5,156 Matching Annotations
  1. May 2023
    1. eLife assessment

      This valuable study investigates the environmental drivers behind termite construction, focusing, in particular, on pellet deposition behavior, with the conclusion that termites likely sense curvature indirectly through substrate evaporation. The findings reconcile discrepancies between previous studies through experimental and computational approaches. The strength of the evidence supporting the claims is solid, although many computational details are still missing, and the are concerns about the repeatability of the results across replicates, the dynamics of evaporation in their experiment, and the termites' ability to sense humidity.

    1. eLife assessment

      This paper describes a useful analysis tool for quantitative assessment of sarcomere structures in healthy and perturbed cardiomyocytes. The work is solid, and the methods, data and analyses broadly support the claims with only minor weaknesses. The tool will be of interest to biologists working on sarcomere structure, function and development.

    1. eLife assessment

      This useful manuscript challenges the utility of current paradigms for estimating brain-age with magnetic resonance imaging measures, but presents inadequate evidence to support the suggestion that an alternative approach focused on predicting cognition is more useful. The paper would benefit from a clearer explication of the methods and a more critical evaluation of the conceptual basis of the different models. This work will be of interest to researchers working on brain-age and related models.

    1. eLife assessment

      This study presents important findings that set a new standard for generating and maintaining monosomic yeast lines, and is the first, to our knowledge, to assess gene expression in yeast monosomies. The research offers an innovative approach to evaluate epistasis between genes on the same chromosome; however, the strength of evidence supporting the conclusions on positive epistasis for fitness is still incomplete due to the need for clarification for the exact calculation method of expected fitness without epistasis, as well as due to a lack of molecular mechanisms. Additionally, the interpretation of transcriptome results would benefit from a more comprehensive consideration of previous studies on genomic balance and the inclusion of further analyses and experiments.

    1. eLife assessment

      This valuable manuscript provides a single-cell RNA sequencing analysis of adult pig skin from different species and anatomical regions. The evidence supporting the conclusions is compelling, with identification molecular and cellular differences in pig skin, yet the analyses are incomplete in the analysis of regional- or species-based differences.

    1. eLife assessment

      This is an important study that defines cell type changes upon the expression of a mutant tau protein and put it into context of human postmortem tissue. Technically, the single cell mRNA sequencing data are convincing but the loss of neurons already at the earliest stages assessed in this model may rather suggest there are also elements of developmental toxicity.

    1. eLife assessment

      This fundamental study substantially advances our understanding of how aging and stress resilience across an organism is determined by identifying a new player in this process and uncovering its mode of action. The evidence is solid as the methods, data and analyses broadly support the claims with only minor weaknesses. The work will be of broad interest to the field of aging and protein homeostasis.

    1. eLife assessment

      Studies of prey behavior have the potential to provide insight into the chemical encoding of stress in the brain and the mechanisms by which this generates behavioral plasticity. In this important work, the authors identify a novel predation-evoked behavior in the nematode C. elegans and implicate dopamine in its implementation. While the support for some claims in the current paper is incomplete, this work provides an exciting foundation for future studies of behavioral plasticity in this powerful system.

    1. eLife assessment

      The toxin mycolactone is produced by mycobacterium ulcerans which is responsible for the Buruli ulcer. The authors performed a valuable study showing the effects of mycolactone on blood vessels integrity. This convincing data provide new therapeutic targets to accelerate healing of Buruli ulcers.

    1. eLife assessment

      This paper is of interest to neuroscientists studying the effects of sex hormones on neural and behavioral plasticity, and more specifically to researchers studying the neural mechanisms underlying birdsong plasticity. The experimental design is excellent, and the work provides a comprehensive resource for understanding the intersection between testosterone's influence on gene expression and behavior. However, the work also makes claims concerning cellular effects and gene regulatory mechanisms that extend beyond the data and under the current analyses are not rigorously supported.

    1. eLife assessment

      This study is an excellent example of how one can use high-throughput technologies to address animal evolution from a cell-type perspective. The authors present a beautiful analysis of single-nucleus RNA-seq data from three embryonic stages in a sea star; this is the first single-cell data from this large group of echinoderms and the first single-nucleus transcriptomic study in any echinoderm. The authors demonstrate the presence of unique as well as previously unnoticed homologous cell types between a sea star and a sea urchin, discovery very intriguing to echinoderm developmental biologists, which will also be of great interest to scientists in the broad fields of evolution and development.

    1. eLife assessment

      The findings of this study yield important new insights into the relationship between the number of close friends and mental health, cognition, and brain structure. Due to the large sample sizes, the evidence is solid but would have been improved if both of the analyzed datasets contained more closely matched measures. This work advances our understanding of how the friendship network relates to young adolescents' mental well-being and cognitive functioning and their underlying neural mechanisms.

    1. eLife assessment

      This potentially important work proposes a novel approach, based on co-evolution analysis, machine-learning protocols and molecular dynamics simulations, to predict structures and energetics of the main states of the alternating access cycle of a family of membrane transporters, the sugar porters. The approach is compelling, especially the application of co-evolution and Alphafold to generate highly accurate models in different conformational states of a given protein, but the work is currently incomplete due to shortcomings in the calculation of the energy landscape. With this aspect strengthened, the manuscript will be of interest to the transporter and computational modeling communities.

    1. eLife assessment

      This study presents useful structural and functional connectivity profiles of patients receiving deep brain stimulation in the posterior hypothalamus for severe and refractory aggressive behavior. The inclusion of data from multiple centers is compelling. However, the imaging analysis is incomplete and the interpretation of the findings is not solid.

    1. eLife assessment

      This study reports a joint experimental and computational investigation of the structural features of biomolecular condensates formed by a specific intrinsically disordered protein. The authors also adapt emerging rules to discuss and physico-chemical determinants of these structures of condensates. Specifically, the authors adapt the analysis of fractal structures, co-opted from the field of colloidal chemistry / physics, and generate important insights regarding the network-like organization of disordered proteins within in silico facsimiles of condensates. The usage of these analyses in the context of studying all atom models for multi-chain assemblies intended to mimic the internal organization of condensates is very interesting. The work is of relevance to cell biology and structural biology.

    1. eLife assessment

      The study of Thiery et al. details the heterogeneous expression of a very large number of genes presumably associated with cell fate decisions in the ectoderm at the neural plate border in early avian embryos. The authors mostly succeed in presenting their very complex strategy of data analysis in a clear way but the work is incomplete with some conceptual weaknesses in how the authors describe and interpret their results. By focusing on one of the earliest cell fate decisions in the ectoderm of a vertebrate embryo, this study will be valuable to a broad range of developmental biologists.

    1. eLife assessment

      This study presents a useful application of a prior model published by the authors to a new dataset. The results from this approach were interesting and solid but the conclusions that one can make from the application of the model to only one paper are limited in scope and would depend on further probing to know if the model itself has face validity as a model of ventral visual stream function.

    1. eLife assessment

      Protein and lipid homeostasis are important for maintaining cellular functions but their crosstalk remains largely unknown. This important manuscript deals with this interesting topic and applies the powerful unbiased tools of somatic cell genetics to discover evidence suggesting a link between sphingolipids/cholesterol ester metabolism and lysosomal protein aggregation. However, in our view the experimental evidence in support of the paper's stated conclusions remains incomplete and measures that (i) go beyond reliance on the ProteoStat stain as the sole metric for aggregation and proteostatic challenge, (ii) biochemically back up the results and provide plausible mechanistic insights into the connection of lysosomal lipid handling and protein aggregation are needed.

    1. eLife assessment

      This paper introduces the python software package Pynapple and a separate package of more advanced routines (Pynacollada) to the Neuroscience/Neural Engineering community. Pynapple provides a set of data objects and methods that have the potential to simplify data analysis for neural and behavioral data types. This represents a valuable contribution to the field. The evidence was judged to be incomplete due to the fact that key details were missing.

    1. eLife assessment

      This is an important paper that revises the canonical model of how olfactory sensory neurons choose which odor receptor to express. The data presented in the paper are convincing and the model proposed is provocative and likely to enable important future work.

    1. eLife assessment

      This important study combines state-of-the art proteomics and genetic manipulation of Chlamydia trachomatis to study the function of a chlamydial effector, Cdu1, with deubiquitination and acetylation activities. Solid evidence is provided to show that Cdu1 is able to protect itself and three other chlamydial effectors, which are involved in the control of chlamydial egress from host cells, from ubiquitin-mediated degradation, and that this depends on the acetylation activity of Cdu1, but not on its deubiquitination activity. This work should be of interest to microbiologists and cell biologists studying host cell-pathogen interactions.

    1. eLife assessment

      This valuable work describes a novel role of Vangl2, a core planar cell polarity protein, in mechanistically linking the inflammatory NF-kB pathway to selective autophagic protein degradation. Using solid methods, the authors also establish the functional significance of the proposed mechanism in sepsis, a biomedically important human ailment. The work may advance our understanding of NF-kB control, particularly in the context of aberrant inflammation. However, some gaps remain, and additional studies are needed to unequivocally establish the role of Vangl2 in regulating NF-kB signaling.

    1. eLife assessment

      This work presents an important methodological advance for single-molecule force spectroscopy of membrane proteins providing a new robust design of the linkage between a target single molecule and solid support. The data provide compelling evidence of the improved mechanical stability of the pulling system. Allowing more statistically reliable force measurements of biomolecules, this method may be broadly applicable in the field of single-molecule biophysics.

    1. eLife assessment

      The authors present an exciting idea about how to integrate morphogens into a gene regulatory network with the dynamics of morphogenesis and cell movement. It represents a novel methodology, but in its current form the hypotheses, data and relationships described do not provide a sufficiently compelling model to disentangle cause and effect or elucidate the impact of cell movements on differentiation dynamics the zebrafish mesoderm.

    1. eLife assessment

      This important work investigates how two distinct processes, morphological changes and synaptic plasticity, contribute to the final shape of neuronal dendrites and the spatial structure of their synaptic inputs. The modelling is solid and could be broadly applied to other similar questions. Some of the findings are a direct result of how the model is constructed, which limits the impact. The work will be of interest to neuroscientists studying dendritic development and connectivity at a single-cell level.

    1. eLife assessment

      This paper presents important findings on the hexametric structure of MCM8/9, which potentially explain its role as a DNA helicase in homologous recombination. Due to the lack of DNA in the complex and the invisibility of HROB the current data only provide an incomplete model of the function of the MCM8/9 complex. This work will be of interest to biologists studying DNA transactions.

    1. eLife assessment

      The authors present a useful analysis of different factors that are required for release of the lipid-linked morphogen Shh from cellular membranes. The evidence is currently still incomplete as experiments rely on over-expression of Shh in a single cell line and are sometimes of a correlative nature. The study confirms and extends previous findings and will be of interest to developmental biologists who work on Hedgehog signaling.

    1. eLife assessment:

      This study introduces a valuable paradigm in the filed of adipose biology field: blocking triglyceride storage in adipose tissue does not lead to lipodystrophy and impaired glucose homeostasis but instead improves metabolic health. The evidence supporting these claims are convincing, with the authors providing a comprehensive metabolic analysis. However, mechanistic studies, which are currently incomplete, would strengthen the study and its impact. Regardless, this study will be of high interest to those in the adipose tissue biology and metabolism fields.

