3,103 Matching Annotations
  1. May 2023
    1. colocalization of Lst1-3xGFP with Atg40-2xmCherry

      To examine the association of two proteins in the cell, colocalization of two fusion proteins with different florescence tagged fused with two proteins are utilized to be visualized under the confocal/florescence microscope, to test whether these two signals (red and green florescence in this study) could be overlapping in the cell.

      LST1 fused with GFP, the green florescence protein. ATG40 fused with mCherry, the red florescence protein.

    2. Because increased levels of autophagy receptors increase ER-phagy and the number of ER-containing autophagosomes (11, 12), ER-phagy receptors are thought to play a role in packaging ER into autophagosomes (12). To address if Lst1 works with Atg40 to perform this function, we induced Atg40 expression with rapamycin (11) and asked if this promotes an association with Lst1

      To investigate how the role of ER-phagy receptor, ATG40, involved in packaging the cargo for recycling in ER specifically, the authors made the connection of observation and results obtained in ATG40, and associated with LST1 to hypothesize that LST1 could be associated with the ER-phagy receptor, ATG40.

    3. ER exit sites (ERES)

      The ER exit sites are specialized ER zones for the transport of cargo proteins from the ER to the Golgi apparatus.

    4. Rapamycin also induced the expression of the nucleophagy receptor Atg39 (11) but did not induce the colocalization of Lst1 with Atg39 (fig. S8, C and D). Furthermore, Lst1 did not contribute to the degradation of the nuclear ER marker Hmg1 (fig. S8, E to H).

      In yeast, the ER consists of 3 subdomains, the cytoplasmic ER, the cortical ER, and the perinuclear ER (also called nuclear envelope).

      Atg39 specifically localizes to the nuclear envelope. Therefore, the Atg39-dependent pathway in selective autophagy terms as nucleophagy.

      Conversely, Atg40 predominantly localizes to the cytoplasmic ER and the cortical ER, and loads fragments (ER tubules or sheets) of these ER subdomains into the phagophore. Thus, Atg40 is exclusively involved in ER-phagy.

      To exclude the possibilities that LST1 is localized to the nuclear envelope and do not involve in nucleophagy, the authors examine the colocalization of Atg39 and Lst1, and rule out the possibility that the Lst1 is localized in nuclear envelope and do not reside on the nuclear envelope and its marker, Hmg1.

    5. ubiquitin-like protein Atg8

      Atg8 protein is a marker protein to observe autophagosome formation. When Atg8 protein engineered with the red florescence protein (RFP), RFP-Atg8, RFP-Atg8 protein will be conjugated to the lipids and enable the membrane fusion to localize on the autophagosome.

    6. Atg8-Lst1 colocalization in wild-type (WT) but not atg40Δ cells

      Atg8 also plays an important role in cargo recognition for selective autophagy by interacting with the receptor protein. When Atg40 is mutant, Lst1 is failed to interact and colocalize with Atg40, indicating that Lst1 is acting together with Atg40 to form autophagosome. And Sec23 is partially required with Atg40 to form autophagosome.

    7. Lnp1 is an ER protein that resides at and stabilizes the three-way junctions that form when two tubules fuse to each other (23). In its absence, ER network rearrangements are disrupted and Atg40 puncta fail to access the autophagy machinery (17). As a consequence, ER is not packaged into autophagosomes in lnp1Δ cells

      Lnp1 is a protein to maintain the structure of ER by stabilizing rearrangements of the ER networks.

      Further reading: https://doi.org/10.1073/pnas.1805032115

    8. we performed binding studies with lysates prepared from untreated and rapamycin-treated cells expressing Atg40-3xFLAG.

      This experiment is an in vitro binding assay by purifying the GST fusion of target coat proteins of the COPII and incubated with Atg40 fusion protein with FLAG epitope tagged expressed in the yeast

    9. Atg40-3xFLAG from both lysates bound to purified, bacterially produced glutathione S-transferase (GST)–Lst1, but not to GST-Sec13, GST-Sec24 (Fig. 3A and fig. S10, A and C), or GST-Sec23 (fig. S10B).

      Only GST-Lst1 purified protein is able to bind with the Atg40 but not other subunits of COP11 coat proteins.

    10. Representative electron micrographs of WT and pep4Δ strains treated for 12 hours with rapamycin

      pep4Δ strain is a vacuolar protease-deficient yeast strain that lost protease activity wihle fail to degrade the autophagic cargo and served as negative control when compared with the wild-type original strain.

    11. vacuolar protease Pep4

      Pep4, a vacuolar protease required for function of multiple hydrolases, is required for autophagic cargo degradation

    12. atg14Δ mutant

      autophagy-deficient yeast strain which fail to form the autophagosomes to degrade and recycle substances.

    13. we examined pathway induction by flow cytometry in cells carrying an integrated UPR-regulated GFP reporter

      To induce the UPR (unfolded protein response), DTT (dithiothreitol) is added to induce protein misfolding in the ER by blocking protein disulfide bond formation, thus activate and induce the UPR.

      The relative intensity of GFP fluorescence signal in the cells was measured using the flow cytometry.

    14. SEC24C

      SEC24C in mammalian cells is the homolog for Lst1 in yeast.

    15. Torin2 (TOR inhibitor2)

      Torin 2 is a potent and selective mTOR inhibitor, which decreases cell viability and induces autophagy and apoptosis.

    16. ULK1, a component of the autophagosome biogenesis machinery

      ULK1 is one of two mammalian homologues of the yeast ATG1 kinase, known for its role in autophagy initiation

    17. There are two major types of autophagy pathways, bulk and selective

      Bulk autophagy also called non-selective macroautophagy. During bulk autophagy, autophagosomes fuse with lysosomes or vacuoles resulting in the degradation of the cargo.

      While during selective autophagy, the cargo is distinguished (mitochondria, ER, ribosomes, peroxisomes and etc.) and recognized by specific cargo receptors, or selective autophagy receptors, to connect with the autophagosome for degradation.

      Here are two videos for more an explanation: 1) The mechanism of autophagy: https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s

      2) Self-Eating Cell Research Wins Nobel in Medicine: https://www.youtube.com/watch?v=Ws0mOmfC9EU

    18. ER-associated degradation (ERAD)

      Misfolded protein are retained in the ER and subjected for proteosomal degradation which occurs in the cytosol.

      Learning from the youtube: https://www.youtube.com/watch?v=fEEbyYjXNUU&t=1s

    19. unfolded protein response (UPR)

      When newly synthesized protein is not properly folded into their correct orientation in the endoplasmic reticulum (ER), the ER now is under the stress to degrade the misfolded protein. To degrade the misfolded proteins and maintain the ER homeostasis, the cellular signaling will turn on the unfolded protein response to help the cell deals with problematic proteins for recycle and degradation.

      Video: https://www.youtube.com/watch?v=vy4m-fUOn9o

    20. isoforms

      Genes are commonly generate isoforms from the same locus to produce different mRNA and thus give rise to different length of amino acid with similar protein functions.

    21. mammalian homolog, SEC24C

      Lst1 and SEC24C, are homologous gene in yeast and mammalian respectively. The protein or DNA sequence of these genes, Lst1 and SEC24C, are highly similar and evolutionary share the common ancestor, termed as homolog.

    22. ER-phagy receptor Atg40

      Protein recycling and self-eating process that selectively happens in endoplasmic reticulum terms as ER-phagy (phagy means eating). Selective autophagy requires a receptor protein to recognize its degradation targets and directs the targets to be sequestrated by autophagosomes, a double membrane vesicle structure, which to be transported into lysosomes or vacuoles.

      A protein named as Atg40, has been recognized as a ER-phagy receptor protein in yeast. FAM134B is a putative mammals homologue of ATG40.

      Literature first explain the Atg40 ER-phagy receptor https://doi.org/10.1038/nature14506 (ATG40)

      https://doi.org/10.1038/nature14498 (FAM134B)

    23. endoplasmic reticulum (ER)

      ER is a transportation system of the eukaryotic cell composed of network of tubules and sheet-like area adjacent with the nuclear envelope and stretches out to the cell periphery.

      Learning corner with video: https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s glossary

    24. How sites on the ER are targeted for ER-phagy is unclear. We reasoned that the cytosolic machinery that recognizes and binds to ER-phagy receptors may play a role in marking specific sites on the ER where autophagy will occur. Because COPII coat subunits are known to participate in membrane-budding events at the ER (1), we investigated whether coat subunits play a role in sequestering ER domains into autophagosomes during ER-phagy.

