Evaluated articles

Evaluation Summary:

This manuscript describes a fluorospot-based assay as a model for a methodical, step-wise and rigorous approach - that combines multiple reagents in a complex system - to study the cross-reactivity of antibody to polymorphic antigens using the malaria vaccine candidate, VAR2CSA, as a model. The authors apply monoclonal antibodies and the corresponding B cells to validate their multiplexed assay before testing small number of samples from malaria exposed donors in a pilot application of the assay. The data support the conclusions. This information will attract the attention of immunologists and vaccinologists, who are primarily but not exclusively, involved in research on malaria.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The authors have engineered an anti-CD73 chimeric antigen receptor (CAR) that they express in NK cells to counteract tumors bearing CD73, which contributes to the generation of immunosuppressive adenosine in the tumor microenvironment. This is a promising approach for a new anti-cancer immunotherapy and will be of interest to oncologists and cancer immunologists. The CAR-bearing NK cells show slightly enhanced tumor killing in vitro, but preliminary data show more promising results in mice. This could be due to the CD73 CAR blocking catalytic activity in the tumor microenvironment more effectively than directly promoting cytotoxicity responses.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The authors report that neurons in V1 and V4 provide multiplex information of simultaneously presented objects. A combination of multi-single unit recordings, statistical modelling of neuronal responses and neuronal correlations analyses argues in favor of their claims. Pairs of neurons having similar object preferences tended to be positively correlated when both objects were presented, while pairs of neurons having different objects preferences tended to be negatively correlated. These patterns and others suggest that information about the two objects is multiplexed in time. There are, however, some unclear points that deserve discussion and further analysis that could more strongly support the claims.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to readers interested ligand-gated ion channels and their evolution. The authors show that ancestral AChR beta subunits reconstructed phylogenetically can form homomeric channels that open spontaneously. The work expands our understanding of agonist-independent AChR gating and highlights intriguing aspects of AChR evolution.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Replication Factor C (RFC) is known to play a role in both DNA replication and DNA repair by loading a protein clamp called PCNA onto DNA junctions with a 3'-recessed end. The current paper elegantly demonstrates that RFC has a second DNA binding site that recognizes a single strand-double strand DNA with a 5'-recessed junction. The paper reports a series of interesting structures and confirms binding to both short gapped DNA and nicked DNA by RFC, causing local unwinding DNA at the ssDNA/dsDNA junctions. The paper, which is of interest to colleagues studying DNA replication and repair, should be improved through a few clarifications.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Using mass spectrometry, Crawford et al. identify aspartate aminotransferase 2 (Aat2) as a protein whose polysome-association is increased under oxidative stress in yeast. Aat2 deletion sensitizes yeast to oxidative stress, which is paralleled by an aberrantly elevated integrated stress response, although polysome-association of Aat2 and its effect on oxidative stress response are independent of its aminotransferase activity. This provides evidence that metabolic enzymes may "moonlight" as post-transcriptional regulators. The study will appeal to experts in the fields of biochemistry, genetics, cellular and molecular biology. The presented data mostly support the authors' conclusions, but there are a few technical issues that should be addressed. These include corroborating Aat2:ribosome association and characterizing the effects of non-catalytic Aat2 mutants on the integrated stress response.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer 3 agreed to share their name with the authors.)

Evaluation Summary:

Ivica et al. provide both functional and structural characterization of a relatively unstudied glycine receptor agonist that is structurally in between a full and partial agonist. The combination of cryogenic electron microscopy and electrophysiological approaches allows for complementary structural and functional investigations into the criteria that determine ligand efficacy at the glycine receptor. This manuscript will be of interest to both biophysical and pharmacological investigations of ligand-gated ion channels.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper is of broad interest to investigators studying the function and regulation of protein scaffolds, dynamic protein structure, and the regulation of the postsynaptic density at excitatory synapses. The authors develop an integrated approach using fluorescence-based biochemical methods, disulfide mapping, and discrete molecular dynamic simulations to study the dynamic supertertiary conformation of the synaptic scaffold protein PSD95.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper introduces Neuroscout, a new web-based platform for the analysis of fMRI data with a particular focus on naturalistic stimuli. It describes a new tool that will potentially be of great use to the neuroimaging community, and whose development is already quite mature and has a number of datasets ready to use online. Neuroscout as a tool will be of particular interest to neuroimagers and cognitive neuroscientists, but the conclusions drawn using the tool should be of interest to neuroscientists more broadly.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Hart et al show that loss of mitochondrial complex I rescues succinate dehydrogenase deficient (SDH) cells. The experiments are well performed and the phenotype is potentially very interesting to researchers of cancer metabolism. The authors propose that rescue of SDH deficiency by complex I inhibition is caused by an increase in mitochondrial NADH which leads to a restoration of aspartate levels, which in turn rescues proliferation. To support the model, the authors do demonstrate that there are possible correlations of this phenotype to restored aspartate biosynthesis. However, they do not unambiguously establish a mechanism that fully defines how complex I inhibition rescues the proliferation of SDH deficient cells.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

