Evaluated articles

Evaluation Summary:

This manuscript is of broad interest to readers in the field of human vision and its cortical topography as well as behavioral and genetic links. The investigation of the neurobiological basis of visual task performance asymmetries represents an important contribution to our understanding of how visual system architecture shapes perception. 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. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Evaluation Summary:

This manuscript describes an interesting regulation of the hexosamine biosynthetic pathway (HBP) that is relative specific to the mouse embryonic stem cells (mESC). HBP produces UDP-N-acetylglucosamine, which is used in various protein glycosylation events, thus regulating many biological pathways. Understanding this pathway and its regulation is thus of fundamental significance.

(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 experiments reported here directly assess the impact of theta burst transcranial magnetic stimulation on neuronal activity. It will be of high potential interest to researchers using non-invasive brain stimulation. Although the results are highly intriguing, several methodological issues limit the inferences that can be drawn from the data as currently presented.

(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 will be of interest to readers in the field of plant evolutionary biology and paleontology, paleobotany in particular. Using novel 3D reconstruction techniques, the authors provide the first evidence-based reconstruction of Asteroxylon mackiei, the Early Devonian Rhynie chert plant known for a century, and demonstrate that it possessed an extinct pattern of root development transitional to the evolution of true roots in modern club-mosses. The use of multiple lines of evidence and 3D reconstructions based on serial sections of petrified materials provides compelling support for the key conclusions of the paper.

(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. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Evaluation Summary:

This paper examines the roles and mechanisms of how subunits of the mitochondrial calcium uniporter complex (MCUcx) regulate calcium uptake by mitochondria, a process that serves to match the rate of ATP generation to cellular metabolic needs. Based on direct electrophysiological recordings of MCUcx, the authors find that the MICU1 subunit potentiates channel activity in a calcium-dependent manner but does not block the channel at low calcium levels, challenging current models of MCU regulation. This work will be of significant interest to biophysicists and cell biologists interested in mitochondrial biology, bioenergetics, and ion channel and calcium signaling mechanisms.

(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:

Tonkin-Hill and colleagues present a large set of deep sequencing data from acute SARS-CoV-2 infections with each sample sequenced in duplicate. They use these data to characterize the within-host mutational patterns and diversity and relate them to SARS-CoV-2 diversity in consensus sequences sampled around the globe. It further allows understanding how this variation can or cannot be used to understand transmission dynamics and other applications in genomic epidemiology.

(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:

This paper provides important data on the contribution of the vmPFC to temporal discounting, by showing differential modulation of two well-known effects in inter-temporal choice (magnitude effect, episodic future thinking). VMPFC damage abolished the magnitude effect, but not a modulation of discounting via future thinking, a finding of interest to cognitive neuroscientists working on prospection, decision-making and executive control.

(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 describes an important feature of within-host acquisition of antibiotic resistance. This is a follow-up to their recent publication (Bakkeren et al. 2019), and complements their finding of persister cells in the tissues, to show that also chronic, tissue residing bacteria can provide plasmid tissue reservoirs. The experiments the authors performed are elegant and timely. This manuscript will be of interest to readers in the fields of infection biology, plasmid ecology, gut microbiomes, and antimicrobial resistance.

(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 interest to a broad audience interested in the coevolutionary arms race between plants and their herbivores. In a thoroughly investigated case study, the detoxification strategy of cockchafer larvae towards the major defensive compound of one of their preferred host plants, dandelion, is revealed and effects on the behavior of the larvae are described.

(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 names with the authors.)

Evaluation Summary:

This study is of potential interest to biologists interested in developmental patterning and the link between cellular identity and behavior. The authors perform experiments in the progenitor zone of avian embryos to propose that heterogeneity of cellular behaviors may drive morphogenesis and underlie cell fate choices. The work is nicely done but might need some additional experimental validation of the proposed hypothesis.

(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 study analyzes publicly available genomic and proteomic data to identify host proteins that may be involved in regulation of COVID-19 susceptibility and severity. Several known and new targets are identified, further revealing the complexity of host genetic variation in COVID-19 disease.