      Key question raised by the authors, how the dispersed site throughout the ER are recognized by the selective autophagy receptors to deliver the cargo for degradation.

      The authors hypothesized that, COP11 coat proteins which involved in membrane-budding at the ER, could involve in ER-phagy.

    25. 11 K. Mochida, Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, H. Nakatogawa, Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 522, 359–362 (2015).

      The endoplasmic reticulum (ER) is a complex network of membranes involved in protein and lipid synthesis, ion homeostasis, protein quality control and organelle communication. It is also a source of membrane-bounded vesicles called autophagosomes, the vehicles for the self-digesting cellular process of autophagy. This paper shows how the ER itself is targeted for degradation by autophagy — a process that could ensure constant ER turnover in response to cellular requirements.

      Authors find the protein FAM134B is an ER-resident receptor that facilitates 'ER-phagy'. Downregulation of this protein — mutations of which can cause sensory neuropathy in humans — resulted in expanded ER structures and degeneration of mouse sensory neurons. In particular, authors demonstrated that this process is conserved in yeast, where Atg40 is enriched in the cortical and cytoplasmic ER, loading these ER subdomains into autophagosomes. A further ER-phagy receptor, Atg39, localizes to the perinuclear ER (or the nuclear envelope) and induces autophagic sequestration of a part of the nucleus, thus ensuring cell survival under nitrogen-deprived conditions.

    26. By contrast, Lst1 acted exclusively in ER-phagy.

      A conclusion summarized by the authors based on experiments that have been done to distinguish the bulk autophagy and selective autophagy that happened in various organelles, and only ER-phagy is required by Lst1 coat protein.

      To draw a conclusion which exclusively functional in one particular experiment, the designs of various experiments are needed in order to rule out other possibilities.

    27. FAM134B

      The mammals homolog of Atg40 in yeast. To verify the evolutionarily conserved function the ER-phagy receptor in higher order and complex organism such as in mammal cell, FAM134B, the homolog protein of Atg40 in mammals, was used to test its functional similarity.

    28. To determine whether any of the SEC24 isoforms are required for ER-phagy in mammalian cells, we knocked down each of the four isoforms by small interfering RNA (siRNA) in U2OS cells

      The authors tested whether or not the defeated of Lst1 in yeast will have the similar observation in mammalian cells by looking at the homologs of the isoforms of Sec24 in mammals.

    29. Thus, although Atg40 was not found to be a UPR target, the UPR responded to the loss of ER-phagy.

      Lst1 and atg40 mutants have higher UPR response before and after DTT treatments, indicates that defeated in ER-phagy proteins will also induce the UPR.

    30. To determine whether ATZ aggregates in the absence of Atg40 or Lst1, microsomal membrane fractions prepared from WT, atg14Δ, atg40Δ, and lst1Δ cells were analyzed on sucrose gradients. Soluble ATZ was primarily found at the top of the WT gradient, whereas ATZ from mutant lysates was largely in the pellet

      ATZ-pYES2 is a vector natively expressing the ATZ, a misfolded protein, in yeast. ATZ-pYES2 used to observe a as substrate targeted for autophagy degradation.

      Wild type, and mutants of the atg40 and lst1 were transformed with ATZ-pYES2 to observe whether loss-of-functions of atg40 and lst1 will lead to the accumulation of aggregated ATZ protein in the ER, which indicates that Atg40 and Lst1 are essential ER-phagy.

    31. These findings implied that Lst1 and Atg40 function in the same pathway.

      No additive effect was observed when double mutant of lst1atg40 is investigated. This finding drawn another summary which LST1 and ATG40 function in the same pathway.

    32. By contrast, Lst1 acted exclusively in ER-phagy.

      A conclusion summarized by the authors based on experiments that have been done to distinguish the bulk autophagy and selective autophagy that happened in various organelles, and only ER-phagy is required by Lst1 coat protein.

      To draw a conclusion which exclusively functional in one particular experiment, the designs of various experiments are needed in order to rule out other possibilities.

    33. we found an unexpected role for Lst1-Sec23 in ER-phagy that was independent from its function in secretion.

      Lst1-Sec23 is a coat adaptor protein that carry the cargo molecules form ER to Golgi, which mainly to help the secretory proteins transportation. The author discovered new function of the Lst1/Sec23 in self-eating and protein recycling process (autophagy), in which the Lst1-Sec23 functions together with the autophagy receptor, Atg40, to localize the ER domains for autophagic degradation.

  2. Apr 2023
    1. First, when Atg40 expression was up-regulated by the TOR inhibitor rapamycin, the Lst1-Sec23 complex associated with Atg40 puncta.

      In response to stress caused by starvation or misfolded aggregate-prone secretory proteins, Lst1 acted to promote an additional function—ER-phagy. Together with autophagy receptors on the ER, Lst1 targeted ER domains for degradation to avert protein aggregation, thus preserving cellular health.

    2. 10 M. Hamasaki, T. Noda, M. Baba, Y. Ohsumi, Starvation triggers the delivery of the endoplasmic reticulum to the vacuole via autophagy in yeast. Traffic 6, 56–65 (2005).

      Known as the first article to described ER-phagy.

      In this article, authors characterized the fate of the ER in response to starvation, and demonstrated a significant linkage to autophagy.

      Abstract: Autophagy is a survival mechanism necessary for eukaryotic cells to overcome nutritionally challenged environments. When autophagy is triggered, cells degrade nonselectively engulfed cytosolic proteins and free ribosomes that are evenly distributed throughout the cytoplasm. The resulting pool of free amino acids is used to sustain processes crucial for survival. Here we characterize an autophagic degradation of the endoplasmic reticulum (ER) under starvation conditions in addition to cytosolic protein degradation. Golgi membrane protein was not engulfed by the autophagosome under the same conditions, indicating that the uptake of ER by autophagosome was the specific event. Although the ER exists in a network structure that is mutually connected and resides predominantly around the nucleus and beneath the plasma membrane, most of autophagosome engulfed ER. The extent of the ER uptake by autophagy was nearly identical to that of the soluble cytosolic proteins. This phenomenon was explained by the appearance of fragmented ER membrane structures in almost all autophagosomes. Furthermore, ER dynamism is required for this process: ER uptake by autophagosomes occurs in an actin-dependent manner.

    3. retrotranslocates

      To cause, or to undergo retrotranslocation.

      Retrotranslocation is the reverse process of translocation.

      Translocation is a transfer of a chromosomal segment to a new position, especially on a nonhomologous chromosome; the segment so transferred.

    4. vesicles

      Vesicles are compartments formed by a lipid bilayer separating its contents from the cytoplasm or a fluid-based extracellular environment. They can contain either liquids or gases and have a wide range of functions in cells across the living world from regulating buoyancy to secreting hormones.

      The word ‘vesicle’ derives from the Latin word vesicula meaning ‘small bladder’

  3. Feb 2023
    1. 28 K. J. Travers, C. K. Patil, L. Wodicka, D. J. Lockhart, J. S. Weissman, P. Walter, Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101, 249–258 (2000).

      It was identified above as previous studies, so why was this article so important?

      Tag as "References"

    2. Although ER-phagy was initially described in 2005 (10), it was not until the first ER-phagy receptors were identified that the process was thought to be selective (11, 12).

      News - why was this such an important discovery about describing the ER-phagy? Tag to "NewsAndPolicy"

  4. Sep 2021
    1. S. Culliney, L. Pejchar, R. Switzer, V. Ruiz-Gutierrez, Ecol. Appl. 22, 1718–1732 (2012).

      This study provides evidence that ‘Alalā, an endangered native bird species in Hawaii, displays seed dispersal behaviors and promotes seed germination of various native plants. Based on these results, the authors suggest that ‘Alalā can contribute toward the restoration of native fruiting plants in Hawaiian forest communities.

    2. E. Burgos et al., J. Theor. Biol. 249, 307–313 (2007).

      Nestedness can contribute toward the robustness of a network. If species that share fewer interactions are the first to go extinct, the remaining mutualistic system has a greater chance of survival. The authors also calculate a coefficient as a parameter of a network’s robustness.

