eLife

Latest preprint reviews

1. Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization

   This article has 4 authors:

   1. Yafan Zhang
   2. Irene Silvernail
   3. Zhuyang Lin
   4. Xingcheng Lin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable work presents an interpretable protein-DNA Energy Associative (IDEA) model for predicting binding sites and affinities of DNA-binding proteins. The study provides a detailed description of the method, making it reproducible. However, the generalizability of the prediction model presents certain concerns, and the supporting evidence appears incomplete. Nonetheless, with a thorough re-examination of the training and testing procedures, this model can be widely applicable for predicting genome-wide protein-DNA binding sites.

   Reviewed by eLife

2. Increased reluctant vesicles underlie synaptic depression by GPR55 in axon terminals of cerebellar Purkinje cells

   This article has 2 authors:

   1. Takuma Inoshita
   2. Shin-ya Kawaguchi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study reporting that activation of the presynaptic GPR55 receptor suppresses synaptic transmission by modulating GABA release through the reduction of the readily releasable pool without affecting the presynaptic AP waveform and calcium influx. The evidence supporting this claim is compelling and based on an impressive array of techniques including patch-clamp recordings from the axon terminals of cerebellar Purkinje cells and fluorescent imaging of vesicular exocytosis. However, a few technical issues leave some questions open, these include uncertainty regarding the specificity of pharmacological agents and the nature of the endogenous process that would activate this pathway in vivo. In the current form, the evidence indicating that synaptic vesicles become insensitive to VGCC activation in the presence of GPR55 is weak and would need to be supported with additional experimental data.

   Reviewed by eLife

3. Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab resistant HER2 positive breast cancer

   This article has 14 authors:

   1. Yijia Hua
   2. Ningjun Duan
   3. Chunxiao Sun
   4. Fan Yang
   5. Min Tian
   6. Yanting Sun
   7. Shuhan Zhao
   8. Jue Gong
   9. Qian Liu
   10. Xiang Huang
   11. Yan Liang
   12. Ziyi Fu
   13. Wei Li
   14. Yongmei Yin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides compelling evidence that SLC7A11 may serve as a potential therapeutic target for trastuzumab-resistant HER2-positive breast cancer. While the findings are well-supported by robust data, the study could have been further strengthened by incorporating additional cell line experiments and providing more detailed clarification on patient sample selection. Nevertheless, this valuable work represents a significant contribution and will be of considerable interest to researchers in the field of breast cancer.

   Reviewed by eLife

4. Combined transcriptomic, connectivity, and activity profiling of the medial amygdala using highly amplified multiplexed in situ hybridization (hamFISH)

   This article has 15 authors:

   1. Mathew D Edwards
   2. Ziwei Yin
   3. Risa Sueda
   4. Alina Gubanova
   5. Chang S Xu
   6. Virág Lakner
   7. Megan Murchie
   8. Chi-Yu Lee
   9. Kristal Ng
   10. Karolina Farrell
   11. Rupert Faraway
   12. Subham Ganguly
   13. Elina Jacobs
   14. Bogdan Bintu
   15. Yoh Isogai

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Overall, this is an important work: the new methodology of hamFISH is a key additional tool for the assessment of the expression of multiple genes simultaneously. The authors provide convincing evidence of the utility of this approach on Medial Amygdala (MeA) tissue leveraging previous a transcriptomic dataset for gene selection. The authors also present a deeper dive into putative relationships between the on-tissue expression of subsets of genes and connectivity and behavioral regulation. The putative biological insights are intriguing, although preliminary, but notably they set up questions for future studies.

   Reviewed by eLife

5. Complex system modelling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria

   This article has 11 authors:

   1. Sromona D Mukherjee
   2. Carlos A Batagello
   3. Ava Adler
   4. Jose Agudelo
   5. Anna Zampini
   6. Mangesh Suryavanshi
   7. Andrew Nguyen
   8. Teri Orr
   9. Denise Dearing
   10. Manoj Monga
   11. Aaron W Miller

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work presents a valuable approach based on a complex systems theoretical framework to characterize diet-host-microbe interactions and develop targeted bacteriotherapies through a three-phase workflow. Despite the partial support of the description and experimental setup of the 'complex systems theoretical approach,' the collected data are solid and advance our understanding of oxalate bacterial metabolism in microbial communities. This study will interest researchers working on gut microbiomes and the possible modulation of host-microbial interactions.

