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Referee #4

Evidence, reproducibility and clarity

In this manuscript, Dilbaz-Gunden, et al. investigate the localization and function of CSPP1 in multiciliated cells (MCCs). Using a combination of mouse tracheal cell cultures and Xenopus embryos, the authors characterize the localization of CSPP1 in MCCs and use gene knockdowns to analyze CSPP1 function. They find similar protein localization in both models and that loss of CSPP1 disrupts centriole organization, basal body migration/docking, basal body polarity, and cilia formation. Overall, the data is high quality and the presentation is clear. The main conclusion that CSPP1 is a conserved regulator of ciliogenesis in MCCs is supported by the evidence presented.

Major comments:

1. For each of the CSPP1 protein localization studies presented in Figure 1, to gauge reproducibility, it would be useful to indicate how many cells were analyzed and how many looked like the representative images.
2. The conclusion that CSPP1 is required for centriole amplification is confusing since CSPP1 depletion does not alter centriole number (Fig. 2D-E). The centriole defect appears to be due to a MCC morphogenesis defect.
3. In CSPP1 loss-of-function treatments, the authors find defects in centriole organization, basal body migration, basal body polarization, cilia formation, cilia length, and cilia motility in MCCs. It is not clear whether the authors propose that CSPP1 has distinct functions in each of these processes or these are pleiotropic phenotypes due to earlier defects in MCC morphogenesis. This is particularly confusing since previous work indicates CSPP1 is a regulator of the cell/cytoplasmic cytoskeleton.

Significance

Mutations in CSPP1 have been identified in patients with the ciliopathies Joubert syndrome and Meckel-Gruber syndrome, so the significance of studying CSPP1 is high. How mutations in CSPP1 can cause two distinct ciliopathies remains unclear. Previous work has identified CSPP1 as a microtubule-associated protein that is localized to the basal body and ciliary tip of primary cilia and is involved in cilia length regulation. In this context, the finding in the current manuscript that CSPP1 is important for establishing ciliary structure is not new or unexpected. However, this is the first analysis of CSPP1 localization and function in MCCs. This new evidence that loss of CSPP1 can disrupt both primary cilia and motile cilia in MCCs supports a model for how mutations affecting core cilia assembly proteins can underlie multiple ciliopathy phenotypes. This work will appeal to a broad audience in the fields of cell biology and ciliopathy. A limitation to the significance of this work is that it stops short of investigating how CSPP1 mechanistically regulates MCCs.

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Referee #3

Evidence, reproducibility and clarity

The report by Dilbaz-Gunden et al characterizes the roles of Joubert syndrome protein CSPP1 in multiciliogenesis. Joubert syndrome is commonly thought of as a sensory ciliopathy as many regions in the brain that are affected in this disorder do not possess motile cilia. However, the authors note in their introduction that there are pathogenic variants in several "cilia" genes that cause both sensory and motile cilia phenotype in the same individuals. This motivates the study to evaluate the role of CSPP1 in multiciliated cell contexts.

The strengths of this report are the analyses in multiple systems and the beautiful imaging and quantifications of these images. However, some of the conclusions are less convincing than others as written and this weakens the paper. My suggestions for strengthening this report are as follows:

1) One major conclusion is that CSPP1 is required for "efficient centriole amplification". This doesn't seem supported by the results in figure 2 as presented. In 2D the conclusion seems to be that the cells have similar number of centrioles, but loss of Cspp1 results in cells with larger apical surfaces that do not fill with centrioles. This doesn't appear to be an inability to make centrioles, but an inability of a cell lacking Cspp1 to recognize that it needs to make more centrioles to fill the larger surface area. Are there other manipulations that increase apical surface area yet the cells compensate appropriately with more centrioles? Given the later results that Cspp1 loss affects the apical microtubule networks, how many of the subsequent defects, (defective basal body docking, apical organization, establishment of rotational polarity, ciliogenesis, and failure of MCCs to integrate properly in the epithelium) are due to that defect alone? The presentation and the interpretations would benefit from thinking about which loss of Cspp1 phenotypes are likely direct roles of Cspp1, versus indirect consequences of an earlier Cspp1 role. The statement on page 20 that "CSPP1 depletion is consistent with a role for CSPP1 in coordinating centriole amplification with apical remodeling" seems more accurate and could be the way to think about reframing the results.