    3. H. A. Mooney, E. E. Cleland, Proc. Natl. Acad. Sci. U.S.A. 98, 5446–5451 (2001).

      Mooney and Cleland describe the evolutionary consequences of invasive species on the invaders themselves and on native species. Modifying behavior to adapt to a new environment, competing for similar resources, predation, or creating hybrid progeny by breeding with native species are just a few examples.

    4. N. Blüthgen, F. Menzel, N. Blüthgen, BMC Ecol. 6, 9 (2006).

      Previously, the majority of network analysis was qualitative. Blüthgen et al. introduce two quantitative measurements that use the frequency of interactions to describe specialization at the species level and across a network.

    5. E. L. Rezende, J. E. Lavabre, P. R. Guimarães, P. Jordano, J. Bascompte, Nature 448, 925–928 (2007).

      The phylogenetic or evolutionary relationship between species can predict the types and quantity of interaction patterns they exhibit in a network. Using a simulation of extinction events, the authors also demonstrated that the extinction of one species can result in the extinction of other species that are evolutionarily related.

    6. A. de Almeida, S. B. Mikich, Oikos 127, 184–197 (2018).

      The authors merged data sets from multiple studies investigating fruit-frugivore interactions and illustrated that most networks across various neotropical areas were significantly nested and modular. The authors also concluded that combining results from different studies can be useful for analyzing the ecological structures of broad regions and supporting conservation efforts.

    7. C. G. Chimera, D. R. Drake, Biotropica 42, 493–502 (2010).

      In contrast to Foster, Chimera found that introduced birds in Hawaii dispersed predominately the seeds of non-native plants. Possible explanations could be that the non-native plants produce larger fruit that are more abundant and have a smaller seed size. These qualities are more enticing to birds and enhance the fruit's chances of getting eaten and its seeds later deposited.

    8. J. T. Foster, S. K. Robinson, Conserv. Biol. 21, 1248–1257 (2007).

      Foster and colleagues investigated how often introduced fruit-eating birds on the islands of Hawaii consume and disperse seeds from native plants versus seeds from exotic plants. They found that seeds from native plants made up the majority of the introduced bird species’ diets. This supports the potential of introduced bird species playing a role in the conservation efforts of native habitats.

    9. A. Traveset, D. M. Richardson, Annu. Rev. Ecol. Evol. Syst. 45, 89–113 (2014).

      The authors studied the feeding behaviors of birds in the Galapagos island. They discovered that these birds ate a not just a select few, but a wide variety of plants on the Islands. They called this behavior interaction release, a survival tactic where animals expand their niches.

    10. S. L. Lewis, M. A. Maslin, Nature 519, 171–180 (2015).

      The Anthropocene is defined as the epoch or geological time when human activity significantly impacted the global environment. Based on the criteria for defining a new epoch and supporting geological evidence, the authors propose two possible dates to mark the beginning of the Anthropocene: 1610 and 1964.

    11. Although these introduced birds on O‘ahu are the only dispersers of native plants, they disperse a much higher proportion of seeds from invasive plants; therefore, their presence is a “double-edged sword” for conservation

      Connects to Learning Standards, A Framework for K-12 Science Education, Disciplinary Core Ideas: LS2.C Ecosystems Dynamics, Functioning, and Resilience:

      "Anthropogenic changes (induced by human activity) in the environment—including habitat destruction, pollution, introduction of invasive species, overexploitation, and climate change—can disrupt an ecosystem and threaten the survival of some species."

    12. introduced plants accounted for 93.3% of dispersal events

      Of all seeds found in bird poops, 93% are of introduced plant species.

    13. well integrated into novel networks,

      ability to establish new interactions with partner species present in the ecosystem

    14. We also estimated robustness (stability to species loss) of each network as the rate of secondary extinction expected under the simulated loss of network partners,

      Connects to Learning Standard, Vision and Change for Undergraduate Biology Education Core Competencies and Disciplinary Practices: VC3 Ability to use modeling and simulation:

      "Use mathematical modeling and simulation tools to describe living systems."

    15. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide

      Connects with Learning Standards, A Framework for K-12 Science Education, Crosscutting Concepts: Scale, proportion, and quantity:

      "In considering phenomena, it is critical to recognize what is relevant at different measures of size, time, and energy and to recognize how changes in scale, proportion, or quantity affect a system’s structure or performance."

    16. J. Memmott, N. M. Waser, M. V. Price, Proc. R. Soc. London Ser. B 271, 2605–2611 (2004).

      By simulating the network patterns between plants and pollinators, the authors demonstrated that plants were more resistant to extinction with the removal of specialized pollinators versus generalized pollinators. Specialized pollinators only interact with a few plant species, whereas generalized pollinators interact with a larger range of plant species. When a generalized pollinator is lost, more plants are affected.

  5. Jul 2020
    1. “something in the piece itself determines that a head shall develop at the anterior cut surface and a tail at the posterior cut surface”

      Here, Morgan suggests that regeneration of a head versus a tail is related to the location of the amputation and the cells that reside there.

    2. “Janus heads”

      Janus was a Roman god and doorkeeper to the heavens. Relevant here, Janus was usually depicted with two heads, one facing the past and the other towards the future.

    3. As part of a systematic effort to define the roles

      Using the process of science to identify and evaluate possible explanations for a natural phenomenon.

      Click here to learn more about the process of science: https://media.hhmi.org/biointeractive/click/understanding-science/#/intro/4

    4. β-catenin antagonist adenomatous polyposis coli

      Adenomatous polyposis coli, or APC, is gene that plays many roles, including acting as a tumor suppressor. APC has also been found to play a role in cell division and directing cells where to go once division takes place. In order to do its job, APC directs β-catenin in the Wnt signaling pathway.

      Read more in the Journal of Cell Science. The PDF is also available in the "Related content" tab.

    5. RNA interference (RNAi)

      A mechanism used by both plant and animal cells to silence a gene using a double-stranded DNA molecule. DNA is converted into the smaller RNAi molecules used to turn genes off. Scientists are now able to use this natural process to turn off genes they are studying so they can learn more about their function.

    1. an array of measures ranging from rotational behavior (Fig. 6D) to head position bias and locomotion

      Motor behavior was assessed using amphetamine-induced rotations, head position bias, and locomotion.

      Rotations were performed by injecting amphetamine 30 minutes prior to trial and placing the animal in an opaque cyclinder. Ipsilateral (same side as) rotations to the 6-OHDA lesion (clockwise) were added and contralateral (opposite side as) rotations were subtracted.

      Head position bias was determined by the number of head tilts over time, where a greater than 10 degree deviation left or right from midline was measured.

      Locomotion was measured using software called Viewer that tracked motion and calculated distance.

    2. DBS can also encounter limitations as a therapy even for the symptoms that typically respond.

      Part of the ambition in this paper was identifying the contributions of different neurons in a parkinsonian brain. Using optogenetics to better understand DBS can theoretically lead to more effective therapies in the future. Read more from The Cellular Scale.

    3. Therefore, optogenetics, in principle, could be used to systematically probe specific circuit elements with defined frequencies of true excitation or inhibition in freely behaving parkinsonian rodents.

      This group has led the field of optogenetics by laying the groundwork for how this "tool" can be employed in neuroscience research.

    4. based on single-component microbial light-activated regulators of transmembrane conductance and fiber optic– and laser diode–based in vivo light delivery

      Opsins are transmembrane proteins (passing through the cell membrane) that are ion channels/pumps which allow for various ions like sodium, potassium, hydrogen, chloride, and calcium to move in or out of the cell.

      There are three main families of opsins: channelrhodopsins, halorhodopsins, and bacteriorhodopsins. Each opsin is light sensitive due to a chromophore retinal molecule within the transmembrane domain of the channel, and each family is sensitive to a specific wavelength of light.

    5. To inhibit the excitatory STN neurons directly, we delivered lentiviruses carrying eNpHR under the CaMKIIα promoter to the right STN of the hemiparkinsonian rats. CaMKIIα::eNpHR labeled with enhanced yellow fluorescent protein (EYFP) expression was specific to excitatory neurons

      Second-generation lentiviruses encoding the enhanced halorhodopsin were created using three plasmids.

      One plasmid containing the gene of interest (eNpHR) under the control of the promoter (CaMKIIα) is called the transfer vector. The transfer vector usually encodes a fluorescent gene to monitor expression: in this experiment, enhanced yellow fluorescent protein (EYFP) was added after the eNpHR sequence.