   Reviewed by eLife

6. Serial ‘deep-sampling’ PCR of fragmented DNA reveals the wide range of Trypanosoma cruzi burden among chronically infected human, macaque, and canine hosts, and allows accurate monitoring of parasite load following treatment

   This article has 7 authors:

   1. Brooke E White
   2. Carolyn L Hodo
   3. Sarah Hamer
   4. Ashley B Saunders
   5. Susana A Laucella
   6. Daniel B Hall
   7. Rick L Tarleton

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important methodological advance to improve the sensitivity of PCR for detecting Trypanosoma cruzi in blood, combining DNA fragmentation, deep sampling, and blood cell pellet analysis. The findings offer solid evidence of enhanced detection sensitivity and shed light on parasite load dynamics during chronic infection in mammalian reservoirs. The evidence is sound for macaques and the method shows promise in expanding detection limits, but there is some variability in the limits of detection and small sample size of human samples. This work will be of interest to parasitologists, epidemiologists, and clinicians using molecular diagnostics to monitor responses to etiological treatments for Chagas disease.

   Reviewed by eLife

7. Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2

   This article has 2 authors:

   1. John Huddleston
   2. Trevor Bedford

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study investigated the influence of genomic information and timing of vaccine strain selection on the accuracy of influenza A/H3N2 forecasting. The authors utilised appropriate statistical methods and have provided solid evidence that is an important contribution to the evidence base. While the study addresses a key aspect of public health, the impact is rather limited by its exclusive reliance on predictive methods using genomic information, without incorporating phenotypic data.

   Reviewed by eLife

8. HERV activation segregates ME/CFS from fibromyalgia while defining a novel nosologic entity

   This article has 4 authors:

   1. Karen Giménez-Orenga
   2. Eva Martín-Martínez
   3. Lubov Nathanson
   4. Elisa Oltra

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study substantially expands observations of HERV expression in the clinical settings. The evidence provided by the authors that HERV activity is an underlying etiological factor in ME/CFS and fibromyalgia is compelling and suggests further investigation into mechanisms. This work will be of broad interest to clinicians and researchers alike.

   Reviewed by eLife

9. RAS–p110α signalling in macrophages is required for effective inflammatory response and resolution of inflammation

   This article has 19 authors:

   1. Alejandro Rosell
   2. Agata Adelajda Krygowska
   3. Marta Alcón Pérez
   4. Cristina Cuesta
   5. Mathieu-Benoit Voisin
   6. Juan de Paz
   7. Héctor Sanz-Fraile
   8. Vinothini Rajeeve
   9. Ana Carreras-González
   10. Alberto Berral-González
   11. Ottilie Swinyard
   12. Enrique Gabandé-Rodríguez
   13. Julian Downward
   14. Jordi Alcaraz
   15. Juan Anguita
   16. Carmen García-Macías
   17. Javier De Las Rivas
   18. Pedro R Cutillas
   19. Esther Castellano Sanchez

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study investigates the impact of disrupting the interaction of RAS with the PI3K subunit p110α in macrophage function in vitro and inflammatory responses in vivo. Solid data overall supports a role for RAS-p110α signalling in regulating macrophage activity and so inflammation, however for many of the readouts presented the magnitude of the phenotype is not particularly pronounced. Further analysis would be required to substantiate the claims that RAS-p110α signalling plays a key role in macrophage function. Of note, the molecular mechanisms of how exactly p110α regulates the functions in macrophages have not yet been established.

   Reviewed by eLife

10. Variations and predictability of epistasis on an intragenic fitness landscape

    This article has 3 authors:

    1. Sarvesh Baheti
    2. Namratha Raj
    3. Supreet Saini

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This paper addresses the important question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are predictable based on the wild-type phenotype. However, these potentially interesting claims are inadequately supported by the analysis, because measurement noise is not accounted for, arbitrary cutoffs are used, and global nonlinearities are not sufficiently considered. If the results continue to hold after these major improvements in the analysis, they should be of interest to all biologists working in the field of fitness landscapes.

    Reviewed by eLife