    1. eLife assessment

      This study presents an important open-source resource for high-throughput behavioral screening. The protocols employ inexpensive, off the shelf hardware, and carry out real-time analysis of hundreds of behaving flies. Although these protocols were developed using Drosophila melanogaster, they could easily be applied to other model systems. The evidence in support of the conclusions is solid although more details on the algorithms used for phenotyping would be helpful in order to better assessing the overall robustness of the platform.

    1. Within the pantheon of types of notes there are: - paraphrasing notes, which one can use to summarize ideas for later recall and review as well as to check one's own knowledge and understanding of what an author has said. - commentary notes, which take the text and create a commentary on them, often as part of having a conversation with the text. These can be seen historically in the Midrashim tradition of commenting on Torah.

      [23:12 - 24:47]


      separately also: - productivity notes - to do lists, reminders of work to be done, often within or as part of a larger complex project

    1. eLife assessment

      This valuable work provides new insights into history-dependent biases in human perceptual decision-making. It provides compelling behavioral and MEG evidence that humans adapt their history-dependent to the correlation structure of uncertain sensory environments. Further neural data analyses would strengthen some of the findings, and the studied bias would be more accurately framed as a stimulus- or outcome-history bias than a choice-history bias because tested subjects are biased not by their previous choice, but by the previous feedback (indicating the category of the previous stimulus).

    1. eLife assessment

      This study presents valuable findings on a cleaved form of METTL3 that may play an essential role in regulating the assembly of the METTL3-METTL14-WTAP complex. The evidence supporting the claims of the authors is solid, but the model and assays can be improved. The work will be of interest to biologists working on RNA epigenetics and cancer biology.

    1. eLife assessment

      This study provides potentially important, new information about the combination of information from the two eyes in humans. The data included frequency tagging of each eye's inputs and measures reflecting both cortical (EEG) and sub-cortical processes (pupillometry). Binocular combination is of potentially general interest because it provides -in essence- a case study of how the brain combines information from different sources and through different circuits. The strength of supporting evidence appears to be solid, showing that temporal modulations are combined differently than spatial modulations, with additional differences between subcortical and cortical pathways. However, the manuscript's clarity could be improved, including by adding more convincing motivations for the approaches used.

    1. eLife assessment

      This study offers new fundamental information on a role for the sodium/potassium pump in sleep regulation. Elegant methods were used to provide compelling evidence supporting the claim. The work will be of interest to sleep researchers in zebrafish as well as in other species.

    1. eLife assessment

      Yang et al. investigate whether distinct sources of conflict are represented in a common cognitive space. The study uses an interesting task that mixes two different sources of difficulty and reports that the brain appears to represent these sources as a mixture on a continuum, in the prefrontal areas involved in resolving task difficulty. While these results are useful, they overlap with previous findings, leave open several design and logical concerns, and rely on novel statistical analyses that may require further validation, so they are currently incomplete.

    1. eLife assessment

      This is an important study demonstrating that vitamin D-bound VDR both increases SIRT1 expression and directly interacts with SIRT1 to cause auto-deacetylation on Lys610, thereby regulating activation of SIRT1 catalytic activity. The data presented to support the presented conclusions are convincing, and the findings are particularly relevant to the actions of VDR on colorectal cancer.

    1. eLife assessment

      This study presents valuable findings on a potential positive feedback loop between ZEB2 and ACSL4 that regulates lipid metabolism and breast cancer metastasis. The evidence supporting the claims of the authors is solid, but more appropriate validation for ACSL4 interacting with ZEB2 would have strengthened the study. The work will be of particular interest to colleagues working on breast cancer.

    1. eLife assessment

      This important study uses calcium imaging in mice to advance our understanding of the effect of antipsychotic drugs on neural functioning. The evidence supporting the conclusions is solid, although the statistical testing of the data may be improved. This work will be of interest to neuroscientists working on visual processing and psychosis researchers.

    1. eLife assessment

      This study will be of interest and valuable to scientists of many different subareas in the study of eukaryotic extracellular vesicles. The authors' efforts to improve the way we analyze EVs are highly appreciated and their results are convincing: they not only used appropriate and validated methodologies in line with current state-of-the-art but also presented alternatives to improve these approaches.

    1. eLife assessment

      This valuable study reports a complete in vitro system where different steps and direct interactions between different components of MHCI maturation can be monitored, hence leading to a better mechanistic understanding of MHC I maturation. The evidence supporting the findings is currently incomplete and would benefit from clarification of some key issues. This work will be of interest to immunologists and biochemists.

    1. GLOBIN

      Globin Gene Switching is a process of sequential activation and inactivation of globin genes during development. Here's how it works:

      1. Transcription factors along with epigenetic elements such as DNA methyltransferases and demethylases interact with enhancers "upstream" of the β-globin gene cluster that contact globin gene promoters.
      2. This process silences the embryonic and fetal genes.
      3. Activation of fetal globin gene repressors during development allows expression of the adult genes.
      4. Developmental factors such as RNA-binding factors and microRNAs also impact hemoglobin switching.

      β-Globin Gene Switching:

      1. An upstream super-enhancer called the β-globin locus control region (LCR) binds erythroid-specific and ubiquitous transcription factors.
      2. The LCR interacts directly with globin gene promoters.
      3. Transcription factors that silence and activate genes also interact with elements of the globin genes.
      4. Competition among the β-like genes for the LCR and autonomous silencing of the embryonic and fetal globin genes depends on transcription factors.
      5. Silencing, first of HBE and then of HBG2 and HBG1, favors the interaction of the LCR with HBB.
      6. When HBG2 or HBG1 is upregulated by rare point mutations in their promoters, expression of the linked HBB is downregulated.
      7. Deletions of the HBB promoter remove competition for the LCR, increasing the expression of HBG2, HBG1, and HBD.
      8. The transcription factors BCL11A and ZBTB7A silence the HbF genes.
      9. BCL11A binds to the HbF gene promoters, repressing them and silencing transcription; ZBTB7A binds upstream of BCL11A with similar repressive effects.
      10. Mutations in these binding sites abolish the normal silencing of the HbF genes, leading to hereditary persistence of fetal hemoglobin (HPFH).
      11. Disruption of the BCL11A regulatory elements or the binding sites for BCL11A by gene editing is a prime therapeutic target for HbF induction.

      α-Globin Gene Switching:

      1. A less complex switch takes place in the α-globin gene cluster.
      2. A regulatory locus of four elements termed R1-R4 is present within introns of the gene NPRL3 that is upstream of HBA2.
      3. A developmental switch from embryonic ζ- to adult α-globin gene expression occurs at about 6 weeks’ gestation.

      Modulation of HbF Level:

      1. Variations in three quantitative trait loci (QTL), BCL11A, MYB, and a locus linked to the HBB cluster, account for a major portion of HbF variation among normal individuals and patients with sickle cell anemia and β thalassemia.
      2. BCL11A, a zinc finger protein that represses HbF genes, binds TGACCA motifs, the most important at position –115 in the promoter of each γ-globin gene.
      3. ZBTB7A binds 85 nucleotides upstream of these BCL11A binding sites; its binding also represses γ-globin gene transcription.
      4. When binding of either BCL11A or ZBTB7A is disrupted, silencing of HBG2 and HBG1 is abrogated.
      5. The MYB gene is essential for hematopoiesis and erythroid differentiation.
      6. MYB inhibits HbF expression directly by activation of KLF1 and other repressors and indirectly through alteration
    2. GLOBIN

      Here are the major points summarizing the text on globin gene clusters and hemoglobin:

      Globin Gene Clusters:

      • Globin is encoded in two nonallelic gene clusters: β-globin gene cluster on chromosome 11 and α-globin gene cluster on chromosome 16.
      • The β-globin gene cluster contains an embryonic ε-globin gene, two fetal γ-globin genes, a major adult β-globin gene, and a minor adult δ-globin gene.
      • The α-globin gene cluster contains an embryonic ζ-globin gene and duplicated α-globin genes with identical proteins.
      • Hemoglobin production begins with embryonic hemoglobins: Gower I, Gower II, Portland I, and Portland II.
      • Fetal hemoglobin (HbF) production starts at 6-8 weeks of gestation, peaks during mid-gestation, and falls to <1% of total hemoglobin during the first 6 months of extrauterine life.
      • Adult hemoglobin A (HbA) production follows a pattern reciprocal to that of HbF.
      • Hemoglobin composition of normal adults is >95% HbA, ~1% HbF, and 2-3% HbA2.
      • Hemoglobin is subject to posttranslational modifications, the most important being the nonenzymatic glycosylation of HbA forming the adduct HbA1c.

      Hemoglobin Structure:

      • All globin polypeptides have similar but not identical primary structures. α-Globins contain 141 amino acids, and β-like globins have 146 amino acids.
      • The primary structure dictates the secondary structure of globin into α-helical sections joined by small nonhelical stretches.
      • Each globin chain folds into a tertiary conformation known as the globin fold, where charged amino acid residues face the exterior of the molecules and uncharged residues face the hydrophobic interior.
      • The iron-containing tetrapyrrole heme moiety is protected from oxidation and located between two of the helical segments; O2 loading and unloading occur when heme iron is in its reduced ferrous form.
      • Globin gene mutations affecting critical heme-binding amino acid residues allow iron to be oxidized, forming methemoglobin, which has high O2 affinity and does not release O2 in tissues.
      • Dimers of α- and non-α-globin chains reversibly assemble into tetramers, forming a quaternary structure.

      Hemoglobin Function:

      • Hemoglobin transports O2 from lungs to tissues and carbon dioxide (CO2) from tissues to lungs.
      • Hemoglobin is a nitrate reductase that releases nitric oxide (NO) from nitrite to promote vasodilation.
      • Oxygen binding is defined by the sigmoidal shape of the hemoglobin-O2 dissociation curve.
      • The P50 is a point on this curve that indicates the partial pressure of O2 where hemoglobin is half saturated.
      • The P50 is influenced by the binding of 2,3-bisphosphoglycerate, pH, and temperature.
      • The conformation of hemoglobin fully saturated with O2 is known as the R or relaxed state; desaturated hemoglobin is in the T or tense state.
      • Hemoglobin variants that decrease P50 are characterized by isolated erythrocytosis as compensation for hypoxia.
      • Variants with increased P50 sometimes are accompanied by cyanosis and anemia as hemoglobin becomes unsaturated and O2 delivery is enhanced.
      • Mutations of residues critical for heme binding, R-T transitions, or tetramer stability cause hemoglobinopathies characterized by hemolytic anemia
    1. eLife assessment

      This work aims to discover the mechanisms governing the switch between conventional DNA replication and telomeric end-replication that requires a specialized mechanism. Genetic and biochemical assays for protein modifications and interactions suggest an interplay between sumoylated PCNA and chromosome terminal capping proteins. The results address an important question that would have implications for several fields interested in genome stability questions. However, several claims, even some that form the basis of the proposed molecular models, are incompletely supported by the data.

