Evaluated articles

Evaluation Summary:

This paper will be of interest to developmental biologists and neuroscientists as it aims to resolve the unknown mechanism by which loss of a key enzyme in cholesterol biosynthesis results in neurodevelopmental defects. It provides a conceptual framework for understanding how altered lipid metabolism can impact brain development. Many of the key claims of the paper are well-supported, but reasonable alternative explanations remain.

(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 work combines experiments and simulations together with previously reported biophysical and structural observations to develop a structure-based model that provides mechanistic insight into the two functions of cohesin: cohesion and loop extrusion. This intriguing and informative manuscript will be of broad interest to those working in the fields of chromatin structure, chromosome biology and molecular machines. While the data and analysis support the authors' conclusions, the presentation of the work can be improved for clarity.

(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 paper is of potential interest to a broad audience of neuroscientists, as it adds to our growing understanding of transcriptional mechanisms that regulate neural connectivity. Specifically, the paper provides support for the idea that transcriptional pathways previously implicated in neuronal cell fate determination can have independent roles in specifying connectivity between neurons. The study is highly technically innovative and cleverly uses a set of newly developed tools to analyze the developmental time window over which transcriptional activity is required to achieve to proper connectivity. However, the paper falls a little short in defining specific mechanisms involved downstream of the transcription factors themselves.

(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:

Redmond et al. use single-cell and single-nucleus RNA-sequencing to reveal the molecular heterogeneity that underlies regional differences in neural stem cells in the adult mouse. Prior work had separate subventricular stem cells as type A and B. By generating bulk and single cell transcriptome sequence data, the authors identified a distinct subtype of both A and B cells that differentiate into dorsal and ventral identities. They also identify a set of genes that constitute a conserved molecular signature of these cell types.

(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.)

Summary:

This paper is of general interest to cancer biologists focusing on identifying new targets for cancer therapy particularly in the context of squamous cell lung carcinoma. The authors demonstrate that genetic ablation of the deubiquitinase USP28 reduces the growth of lung squamous cell carcinomas but not lung adenocarcinomas in a mouse model of lung cancer, and that that this restriction of growth is accompanied by loss of expression of several USP28 targets. They also describe activity of a new small molecule compound in controlling the growth of lung squamous cell carcinomas in mouse genetic and xenograft models, and reducing expression of USP28 targets. They demonstrate that USP28 is one target of the newly identified compound, but they do not establish whether it is the only and biologically relevant target of this compound.

Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

Evaluation Summary:

This manuscript considers an important open problem in molecular biology, that is how distal chromosomes can recognise each other at a distance and become paired, as happens for example in homolog paring in Drosophila. To address this question, the authors combine theoretical models and experiments, which return valuable insights. However, a final proof of the envisaged mechanisms remains to be determined.

(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:

This work explores the cellular and behavioural effects of a genetically induced reduction of the expression of a glutamate (excitatory) receptor (GluA4), focusing on the cerebellum , a structure involved in the acquisition of arbitrary, complex motor reflexes. The authors show that synaptic transmission at the input layer to the cerebellar cortex is reduced, despite some compensation by other mechanisms, which are characterised. Locomotion is little affected while acquisition of a "conditioned eyeblink" is abolished. The authors try to link the cellular and behavioural phenomena via modelling of the cerebellar computation, although this is not definitive. The work is of high quality, of interest to cerebellar physicists and neurocomputational modellers in particular.

(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 have elucidated the biochemical and regulatory apparatus for the biosynthesis of sulfated exopolysaccharides, an entire class of molecules not previously studied in cyanobacteria. The work has broad implications for the microbiology and ecology of these organisms and also opens the possibility to use these compounds in biotechnology and modify their structures by combinatorial synthesis.

(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 names with the authors.)

Evaluation Summary:

This is a very important paper that challenges the generally accepted dogma that full zippering of SNARE complexes is essential for intracellular membrane fusion. Previous work had already shown that C-terminal truncation of one SNARE arrested liposome fusion mediated by the yeast vacuolar SNARE complex and that Sec17/Sec18 could rescue fusion, but it was argued that such rescue could arise because Sec17/Sec18 restored C-terminal zippering. This paper now shows that Sec17/Sec18 rescue fusion even when three SNAREs are crippled -by truncation or mutation- to definitively prevent zippering, thus showing that Sec17/18 have a direct, positive role in membrane fusion.

(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 of interest to several fields in biology and medicine including evolutionary genomics and antibiotic stewardship. Ma et al. sought to investigate the breadth of genetic mechanisms for evolution of carbapenem resistance across various lineages of the bacterial pathogen Klebsiella pneumoniae. The authors performed systematic and thorough bioinformatic and genetic analyses to identify how transposon activity and CRISPR-Cas systems facilitate the evolution of antibiotic resistance and restriction of horizontally acquired genetic elements, respectively. The study's results emphasize the importance of additional factors, other than MIC values, such as genetic background, plasmid/transposon activity, and drug identity and choice in determining the rate at which resistance can evolve in K. pneumoniae.