      A second plasmid containing the envelope gene, usually VSV-G (vesicular stomatitis virus), allows for a broader degree of infectivity in various cells. The third plasmid contains all of the packaging genes necessary to create a functional viral unit.

      When all three plasmids are added to HEK293 (human embryonic kidney) cells, viral particles are released from the cells and suspended in the culture media. Learn more about lentiviruses here.

    6. this would be consistent with recent findings (33) indicating that a glial-derived factor (adenosine) accumulates during DBS and plays a role in DBS-mediated attenuation of thalamic tremor.

      In 2008, Bekar et al. demonstrated that the adenosine triphosphate (ATP) byproduct, adenosine, accumulated following deep brain stimulation. Adenosine would then activate adenosine A1 receptors which in turn depressed excitatory transmission in the thalamus and reduced tremors.

    7. the direct activation of local glial cells appeared not to be sufficient to treat parkinsonian symptoms, pointing to consideration of other circuit mechanisms.

      When blue light passed through the optrode to the STN, neuronal firing was inhibited by activating ChR2-expressing astrocytes. ChR2 allowed for the influx of calcium into astrocytes, causing a release of glutamate and adenosine into the cellular environment. Adenosine would then bind to adenosine A1 receptors and inhibit neuronal firing. Even though they were able to inhibit firing, motor pathology was still unaffected by this intervention, alluding to other circuit mechanisms.

    8. Because simple inhibition of excitatory cell bodies in the STN did not affect behavioral pathology and because HFS (90 to 130 Hz) is used for electrical DBS, we used ChR2 to drive high-frequency oscillations in this range within the STN.

      Since inhibiting excitatory neurons in the STN with eNpHR and activating glial cells with ChR2 were both insufficient at correcting motor deficits in hemiparkinsonian rats, the authors attempted to mimic the high-frequency stimulation using ChR2 in the excitatory neurons.

    9. Therapeutic effects could arise from driving axonal projections that enter the STN

      In other words, beneficial effects could arise by activating or targeting axonal projections entering the STN as opposed to direct STN interventions.

    10. matter of controversy

      Check out this 2019 episode of NPR's podcast Invisibilia for more on what it's like to be a patient treated with DBS. https://www.npr.org/2019/03/28/707639854/the-remote-control-brain

    11. optogenetics allows genetically targeted photosensitization of individual circuit components

      The specificity of optogenetic treatments is of particular clinical interest and relevance for neuroscientists. Because individual cells can be targeted in the living organism, optogenetics allows scientists to better understand how different brain cells function and communicate.

    12. We have developed and employed optogenetics technology

      One of the paper authors, Karl Diesseroth, is attributed with implementing light-sensitive proteins called opsins in neurons to control their activity. He coined the term "optogenetics" to signify that neurons can be selectively targeted using genetics which in turn encodes proteins that are optically controlled.

    13. channelrhodopsins

      This family of proteins is employed to activate neurons by driving cations (including sodium, calcium, hydrogen, and potassium) into the cell and causing the membrane potential to become more positive, leading to depolarization.

    14. halorhodopsins

      Halorhodopsins and bacteriorhodopsins typically inactivate neurons by driving chloride ions into the cell or hydrogen ions out of the cell and causing the membrane potential to become more negative, leading to hyperpolarization.

    1. continental plume–related basalts

      Both ocean island basalts and continental plume-related basalts come from deep within the mantle. OIBs intruded into oceanic (basaltic) crust, whereas continental plumes intrude into continental crust (for example, Deccan traps in India).

    1. The gender gap in the learning of physics concepts was substantial in the control condition (d = 0.46) (F1,304 = 6.23, P = 0.01), indicating that men improved their FMCE scores more than women over the semester. In the affirmation condition, however, this gender learning gap entirely disappeared

      Values affirmation erased the gender gap in the Force and Motion Conceptual Evaluation (FMCE).

      Women who did not affirm values did not increase their scores on the FMCE from the first test to the second test as much as men did. However, women who did values affirmations had score increases similar to men.

  6. Apr 2020
    1. Here we report a directly documented example from its origin to reproductive isolation.

      As a well documented case of natural selection, mechanisms of evolution are clearly described among finches on the Galápagos islands. Learn more with these activities from HHMI BioInteractive. https://www.biointeractive.org/classroom-resources/natural-selection-and-evolution-darwins-finches

    2. surrogate experiment, for example with finch models and/or playback of tape-recorded song (27)

      Grant et al. did the experiment described here with a population of G. difficilis on Isla Genovesa.

      They played tape-recorded songs from several G. difficilis populations (Isla Genovesa, Isla Wolf, and Isla Darwin) and demonstrated that the finches responded strongly to their own population's song, weakly to the Isla Darwin population's song, and not at all to the Isla Wolf population's song.

    3. The low values probably represent low additive genetic variation because the traits are highly heritable in Geospizaspecies

      The authors conclude that their measurements, both genetic (inbreeding coefficient, admixture, average nucleotide diversity) and bill shape (length and depth), do show low levels of variation in the Big Bird population.

      They conclude that this is expected because the bill shape traits are highly determined by genes, and so low genetic diversity would lead to low physical diversity of certain traits, such as bill shape.

    4. The ability of finches to efficiently exploit the large woody fruits of Tribulus cistoides in dry seasons, and particularly during droughts and limited food supply, is a function of bill size, especially bill depth (12)

      By measuring bill size and recording bird mortality on Daphne Major during a drought that occurred in 2004-05, scientists were able to establish the characteristics of bills that were adaptive during this period of decreased food supply.

      The plant species mentioned is a food supply for the Big Bird lineage, so this data on bill morphology is relevant to understanding this hybrid population.

    5. We followed the survival and breeding of this individual and its descendants for six generations over the next 31 years.

      The Grants began studying finches on Daphne Major Island in 1972. Along with team members, they returned there every year until 2012 to observe the finches. Observations included identities of mating pairs, number of offspring (used to construct pedigrees) and mortality of birds (recording deaths of birds).

      The techniques used included catching the birds and banding them (installing identification bands around their legs), as well as taking measurements of the birds (including body mass and beak measurements). Blood samples were also collected for later DNA analysis.

    6. bill

      As in a bird's beak.

    1. Diamonds recovered from kimberlite pipes are less likely to have been exposed to cosmic rays,

      An elevated R/Ra ratio indicates that there has been exposure to cosmic rays in the past. This means some meteorites may have crashed onto ancient Earth and the He concentration in the rock has remained relatively undisturbed since then.

    2. Thus, our studied diamonds provide the most direct and undegassed evidence of the variation in helium isotope compositions in Earth’s transition zone.

      In the diamond fluid inclusions richest in helium-3, the <sup>3</sup>He/<sup>4</sup>He ratio is about 50 times to that of air. This considerably high isotope ratio suggests that the real age of these fluid inclusions date back to the early days of Earth's formation.

    3. Preservation of He and its isotope signatures in diamond is supported by He heterogeneities within individual diamonds

      In conducting their experiments, the research team acknowledged the inherent variability in the <sup>3</sup>He/<sup>4</sup>He ratio inside each diamond. To minimize these differences, the scientists used diamonds that were free of inclusions thereby eliminating the possibility of inconsistencies in helium ratios originating from these inclusions. Then, they crushed the diamond in a vacuum to verify that 90% of the helium is present in the groundmass of the diamond. This was then followed by step-heating the crushed diamond to measure the variability in the <sup>3</sup>He/<sup>4</sup>He ratio in the diamond.

    4. Resolving the existence and location of a long-term preserved, primordial, undegassed, high-3He/4He reservoir, and where it interacts with other reservoirs in the mantle, is key to understanding the evolution of Earth and deep mantle convection.

      The research team sought to identify an untouched, untapped chemical reservoir. To do this, they decided to examine primordial diamonds that contained both helium-4 and helium-3 isotopes.

      The helium-4 isotopes are formed from radioactive decay of trace elements and hence take a long time to form. Conversely, the helium-3 isotopes exist inside Earth from the early days of formation and there has been no new generation of helium-3 isotope since then.

