Evaluated articles

eLife assessment

This manuscript presents useful findings on several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2 that further our understanding of deep sea microbial life. The manuscript's primary claim is that phage isolates augment polysaccharide use in Pseudomonas bacteria via auxiliary metabolic genes (AMGs). However, the strength of the evidence is incomplete and does not support the primary claims. Namely, there are not data presented to rule out phage contamination in the polysaccharide stock solution, AMGs are potentially misidentified, and there is missing evidence of successful infection.

eLife assessment

The authors analyze the relationship between human mobility and genomic data of SARS-CoV-2 using mobile phone mobility data and sequence data and present a solid proof of concept. This useful work was conducted on a fine spatial scale and provides suggestions on how mobility-derived surveillance could be conducted, although these results are mixed. The primary significance of this work is the strong use of large datasets that were highly granular. The authors provide a rigorous study, but with less clear predictive power of mobility to inform transmission patterns.

eLife assessment

This is a valuable study on the efficacy of a live attenuated vaccine that was tested in different animal models. The evidence is convincing, but it could be further strengthened by comparing the efficacy of their platform with an mRNA vaccine and further investigating mucosal protection.

eLife assessment

This fundamental study uses a creative experimental system to directly test Ohno's hypothesis, which describes how and why new genes might evolve by duplication of existing ones. In agreement with existing criticism of Ohno's original idea, the authors present compelling evidence that having two gene copies does not speed up the evolution of a new function as posited by Ohno, but instead leads to the rapid inactivation of one of the copies through the accumulation of mostly deleterious mutations. These findings will be of broad interest to evolutionary biologists and geneticists.

eLife assessment

This important study provides solid evidence, both from biochemical analyses and in vivo mouse models, that soluble uric acid serves as an enzymatic inhibitor of the NADase CD38, thereby impacting inflammatory responses. By shedding light onto the intricate interplay between uric acid and CD38, the authors highlight potential therapeutic avenues for inflammatory and age-related conditions, which may be of interest to medical biologists, biochemists, and cell biologists. Further in vivo and in vitro validation suggested would be helpful to cement the significance and implications of these findings.

eLife assessment

The authors examined whether the frequency of alternative splicing across entire genomes correlates with measures of complexities across prokaryotes and eukaryotes. Although the question is very interesting and important for our general understanding of the evolution of life forms, the work is inadequate: the methods, data, and analyses do not support the primary claims. The measure of alternative splicing frequency used by the authors is problematic; the method is inappropriate; the observed correlations may also be explained by known population genetics principles; and parts of the manuscript are difficult to understand.

eLife assessment

This study presents valuable information on the mechanism of how birnavirus VP3 protein interacts with PI3P in early endosomes. Evidence supporting the proposed two-stage mechanism is incomplete and would benefit from additional supporting experiments, and additional experimentation would also address concerns about data consistency.

eLife assessment

This valuable work by Zheng and colleagues uses a large cohort database from Shanghai to identify that post-infection vaccination among previously vaccinated individuals provides significant low to moderate protection against re-infection. The evidence supporting the conclusion is solid with some limitations, e.g., lack of symptom severity as an outcome, no inclusion of time since infection as an independent variable, improper definitions of some key variables, difficult-to-interpret figures, and exclusion of key groups (infected and then vaccinated). This study will be of interest to vaccinologists, public health officials and clinicians.

eLife assessment

This important study develops a high throughput version of expansion microscopy that can be performed in 96-well plates. The engineered technology is convincing and compatible with standard microplates and automated microscopes and thus will be of broad interest. However, the application is incomplete and would benefit from additional experiments.

eLife assessment

Peng et al. reported important findings that 36THz high-frequency terahertz stimulation (HFTS) could suppress the activity of pyramidal neurons by enhancing the conductance of voltage-gated potassium channels. The significance of the findings in this paper is that chronic pain remains a significant medical problem, and there is a need to find non-pharmacological interventions for treatment. The authors present convincing evidence that high-frequency stimulation of the anterior cingulate cortex can alter neuronal activity and improve sensory pain behaviors in mice.

eLife assessment

This study presents valuable data on the increase in individual differences in functional connectivity with the auditory cortex in individuals with congenital/early-onset hearing loss compared to individuals with normal hearing. The evidence supporting the study's claims is convincing, although additional analyses and a deeper conceptual framing would have strengthened the study. The work will be of interest to neuroscientists working on brain plasticity and may have implications for the design of interventions and compensatory strategies.