2) Another major issue is that how quantifications are conducted aren't always clear. For example, saying a control cell has "dense and uniform" centriole distribution and a Cspp1 depletion cell is abnormal and disorganized doesn't clarify how the person doing the analysis decided what was normal versus abnormal. In some cases this can be found in figure legends, but it would be helpful to include an analysis section in materials and methods that explains how decisions were made regarding normal and abnormal for each analysis.

3) Minor - It would be nice to add some thought to the discussion about why some mutations cause both sensory and motile cilia defects, while others do not.

4) Figure 1A - please add the ALI stages to the diagram outlining the stages of MCC formation.

5) Figure 2 B-J it would be helpful to add these category labels to the panels to help the reader understand what each group of stainings is meant to analyze.

6) Figure 1E bottom panel - the inset isn't from the outlined cell? Why is this?

7) Figure 1F and S1B - in detached cilia, CSPP1 expression is throughout the axoneme and at the tip, but in other images the concentration at the tip is emphasized as the localization for this protein. Is the staining in detached cilia an artefact? Or is it just less obvious that CSPP1 is throughout the cilia body in intact MCCs?

8) Figure 2B - As per the major comment above - how did the researcher set the threshold for amplified versus less amplified?

9) Was there rationale for using the SB versus TB morpholino?

10) In Figure 3A, why is there so much less ZO1 in the shCspp1 image? Is this a defect with loss of CSPP1 or an imaging plane issue?

11) Figure 4A add the stage of analysis to the images.

12) Figure S2A How was quantification of CSPP1 protein levels conducted?

13) Figure S2E was the new product produced by SB MO sequenced to confirm this is intron retention as opposed to some other splicing defect?

14) Define GFP-GPI in material and methods. I assume membrane associated GFP marker?

15) Figure S2F - the traced outlines do not look like the cells indicated by the boxes.

16) Figure S3B - Which cells is which of the callouts? Why are there no traced outlines as in other figures?

Significance

This work is important and will be of interest to the cilia community. The images are fantastic and the ultimate findings of CSPP1 affecting multiciliated cells is novel and intriguing. My issues with the paper have to do with interpretation of the results which seems to be incomplete. The authors should be able to fix the issues I have with text edits and I do not think they need to do additional experiments.

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Referee #2

Evidence, reproducibility and clarity

The paper by Dilbaz-Gunden and colleagues describe the results of experiment to understand the function of the CSPP1 protein in multiciliated cells (MCCs). Mutations CSPP1 have been identified in Joubert syndrome patients and although the protein has been studied with reference to primary cilia, there are clinical issues reported in these patients that suggest functions in motile ciliated cells as well. The authors first describe a detailed localization pattern of CSPP1 in differentiating MCCs, using mouse trachea and Xenopus epidermal MCCs. Then they use knockdown studies to uncover apparently multiple roles of CSPP1 in basal body biogenesis, apical migration and docking as well as axoneme formation and cilia motility. While the localization studies provide solid data, I am not convinced with the loss-of-functions approaches adopted in this study. A stable genetic knockout is essential to properly dissect the role of CSPP1 in MCCs: Either a mouse mutant or knockout in cultured cells then differentiated into MCCs. There are many papers with knockdown studies in cultured cells and Xenopus embryos which do not even up with findings from stable knock outs. Of relevance to this work is the initial description of Deup1 as a protein essential for basal body generation in MCCs using similar knock down studies in mammalian cells and Xenopus embryos (PMID: 24240477), which has been subsequently refuted using stable knockout mice (PMID: 31792378). The other shortcoming is that the data are largely descriptive, with no new or mechanistic insights into CSPP1 function in centriole or cilia formation. Furthermore, the knockdown effects seem to produce pleiotropic effects, so it is not easy to appreciate if CSPP1 indeed has multiple functions or it is principally required for generating proper basal bodies, for example, and failure in this early event in the knockdown conditions triggers other downstream manifestations like problem in their migration and docking and axonemal extension.