  7. Feb 2020
    1. Although unexpected, a high-3He/4He source dominating the isotope ratio could explain why the R/Ra values are higher than those found for MORBs. This would be most visible in rocks that have low helium concentrations and low U-Th-Sm contents, such as recycled pelagic sediments strongly depleted in almost all their helium and U-Th during subduction

      Could use further explanation

    2. sublithospheric diamonds

      Identified by mineral inclusions consistent with being exposed to high pressures found at depths of more than 400 kilometers.

    3. [8 ± 1 R/Ra (SD)]

      What does this mean? Needs some translation

    4. Sr-Nd-Hf-Pb


    5. He-Sr-Pb


    6. compositions of basalts provide information

      Measurement of isotopic content of primitive basaltic rocks has been a useful method to understand the exact chemical composition of these old rocks. Learn more in this article from Eos explaining the importance of using these techniques. https://eos.org/features/isotope-geochemists-glimpse-earths-impenetrable-interior

    7. Isotope

      Chemical elements that have the same number of electrons and protons but a different number of neutrons are called isotopes. For example, both carbon-12 and carbon-14 have six electrons and six protons, but they have 12 and 14 neutrons, respectively. These isotopic differences change the atom's atomic mass and other chemical properties.

  8. Oct 2019
    1. Without bold new ideas and management strategies, current recycling rates will no longer be met, and ambitious goals and timelines for future recycling growth will be insurmountable.

      In response to China's plastics import ban, 187 governments have agreed to alter a pre-existing global waste treaty called the Basel Convention.

      In May 2019, all countries that have ratified the Basel Convention (notably excluding the United States) approved major plastics-related changes. These changes are set to take effect started in 2021.

      Read more from the UN Environment Programme

    2. China has increasingly implemented more rigid waste import policies, starting prior to 2010

      The Basel Convention, which governs the international waste trade, was adopted in 1989 in response to hazardous waste dumping on communities in Africa, the Caribbean, and Asia. China and the United States signed onto the Basel Convention in 1990. China ratified the treaty in 1991, while the United States has yet to ratify.

      Read more from The Conversation

    3. This operation was referred to as the “Green Fence” and highlighted the fragility of global dependence on a single importer.

      Shortly after taking office, China's new president Xi Jinping enacted the 2013 "Green Fence" policy directive aimed to lessen the contamination levels and boost the quality of imported recycled materials. Shipping containers that did not pass import inspection were rejected from entering the country.

    4. China, which has imported a cumulative 45% of plastic waste since 1992, recently implemented a new policy banning the importation of most plastic waste, begging the question of where the plastic waste will go now.

      Enacted in January 2018, China's "National Sword" policy banned 24 types of solid waste, including various plastics, and set a much tougher standard for contamination levels.

      The new policy ups the ante with a ban on plastic waste containing more than 0.5% contamination. Some view this move as an unintended consequence of single-stream recycling.

    5. the emerging markets in China in the 1990s found that the material could be used profitably

      In the 1990s, China emerged as a global manufacturing powerhouse generating a huge increase in demand for raw materials. This offered a market for products that come out at the end of the recycling process, such as the plastic pellets made from recycled materials. For example, these pellets can be turned into the soles of shoes. Read more in the Financial Times

    6. Commingled and single-stream recycling

      Refers to the collection of recyclables including glass, paper, and plastic, all in the same recycling bin.

    7. additives

      These are chemicals added in the manufacturing process that can make plastics more flexible, durable, and transparent. A notorious example of a plastic additive includes bisphenol A (BPA). In high doses, BPA has possible health effects on the brain and prostate glands of fetuses, infants, and children.

      Read more from Mayo Clinic.

    8. Management of this large increase and quantity of plastic waste has been challenging, particularly in areas of rapid economic development and population growth. Only 9% of plastic waste has been recycled globally, with the overwhelming majority of global plastic waste being landfilled or ending up contaminating the environment (80%)

      The World Bank estimates that annual waste generation will increase by 70% from 2016 to 3.4 billion MT in 2050. Over 90% of waste, including plastics, produced in low-income countries is disposed of in unregulated dumps or openly burned.

    9. solid waste management systems

      Refers to the range of garbage materials that are discarded as unwanted and useless. Landfills are often used as solid waste management systems.

    10. historic growth in production

      A chemist at Dupont named Wallace Carothers invented a synthetic polymer that became known as nylon. Nylon and other early plastics became wide spread in the late 1930s and early 1940s. During World War II, plastic production in the United States increased by 300%.

      Read more about the history of early plastic production from the American Chemical Society and the Science History Institute.

    11. metric tons (MT)

      One metric ton is equal to 1,000 kilograms or 2,204.6 pounds. One black rhinoceros weights approximately one metric ton. Source: Wikimedia

    12. However, plastic packaging for food, beverage, and tobacco items is often used only once, which has contributed to 61% of global beach litter

      The Institute for European Environmental Policy found that plastics make up 85% of beach litter worldwide, 61% of which are single-use plastics, such as those used in food packaging.

  9. Sep 2019
    1. this coincides with COF values dropping substantially, leading to a superlubric state that is maintained until the end of the simulation.

      Learn more about how the computer simulation led to the discovery of a novel superlubric combination of materials.

    2. reduced contact area that slide against the DLC surface, achieving an incommensurate contact

      With a combination of materials (graphene, nanodiamond particles, and DLC), the researchers were able to demonstrate the formation of nanoscrolls, which reduced the overall contact area between two sliding interfaces, leading to substantially decreased friction.

    1. Our study provides a potential explanation for why clinical deep brain stimulation in the ventral thalamus near the ZI can increase binge eating.

      Deep brain stimulation sometimes causes binge eating in Parkinson’s patients; now scientists might know why.

      Read more in Scientific American: https://www.scientificamerican.com/article/electric-brain-stimulation-offers-binge-eating-clue/

    2. Intraperitoneal CNO

      The CNO was injected into the peritoneum, the thin membrane that lines the walls of the abdominal cavity. It travels through the circulation system, crosses the blood-brain barrier, and affects its target cells.

    3. by using a two-chamber place preference test

      The authors hypothesized that because the ZI to PVT projection promotes intake of foods that are pleasurable to eat and also makes mice overcome their aversion to light in order to eat that food, that stimulation of this pathway is pleasurable or rewarding for the mice.

      They tested this by placing the animals in a box with two identical compartments. The mice were able to freely move around the box. On one side of the chamber the mice received stimulation of their ZI-PVT neurons, whereas the stimulation was turned off when the mice were on the other side.

    4. This is almost 100 times faster than that reported for optogenetic stimulation of the AgRP neuron soma and 500 times faster than stimulation of AgRP-PVT axon terminals (19, 20). As soon as the laser was turned off, the mice stopped eating.

      The authors wanted to compare the latency of eating onset upon stimulation of ZI projections to the PVT versus that of agRP neurons, which are known to promote food intake in response to hunger.

      They found that mice start to eat much faster than mice did in previous reports where AgRP neurons were stimulated or when agRP projections to the PVT were stimulated.

    5. optogenetic stimulation

      A technique that uses light to control the activity of cells, most commonly neurons, in living animals. The cells are genetically modified to express ion channels that are sensitive to light. Shining light on the neurons changes their activity, allowing scientists to understand the role of the neuron in a given behavior or physiological process.

    1. polymer

      Materials made of long, repeating chains of molecules. The term polymer is often used to describe plastics, which are synthetically made, but natural polymers also exist.

    2. single-use plastic food packaging (polyethylene, polypropylene, and polyethylene terephthalate)

      As the most common plastic, polyethylene is used for everything from plastic bags to bulletproof vests. Polypropylene is commonly used in chip bags, microwave dishes, and bottle caps. Some fabric textiles and many water bottles are made of polyethylene terephthalate (PET).

      Plastics are notoriously persistent pollutants. It is estimated that a PET plastic water bottle will take anywhere from 100-500 years to degrade.

    3. lower-income countries in the East Asia and Pacific for decades.

      Since China's 2018 policy went into effect, many of the "replacement countries" have also started to crack down.

      Malaysia, Thailand, and Vietnam have enacted stricter quality standards for waste coming from countries such as the US, UK, and Australia.

      Read more here: http://wastemanagementreview.com.au/battling-sovereign-risk/

    4. circular economy

      An economic system where waste and pollution are designed out, keeping products and services in closed loops or cycles. The circular economy is an alternative to a traditional linear economy in which products and materials are made, used, and disposed of.