    1. eLife assessment

      This study presents convincing evidence of the correlation between social tolerance and communicative complexity in a comparison of three macaque species. Notably, the authors use an innovative, detailed methodology for quantifying facial expressions during social interactions that provides a valuable framework for future comparative research in animal communication. These findings would be further strengthened with some conceptual clarity regarding the basis of the hypotheses being tested and the addition of an interobserver reliability test.

    1. eLife assessment

      This study provides valuable information on the biogenesis of eccDNAs during spermatogenesis, i.e., eccDNAs in spermatogenic cells are not derived from miotic recombination hotspots but represent oligonucleosomal DNA fragments from apoptotic male germ cells, whose ends are ligated through microhomology-mediated end-joining. The study is currently incomplete because the method of bioinformatics needs more details and data interpretation should take the amplification bias into consideration.

    1. Secretory

      Sure, here's a summary of the causes of secretory diarrhea presented in the text:

      Causes of secretory diarrhea:

      1. Medications: Regular ingestion of drugs and toxins, including prescription and over-the-counter medications, may produce diarrhea. Stimulant laxatives and chronic ethanol consumption may also cause secretory-type diarrhea.

      2. Bowel resection, mucosal disease, or enterocolic fistula: These conditions may result in secretory-type diarrhea because of inadequate surface for reabsorption of secreted fluids and electrolytes.

      3. Partial bowel obstruction, ostomy stricture, or fecal impaction: These may paradoxically lead to increased fecal output due to fluid hypersecretion.

      4. Hormones: Secretory diarrhea may be caused by hormones, including those released by metastatic gastrointestinal carcinoid tumors, gastrinomas, VIPomas, medullary carcinoma of the thyroid, and systemic mastocytosis.

      5. Bacterial infections: Certain bacterial infections may occasionally persist and be associated with a secretory-type diarrhea.

      6. Environmental toxins: Inadvertent ingestion of certain environmental toxins (e.g., arsenic) may lead to chronic rather than acute forms of diarrhea.

      7. Idiopathic bile acid malabsorption (BAM): Reduced negative feedback regulation of bile acid synthesis in hepatocytes by fibroblast growth factor 19 (FGF-19) produced by ileal enterocytes results in a degree of bile-acid synthesis that exceeds the normal capacity for ileal reabsorption, producing BAD. An alternative cause of BAD is a genetic variation in the receptor proteins (β-klotho and fibroblast growth factor 4) on the hepatocyte that normally mediate the effect of FGF-19.

      8. Colonic transit: Genetic variation in the bile acid receptor (TGR5) in the colon may result in accelerated colonic transit.

      It's worth noting that some of these causes may overlap or occur in conjunction with each other.

    2. The

      Points:

      The cornerstone of diagnosis in those suspected of severe acute infectious diarrhea is microbiologic analysis of the stool.

      Workup includes cultures for bacterial and viral pathogens; direct inspection for ova and parasites; and immunoassays for certain bacterial toxins (C. difficile), viral antigens (rotavirus), and protozoal antigens (Giardia, E. histolytica).

      Clinical and epidemiologic associations may assist in focusing the evaluation.

      If a particular pathogen or set of possible pathogens is implicated, either the whole panel of routine studies may not be necessary or, in some instances, special cultures may be appropriate.

      Molecular diagnosis of pathogens in stool can be made by identification of unique DNA sequences, and evolving microarray technologies have led to more rapid, sensitive, specific, and cost-effective diagnosis.

      Persistent diarrhea is commonly due to Giardia, but additional causative organisms that should be considered include C. difficile, E. histolytica, Cryptosporidium, Campylobacter, and others.

      Flexible sigmoidoscopy with biopsies and upper endoscopy with duodenal aspirates and biopsies may be indicated if stool studies are unrevealing.

      Structural examination by sigmoidoscopy, colonoscopy, or abdominal computed tomography (CT) scanning may be appropriate in patients with uncharacterized persistent diarrhea to exclude IBD or as an initial approach in patients with suspected noninfectious acute diarrhea.

      Fluid and electrolyte replacement are of central importance to all forms of acute diarrhea.

      Oral sugar-electrolyte solutions (iso-osmolar sport drinks or designed formulations) should be instituted promptly with severe diarrhea to limit dehydration, which is the major cause of death.

      Profoundly dehydrated patients, especially infants and the elderly, require IV rehydration.

      In moderately severe nonfebrile and nonbloody diarrhea, antimotility and antisecretory agents such as loperamide can be useful adjuncts to control symptoms.

      Such agents should be avoided with febrile dysentery, which may be prolonged by them, and should be used with caution with drugs that increase levels due to cardiotoxicity.

      Bismuth subsalicylate may reduce symptoms of vomiting and diarrhea but should not be used to treat immunocompromised patients or those with renal impairment because of the risk of bismuth encephalopathy.

      Judicious use of antibiotics is appropriate in selected instances of acute diarrhea and may reduce its severity and duration.

      Many physicians treat moderately to severely ill patients with febrile dysentery empirically without diagnostic evaluation using a quinolone, such as ciprofloxacin (500 mg bid for 3–5 d).

      Empirical treatment can also be considered for suspected giardiasis with metronidazole (250 mg qid for 7 d).

      Selection of antibiotics and dosage regimens are otherwise dictated by specific pathogens, geographic patterns of resistance, and conditions found.

      Newer agents such as nitazoxanide may be required for Giardia and Cryptosporidium infections because of resistance to first-line treatments.

      Antibiotic coverage is indicated, whether or not a causative organism is discovered, in patients who are immunocompromised, have mechanical heart valves or recent vascular grafts, or are elderly.

      Bismuth subsalicylate may reduce the frequency of traveler’s diarrhea.

      Antibiotic prophylaxis is only indicated for certain patients traveling to high-risk countries in whom the likelihood or seriousness of acquired diarrhea would be especially high.

      Use of ciprofloxacin, azithromycin, or rifaximin may reduce bacterial diarrhea in such travelers by 90%, though rifaximin is not suitable for invasive disease but rather as treatment for uncomplicated traveler’s

    3. Infectious

      Sure, here are some additional sub points for each category of infectious agents:

      1. Travelers:
      2. Enterotoxigenic E. coli (ETEC) and enteroaggregative E. coli (EAEC)
      3. Campylobacter
      4. Shigella
      5. Aeromonas
      6. Norovirus
      7. Coronavirus
      8. Salmonella
      9. Vibrio cholerae

      10. Consumers of certain foods:

      11. Salmonella (from chicken, eggs)
      12. Campylobacter (from undercooked hamburger)
      13. Shigella (from undercooked pork)
      14. Enterohemorrhagic E. coli (EHEC) O157:H7 (from undercooked hamburger)
      15. Bacillus cereus (from fried rice or other reheated food)
      16. Staphylococcus aureus (from mayonnaise or creams)
      17. Listeria monocytogenes (from fresh or frozen uncooked foods, mushrooms, or dairy products)
      18. Vibrio species (from seafood, especially if raw)

      19. Immunodeficient persons:

      20. Mycobacterium species
      21. Cytomegalovirus
      22. Adenovirus
      23. Herpes simplex virus
      24. Cryptosporidium
      25. Isospora belli
      26. Microsporidia
      27. Blastocystis hominis
      28. Neisseria gonorrhoeae
      29. Treponema pallidum
      30. Chlamydia

      31. Daycare attendees and their family members:

      32. Shigella
      33. Giardia
      34. Cryptosporidium
      35. Rotavirus
      36. Adenovirus
      37. Norovirus

      38. Institutionalized persons:

      39. Clostridioides difficile (C. difficile)
      40. Norovirus
      41. Rotavirus
      42. Adenovirus
      43. Salmonella
      44. Shigella
      45. Campylobacter
      46. Vibrio cholerae

      Additionally, some infectious agents may cause specific clinical features: - Small-bowel hypersecretion: preformed bacterial toxins, enterotoxin-producing bacteria, and enteroadherent pathogens (resulting in profuse, watery diarrhea) - Marked vomiting and minimal or no fever: preformed bacterial toxins and enterotoxin-producing bacteria - Abdominal cramping or bloating, higher fever: enteroadherent pathogens - High fever and abdominal pain: cytotoxin-producing and invasive microorganisms - Bloody diarrhea (dysentery): invasive bacteria and Entamoeba histolytica - Severe abdominal pain with tenderness mimicking acute appendicitis: Yersinia invades the terminal ileal and proximal colon mucosa

    1. Other

      Here's a simplified list of causes of different types of gastrointestinal symptoms:

      1. Heartburn: Opportunistic fungal or viral esophageal infections, GERD, hiatal hernia, peptic ulcer disease, and gastritis.

      2. Odynophagia (painful swallowing): Opportunistic fungal or viral esophageal infections.

      3. Upper abdominal pain: Biliary colic, pancreatic disease (chronic pancreatitis, malignancy), hepatocellular carcinoma, Ménétrier’s disease, infiltrative diseases (sarcoidosis, mastocytosis, eosinophilic gastroenteritis), mesenteric ischemia, thyroid and parathyroid disease, and abdominal wall strain.

      4. Nausea and vomiting: Gastroparesis, viral or bacterial gastroenteritis, chemotherapy-induced nausea and vomiting, motion sickness, and vestibular disorders.

      5. Gas, bloating, and discomfort: Intestinal lactase deficiency, intolerance of other carbohydrates (e.g., fructose, sorbitol), and small-intestinal bacterial overgrowth.

      6. Dyspepsia (indigestion): Peptic ulcer disease, gastritis, GERD, celiac disease, nonceliac gluten sensitivity, pancreatic disease (chronic pancreatitis, malignancy), hepatocellular carcinoma, Ménétrier’s disease, infiltrative diseases (sarcoidosis, mastocytosis, eosinophilic gastroenteritis), mesenteric ischemia, thyroid and parathyroid disease, and abdominal wall strain.