eLife assessment

Hou and colleagues describe the the use of a previously characterized FRET sensor for use in determining gamma secretase activity in the brain of living mice. In an approach that targeted the sensor to neurons, they observe patterns of fluorescent sensor readout suggesting clustered regions of secretase activity. These results once validated would be valuable in the field of Alzheimer's Disease research, yet further validation of the approach is required, as the current evidence provided is inadequate to support the conclusions.

eLife assessment

This valuable study explores the neural basis for a well-known auditory illusion, often utilized in movie soundtracks, in which a sequence of two complex tones can be perceived as either rising or falling in pitch depending on the context in which they are presented. Solid single-neuron data and analyses are presented to show that correlates of these pitch-direction changes are found in the ferret primary auditory cortex. The manuscript is, however, difficult to assess in places and would benefit from greater consideration of how the results fit more broadly into models of auditory coding.

eLife assessment

This useful study has identified a subset of neurons in the preoptic hypothalamus that promote social behavior in single-housed female mice. The approach is solid; however, due to a lack of significance in the key findings and competing outcomes between different manipulation methods, the evidence is incomplete. The authors have the potential to demonstrate evidence by either increasing the number of experimental animals represented in the study or by adjusting the language in the conclusions to reflect the findings.

eLife assessment

This important study uses the Jurkat T cell model to study the role of Formin-like 1 β phosphorylation at S1086 on actin dynamics and exosome release at the immunological synapse. While the evidence is compelling within the framework of the Jurkat model, it is limited in a broader immunological and cell-biological context due to the limitations of the model system. Jurkat is known to have a bias toward formin-mediated actin filament formation at the expense of Arp2/3-mediated branched F-actin foci observed in primary T cells. In this light, confirming major findings in primary T cells will be of importance.

eLife assessment

This study presents a useful reassessment of the potential role of dendritic cell-derived IL-27 p28 cytokine in the functional maturation of CD4+CD8- thymocytes, and CD4+ recent thymic emigrants. The evidence supporting the claims of the authors is solid and serves to reaffirm what has been previously described, with the overall advance in understanding the mechanism(s) responsible for the intrathymic functional programming of CD4+ T cells being limited.

eLife assessment

The study reports on a previously unrecognized function of ATG6 in plant immunity. The work is valuable because it proposes a direct interaction between ATG6 and a well-studied salicylic acid receptor protein, NPR1, which may interest researchers investigating plant immunity regulation. While the data presented are compelling, more information regarding the specificity of ATG6's role would improve the overall impact of the study, especially with an eye towards consistency with prior work.

eLife assessment

This important mouse study shows that wild-type female progeny of Khdc3 mutants have abnormal gene expression relating to hepatic metabolism, which persists over multiple generations and passes through both female and male lineages. Information about litter size and a full phenotypic description of the phenotype of each progeny should be included to evaluate the impact of KHDC3 mutation on the progeny; in its current state, the evidence for the authors' claims is incomplete. A role for small RNAs on this phenomenon is proposed but has not been functionally validated. The work will be of interest to researchers in the field of DNA-independent mechanism of inheritance. Mentioning the experimental organism in title and abstract would ensure that it targets the appropriate audience.

eLife assessment

Through a genome-wide screen for functional alternative transcription start sites (TSS) in Arabidopsis, the authors provide evidence for widespread transcription of potential microproteins from previously annotated protein-coding genes. Functional analysis of AtHB2-miP, derived from the C-terminal region of transcription factor AtHB2 and predicted to form non-productive dimers with ATHB2, suggested that this microprotein could affect AtHB2 functions in shade responses, root growth, and iron homeostasis. The work is valuable as a case study of how new microproteins could act to modulate gene regulation in response to environmental change, but the focus on a single gene, the lack of precision in AtHB2-miP measurement with missing controls, and the relatively minor phenotypic effects in the specific case investigated, leave it unclear how important microprotein production is as a general regulatory strategy.

eLife assessment

This potentially important paper reports on interactions between L1TD1, an RNA binding protein (RBP), and the ancestral LINE-1 retrotransposon from which it originates. Overall, the results support a model in which L1TD1 and LINE-1 ORF1p have synergistic effects on LINE-1 retrotransposition, but the evidence for whether this is through direct protein-protein interaction or through simultaneous interaction with LINE-1 RNA is currently incomplete.