  10. Aug 2019
    1. Depolarizing concentrations of K+

      Learn more about action potentials and membrane depolarization with Khan Academy. See also their video here.

    2. sympathetic superior cervical ganglion in adult rats

      Prior to this research, studies primarily focused only on the transmitter expression during development. Is there a similar phenomenon in adult stages? The cervical ganglia are separated by denervation technique. The denervated ganglia were measured for the activity of substance P. Two-fold increase in substance P was observed in the ganglia compared to controls.

    3. Since some trigeminal neurons are derived from the neural crest, whereas nodose neurons are epibranchial placode derivatives, heterogeneous populations, differing embryologically, geographically, and functionally, may exhibit transient catecholaminergic expression during development.

      Two types of neurons—trigeminal neurons and nodose neurons—are discussed here.

      Trigeminal neurons are derived from the neural crest. Epibranchial placodes help in the generation of the neurons found in the back of the brain/cranial nerves (or nodose). Hence, both neurons differ in embryonic origin.

      Trigeminal neurons are derived from one source and hence they are homogenous. However, the epibranchial placode helps in the generation of several cranial nerves, namely hypoglossal and glossopharyngeal. This results in a heterogenous population.

      As both sets of neurons differ in their embryonic origin and location in the brain, it is fair to state that the functions of these neurons to express catecholamines will also be different.

    4. grown in dissociated cell culture

      Neurons are separated from the animal through mechanical or enzymatic disruption. The separated neurons are transferred to a dish or culture plate. The neurons are maintained in the dish.

    5. At this early stage in our understanding,

      The field of neuroplasticity evolved and expanded since this exploratory 1984 research. While there is still ample debate on the plasticity of our brain cells in adulthood, scientists generally agree that neurons are less flexible as we age. Read more in Science. (This resource can also be found in the Related Content tab).

    6. neuronal plasticity

      Check out this video primer on neuroplasticity from Khan Academy.

  11. Jun 2019
    1. biogeochemical exchanges among Earth’s soil, water, and atmosphere.

      A 2019 study highlighted the need to update how the water cycle is taught in school to include human interference.

      Read more in Science Daily.

    1. resulting in a significant gender × condition interaction

      Interaction effects occur when the effect of one variable depends on another variable.

      In this case, the effect of the intervention (values affirmation or control) depended on the student gender (male or female).

    2. improve the performance of stereotype-threatened individuals

      Values affirmation can reduce the effect of stereotype threat for women taking a math test under laboratory conditions.

    3. lab studies show

      It has been shown that values affirmation can significantly reduce a person's physical response to a subsequent stressful situation.

      Specifically, participants that performed a values affirmation task before undergoing a stress test produced less cortisol (a hormone that is released when we are stressed) than participants who did not get the intervention.

    1. Our observations suggested, consequently, that opiate peptidergic and catecholaminergic traits may be differentially regulated in the adult medulla.

      The results described in the previous two sentences suggest that each class of transmitters are regulated differently in the adult medulla.

    2. petrosal and nodose neurons

      Brain cells in a group of nerves found at the base of the skull. The nodose and petrosal neurons are part of the vagus and glossopharyngeal nerves, respectively.

    3. methylates

      Introduces a methyl (CH<sub>3</sub>) group. Here, PNMT adds a CH<sub>3</sub> group onto norepinephrine creating epinephrine (also known as adrenaline).

    4. caudal thoracic

      Situated in the tail part of the body.

    5. Recent work with bullfrog sympathetic ganglia suggests another mechanism for alteration of site of transmitter action.

      Previously, researchers found that neurons in frog sympathetic ganglia are also depolarized by substance P, making them an appropriate model organism to study.

    1. zona incerta (ZI)

      A part of the brain.

      The function of this area is poorly understood but is thought to regulate behavior of an animal in response to internal (such as hunger) and external (such as pain) sensory cues.

    2. γ-aminobutyric acid (GABA)

      An inhibitory neurotransmitter. Neurons communicate with each other by releasing neurotransmitters. Neurons respond to inhibitory neurotransmitters by reducing their activity.

    3. Based on retrograde rabies virus and anterograde AAV tracing, ZI axonal projections to the excitatory neurons of the PVT appear more robust than those from other known regions of the brain involved in food intake, suggesting the ZI is not a minor component

      More so than any region of the brain studied so far, ZI GABA neurons and their projections promote binge-like eating behavior.

    4. type A GABA (GABAA) receptor antagonist bicuculline (Bic)

      A light-sensitive competitive agonist of GABA<sub>A</sub> receptors. It was originally isolated and identified over 40 years ago in the Dicentra cucullaria plant.

    5. Bic attenuated photostimulation-evoked feeding (Fig. 2K). That Bic did not completely block photostimulation-evoked food intake could be a diffusion limitation of Bic after application, or ZI VGAT-Cre neurons may coexpress other neurotransmitters responsible for the remaining action.

      The authors found that blocking the function of the GABA receptor (GABA<sub>A</sub> receptor) in the PVT could blunt the increase in food intake mediated by stimulation of ZI terminals in the PVT. This suggests that GABA is an important neurotransmitter underlying this effect.

      The limitations of this approach include that the authors cannot control the spread of the GABA<sub>A</sub> receptor blocker or that other neurotransmitters might be involved.

  12. May 2019
    1. Brain slice electrophysiology confirmed that optogenetic activation of PSTh glutamatergic neuron terminals in the PVT evoked strong glutamate-mediated postsynaptic excitatory currents in PVT vGlut2-GFP neurons, suggesting a functional role for PSTh glutamate neurons in the synaptic excitation of PVT glutamate neurons

      The authors confirmed that stimulation of the PSTh terminals in the PVT was able to activate PVT neurons, i.e. induce excitatory activity in the PVT cells.

      This confirms the rabies tracing result and shows that the connection between the PSTh and the PVT is functional.

    2. That the PSTh may be involved in feeding is suggested by increased c-fos expression in the PSTh during anorexia induced by amino acid deficiency

      Anorexia induced by dietary deficiency in a single indispensable amino acid was found to induce expression of c-fos—a protein known to be present in active neurons—in the PSTh.

    3. In the absence of available food, optogenetic activation of the VGATZI-PVT pathway evoked a significant preference for the chamber associated with laser stimulation compared with the control chamber

      The mice preferred to spend more time in the compartment where they received stimulation of the ZI-PVT pathway. This suggests that stimulation of the neurons is pleasurable for the animal.

    4. motivational valence

      The degree to which something is perceived as pleasurable (positive valence) or unpleasant (negative valence).

    5. To test the time course and efficiency of optogenetic activation of VGATZI-PVT inhibitory inputs to evoke feeding, we used a laser stimulation protocol of 10 s ON (20 Hz) followed by 30 s OFF for more than 20 min to study ZI axon stimulation in PVT brain slices and feeding behavior. Stimulation of ZI axons with this protocol hyperpolarized and inhibited PVT glutamatergic neurons each time the light was activated (Fig. 3A). Mice immediately started feeding for each of the 30 successive trials of ZI axon laser stimulation (Fig. 3B and movie S4). The mean latency to initiate feeding was 2.4 ± 0.6 s when we used laser stimulation of 20 Hz (Fig. 3C).

      The authors followed an optogenetic protocol by intermittently turning on the stimulation light for 10 seconds followed by 30 seconds of no stimulation. With each 10 seconds of light on, they measured how long it took for the mice to begin eating.

    6. ZI GABA neurons project to multiple brain regions, including the hypothalamus and midline thalamus (fig. S6). We therefore measured the relative contribution of stimulation of ZI somata with selective stimulation of ZI axons targeting the PVT. Stimulation of ZI VGAT cell bodies or VGATZI-PVT terminals in the PVT evoked similar levels of feeding

      This suggests that even though ZI GABA neurons project to other brain regions in addition to the PVT, the PVT projection appears to be the most important mediator of increased food intake.

      This is because ZI GABA cell body stimulation and stimulation of the projections to the PVT evoked similar degrees of food intake.

    7. Anterograde

      Occurring along the nerve processes away from the neuron body, as opposed to retrograde.

    8. Food deprivation lasting 24 hours increased inhibitory synaptic neurotransmission to PVT glutamate neurons

      In food-deprived mice, PVT glutamate neurons receive more inhibitory inputs compared to fed mice. These may come from ZI inhibitory GABA neurons, which the authors demonstrated to have increased activity upon food deprivation.