      7. Other causes of indigestion: Congestive heart failure and tuberculosis.

    2. Intraperitoneal

      Sure, here are some variants and examples of the conditions mentioned in the text:

      Intraperitoneal Disorders: - Ulcers: peptic ulcers, stress ulcers - Malignancy: stomach cancer, colon cancer - Benign or malignant tumors: intestinal tumors, colon polyps - Inflammatory diseases: Crohn's disease, ulcerative colitis - Superior mesenteric artery syndrome: Wilkie's syndrome - Median arcuate ligament syndrome: Dunbar syndrome - Biliary colic: gallstones, cholecystitis - Enteric infectious causes: norovirus gastroenteritis, bacterial food poisoning (e.g. Staphylococcus aureus, Bacillus cereus), cytomegalovirus enteritis

      Gut sensorimotor dysfunction: - Gastroparesis: diabetic gastroparesis, idiopathic gastroparesis, postsurgical gastroparesis - Intestinal pseudoobstruction: Ogilvie's syndrome, chronic idiopathic intestinal pseudoobstruction, secondary pseudoobstruction (e.g. from scleroderma, amyloidosis, small-cell lung carcinoma) - Gastroesophageal reflux: GERD - Irritable bowel syndrome: IBS - Chronic constipation: functional constipation, slow-transit constipation

      Other functional gastroduodenal disorders: - Chronic nausea vomiting syndrome: functional nausea vomiting disorder - Cyclic vomiting syndrome: CVS - Cannabinoid hyperemesis syndrome: CHS - Rumination syndrome: regurgitation disorder

      Extraperitoneal Disorders: - Myocardial infarction: heart attack - Congestive heart failure: CHF - Postoperative emesis: postoperative nausea and vomiting (PONV) - Increased intracranial pressure: intracranial hypertension, pseudotumor cerebri - Anorexia nervosa: restrictive eating disorder - Bulimia nervosa: binge-eating disorder

      Medications and Metabolic Disorders: - Analgesics: opioids, nonsteroidal anti-inflammatory drugs (NSAIDs) - Antibiotics: macrolides, fluoroquinolones, tetracyclines - Cardiac antiarrhythmics: amiodarone - Antihypertensives: calcium channel blockers, ACE inhibitors, beta blockers - Oral hypoglycemics: sulfonylureas, meglitinides - Antidepressants: selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), tricyclic antidepressants (TCAs) - Smoking cessation drugs: varenicline, nicotine replacement therapy (NRT) - Contraceptives: combined oral contraceptives (COCs), progestin-only contraceptives (POCs) - Cancer chemotherapy: cisplatin, carboplatin, paclitaxel, docetaxel, doxorubicin - Metabolic disorders: pregnancy (nausea of pregnancy, hyperemesis gravidarum), uremia, diabetic ketoacidosis, Addison's disease, hypoparathyroidism, hyperthyroidism, hypothyroidism - Circulating toxins: fulminant liver failure, enteric bacterial infections (e.g. Salmonella, Shigella, Escherichia coli), ethanol intoxication.

    3. MECHANISMS

      Start | |---Brainstem nuclei (including the nucleus tractus solitarius; dorsal vagal and phrenic nuclei; medullary nuclei regulating respiration; and nuclei that control pharyngeal, facial, and tongue movements) | |---Coordinate initiation of emesis | |---Neurokinin NK1 pathway | |---Serotonin 5-HT3 pathway | |---Endocannabinoid pathway | |---Vasopressin pathway | |---Activators of emesis | |---Emetic stimuli act at several sites | | | |---Unpleasant thoughts or smells (brain) | | | |---Motion sickness and inner ear disorders (labyrinthine pathways) | | | |---Gastric irritants and cytotoxic agents (gastroduodenal vagal afferent nerves) | | | |---Nongastric afferents (bowel obstruction and mesenteric ischemia) | | | |---Bloodborne stimuli (area postrema) | |---Neurotransmitters mediating vomiting are selective for different sites | |---Vestibular muscarinic M1 and histaminergic H1 receptors (labyrinthine disorders) | |---5-HT3 receptors (vagal afferent stimuli) | |---5-HT3, M1, H1, and dopamine D2 subtypes (area postrema) | |---NK1 receptors in the CNS (nausea and vomiting) | |---Cannabinoid CB1 pathways (cerebral cortex and brainstem) | |---Somatic and visceral muscles respond stereotypically during emesis | |---Inspiratory thoracic and abdominal wall muscles contract | |---Distally migrating gut contractions are abolished | |---Orally propagating spikes evoke retrograde contractions to facilitate expulsion of gut contents | |---Therapies for vomiting act on receptor-mediated pathways End

    4. ausea is the feeling of a need to vomit. Vomiting (emesis) is the oral expulsion of gastrointestinal contents resulting from gut and thoracoabdominal wall contractions. Vomiting is contrasted with regurgitation, the effortless passage of gastric contents into the mouth. Rumination is the repeated regurgitation of food residue, which may be rechewed and reswallowed. In contrast to emesis, these phenomena exhibit volitional control. Indigestion encompasses a range of complaints including nausea, vomiting, heartburn, regurgitation, and dyspepsia (symptoms thought to originate in the gastroduodenal region). Some individuals with dyspepsia experience postprandial fullness, early satiety (inability to complete a meal due to premature fullness), bloating, eructation (belching), and anorexia. Others report predominantly epigastric burning or pain. Nausea, vomiting, and dyspepsia have been correlated with a condition now called avoidant/restrictive food intake disorder.
      • Nausea: the sensation or feeling of an urge to vomit.
      • Vomiting (emesis): the act of expelling the contents of the stomach through the mouth due to the contraction of the gastrointestinal and thoracoabdominal muscles.
      • Regurgitation: the effortless movement of food or liquid from the stomach back into the mouth without the forceful contractions seen in vomiting.
      • Rumination: the repeated regurgitation of food residue, which may be rechewed and reswallowed voluntarily.
      • Indigestion: a collection of symptoms that includes nausea, vomiting, heartburn, regurgitation, and dyspepsia. Dyspepsia is a group of symptoms that originate in the gastroduodenal region and include postprandial fullness, early satiety, bloating, eructation, and anorexia. Epigastric burning or pain may also be present.
      • Avoidant/restrictive food intake disorder: a condition in which individuals have difficulty consuming certain types of food or food in general, leading to weight loss or nutritional deficiencies. Nausea, vomiting, and dyspepsia have been associated with this disorder.
    1. Oral

      summary Oropharyngeal Dysphagia: - Poor bolus formation and control, drooling, and difficulty initiating swallowing are characteristic signs. - May result in premature spillage of food into the hypopharynx, aspiration into the trachea, or regurgitation into the nasal cavity. - Causes include neurologic, muscular, structural, iatrogenic, infectious, and metabolic factors, with iatrogenic, neurologic, and structural pathologies being the most common. - Iatrogenic causes include head and neck cancer treatments such as surgery and radiation. - Neurogenic dysphagia resulting from cerebrovascular accidents, Parkinson’s disease, and amyotrophic lateral sclerosis is a major cause of morbidity related to aspiration and malnutrition. - Asymmetry in the cortical representation of the pharynx provides an explanation for the dysphagia that occurs as a consequence of unilateral cortical cerebrovascular accidents. - Structural lesions causing dysphagia include Zenker’s diverticulum, cricopharyngeal bar, and neoplasia. - Rapid-sequence fluoroscopy is necessary to evaluate for functional abnormalities. - Adequate fluoroscopic examination requires that the patient be conscious and cooperative. - Timing and integrity of pharyngeal contraction and opening of the UES with a swallow are analyzed to assess both aspiration risk and the potential for swallow therapy. - Structural abnormalities of the oropharynx should be assessed by direct laryngoscopic examination.

      Esophageal Dysphagia: - The adult esophagus measures 18-26 cm in length and is anatomically divided into the cervical esophagus and the thoracic esophagus. - Solid food dysphagia becomes common when the lumen is narrowed to <13 mm. - The most common structural causes of dysphagia are Schatzki’s rings, eosinophilic esophagitis, and peptic strictures. - Propulsive disorders leading to esophageal dysphagia result from abnormalities of peristalsis and/or deglutitive inhibition, potentially affecting the cervical or thoracic esophagus. - Rapid-sequence fluoroscopy is necessary to evaluate for functional abnormalities. - Adequate fluoroscopic examination requires that the patient be conscious and cooperative. - High-resolution manometry is used to measure pressure changes along the length of the esophagus during swallowing. - Structural abnormalities of the esophagus should be assessed by endoscopic examination.

      Here's a table summarizing the information:

      | Category | Oropharyngeal Dysphagia | Esophageal Dysphagia | | --- | --- | --- | | Signs and Symptoms | Poor bolus formation and control, drooling, difficulty initiating swallowing | Solid food dysphagia, potentially accompanied by altered esophageal sensation, reduced distensibility, or motor dysfunction | | Causes | Neurologic, muscular, structural, iatrogenic, infectious, metabolic | Structural causes include Schatzki’s rings, eosinophilic esophagitis, and peptic strictures; propulsive disorders due to abnormalities of peristalsis and/or deglutitive inhibition | | Iatrogenic Causes | Head and neck cancer treatments such as surgery and radiation | N/A | | Diagnosis | Rapid-sequence fluoroscopy, direct laryngoscopic examination | Rapid-sequence fluoroscopy, high-resolution manometry, endoscopic examination |

    1. iron-bearing transferrin interacts with its receptor
      1. Iron is transported in the blood by the iron-transferrin complex.
      2. The complex interacts with specific transferrin receptors on the surface of cells that express transferrin receptors, such as developing erythroblast cells.
      3. The iron-bearing transferrin is internalized via clathrin-coated pits and transported to an acidic endosome.
      4. Iron is released from the transferrin at the low pH of the endosome.
      5. Iron is made available for heme synthesis.
      6. The transferrin-receptor complex is recycled to the surface of the cell.
      7. The bulk of the transferrin is released back into circulation, and the transferrin receptor re-anchors into the cell membrane.
      8. Iron in excess of the amount needed for hemoglobin synthesis binds to a storage protein, apoferritin, forming ferritin.
      9. Senescent red cells are recognized by the cells of the reticuloendothelial system and undergo phagocytosis.
      10. Hemoglobin is broken down, and the iron is shuttled back to the surface of the RE cell.
      11. Iron is presented to circulating transferrin via the iron export channel, ferroportin.
      12. Iron is then available for reutilization for hemoglobin synthesis
    1. eLife assessment

      This work explores how centrosomes, which function as the primary microtubule organizing center in animal cells, regulate cell division by examining the process in cells in which centrosome formation has been inhibited. The carefully conducted experiments provide convincing support for the important observation that elongated, but successful, mitosis observed in cells lacking centrosomes is due to delays in cell cycle progression, though the reviewers highlight some caveats that merit further discussion.

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      This valuable work fills a gap in the mapping of gene expression patterns in the early embryo of C. elegans. The presented data are solid and provides a resource for future analysis. The manuscript can still be improved in order to strengthen some of the conclusions made.

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      In this important study, the authors provide convincing evidence that current DNA-based microbial genomics for skin bacteria cannot always detect the source of sequenced DNA and whether it originated from viable or non-viable bacteria. Additionally, the authors demonstrated in humans and mice that most of the viable bacteria reside inside hair follicles rather than the surface of the skin per se. Overall, the work has significance beyond a single discipline and will be of interest to those studying microbiomes.

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      In its current form, the reviewers felt that the work describing the use of a CycleGAN for alignment of neural activity from a neural interface across sessions was useful, with solid evidence showing that it improved performance over similar-concept previous approaches.

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      Protein abundance is the result of many layers of regulation, including at the levels of transcription, mRNA stability, translation and protein degradation. Many transcripts contain short upstream ORFs (uORFS), but their effects on the translation of the main ORFs are difficult to predict as they are sometimes negative, positive and of different magnitudes. Here, the authors identify features of uORFs using massively parallel reporter assays, and these features help predict uORF effects on translation of main ORFs. The results will be an important resource for the community of researchers using this model organism and for the molecular and cell biology community in general as they allow to better understand how genes are regulated. There are also areas in which the authors' claims or conclusions are not fully justified and require either additional statistical analysis or new experimentation.

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      Early life stress can have profound effects on animal behavior, including potential influences on individuality. In this valuable work, the authors use a rich new dataset to solidly demonstrate that the behavioral consequences of early life stress in C. elegans can be buffered by neuromodulators previously implicated in patterns of individuality. While much remains to be learned about the mechanisms by which stress might influence individuality, these studies provide an important entry point that will be of interest to neurobiologists studying interactions between behavior, neuromodulation, stress, and individuality.

