eLife

Latest preprint reviews

1. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition

   This article has 10 authors:

   1. Kerry Marie Goodman
   2. Phinikoula S Katsamba
   3. Rotem Rubinstein
   4. Göran Ahlsén
   5. Fabiana Bahna
   6. Seetha Mannepalli
   7. Hanbin Dan
   8. Rosemary V Sampogna
   9. Lawrence Shapiro
   10. Barry Honig

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of interest to cell biologists, biochemists and biophysicists interested in how adhesion and signaling proteins at the cell surface help cells (and especially neurons) interact and perform self/non-self-recognition and self-avoidance. The authors provide the first extensive biophysical dataset examining a large subset of potential trans (across two cells) and cis (on the surface of the same cell) interactions between different isoforms of the ~60 clustered protocadherins (cPcdhs). There data show that all tested trans interactions are strictly homophilic and that not all possible cis interactions are equivalent. These results provide additional layers of complexity and constraints on how this protein family can provide neurons with the ability to perform self-recognition and self-avoidance.

     (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.)

   Reviewed by eLife

2. Autophagosomes fuse to phagosomes and facilitate the degradation of apoptotic cells in Caenorhabditis elegans

   This article has 7 authors:

   1. Omar Peña-Ramos
   2. Lucia Chiao
   3. Xianghua Liu
   4. Xiaomeng Yu
   5. Tianyou Yao
   6. Henry He
   7. Zheng Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study presents evidence that autophagosomes fuse with phagosomes and that this promotes the degradation of phagocytosed cell corpses. The study also resolves controversy in the field about the question why genes involved in autophagy affect cell corpse engulfment and degradation. With some additional data to solidify the main conclusions, the work will be of interest to a broad cell biology 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 and Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

3. Structural and functional insights of the human peroxisomal ABC transporter ALDP

   This article has 6 authors:

   1. Yutian Jia
   2. Yanming Zhang
   3. Wenhao Wang
   4. Jianlin Lei
   5. Zhengxin Ying
   6. Guanghui Yang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to the lipid metabolism and transporter communities. Fatty acids that are too long to be transported into mitochondria are instead transported into peroxisomes for their break down i.e., beta-oxidation. The authors have determined the cryo-EM structure of human ABC transporter ABCD1 (ALDP), which translocates very-long-chain fatty acids (VLCFA) conjugated to coenzyme A across peroxisomal membranes, in complex with its substrate. While the work is well done, it is unclear what new mechanistic insights are gained from the ALDP structure. Also, the proposed conformational differences based on AlphaFold models should be taken with caution.

     (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.)

   Reviewed by eLife

4. Zinc finger protein Zfp335 controls early T-cell development and survival through β-selection-dependent and -independent mechanisms

   This article has 12 authors:

   1. Xin Wang
   2. Anjun Jiao
   3. Lina Sun
   4. Wenhua Li
   5. Biao Yang
   6. Yanhong Su
   7. Renyi Ding
   8. Cangang Zhang
   9. Haiyan Liu
   10. Xiaofeng Yang
   11. Chenming Sun
   12. Baojun Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors have discovered that the transcription factor Zfp335 is an important regulator of early T cell development in the thymus. This paper will be of interest to scientists within the field of T cell development. The approaches used are thoughtful and rigorous and the key claims are supported by the data. Whether or not Zfp335 specifically controls beta-selection via the gene targets described requires additional experimentation.

     (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.)

   Reviewed by eLife

5. Developmental single-cell transcriptomics of hypothalamic POMC neurons reveal the genetic trajectories of multiple neuropeptidergic phenotypes

   This article has 3 authors:

   1. Hui Yu
   2. Marcelo Rubinstein
   3. Malcolm J Low

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript by Yu et al. captures the transcriptional heterogeneity of mouse POMC neurons across hypothalamic development. This study unifies multiple other observations about the role for other neuron al cell types that express POMC transiently during development. The paper is an important resource understanding of the diversity of POMC neuron classes and their relationship to other cell types in the arcuate nucleus.

     (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.)