    9. confirmed that PVT glutamate neurons receive strong and direct innervation from ZI neurons

      The authors confirm their anterograde tracing findings using retrograde tracing to show that ZI GABA neurons send projections to excitatory neurons in the PVT.

    1. will stand for no amino acid—that is, will be nonsense

      As a general rule, there are four kinds of codons: codons that initiate the reading frame, codons that stop the reading frame, codons that code for amino acids to make proteins, and codons that don't code for anything at all (called nonsense codons).

    2. The experimental proof of the colinearity of a gene and the polypeptide chain it produces may be confidently expected within the next year or so.

      Crick proposed that a gene was a linear sequence of nucleotides, where each gene encoded a single protein. However, this explanation is a bit too simplistic, especially for higher-level and multicellular organisms.

      In fact, we now know that colinearity is generally the exception, not the rule, in eukaryotic genomes.

      For more information, check out this piece in Nature Education: https://www.nature.com/scitable/topicpage/what-is-a-gene-colinearity-and-transcription-430

    3. In spite of the uncertainty of many of the experimental data, there are certain codes which have been suggested in the past which we can now reject with some degree of confidence.

      Science is a way of knowing.

      Science is both a body of knowledge that represents a current understanding of natural systems and the processes used to refine, elaborate, revise, and extend this knowledge.

    4. If the code does indeed have some logical foundation, then it is legitimate to consider all the evidence, both good and bad, in any attempt to deduce it. This is not true if the codons have no simple logical connection.

      Scientific knowledge is open to revision in light of new evidence.

      Scientific argumentation is a mode of logical discourse used to clarify the strength of relationships between ideas and evidence that may result in revision of an explanation.

    5. in response to a letter of

      Science benefits when scientists communicate and collaborate across disciplines.

      Science would make little progress without the exchange of ideas, especially across different disciplines. Here George Gamow, a theoretical physicist, shares his ideas about the genetic code with Linus Pauling, one of the pioneers of quantum chemistry.


    6. Deductions

      Crick relies on deductive reasoning to make his argument for the nature of the genetic code.

      Deductive reasoning draws specific conclusions from general principles or premises, whereas inductive reasoning infers general principles from specific instances.

    7. The code is probably much the same in different organisms.

      You may have heard about this concept before, maybe even hearing that we humans share 50% of our genes with bananas!

      However, the story is a bit more complicated; in fact, genes (that is, regions coding for proteins) comprise only about 2% of our DNA. About 8% of our genes are involved in regulatory functions and the other 90% is mostly non-functional.

      Because of our shared evolutionary ancestor (approximately 1.6 billion years ago), bananas and humans have a lot in common!

    8. It is possible that some triplets may code more than one amino acid—that is, they may be ambiguous.

      While most amino acids are encoded by at least two codons (with the exception of methionine and tryptophan), the reverse is not true. Each codon specifies just one amino acid or stop signal. Thus, the genetic code is unambiguous.

    9. In general, more than one triplet codes each amino acid.

      In other words, the same amino acid is coded by more than one base triplet. For example, there are six different codon combinations to encode arginine. This property is now known as degeneracy.

    10. We’re often told that DNA is genetic information. But how exactly does DNA, a molecule, contain information? Francis Crick—who discovered the structure of DNA along with Rosalind Franklin, James Watson, and Maurice Wilkins—had the same question. In this 1963 review, Crick lays out his hypotheses and analyzes the evidence that supports a genetic code. He concludes with a wondrous inquiry: Do all living things share the same code? Do plants, bacteria, animals and humans all share the same language of life?

      BR suggestions:

      We’re often told that DNA is "genetic information." But how exactly does DNA, a molecule, contain information? Francis Crick—who discovered the structure of DNA along with Rosalind Franklin, James Watson, and Maurice Wilkins—had the same question. In this 1963 review, Crick lays out his hypotheses and analyzes the evidence that supports an organized system of information within DNA that can be converted into other information--a genetic code. He concludes with a wondrous inquiry: Do all living things share the same language of life?

    1. protospacer flanking sites (PFSs)

      The group that described targeting preferences of Cas13 suggested that PFS should be used for Cas13 instead of PAM, since PAM is used for Cas9. Additionally, PFS is different than the PAM because the PAM is used for discriminating self from non-self sequences. The PFS is not used for that as there is no concern for self targeting when targeting RNA molecules. Therefore, the PFS is just some sequence preference of Cas13.

    2. DNA base editors, consisting of a fusion between Cas9 nickase and cytidine deaminase, can mediate efficient cytidine-to-uridine conversions within a target window and substantially reduce the formation of double-strand break–induced indels

      DNA base editing is a technique which allows precise conversion of one nucleotide into another without any template sequence.

      A base editor is a fusion protein made up of a protein that recognizes specific DNA sequences (for example, Cas9), and a deaminase that can convert one amino acid to another (i.e., cytidine [C] to uridine [U] or adenosine [A] to inosine [I]).

      Because of the geometry of the proteins, this conversion can only happen in a certain range of nucleotides, called the target window.

  13. Apr 2019
    1. This prototype includes a MOF-801 layer (packing porosity of ~0.85, 5 by 5 by 0.31 cm, containing 1.34 g of activated MOF), an acrylic enclosure, and a condenser

      Since this paper was published, the authors refined and optimized the devise and tested it under desert conditions with record high efficiency.

      See "Related Content" tab for: Kim, Hyunho, et al. "Adsorption-based atmospheric water harvesting device for arid climates." Nature communications 9.1 (2018): 1191.

    1. biclustering

      A technique that identifies and clusters groups, specifically for two separate clusters.

    2. This, together with the results from Fig. 1B, suggested that although not discrete, enterotypes do indeed represent “densely populated areas in a multidimensional space of community composition,” as stated in the original publication

      The authors of this paper agree with Bork and colleagues' original proposition that enterotypes are "densely populated areas in a multidimensional space of community composition." However, they argue that these enterotypes are not discrete but rather overlapping microbial configurations.

    3. Some early-life events that are generally thought to affect adult microbiota composition were not associated with microbiota composition variation in our study, including mode of birth [cesarean section (N = 36) or vaginal delivery (N = 1036)], place of birth [home (N = 207) or hospital (N = 899); increased diversity in home-born individuals, FDR>5% when controlling for age], and infant nutrition [breastfed (N = 537) or not breastfed (N = 359)]

      Their study suggests that early-life events, such as birth method or nutrition, do not have any significant correlations with the adult microbiome.

    4. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate.

      The study found 69 dependent factors from clinical-based—that is, measurements taken by doctors—and questionnaire-based—that is, provided by the patients about their lifestyle—data. They found that for 92% of the factors that had a counterpart in an independent study (=LLDeep study), these factors were still significantly associated to variation in microbiome composition.

    5. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota

      The Human Microbiome Project launched by the U.S. National Institutes of Health was one of the first initiatives to research the impact of our microbiomes on human health and disease. This was one of the first large scale projects based on 16S rRNA sequencing and has become the basis of important database systems for current metagenomic studies. The goal of this study was to establish a core human microbiome in healthy individuals and observe how it changes during different disease states.

      The FGFP and the LLDeep projects share similar sequencing approaches and goals to the Human Genome Project, with a distinct focus on the gut microbiome and its links to lifestyle and health.

    1. polynucleotide

      Poly means many, and a nucleotide is the building block of genetic material. Therefore, a polynucleotide is a chain of many nucleotides—or one strand of genetic material.

    2. having about equal amounts of uracil and cytosine in (presumably) random order, will increase the incorporation of the amino acids phenylalanine, serine,  leucine, and proline, and possibly threonine.

      As seen in the figure below, random triplet combinations of U and C are now known to encode for the amino acid residues Crick suspected.

    1. Type VI CRISPR-Cas systems

      CRISPR is a family of DNA sequences that are part of the immune system of bacteria. CRISPR enzymes detect specific viral DNA or RNA sequences, and can cleave the invading sequences and destroy them. Recently, researchers have begun to use CRISPR as a highly accurate tool for detecting specific DNA sequences in their research.

      Type VI CRISPR-Cas systems are those that involve the protein Cas13, which can cut RNA molecules.

    2. ortholog

      Genes in different species that can be traced to a common ancestral DNA sequence.