    1. eLife Assessment:

      In addition to identifying several components regulated by checkpoint kinases, the authors identify a novel non-canonical activation mode for the central checkpoint kinase Rad53, a phosphorylation event that does not depend on Mec1 and instead depends on proteins involved in retrograde signaling through Rtg3. The study thus reveals unanticipated complexities in the DNA replication stress response. Overall, the work is well done and the data support the main conclusions.

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  2. Apr 2023
    1. To summarize what I have read here (correct me if I am wrong) @mayhewluke described some real drawbacks of how derivations are currently implemented: Derivations cannot use a specific version of a package. Derivations are limited to a very small subset of real versions for dependencies.

      This entire comment is gold

    1. eLife assessment

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    1. eLife assessment

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    1. What, then, are we to do? How can we transform a disorganized group into one that is organized enough to take on a collective obligation to prevent harm? A promising solution here might be to revisit the place of individual moral agents in ascribing forward looking collective responsibility in cases where a group is not yet organized enough to be ascribed such responsibility. In particular, we might want to ask how, if at all, individual moral agents might be motivated and even obligated to create the kind of organized collective that is needed here.
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      This important study identifies more than 1500 genes that are differentially transcribed over the cell cycle of the single-celled eukaryotic pathogen, Trypanosoma brucei. Analysis of the two major developmental stages of these pathogens suggests that a core set of genes are similarly regulated in both stages, while many cell cycle-related changes in gene expression were unique to one stage. Intriguingly, the levels of far fewer proteins are differentially regulated over the trypanosome cell cycle, indicating that protein levels are primarily regulated by post-transcriptional processes. The study represents a significant technical advance in analyzing gene expression at the single-cell level in unfractionated trypanosome cultures.

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    1. eLife assessment

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      This study provides a clearly presented and thoughtfully analyzed single cell-resolution dataset of gene expression in wildtype and mutant zebrafish skin. These data are used by the authors to develop and test hypotheses about cell lineage relationships and signaling interactions between cell types in the skin, allowing them to identify roles for several signaling pathways and the hypodermis in scale and pigment cell development. The reviewers have suggestions for clarifications and acknowledging caveats to some experiments, but overall assess the significance of the manuscript to be fundamental and the quality of the data compelling.

    1. eLife assessment

      This study presents valuable findings on the changes of immune cell populations and stromal cells occurring at the CNS borders in a neonatal bacterial meningitis model, focusing on fibroblasts, macrophages and endothelial cells. The study provides solid snRNA-seq dataset and high quality immune fluorescence images of dissected brain border regions, that will be useful for the community. These observations and datasets will be of interest to the neuro-immunology community.

    1. eLife assessment

      This study represents a valuable body of work in which the authors assemble a molecular description of colorectal cancer and classification into subtypes. Overall, the evidence supporting the findings is solid and could be improved with more detail. Consensus over a diverse range of data from publicly available sources is convincing. When added to existing knowledge this work may contribute to future biomarker discoveries for colorectal cancer.

    1. eLife assessment

      This important study advances our understanding of the metabolic and hemodynamic underpinnings of different brain networks. The evidence is convincing, drawn from multiple datasets and including simultaneous fMRI and PET, although the authors should make clear which claims are supported by their evidence and which are speculation based on the literature. The study will be of interest to neuroscientists and researchers who use functional neuroimaging tools to study brain activity.

    1. eLife assessment

      This study presents useful information on the environmental and epigenomic associations of obesity in children and adolescents. The data were collected and analyzed using a solid and validated methodology and can be referenced at the clinics and health authorities to make a guideline and a policy strategy.

    1. eLife assessment

      This manuscript presents an exciting set of experiments on the mechanisms through which PSD proteins induce actin bundle formation. The work included deep mechanistic analyses which determine the necessity of upper vs. lower levels of PSD proteins for actin bundle formation, identify the domains and interactions of these proteins that are necessary and sufficient to induce actin bundles, and provide a first assessment in neurons of potential roles of the newly discovered mechanisms.

    1. eLife assessment

      This paper presents a valuable cross-validation study of mesoscopic measurements of axonal orientations from three different modalities: x-ray tomography, scattered light imaging, and diffusion MRI. The authors show convincing similarities and differences in fibre orientations from all three methods over partial ex vivo brain samples, though as only a single diffusion method is investigated, there is inadequate evidence to support conclusions about diffusion MRI reconstruction methods in general. As a first example of work comparing these three modalities, it is of interest to researchers who want to apply x-ray tomography or scattered light imaging to image the white matter ex vivo or use these methods for future validation of diffusion MRI methods.

    1. eLife assessment

      This study has important implications for the impact of sexual conflict on population viability under different temperatures. The authors propose that male harm to females in sexual conflict can be reduced as a function of temperature within the optimal reproductive range of a species. The evidence for this proposal is currently incomplete because there is methodological detail that needs to be further clarified. The results could have implications for the likelihood of the evolutionary rescue of species facing the climate crisis.

    1. eLife assessment

      The authors use computational modeling of the mammalian visual system to address an important and understudied problem: how precise temporal properties of synaptic transmission might impact the kinds of neuronal correlations that instruct development. The present description of the simulations provides mixed evidence for the authors' conclusions. That slow NMDA currents help to minimize rapid timescale correlations is compelling, but other aspects of the simulations, such as neuronal heterogeneity may also contribute.

    1. eLife assessment

      In this important study, the authors generate and analyse single-cell datasets for the human parasitic nematode Brugia malayi. The new resource has the potential to uncover new details of the biology of secretory systems in this filarial nematode but the main claims are only partially supported and strengthening them would require additional experimental support and new analyses. With the methodological part strengthened, the new resource would be of broad interest to parasitologists and nematode biologists and would have the potential to accelerate research in the search of new anthelmintics and vaccines.

    1. eLife assessment

      We believe this study has the potential to be fundamental for the field of microbial communication and compelling evidence with the chance of changing the current state-of-the-art in this area has been presented. This is will be of natural interest to the field of parasitology, but scientists in the general area of cell-to-cell communication will certainly benefit from this contribution too. A major strength of this manuscript is the clear demonstration of the role of cytoneme-like structures and extracellular vesicles in parasite communication using the Trichomonas vaginalis model. Given the potential of these findings, the authors could deepen their discussion and perspectives for other areas.

    1. eLife assessment

      This study reports a cutting-edge set of experiments examining evolutionary models of paralog function differentiation for the mammalian ribosomal proteins eS27 and eS27L. No differentiated roles were identified for either paralog, but the paralogs are differentially expressed, and they preferentially associate with different transcript classes. Reciprocal switching of their coding sequences yielded no detectable phenotypes, but loss of either paralog resulted in lethality at different developmental stages, suggesting that subfunctionalized expression patterns underlie the retention of these paralogs. The work will be of interest to colleagues studying the evolution and diversification of ribosomes.

    1. eLife assessment

      The authors show that tunneling nanotubes or TNTs are used by cells to transfer full-length mRNAs. The data show that as much as 1% of the endogenous mRNA are passed between cells by this procedure. The transferred mRNA affect the transcriptome of the acceptor cells thus highlighting the significance of this nanotube mediated trafficking of mRNA between cells. We appreciate the difficulty of this exercise. The strength of the presented evidence could be questioned based on technical limitations.

    1. eLife assessment

      After mating, animals show a repertoire of behavioural changes. In flies, this includes an increase in egg-laying, salt, and food (particularly protein) consumption, and a concomitant decrease in sexual receptivity. This valuable study compellingly shows that flies also have an increased sugar appetite and they identify the central brain circuitry that controls this increase in the mated condition.

    1. eLife assessment

      The large genetic association studies conducted in East Africa have shown that the Dantu blood group provides substantial protection against severe malaria since it increases the surface tension of red blood cells making it harder for malaria parasites to invade. In this important work, the authors show that parasite growth is indeed restricted in vivo by testing this hypothesis in adult Kenyan volunteers infected with P. falciparium under careful monitoring. They were able to show convincingly that indeed, parasite growth was reduced amongst Dantu adults.

    1. eLife assessment

      Seelbinder et al. describe a new method for perturbing chromatin in living cells by local heating. Employing this approach, the authors uncover interesting behaviors that underscore the variability in the mechanical response of subnuclear domains and structures. The study is timely, and if some conceptual and technical aspects are improved, it should be of broad interest to both the cell biophysics and cell biology communities, in particular since the method can also be applied to study mechanical relationships of subcellular compartments in other cellular and multicellular systems.

    1. eLife assessment

      This study presents a useful inventory of chromatin modifications and genes that are up- and down-regulated during cerebellar development in vivo and in primary culture. The main claims were incomplete and would benefit from further analysis and/or additional experiments. The work will be of interest to biologists working on brain development.

    1. eLife assessment

      This study presents important findings regarding the quantification of dynamics in fish communities in changing ecosystems by combining a large-scale environmental DNA metabarcoding time series with novel statistical approaches. The methods are convincing, with controlled experiments, thorough statistical analyses, and a substantial dataset covering two years of detailed observation, which can provide sufficient power to detect fine-scale ecological interactions. This work is relevant for informing future research on assessing community stability under climate change.

    1. eLife assessment

      The authors use a combination of structural and MD simulation approaches to characterize phospholipid interactions with the pentameric ligand-gated ion channel, GLIC. The general agreement between structures and simulations increases confidence in the description of the lipid interaction poses, and provides a solid basis for the prediction of a state dependent interaction site where lipids could dynamically modulate channel gating. The results will be very useful to understand the nature of phospholipid interactions with pentameric ligand-gated ion channels, although the functional or structural significance of these lipid interactions remains unclear.

    1. eLife assessment

      This interesting study builds on previous work by the PI implicating Greatwall/MASTLKinase in recovery from DNA damage in cultured human cells. This study identifies a ubiquitin ligase that may regulate the stability of Greatwall/MASTL protein stability, and the authors propose that this constitutes a molecular "timer" that controls recovery from DNA damage. Should this be validated it would be an important advance for the field, but the data presented are currently incomplete and do not yet fully support this claim.

    1. eLife assessment

      The authors have uncovered a new target that may be exploited to selectively kill BRCA2 mutant cancer cells. Strengths of the study include the novel pathway uncovered (ROCK kinases) and the strong data in support of the findings. Weaknesses include limited detail regarding the mechanism of BRCA2-specific cell death by ROCK kinase inhibitors, limited information on why some ROCK kinase inhibitors are not effective, as well as whether the cell killing in BRCA2 wild-type cells by ROCK kinase inhibitors is the same mechanism but just attenuated. The work will be of interest to cancer biologists and colleagues studying kinases.

    1. eLife assessment

      This manuscript is of interest to readers in the field of neural development. The study is important as it examines two mutations within a homeodomain transcription factor called Cone-Rod Homeobox (CRX) that cause retinopathy in humans. The data are solid, and the work contributes to our understanding of the underlying pathogenetic mechanisms.