A pathogen's generation interval directly affects estimates of its transmissibility (R), and the period of self-isolation or quarantine needed to prevent transmission. This study shows that the unmitigated generation interval of the original variant of SARS-CoV-2 is several days longer than previously estimated and that interventions have substantially decreased the effective generation interval. These findings improve our ability to model counterfactual intervention-free scenarios. Overall technically sound analyses support the conclusions, and extensive sensitivity analyses show that the findings are robust. However, sampling or ascertainment bias in this relatively small pre-intervention dataset or biased inputs could affect the accuracy of the reported estimates.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript describes randomly generated small proteins of <50 amino acids that can rescue the growth of an auxotrophic mutant of Escherichia coli. The authors suggest that these proteins function by binding specifically to a regulatory element in the 5' UTR of the his operon RNA, altering RNA structure to increase expression. The study suggests that functional small proteins can evolve de novo and that newly evolved small proteins can function as regulators by binding RNA. This is an exciting idea, but the suggested mechanism involving the binding of the small proteins to RNA requires additional experimental support.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors provide novel evidence that semaphorin signaling (SEMA3F) is engaged in the vascular endothelium and smooth muscle to confer atheroprotection. They show that SEMA3F reduces the activity of key enzyme Phosphoinositide 3-kinase to decrease smooth muscle cell proliferation, migration, and phenotype switching, which contributes to atheroprotection. The study has significant translational potential and yields a new therapeutic target.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript could be of interest to physicians and researchers in the field of vascular anomalies. The cohort of patients with lymphatic malformations is reasonably sized (n=30) and the claims made by the authors are supported by the data as well as by current knowledge in the field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript analyzes human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. These studies are the first of their kind and of translational relevance for the field of clinical genetics and prenatal genetic testing, with the potential to contribute to strategies to reduce genetic disease risk in future offspring.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This interesting study identifies why or how the integrated stress response pathway regulates cell recovery upon proteotoxic stress, which is especially interesting in cancer cells resistant to proteasome inhibitors. The authors conclude that translation initiation of mRNAs encoding microtubule cytoskeleton, centrosome and ATF5 proteins is necessary to recover from proteotoxic stress. This paper will make a strong contribution to the literature.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Mahalingam et al. report on a new software suite, ASAP, the assembly stitching and alignment pipeline, capable of montaging and aligning serial sections at a speed leading to total time shorter than image acquisition time. The software applies to both electron microscopy and array tomography, and more generally to any data set consisting of collections of 2D images in need of in-section montaging and cross-section registration. The result is a coarsely registered volume, ready for refining with existing software suits such as SEAMLESS by Macrina et al. (2021) towards subsequent processing, such as image segmentation and neuronal arbor reconstruction for cellular connectomics. This paper will be of special interest to researchers within the field of connectomics, but also to the broad class of scientists who perform large-scale microscopy. The establishment of fast, reliable and scalable image alignment software to process the millions of images produced by modern microscopes at the same speed as they are acquired is key to accelerate research in neuroscience and other fields. The key claims of the manuscript are well supported by the data, and the approaches used are thoughtful and rigorous.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Wang et al., present a thorough analysis of specific neuronal lineages in the early larval ventral nervous system with the objective to relate the birth order to circuit connectivity and function. The stated key findings of the work are (1) the identification of sharp temporal cohort divisions for the lineages under investigation, (2) synapse formation between neurons of different lineages and temporal cohorts, and (3) the observation that output neurons in this instance are born prior to input neurons. The study raises the question of to what extent these findings can be generalized.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is one of the first broad epigenetic analyses in lung development and will be of interest to not only lung biologists but also to the field of epithelial developmental biology. Using paired transcriptomic and epigenetic data, they have uncovered a vast repertoire of signaling mechanisms underlying lung development. These findings have opened up the field's opportunities to understand and study novel pathways and have further defined a role for PI3 kinase signaling in lung development.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Clement and colleagues describe and illustrate the endocasts of six Palaeozoic lungfish genera from superb 3D fossil material, which are very informative for the understanding of brain evolution of lungfishes, the extant sister group to land vertebrates. Rendering important anatomical details regarding brain evolution in lungfishes, and sarcopterygians in general, this work will be of broad interest to zoologists, including vertebrate paleontologists and neuroanatomists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)