Significance

The study provides limited conceptual novelty and does not substantially advance mechanistic understanding of CSPP1 function.

I have expertise in cilia and ciliopathies, particularly multiciliated cells

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Referee #1

Evidence, reproducibility and clarity

The Joubert syndrome protein CSPP1 is a conserved regulator of vertebrate multiciliogenesis and motile cilia function

By: Irem S. Dilbaz-Gunden, Clothilde Boitel, Jovana Deretic, Marine Touret, Mehmet S. Aydin, Esra N. Yigit, Ozgecan Kayalar, Hasan Bayram, Virginie Thomé, Olivier Rosnet, Nicolas Brouilly, Laurent Kodjabachian, Camille Boutin and Elif Nur FiratKaralar

I have only some Minor remarks:

Introduction:

• Motile cilia not always have 9+2 configuration.
• Authors present a excellent introduction explaining how a number of findings suggest that ciliogenesis relies on shared molecular modules, including microtubule-associated proteins, that govern organelle biogenesis and function across both primary and motile cilia.

Results:

• The authors establish CSPP1 as a conserved component of the multiciliogenesis machinery in mouse, human and Xenopus. Its localization to fibrous granules and deuterosomes during centriole amplification, and to basal bodies and ciliary axonemes in mature cells.

• Figure 1: is flawless.

• Figure 2: data from 2 animal models strongly supports that CSPP1 depletion reduced the efficiency of centriole amplification and disrupted formation of the dense centriole arrays characteristic of MCCs.
• Figure 3: data is robust and presents an excellent quantification in 3 axis of milder defects for centrin signal spacing and stronger defects for polarity direction.

I would ask the authors to make the figures even more clear by iserting a small diagram of the animal model being used in each case. In all images presented.

• Figure 4 title: CSPP1 loss leads to defective cilia formation, axonemal structure, and motility (please add in which cells from which animal model) I like the way the authord show the "normal defects" in the control figures and make the comparison with the treatment defects in all cases. Transparency is important. Congratulations. Again, here if one does not read the main text cannot undestand which model is being used. Legends also ommit the model. Please make sure each figure is understandable on its own. Images are of high quality. The number of methodologies used to reach their conclusions is impressive and data is well quantified. The TEM data (h) supports the claims and images were taken at the same cilia longitudinal focus planes supporting sh Cspp1 cilia are indeed very deffective.

• Figure 5:

The xenopus experiments are very convincing and robust as cells were stained for the MO lineage tracer (green), the Rescue tracer (RFP, magenta), and cilia (Acetylated alphatubulin, yellow). All images are impecably presented. The authors provide a detailed framework along MCC development for understanding how a Joubert syndrome-associated gene can contribute to respiratory phenotypes.

Discussion:

• In the discussion (final paragraph) please add a reference for the HH signalling defects in seen in primary cilia as these were not evaluated here. Are these for the same gene or for other genes? Please specify to make it clearer. In JS patients is there any reason why the symptoms are more related to the upper airways? Perhaps discuss this here. Any data from bronchoscopy available? is this a very mild phenotype in humans?

Significance

The manuscript is very well written, supported by great imaging and beautiful figures. I agree that the findings support a model in which disruption of a shared cytoskeletal assembly pathway can link primary and motile ciliopathy phenotypes across multiple ciliary tissues and species. I have some minor remarks that would improve the clariry of the manuscript but I think the work is of excellent quality and will be an important contribution to the field. Publication should be fast.

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here is how I see it: I lay the boys off and that reduces 12mil every two weeks but I am replacing the same amount with skilled workrs that can do tiles, ceiling, electrical, plumbing, soffits and finishing. One month they will be here. In that period I will have to spend as follows, tiles, electrical wiring, switches and plugs, I will shop aggressively and see if I can keep in under 12 mil, tiles under 35 mil, ceiling board is confirmed at 125,000 per sheet and each sheet is 2.80 m2, 30 sheets is 3.71 mil kip and that include the soffits (roof overhang) so thats good. more to do yet tonight

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