(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:

Mandal and colleagues identified novel functions of the Imd pathway transcription factor Relish in the hematopoietic niche development. The authors found that Relish is required for the maintenance of hematopoietic progenitors downstream of hormonal control. This is the first study showing critical roles of Relish in blood development, and therefore, this study will draw broad attention and contribute to understanding of insect hematopoiesis and immunity.

(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:

The manuscript has the potential to be of broad interest to neuroscientists who are aiming to leverage concepts and tools of evolutionary biology to identify novel gene targets and much-needed therapeutic interventions. The follow up experiments are detailed, well thought out, and do a good job of proving the potential of the identified drugs in alleviating molecular signatures in in vitro disease models. However, the link between comparative genomic analysis and identification of specific drugs is not yet sufficiently established and doesn't convincingly demonstrate the usability of the evolutionary pipeline in identifying novel therapeutics.

(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:

Over the past decade, the role of ATP levels in the material properties of cells has gathered substantial interest in part because of the potential role of ATP in solubilizing biomolecular condensates. This study uses a quantitative imaging-based measurement of ATP levels in live cells to assess the impact of mutants in ATP homeostasis on ATP levels and protein aggregation. The strength of this paper is the quantitative, single cell analysis, and the manipulation of ATP using native control pathways. The authors suggest that fluctuations in ATP concentrations can lead to protein aggregation, which would be of broad interest to many fields, including cell biology, aging and neurodegeneration.

(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:

Convergent evolution is often observed in nature, but the molecular mechanisms allowing similar functions to independently emerge are rarely understood. This work determines how the high-affinity recognition of a pathogenic effector produced by the rice blast fungus, Avr-PikD, evolved in the immune receptor Pik-1. The integration of molecular evolution analyses with structure-function biochemical testing is novel to the field and the data quality is exceptional. In addition to advancing knowledge of host-microbe co-evolution, this work is exemplary in its transparency and the breadth of approaches utilized to understand protein evolution, and we expect that this study will provide a conceptual framework for similar studies in the future.

(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:

Cucinotta et al. describe mechanisms that support an intense burst of transcription from many genes within minutes of nutrient repletion as Saccharomyces cerevisiae cells emerge from quiescence. They focus primarily on the role of the nucleosome remodeler RSC in managing chromatin architecture over promoters during quiescence and as cells re-enter the cell cycle using a broad range of genome-wide measurements that strongly support the conclusions. This important process of cell cycle re-entry from quiescence is understudied but impacts areas as diverse as development and carcinogenesis in multicellular organisms to long-term survival and adaptation of microorganisms to environmental cues, so the results will be of interest to a broad audience.

(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:

In this study, Leydon et al. use an elegant multi-component genetic system to address the mechanisms of repression by the Arabadopsis TOPLESS (Tpl) protein. Taking advantage of the genetic tools and knowledge of the structure of the Tpl protein, the authors determine two short alpha helical regions that act as independent repression domains, with the target of one of these domains being the N-terminal region of the Med21 subunit of the mediator complex. Experiments are presented that indicate that Tpl mediated repression involves formation of a promoter complex comprising the mediator complex along with several general transcription factors, but lacking RNA polymerase II. The experimental data comes from both heterologous experimental systems in yeast and the native plant setting and involves diverse but complementary experimental approaches that converge towards a model for gene repression. This paper will be of interest to researchers investigating the mechanisms regulating gene expression, in particular how specific protein-protein interactions repress gene expression.

(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 names with the authors.)

Evaluation Summary:

The manuscript uses a new approach to model the infectiousness profile of COVID-19 infected individuals. The work suggests a higher proportion of pre-symptomatic infectiousness in COVID-19 than the current evidence. The findings are of great interest to public health policy makers. The methodology is of general interest to modellers working on COVID-19.

(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 names with the authors.)

Evaluation Summary:

The authors address the spatial spread of glutamate outside of synapses, with the surprising conclusion that glutamate released at one synapse can strongly activate receptors at neighboring synapses. This manuscript should interest those studying neural signaling and techniques associated with that field. However, caveats of the advanced techniques used to address this difficult question limit the strength of the main conclusion.

(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:

In this study, the authors present a high-resolution single-cell transcriptomic atlas of the pancreatic ductal tree. Their analysis unveiled important heterogeneity within the pancreatic ductal tree and identified unique cellular states. Overall, the results presented here suggest distinct functional roles for subpopulations of duct cells in maintenance of duct cell identity and implication in chronic pancreatic inflammation. Finally, such detailed analysis of the pancreatic duct tree is relevant also in the context of cancer biology and might help elucidating the transition from pancreatitis to pancreatic cancer and/or different predisposition to cancer.

(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:

The technical challenges of identifying and quantifying the frequency of structural variants (SV) on a population scale has been a major limitation to the study of recent human adaptation. This manuscript applies a recent graph-based genotyping method that leverages a library of SVs identified by long-read sequencing to identify SVs in large short-read based cohorts. This is a sensible and powerful approach that highlights several examples of likely adaptive SV evolution in different human populations. The key findings and examples are well supported by the data and methods used. However, the manuscript would benefit from further comparisons and context from previous studies, and deeper exploration of the biological significance. In addition to providing novel examples of adaptive SV evolution, this analysis may serve as a template for future analyses that merge long-read and short-read datasets.

(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.)