    1. eLife assessment

      This study combines experiments in developing embryos and embryo extracts to investigate a fundamental relationship in biology - how the size of mitotic chromosomes scales with changes in cell size during development. By combining the unique tools available in the Xenopus system with modern genomic approaches, the authors convincingly demonstrate that mitotic chromosome scaling is mediated by differential loading of maternal chromatin remodeling factors during interphase. Although it remains unclear exactly how these factors impact chromosome size, the findings reported here will be of broad interest to the cell biology community and are likely to spawn new avenues of experimental inquiry aimed at understanding intracellular scaling relationships.

    1. eLife assessment

      This study provides important estimates from international cancer screening data repository about the impact of the COVID-pandemic related disruptions on cancer screening programs in selected low- and middle-income countries. The evidence supporting the study is solid and relies on national-level screening program attendee volumes and assessments of screen positives during 2019 (pre-pandemic) and 2020 (during the pandemic). The study provides real-world data estimates of proportions/volumes of missed screenings due to pandemic control measures (lockdowns and closures) and may contribute to future modelling efforts for measuring the impact on late/advanced stage detection and excess case burden and mortality.

    1. eLife assessment

      This paper addresses an important clinical concern which is how the antidepressant ketamine exerts its effects acts rapidly. The authors suggest the reason is that ketamine increases glutamatergic transmission in the hippocampus. The strengths are the data are mostly very good, and the limitations are a lack of compelling evidence that the hippocampus is the location where effects occur, as well as several other issues.

    1. eLife assessment

      This important study will be of interest to those working on mycobacterial signal transduction. A combination of experiments provides convincing evidence to show how universal stress proteins bind to cAMP and function by direct sequestration of the second messenger. Although the methods, data and analyses broadly support the conclusions, the main claims are only partially supported and can be strengthened through further analytic approaches.

    1. eLife assessment

      Villalobos-Cantor et. al. describe a new technique for cell-type specific in vivo labeling of nascent peptides, which they call POPPi. POPPi is based on sequence-independent incorporation of the puromycin analog OPP into an elongating peptide, which also simultaneously terminates the growing peptide. To achieve cell-type-specific labeling, the authors used an OPP derivative, PhAc-OPP, as the labeling substrate. The method is potentially interesting but needs further characterization to be able to assess its use.

    1. eLife assessment

      This important study combines a screen of known N6-methyladenine (m6A)-dependent RNA modifying factors to identify ALKBH5 as critical in crush injury response. They demonstrate through gain and loss of function an effect on ALKBH5 m6A-dependent Lpin2 mRNA stability during injury-induced axon regeneration in both dorsal root ganglia nerve and optic nerve regeneration. The results provide new insight into the role of RNA modification on neural injury. However, the limitations of the experimental design on the conclusions drawn require additional consideration. With additional control experiments and further consideration of the limitations, the paper will provide a link between N6-methyladenine and neurotrauma.

    1. eLife assessment

      This study describes important results and convincing evidence linking myofibroblast senescence in the aged heart with a pro-arrhythmogenic phenotype. This is in turn related to higher mortality after myocardial infarction in the aged rabbit heart. These constitute important empiric as opposed to detailed findings. They nevertheless will be of interest to clinician scientists studying cardiac function and disease.

    1. eLife assessment

      Non-communicable diseases (NCDs) are rising rapidly in urbanizing populations in many parts of the developing world, including in sub-Saharan Africa. Temba and colleagues show important evidence that healthy Tanzanians display a pro-inflammatory phenotype with enrichment of specific immune-metabolic pathways. Dood-derived metabolites were identified as an important driver of inflammation-related molecules. These findings provide solid evidence that the dietary transition that occurs in urbanizing areas in sub-Saharan Africa may contribute significantly to the increased incidence of non communicable diseases in this part of the world.

    1. eLife assessment

      This important interdisciplinary study substantially advances our understanding of the prolactin receptor interactions with the membrane lipids and the effect of these interactions on cell signaling. The authors use a combination of state-of-the-art NMR structural analysis, simulations, and cellular assays to provide compelling experimental evidence for protein complexes being regulated by IDR-membrane interactions. The work will be of broad interest to structural biologists and biochemists, and the results presented herein are likely relevant for other non-tyrosine kinase receptors.

    1. eLife assessment

      This important study demonstrates that the transcription factor Chinmo is a master regulator that maintains larval growth and development as part of the metamorphic gene network in Drosophila. Chinmo does so in part by regulating Broad expression in imaginal tissues (exemplified in the wing disc) and in a Broad-independent manner in other larval tissues such as the salivary gland. Finally, they demonstrate that the role of Chinmo in promoting larval development is conserved between holometabolous insects and hemimetabolous insects, which lack a pupal stage. The data were collected and analyzed using solid and validated methodology and will be of interest to a broad audience including those interested in development and evolution.

    1. eLife assessment

      Using surface micropatterning, optical activation, and theoretical analysis, the authors provide compelling evidence that adjacent cells actively propagate mechanical stress in epithelial tissues. The response of the receiver cell is active and enhanced when the principal stress direction is perpendicular to the orientation of actin fibers. This work is important and a must-read for everybody wanting to understand tissue mechanics.

    1. eLife assessment<br /> <br /> This is an important study that uses the song system in a bird model to understand the transcriptional mechanisms underlying neuronal adaptations to sensory deprivation. The manuscript offers compelling data in support of their hypothesis that these transcriptional changes are related to song plasticity. The work will be of interest to biologists who study neuronal plasticity mechanisms.

    1. eLife assessment

      Inferior olivary neurons drive complex spiking activity in Purkinje neurons of the cerebellar cortex, ultimately playing critical roles in controlling motor coordination and plasticity. Using transgenic mice or optogenetic techniques to independently control a major excitatory and inhibitory pathway to the inferior olive, the authors show that the probability and phase of olivary neuron output depend critically on the relative timing of excitation and inhibitory inputs. Network models predict that appropriately timed excitatory and inhibitory input patterns efficiently synchronize larger clusters of inferior olivary neurons, raising the possibility that input timing can gate the output of the motor commands. These valuable findings have the potential to impact the field's understanding of sensorimotor processing, but the strength of evidence is currently incomplete.

    1. eLife assessment

      The study provides evidence that the hormone PTH increases bone mass by, at least in part, regulating the factor Zfp467. In turn, Zfp67 controls expression of the receptor for PTH, thus creating a feedback loop that overall augments bone mass. The findings are novel and of potential great interest. Overall, the study is of interest to a broad audience and significant as it unveils a novel feedback loop involving PTH, a critical endocrine regulator of calcium, phosphate, and bone mass.

    1. eLife assessment

      This paper describes a new method to investigate Staphylococcus aureus intracellular virulence that has produced important insights into the mechanisms of staphylococcal pathogenesis. The results are convincing and the methodology is state-of-the-art. This paper will be of interest to scientists studying microbial intracellular pathogenesis and cell biology.

    1. eLife assessment

      This paper demonstrates the genetic architecture of heart mitochondrial proteome that influences cardiac hypertrophy, using a panel of inbred mouse strains called the Hybrid Mouse Diversity Panel (HMDP). The HDM panel is a very powerful tool to study the genetic basis of various physiological and pathological processes in mice. The authors have used this panel extensively before, and in this paper, they extend their proteomic studies to demonstrate the genetic basis of cardiac hypertrophy. The studies will allow us to better understand the genetics of hypertrophic cardiomyopathy.

    1. eLife assessment

      This important study greatly expands our knowledge of the fossil record of Mermithid nematodes, modern members of which are ecologically important parasitoids of arthropods, annelids and mollusks today. The most important finding, convincingly presented, is that mermithids parasitized a number of insect clades in the Cretaceous that they are not known to infect today or in Cenozoic amber. The evidence for a shift in exploited hosts from heterometabolous insects in the Cretaceous to holometabolous ones in the Miocene is solid but could be made exceptional by adding a small quantitative analysis with confidence intervals and bar plots from the data already compiled in the supplementary material; potential collection bias should be addressed as well.

    1. eLife assessment

      This fundamental work uses deep neural networks to simulate activity evoked by a wide range of stimuli and demonstrates systematic differences in latent population representations between hearing-impaired and normal-hearing animals that are consistent with impaired representations of speech in noise. While the evidence supporting the conclusions is compelling, additional analyses would facilitate the generalizability of the neural-network approach. The research will be of interest to auditory neuroscientists and computational scientists.

    1. eLife assessment

      This manuscript provides valuable data gathered using a new video fluoroscopy method by which movements of artificial joints can be visualized in real time. These solid data add to the understanding of the links between symptoms of unstable joints after total knee replacement and actual joint instability. The paper should be of interest to those who study biomechanics after total joint replacement.

    1. eLife assessment

      In this study, Li and al describe valuable insights into the mechanisms underlying sex-differences diet-induced obesity in mice, with a role of macrophage-derived RELMa secretion in female-specific protection. They provide solid evidence for the impact of RELMa signaling in eosinophil recruitment for diet-induced obesity protection in female mice. Single-cell RNA-seq analysis of the stromal vascular fraction of control and RELMa deficient animals methods were used to investigate molecular mechanisms underlying the protection as a powerful method, although the analysis of this data is difficult to evaluate with incomplete methodological information.

    1. eLife assessment

      In vertebrates, ciliary motility is powered by axonemal dyneins, known as OADs, tethered to doublet microtubules by a pentameric docking complex including the Armc4 and Calaxin subunits. This valuable study combines zebrafish genetics with cryo-electron tomography to convincingly show that Armc4 plays a critical role in the docking of OAD and that Calaxin stabilizes the molecular interaction. The work will be of interest to those studying the structure and function of the axoneme, and motile cilia in general.

    1. eLife assessment

      This important study combines behavior, computational modelling and magnetic resonance spectroscopy to address the question whether age-related declines in learning are driven by declines in working memory or deficiencies of the RL system. The general approach is solid, but the presented evidence to support the papers' main claims could be stronger. With additional analyses and adaptation of the main claims, the paper could be of high interest for researchers in the field of cognitive aging and decision making.

    1. eLife assessment

      The authors present a manuscript aiming to understand the mechanism(s) underlying myeloid bias in HSCs, specifically focused on the role of Pcgf1, and therefore PRC1.1, in the regulation of hematopoiesis. This important work is of interest to the community of researchers interested in myeloid differentiation, lineage fate decisions in hematopoietic stem cells, and the molecular mechanisms that contribute to the initiation of myeloid malignancies. The methods are rigorous and the results convincingly support the authors' conclusions.

    1. eLife assessment

      This is a valuable paper describing an attempt to reconstruct the evolution of Dicer. Using ancestral reconstruction approaches, the authors carefully examine the biochemical characteristics of reconstructed proteins at various junction points in the animal lineage. They provide solid evidence that the deepest ancestrally reconstructed protein has double-stranded RNA stimulated ATPase activity and that this characteristic was lost along the vertebrate lineage. This paper will be of interest to scientists in the RNA-protein interaction and protein evolution fields.

    1. eLife assessment

      The authors have established new formulas to predict maximum oxygen uptake for cyclists and runners based on submaximal exercise testing and anthropometric characteristics. This is an important study with a large and comprehensive dataset, which may be helpful for many exercise labs. The work is convincing, using appropriate and validated methodology in line with the current state-of-the-art, as shown by references to common exercise books.