      There are many different Cas9 and Cas13 orthologs from different bacterial organisms. As engineers, the researchers test many of them as they will have different levels of activity in mammalian cells (as compared to bacterial) and some might not work at all.

    3. nonhomologous end joining (NHEJ)

      When both strands of DNA are cut, a cell can repair the DNA by rejoining the two strands. Nonhomologous end joining is one way this repair can happen, and it does not require homologous (similar) sequences.

      Because the sequences do not have to be homologous, this process is imprecise and can result in deletions or insertions.

    4. homology-directed repair (HDR)

      A process of precise DNA editing in which a cell uses homologous (similar) sequences as a template to repair DNA.

      This method is more precise than nonhomologous end joining (NHEJ), but takes more time. It's also generally less efficient and does not operate on non-dividing cell types like neurons.

    5. catalytically inactive

      The job of enzymes is to make chemical reactions happen faster. An enzyme that is catalytically inactive does not accelerate chemical reactions.

      Cas13 catalyzes the cleavage (cutting) of RNA molecules. This is an important function of the bacterial immune system, where Cas13 helps protect the organism from invading RNA.

      To use Cas13 for RNA editing, the researchers created a catalytically inactive enzyme (dCas13) that can be used to target RNA without cutting it and allowing for recruitment of other enzymes to the RNA.

    6. Endogenous

      Native to a system (i.e. not the result of changes by external factors). Endogenous targeting here means the normal target sites for the ADAR protein in the cell.

  14. Mar 2019
    1. The key features of success of the new lineage are reproductive isolation based on learned song and morphology, transgressive segregation producing novel phenotypes, and the availability of underexploited food resources.

      Here, the authors list the main reasons that this hybrid lineage survived and reproduced rather than dying out or mating with members of the parental species.

    2. A gradual increase in homozygosity was then observed over the next five generations (Fig. 2D), as expected from the small number of breeding pairs

      The authors measured genetic diversity through the inbreeding coefficient and average nucleotide diversity, finding that the pattern of decreasing genetic diversity was as expected for an inbreeding population.

    3. the founder male (5110) was not a G. fortis x G. scandens hybrid as previously hypothesized (12), but a G. conirostris

      This conclusion of the authors is a reclassification of the founder male into a different species than previously thought, based on the genetic analysis.

    4. homoploid hybrid speciation, is rare

      This type of speciation could be rare, but as it is also hard to detect, it may be less rare than currently estimated.

    5. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

      Read more from two of the authors of this paper explaining how Darwin's finches in the Galapagos provided the basis for novel insights into genetic divergence.

      In Science: http://science.sciencemag.org/content/355/6328/910

    1. A major promise of optogenetics has been the potential for dissection of disease circuitry and treatment mechanisms.

      Learn more about the history and potential of optogenetics from Karl Deisseroth's piece in Scientific American.

    2. To probe the functional connectivity between these layer V projection neurons and STN in the PD animals, we conducted a separated-optrode experiment in anesthetized animals in which the fiber-optic and recording electrodes were placed in two different brain regions in Thy1::ChR2 animals

      Based upon previous findings that the cortex and STN are connected, the investigators wanted to know if driving M1 layer V neurons had an effect on STN neuronal firing and subsequent behavioral output. So they placed an optrode over M1 and a recording electrode in the STN.

    3. ameliorated


    4. we used Thy1::ChR2 transgenic mice (22, 23) in which ChR2 is expressed in projection neurons, and we verified that in Thy1::ChR2 line 18, ChR2-YFP is excluded from cell bodies in the STN but is abundant in afferent fibers

      Thy1 (thymocyte differentiation antigen 1) is expressed in the axonal projections of mature neurons. When its promoter is placed in control over ChR2 expression, the protein would be expressed in the projection neurons as opposed to the somata of local neurons.

    5. indeed, as expected from our light-scattering measurements and tissue geometry, we found that at least 0.7 mm3 of STN is recruited by light stimulation, which closely matched the actual volume of the STN

      Measuring the area of c-fos activated neurons upon light stimulation provided the authors with support for using an optrode to stimulate the STN since the area activated closely matched the true volume of the STN.

    6. nigral

      Referring to the substantia nigra, a part of the brain rich in dopamine neurons.

    7. The STN is a predominantly excitatory structure (30) embedded within an inhibitory network. This anatomical arrangement enables a targeting strategy for selective STN inhibition (Fig. 1B), in which enhanced NpHR (eNpHR) (21) is expressed under control of the calcium/calmodulin-dependent protein kinase IIα (CaMKIIα) promoter, which is selective for excitatory glutamatergic neurons and not inhibitory cells, fibers of passage, glia, or neighboring structures

      Since the subthalamic nucleus is excitatory, meaning the neurons within release the neurotransmitter glutamate, selectively targeting this region can be accomplished via the promoter calcium/calmodulin-dependent protein kinase II alpha (CaMKIIα). Placing a gene downstream of the CaMKIIα promoter will cause the gene to be selectively expressed only in excitatory neurons.

      The authors placed the gene sequence for halorhodopsin under the control of the CaMKIIα promoter and were able to selectively inhibit the firing of excitatory glutamatergic neurons in the subthalamic nucleus.

    8. major depression

      To learn more about deep brain stimulation as a treatment for depression, check out this 2018 article in The Atlantic.

    1. opiate peptides

      Peptides that bind to opioid receptors in the brain.

    2. de novo

      Meaning "from the new;" in this case, the first appearance of the enzyme.

    3. putative

      Generally considered or reputed to be.

    1. Focusing on the prevalent concern of BMI increase and suboptimal health, we assessed the sample size needed to evaluate microbiota compositional changes associated to obesity. To do so, we calculated the independent effect sizes of obesity status, gender, age, and BSS on microbiota variation (table S16). This allowed us to estimate that 865 lean (BMI <25) and 865 obese (BMI ≥30) volunteers would be necessary to study microbiota compositional shifts with P < 5% significance level and a power of 80%. When taking into account gender, age, and BSS score as covariates, the estimated sample size was reduced to 535

      Since there is recent concern regarding the association of BMI increase and poor health, the authors wanted to know how large a sample they would need to identify microbiota changes that could be associated with BMI. They did this by conducting a power analysis which allowed them to determine that the sample size needed to detect changes in microbiome composition associated with obesity (with a false positive score below 5% and 80% probability of detecting a real effect if it is present) is 535 samples when taking into account gender, age, and BSS score as covariates.

    2. Residence type [ranging from countryside (N = 77) over rural village (N = 500), small town (N = 272), suburb (N = 137), to city (N = 102)] during early childhood (up to 5 years old), one of the 69 FGFP microbiome covariates, was linked to adult microbial community composition, with a positive correlation between evenness and residence in more industrialized areas, though not statistically significant (FDR >5%) when correcting for age, gender, and BMI

      They found an association between the type of residence the participants lived in as a child (i.e. rural, urban) and their adult microbiota composition. Moreover, individuals that grew up in industrialized areas showed a more even microbial composition than those that grew up in rural areas—however these results were not statistically significant when correcting for age, gender, and BMI.

    3. potential niche differentiation within the colon ecosystem

      Different species may coexist in the colon differently to reduce competition and extinction in either species as several components (nutrients) will be differentially available throughout the colon with changing transit time.

    4. Dirichlet multinomial mixtures

      Refers to a computational technique to model the probability of microbial metagenomics data by representing the data as a frequency matrix of the number of times each taxa is observed in a sample.

    5. Interindividual variation in microbiota composition mainly resulted from changes in relative abundance of core taxa

      Microbiome variation between individuals was largely a result of changes in relative abundance of the core taxa.

    6. Early-life events such as birth mode were not reflected in adult microbiota composition.

      Researchers, like Bokulich and colleagues, had previously demonstrated that birth mode (i.e., vaginal, caesarian) affected the gut microbiome in adults. This study was not able to demonstrate that these differences were still present later in life.

    7. Sequencing-based assessment of microbial communities in human fecal material has linked alterations in gut microbiota composition to disease, as well as chronically suboptimal health and well-being

      Microbiome assessments can have different goals. The U.S. National Institutes of Health Human Microbiome Project (HMP) aimed to characterize the microbial communities from 300 healthy individuals across different sites on the human body; whereas, the Flemish Glut Flora Project (FGFP) targeted a general sample of the population.

      Read more: https://commonfund.nih.gov/hmp