   Reviewed by eLife

6. Structure of the human ATM kinase and mechanism of Nbs1 binding

   This article has 2 authors:

   1. Christopher Warren
   2. Nikola P Pavletich

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation summary

     This manuscript is of broad interest to the DNA-repair and structural biology field. The paper describes new insights into the interaction between ATM and Nsb1, proteins central to repairing DNA double-strand breaks in humans. Overall, the structural cryo-electron microscopy data is solid and the data well analyzed and presented with key claims directly related to and supporting previous known findings.

     (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.)

   Reviewed by eLife

7. High-throughput Plasmodium falciparum hrp2 and hrp3 gene deletion typing by digital PCR to monitor malaria rapid diagnostic test efficacy

   This article has 18 authors:

   1. Claudia A Vera-Arias
   2. Aurel Holzschuh
   3. Colins O Oduma
   4. Kingsley Badu
   5. Mutala Abdul-Hakim
   6. Joshua Yukich
   7. Manuel W Hetzel
   8. Bakar S Fakih
   9. Abdullah Ali
   10. Marcelo U Ferreira
   11. Simone Ladeia-Andrade
   12. Fabián E Sáenz
   13. Yaw Afrane
   14. Endalew Zemene
   15. Delenasaw Yewhalaw
   16. James W Kazura
   17. Guiyun Yan
   18. Cristian Koepfli

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The study reports the development of high-throughput droplet digital PCR to detect Plasmodium falciparum parasites carrying pfhrp2 and pfhrp3 gene deletions. These mutations usually cause false-negative RDT results on malaria tests. Although there are several PCR-based detection methods already available, the assay is useful as an alternative, particularly in countries and settings where droplet digital PCR is routinely used. The strength lies in its capability to detect hrp2 and hrp3 deletions in samples with multiclonal (more than one clone) infections. This has the potential to assist in surveillance for pfhrp2/3 deletions programs where RDTs designed to detect HRP2 are the primary test leading to false negative results, particularly in medium to high transmission settings. The study will be of interest to those studying infectious diseases.

     (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.)

   Reviewed by eLife

8. High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

   This article has 8 authors:

   1. Mingrui Duan
   2. Smitha Sivapragasam
   3. Jacob S Antony
   4. Jenna Ulibarri
   5. John M Hinz
   6. Gregory MK Poon
   7. John J Wyrick
   8. Peng Mao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest for researchers interested in DNA repair and transcriptional regulation. The authors provide a series of well-executed and designed high-resolution sequencing data demonstrating that transcription factor (TF) binding perturbs alkylation base damage formation as well as inhibits its repair via base excision repair (BER) at TF binding sites. Moreover, they demonstrate differences between nucleotide excision repair and BER at TF binding sites that are consistent with the different repair mechanism of these two pathways. These results should have an important and timely impact on 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 and Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

9. Hippocampal-hypothalamic circuit controls context-dependent innate defensive responses

   This article has 7 authors:

   1. Jee Yoon Bang
   2. Julia Kathryn Sunstrum
   3. Danielle Garand
   4. Gustavo Morrone Parfitt
   5. Melanie Woodin
   6. Wataru Inoue
   7. Junchul Kim

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to neuroscientists, particularly those studying defensive behaviors. The authors provide novel insights into the mechanisms by which the brain computes contextual information associated with innate threats in mice. The experimental approach and data analysis are mostly adequate and the study provides the first causal evidence of a hippocampus-anterior hypothalamic pathway mediating spatial fear memory of ethological threats. The implementation of more robust statistical tests, as well as more detailed Methods and Discussion sections should serve to strengthen an already elegant study.

     (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.)

   Reviewed by eLife

10. Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents

    This article has 10 authors:

    1. Nikoloz Sirmpilatze
    2. Judith Mylius
    3. Michael Ortiz-Rios
    4. Jürgen Baudewig
    5. Jaakko Paasonen
    6. Daniel Golkowski
    7. Andreas Ranft
    8. Rüdiger Ilg
    9. Olli Gröhn
    10. Susann Boretius

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study reveals that anesthesia-induced burst suppression's spatial patterns differ across humans, macaques, marmosets, and rats. Given that burst suppression is considered a hallmark of unconscious states, these findings are potentially important for us to understand the evolution of the neural correlates of consciousness. In addition, a novel, purely MR-based method is presented to identify and map burst suppression, which may have relevance in both clinical and experimental studies.

      (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.)

    Reviewed by eLife