    1. eLife assessment

      In the current manuscript, the authors study the effects of hypoxia or genetic and pharmacologic modulation of the hypoxic pathways on T cells. The findings about T cells sense hypoxia and how hypoxia affects T cell (and CAR T cell) differentiation and function are significant and interesting for the field. The data supporting these findings are mostly robust, yet some questions remain open and some statements seem unsupported by evidence.

    1. eLife assessment

      This fundamental work substantially advances our understanding of polymer physics underpinnings of genome folding, organization, and regulation. The conclusions are supported by both convincing computer simulations and analytical theory. The work will be of significant interest to the genome folding community.

    1. eLife assessment

      This manuscript will be of interest to scientists in the field of tissue injury and repair. It provides novel molecular mechanisms of a transcription factor, Prrx1, in fibroblast activation following lung injury. Overall, the work suggests that PRRX1 plays a functional role downstream of TGFb1 to elicit some aspects of the fibrotic response and that PRRX1 could represent an important therapeutic target to treat fibrosis. The strengths of this work are the multiple approaches applying human and mouse lung tissue used by the authors to test the role of PRRX1 in lung fibrosis, however, in its current form, major limitations need to be addressed.

    1. eLife Assessment

      The study has advanced our mechanistic understanding of lung regeneration. While the importance of regeneration of alveolar capillaries for long response to injury has been long recognized, the regulation of this process has not been well understood. Your study provides novel, comprehensive, and compelling evidence that the expression of the transcription factor Atf3 in alveolar capillary endothelial cells plays a critical role in the regeneration of alveolar capillaries following lung injury.

    1. eLife assessment

      This study concerns an important area, that of monoallelic expression, but the study does not provide sufficient information about the candidate regulatory RNA to provide a significant advance over previous work, which should also be discussed in more detail.

    1. eLife assessment

      This important study provides convincing evidence that locus coeruleus is activated during visuomotor mismatches. Gain of function optogenetic experiments complement this evidence and indicate that locus coeruleus could be involved in the learning process that enables visuomotor predictions. This study, therefore, sets the groundwork for the circuit dissection of predictive signals in the visual cortex. Loss-of-function experiments would strengthen the evidence of the involvement of locus coeruleus in prediction learning. These results will be of interest to systems neuroscientists.

    1. eLife assessment

      The study examines the principles according to which neurons connect to each other in the brain. The authors find that data could be best explained by the homophillic wiring principle where neurons preferentially connect to neurons within overlapping groups. The work will provide a valuable resource to the neuroscience community once analyses are standardized across various datasets included.

    1. eLife assessment

      This valuable work advances our understanding of the acoustic features driving the attraction of female mice to male vocalizations. The evidence supporting the conclusions is solid, with well-designed place preference assays and manipulations of male song structure. The work will be of broad interest to neurobiologists and ethologists working on mouse social interactions, auditory processing and communication.

    1. eLife assessment

      This manuscript combines cryo-EM and a suite of compelling whole cell and proteoliposome transport assays to establish the mechanism and structure of the full-length human SLC26A6 chloride/bicarbonate exchangers, including the first partial view of the previously unresolved IVS region of an SLC26 STAS domain. In combination with prior studies on additional SLC26 paralogs, including the SLC26A9 paralog initially reported by the same group, the current study provides important insight into the mechanistic diversity of the SLC26 transporters. This study is of interest to the biophysics community and the field of membrane transport.

    1. eLife assessment

      This study evaluated how naturalistic behaviors are encoded in the striatum by analyzing neural ensembles engaged during grooming behavior. The study shows that neural responses are highly heterogeneous during grooming, but ensembles were detected in which units were more correlated during grooming than during the entire session. This study presents an important contribution to the field by shedding light on how ensembles of neurons encode innate behavior. The results are convincing.

    1. eLife assessment

      This important study uses an innovative genome-wide approach and targeted testing to identify S. aureus genes that affect susceptibility to serum, serum-derived antimicrobial products, and commonly used antibiotics. The findings are significant in that they highlight evidence of evolution of virulence determinants in the setting of exposure to host stressors expected to be present during bacteremia and antibiotic therapy. The evidence is solid, but the presentation could be improved by providing details that clarify the methods and highlighting the limited current understanding of the major target, tcaA.

    1. eLife assessment

      This contribution provides important insights into the thermodynamic landscape of cation transporters of the Cation Diffusion Facilitator (CDF) superfamily, together with a detailed structural investigation of the role of the three zinc(II) binding sites of YiiP. Despite the relatively low resolution of the cryo-EM structures presented in this work, the combination of structural, functional and modeling techniques yields solid evidence for the proposed model. This work will be of interest to biologists and biophysicists that work with membrane transporters; it is an excellent example of how different techniques can be combined to obtain relevant information on the complex mechanism of action of a transporter.

    1. eLife assessment

      This important study combines behavioral and imaging experiments to understand how levels of important brain chemicals shape the processing of information in the brain in children and young adults. The sample size and data quality are outstanding and some of the data are quite convincing. However, the calculation and interpretation of the brain chemical concentration measurements as well as the interpretation of the model-based behavioral parameters are not fully justified and support for the overall conclusions is incomplete. This work will be of interest to neuroscientists, psychologists, and neuroimaging researchers investigating the developing brain in health and disease.

    1. eLife assessment

      This is a valuable addition to the literature as it helps us understand the role of tRNA modifying enzymes in Mycobacterium tuberculosis. By knocking out one of the enzymes, the authors convincingly demonstrate the importance of tRNA-modifying enzymes for intra-host growth of tubercle bacteria. Some of the claims regarding modification as well as the role in virulence could be strengthened through further bioinformatics and phylogenetic analyses as well as experimental approaches. The work will be of interest to microbiologists.

    1. eLife assessment

      Müller glial cells of the zebrafish retina can differentiate into all neural cell classes following injury, providing full regenerative capabilities of the zebrafish retina. This study presents a valuable description of transcriptional changes of Müller glia cells in the adult and regenerating retina using single-cell RNA sequencing. The overall evidence supporting the main claims of the authors is solid, but some aspects of the analysis are incomplete and would benefit from additional experimental evidence to support the existence of different types of Müller glia and their distribution in the retina.

    1. eLife assessment

      This valuable study provides insights into mechanisms of placental aging and its relationship to labor initiation. The authors provide solid evidence and have thoroughly investigated the molecular characteristics of normal placental aging using in vivo and in vitro model systems and human placental tissue analysis to corroborate their findings. This work contributes to existing work in placental aging and preterm birth and will be of interest to reproductive scientists.

    1. eLife assessment:

      This valuable study presents convincing evidence that metabolite levels in Escherichia coli bacteria from a long-term evolution experiment have changed in consistent ways, which in turn can be explained by recurrent mutations in regulatory genes that affect enzyme expression levels. The use of high-resolution mass spectrometry measuring bulk metabolite levels, in combination with existing gene expression and DNA sequencing datasets provides valuable information linking changes in an organism's genome, transcriptome, and metabolome. The current version of the paper lacks clarity in parts, most critically in the introduction, and would benefit from some rewriting to improve its structure, precision, and readability.

    1. eLife assessment

      This study reports important findings regarding the systemic function of hemocytes controlling whole-body responses to oxidative stress. The evidence in support of the requirement for hemocytes in oxidative stress responses as well as the hemocyte single-nuclei analyses in the presence or absence of oxidative stress are convincing. In contrast, the genetic and physiological analyses that link the non-canonical DDR pathway to upd3/JNK expression and high susceptibility, and the inferences regarding the function of hemocytes in systemic metabolic control are incomplete and would benefit from more rigorous approaches. The work will be of interest to cell and developmental biologists working on animal metabolism, immunity, or stress responses.

    1. eLife assessment

      Muroňová et al. provide valuable information about CDCC146 as a centriole and microtubule associated protein essential for sperm flagellar formation and male fertility. Mutations were identified in human patients suffering from MMAF syndrome, but the evidence that these human mutations were causative of the abnormal phenotype is incomplete. To further explore the causality, mouse models are generated and the findings from the mouse study, support that the key roles of CCDC146 for microtubule-based structures throughout sperm development in general but requires statical analysis.

    1. eLife assessment

      This important study reports investigation of the dynamics of PKA at the single-cell level in in vitro and in epithelia in vivo. Using different fluorescent biosensors and optogenetic actuators, the authors dissect the signaling pathway responsible for PKA waves, finding that PKA activation is a consequence of PGE2 release, which in turn is triggered by calcium pulses, requiring high ERK activity. The evidence supporting the claims is solid. At this stage the work is still partly descriptive in nature, and additional measurements would increase the strength of mechanistic insights and physiological relevance.

    1. eLife assessment

      This manuscript reports important findings regarding the potential for self-policing and a division of labor among biofilm-inhabiting Bacillus cells. Overall, this work is robust in its use of various techniques and provides solid insights into the intersections of well-understood regulatory controls and the suppression of cheaters. Despite some concerns about the data, all reviewers were excited by the potential impact of this work. Colleagues interested in microbial social interactions should find this study's narrative about the internal mediation of cell differentiation particularly valuable.

    1. eLife assessment

      This study presents important findings on the mechanism as to how Mycobacterium-containing vacuoles are recognized by host cell factors and subjected to membrane repair or autophagic degradation using Dictyostelium discoideum as a useful model. The evidence for the role of TrafE in damaged-membrane repair and xenophagy induction is convincing, but that in autophagosome closure is rather incomplete.

    1. eLife Assessment:

      Zemel and colleagues provide a report on the fundamental electrophysiological properties of motor neurons driving song in the zebrafish and provide complementary information about cell morphology, pharmacological sensitivity, and ion channel expression and heterogeneity. They provide mainly convincing data supporting the claim of a particular ion channel class, Kv3, that plays an important role in fast electrical spiking (action potentials) in song-related neurons.

    1. eLife assessment<br /> <br /> Within this paper, the authors describe a rapid and easy-to-implement CRISPR/Cas9-mediated knock-in approach to precisely insert large transgenes in the African turquoise killifish. The established method will be instrumental for many researchers working with unusual model species, and, in particular, will expand the killifish community toolbox. It will revolutionize the field and bring the killifish, an emerging animal model in aging biology and disease modeling in vertebrates, into the spotlight even more.

    1. eLife assessment

      This valuable study addresses the anticipated but poorly understood interconnections between ER proteostasis and lipid metabolism. The authors discovered key metabolic enzymes required for integration of ER stress and lipid synthesis and followed up with several direct experiments that provide solid evidence for a broad conservation of the described interactions.

    1. eLife assessment

      Motivated by previous demonstrations that cognitive modulation of heart beat evoked responses (HER) might distinguish minimally consciousness state and unresponsive wakefulness syndrome patients, the present work sought to determine whether contextual processing of auditory regularities (local-global paradigm) differentially affects HER in these patient groups. The results provide preliminary evidence for the usefulness of EEG and oddball paradigms in informing diagnosis of the state of consciousness. This paper will be of interest to those researchers studying signs of consciousness in post-comatose patients and more broadly to those studying brain-body interactions. However, some aspects of the study design and data analysis need to be clarified, particularly as these affect the conclusions that can be drawn.