(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 builds upon the recent observation that Schwann cell (SC)-specific loss of the mitochondrial protein Prohibitin-1 results in a rapid, progressive demyelinating peripheral neuropathy in mice associated with mitochondrial dysfunction. They establish pathways as downstream effectors of mitochondrial dysfunction in Schwann cells. The authors provide a comprehensive evaluation of these pathways following the loss of Prophibitin-1 and identify JUN and mTORC1 as potential mediators of myelin disruption.

(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:

Sitaraman and colleagues address the fundamental question of whether gap junctions facilitate the formation of chemical synapses. To do so they test the function of the gap junction protein, Gjd2b, in early stages of synaptogenesis in larval Zebrafish cerebellar Purkinje neurons. They provide convincing evidence that Gjd2b is necessary for the development of glutamatergic synapses and dendritic arbor growth Purkinje neurons in vivo and that CaMKII plays a role in regulating arbor development. This study will be an important contribution to our understanding of molecular and cellular mechanisms underlying brain 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. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

This paper will be of interest to scientists interested in the biology of the G-protein-coupled receptor Gpr161 and its ciliary regulation of Hedgehog (Hh) signaling. The phenotypes observed in a new GPR161 mutant mouse carrying a hypomorphic allele provide additional information showing which developing tissues are more sensitive to Gpr161 function. However, the data at this stage are insufficient to support the main novel conclusion: the ciliary function of Gpr161 is to regulate Gli3 repressor while the extra-ciliary function is to regulate Gli activator.

(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:

In this work, the authors provide a useful compendium of proteins labeled within SNpc dopaminergic cells using a novel approach. AAV virus was used to conditional express the APEX2 enzyme in dopaminergic neurons (based on DAT-1 Cre genetic technology) to rapidly biotinylate nearby proteins in oriented sections of brain whereby the striatonigral circuit can be spatially parsed for proteomic dissection. In addition to providing a useful new database of proteins for investigators interested in this circuit, the results also provide a more general approach to examining a compartment proteome in neurons and what might be expected in that analysis.

(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:

Light and light perception are important factors that modulate several aspects of behavior and physiology in all animals, including humans. More specifically, the paper examines circadian cycling of phototransduction regulators in diurnal zebrafish and nocturnal mice, and links them to function at the level of ERGs. Interestingly, the transcriptional cycling is shifted between zebrafish and mice. This work is of relevance to vision researchers, but also of interest to a broader audience of behavioral (neuro)scientists and chronobiologists.

(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:

This manuscript provides evidence that loss of N1-methylation of G37 of tRNAs in bacteria on depletion of TrmD results in defects in aminoacylation and peptidyl-transfer, leading to ribosome stalling and phenotypes indicating activation of the stringent 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors developed an aorta-on-a-chip system to investigate the potential mechanism of Bicuspid Aortic Valve-Thoracic Aortic Aneurysm, BAV-TAA, and to test candidate pharmacologic agents. This study is of broad interest to readers in the field of lab-on-a-chip, biomedicine, biomaterials, etc. However, some important details regarding the development of the model are missing, as are some control data. The authors need to discuss the limitations of this model, such as the inability of their on-a-chip model to recapitulate aortic changes associated with complex pathologic processes such as ECM degradation, inflammation, etc, and discuss the importance of follow-up studies in in vivo models.

(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 interest to a broad audience in the blood coagulation and fibrinolysis field. Previously undescribed roles in a range of blood clot properties are attributed to a region of the clotting protein fibrinogen, using state-of-the-art methodology. The data support the main conclusions of the paper, open new avenues of investigation for understanding clot properties, and have clinical implications.

(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 study is significant because it addresses a debated question in the field about whether different opioid receptor subtypes expressed in the same cells must function as a unit or function independently. Here the authors show that while mu and delta opioid receptors each signals in a similar manner in response to specific treatments, their interactions are largely independent of one another in modulating the firing and regulation by desensitization and internalization mechanisms in striatal cholinergic interneurons.

(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.)