    1. eLife assessment

      Hernandez-Perez et al. perform a detailed analysis of Kazrin, a widely expressed protein that appears to be involved in many diverse cellular processes, but whose exact function is unknown. The authors employ mouse embryonic fibroblasts and biochemistry to investigate the function of Kazrin and determine that Kazrin promotes the dynein/dynactin-dependent transport of early endosomes. These findings are valuable to those in the field of intracellular transport, but the story will benefit from additional experiments to prove the main claims, or from textual modifications.

    1. eLife assessment

      In the current study, Mondoloni and colleagues reveal how a selective nicotine receptor in the interpeduncular nucleus is involved in nicotine consumption, which is an important contribution to the understanding of individual differences in drug addiction. However, the preferred hypothesis would benefit from testing in additional experimental models, metabolic assessment, and cell-type specificity.

    1. eLife assessment

      The cerebellum plays a critical role in motor learning, but exactly which forms of synaptic plasticity contribute to learning, as well as the underlying molecular mechanisms, remain poorly understood. In this study, Wang and colleagues show that presynaptic long-term potentiation at the parallel fiber to Purkinje cell synapse is required for one form of motor learning, and involves a previously-unknown signaling cascade, where EPAC activation leads to PKCε-dependent threonine phosphorylation of RIM1α. This study provides new insights into the underlying mechanisms and functional consequences of presynaptic LTP.

    1. eLife assessment

      This paper expands on prior work by using whole-brain calcium imaging in Drosophila to examine how spontaneous and forced walking and turning affect neural activity in the brain. The measurements presented will serve as a valuable resource for the fly systems neuroscience community and suggest many testable hypotheses that may serve as the basis for future studies. Analyses of the data are solid, but conclusions drawn should be presented with more caveats. This article will be of interest to neuroscientists engaged with the central problem of how behavior modulates neural activity.

    1. eLife assessment

      This paper provides valuable new information on the mechanisms by which Vibrio cholerae integrates and responds to environmental signals. While the strength of the evidence provided in the paper in support of the conclusions made and the model proposed is solid, there are several issues that if addressed will strengthen the study further. The work is relevant for a broad audience of microbiologists interested in the mechanisms by which bacteria sense their environment.

    1. eLife assessment

      This is a valuable study on DNA gyrase that provides further evidence for its mode of action via a double-stranded DNA break and against a recently-proposed alternative mechanism. The evidence presented is solid and is derived from state-of-the-art techniques. The work casts new light on the interactions that occur between gyrase molecules and will be of interest to biochemists and cell biologists.

    1. eLife assessment

      This study makes a valuable contribution to our functional understanding of the atypical amino-acid transporter SLC6A177 at nerve cell synapses and the role of SLC6A17 variants in certain forms of intellectual disability. The reported evidence that disease-linked SLC6A17 variants cause behavioral abnormalities is convincing. However, corresponding molecular underpinnings, i.e. the molecular role of SLC6A17 in synapses and the functional molecular consequences of disease-related SLC6A17 variations, remain unclear because corresponding informative experimental approaches are missing - most importantly direct measurements of the transport activity of SLC6A17 in the various genetic contexts studied. This limits the robustness and validity of key mechanistic conclusions drawn from the present work.

    1. eLife assessment

      This valuable work in human subjects reports that sounds that were associated with specific memories during waking behaviors can trigger the reactivation of these memory representations during REM sleep. However, the evidence supporting the conclusions is currently incomplete. Still, the work has the potential to expand our understanding of memory processing during sleep.

    1. eLife Assessment

      Using a novel multi-depth plan display, this study reveals a valuable finding regarding crowding - it decreases with small depth differences between the target and flankers but increases with larger depth differences. The evidence supporting this finding is convincing, although the explanation of the findings is somewhat speculative. This paper will be of interest to visual scientists, neuroscientists, and ophthalmologists, especially those working on visual crowding and depth perception.

    1. eLife assessment

      This study presents useful findings on an important question in cognitive neuroscience - whether the brain can form sensory predictions during sleep. The paradigm used is compelling but evidence supporting the claims of the authors is incomplete. Major issues pertaining to large differences between the pattern of brain responses observed here relative to effects reported in the literature previously, and some evidence that the study might be underpowered to make strong conclusions about certain aspects of the data.

    1. eLife assessment

      The authors ask if brain regions change based on the functional constraints or developmental constraints. To address this, they introduce an automated method for brain segmentation based on the zebrafish tool to study brain evolution in Astyanax. A caveat is that it is difficult to test the functional constraint hypothesis using this method, though it works well for testing developmental constraints.

    1. eLife assessment

      Antimicrobial peptides (AMP) are a class of antibiotics that are inspired by natural components of innate immunity, which raises the specter of bacteria becoming resistant to both. The author this important study test this idea and find compelling evidence that a plasmid that encodes resistance to the AMP colistin also increases resistance to AMPS produced by humans, pigs, and chickens, enables the bacteria to grow better in low levels of AMP, and increases bacterial virulence in an insect model of infection. The study will be of interest to both evolutionary biologists and microbiologists focused on antimicrobial therapy and suggests that the evolution of resistance to these compounds can have collateral effects on immune evasion as well.

    1. eLife assessment

      This important study provides compelling observations of the organization and architecture of haptomonads, a distinct and poorly understood developmental form of Leishmania found in sand fly vectors at later stages of infection. The authors used 3D electron microscopy techniques, including serial block face scanning electron microscopy and electron tomography, to visualize the colonization sand fly by haptomonads in impressive detail.

    1. eLife assessment:

      Sampaio and colleagues utilize an elegant approach to manipulate fluid dynamics in zebrafish Kupffer's vesicle to ask if fluid movement or something in the fluid governs the break in symmetry. These valuable results support a role for fluid movement and detection as important in breaking symmetry in a ciliated left-right organizer and help set a time window when fluid flow is critical for this process. However, as the fluid extraction experiments affect both chemical and physical features, the authors need to provide further convincing evidence to support their mechanosensory hypothesis or temper the claims.

    1. eLife assessment

      In this important study, the role of NBR1 in the degradation of photodamaged chloroplasts is analyzed, advancing our knowledge of chloroplast homeostasis in response to environmental stress. The evidence presented is convincing, in some parts even compelling, and the results are valuable for the plant and the autophagy research community.

    1. eLife assessment

      This valuable manuscript presents resources for genome-wide genetic perturbation in the fruitfly, Drosophila. The evidence for the usefulness is solid, with the authors demonstrating that they can identify novel genes that affect an important pathway, the mTOR pathway, which plays key roles in cell proliferation and cell death. The genetic resources are significant for their availability to colleagues in the Drosophila community seeking to to identify genes with important cellular functions.

    1. eLife assessment<br /> <br /> Descovich et al examine the important decision between proliferative (planar) and differentiation (perpendicular) divisions in the basal layers of the skin and find a key promoter of perpendicular divisions is inhibited by its paralog to specify planar divisions. The authors use sophisticated mouse genetics and imaging and discover that LGN and its paralog AGS3 function antagonistically in determining perpendicular vs. planar divisions. Some statements need to be tamed or further backed up, but overall this study provides a significant advance in the field.

    1. eLife assessment

      This is an important study on the role of a bacterial cell wall component, D-alanylated lipoteichoic acid, as a bacteria cue in Drosophila melanogaster-microbiome interactions. Overall, the evidence supporting the conclusions is compelling, with a solid approach combining crystallography with biochemical and cellular assays, that take advantage of both fly and bacterial mutants, to demonstrate a physiological role in juvenile growth promotion. The work will be of broad interest to those studying host-microbe interactions, especially as it is related to immunology and metabolism mediated by the microbiome.

    1. eLife assessment

      The manuscript describes a fundamental study of the atypical MAPK, ERK3, in the activation of RhoGTPase Cdc42 and the formation of actin-rich protrusions and cell migration. The results show that ERK3 is required for the motility of tumor cells in vivo, providing a new target for fighting metastasis.

  3. Mar 2023
    1. eLife assessment

      These are important findings that show that pupil size is not only governed by the locus coeruleus but also by other neuromodulatory subcortical systems. Furthermore, the authors demonstrate that using a standard hemodynamic response kernel is not appropriate for capturing the activity of these systems, at least at rest. Thus, this paper presents compelling evidence against two prevalent working assumptions among researchers in the field.

    1. eLife assessment

      This important work utilizes a model organism, zebrafish, to explore changes to the proteome and the role of KLHL40, a component of the ubiquitin-proteasome system, in the development of skeletal muscle disease. Using mass spectrometry, the authors demonstrate a major and selective role for proteome remodeling in development. They identify a specific role for KLHL40 deletion in regulating the expression of Sar1 - a key component of biosynthetic secretion, where the resulting elevated levels of Sar1 expression potentially lead to collagen secretion defects in the disease state. The findings are incomplete as further experimental characterization of the overall morphological changes and secretion defects, in particular ones derived from the deregulation of Sar1 levels, is required.

    1. eLife assessment

      In this useful study, a GWAS-type analysis is applied to clinical Mycobacterium tuberculosis isolates to discover genetic polymorphisms linked to poor tuberculosis outcomes. The evidence for the detected associations is still incomplete, as the corresponding polymorphisms are not adequate to power a prediction model for infection outcome, although key host factors - including patient age, sex, and duration of diagnostic delay (which have stronger predictive value) - appear to enhance predictive capacity.

    1. eLife Assessment:

      The manuscript by Godoy and colleagues is an important contribution to the understanding of how lung endothelial regeneration progresses following endothelial ablation. The novelty and elegance of this study are rooted in the regional and specific ablation of lung endothelial cells using diphtheria toxin without the massive inflammatory activation that is seen with lung injury induced by bacterial infections, viral infections, or lipopolysaccharide. The data convincingly demonstrate that there is an emergence of a highly proliferative lung endothelial subpopulation that drives endothelial regeneration. The translational implications of the study include the identification of potential therapeutic targets to augment endothelial regeneration as a treatment for ALI/ARDS. This study will be of interest to vascular biologists, lung biologists, and researchers studying adult tissue regeneration.

    1. eLife assessment

      This is an important contribution to colorectal cancer research to understand how we can predict high-risk patients for recurrence. The strength of the evidence is solid and looks at a novel approach but an approach that still has opportunities to improve.

    1. eLife assessment

      This study provides an important demonstration that loneliness is associated with smaller hippocampal volume, reduced cortical thickness, and worse cognition in healthy older adults. This has theoretical or practical implications beyond a single subfield. The strength of evidence is solid given the cross-sectional and longitudinal design with a few weaknesses. With the analytical and interpretational part strengthened, this paper would be of interest to gerontologists, and dementia/cognitive aging researchers.

    1. eLife assessment

      This paper provides strong evidence for the important point that microtubule function is required for the proper localization of Glut4 glucose transporters in an insulin responsive compartment. This membrane localization is required in turn for effective translocation of Glut4 to the muscle cell surface in response to the hormone.

    1. eLife assessment

      This paper deals with an important unsolved problem in developmental biology of how cells execute their dynamics at the right time. The study combines compelling quantitative single cell and single transcript experiments with genetic perturbations and computational modelling and provides important insights into how the timing of transcription is regulated. The work would be strengthened by better integration of modeling and data.