eLife

Latest preprint reviews

1. Combining mutation and recombination statistics to infer clonal families in antibody repertoires

   This article has 5 authors:

   1. Natanael Spisak
   2. Gabriel Athènes
   3. Thomas Dupic
   4. Thierry Mora
   5. Aleksandra M Walczak

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study provides a new, apparently high-performance algorithm for B cell clonal family inference. The new algorithm is highly innovative and based on a rigorous probabilistic analysis of the relevant biological processes and their imprint on the resulting sequences, however, the strength of evidence regarding the algorithm's performance is incomplete, due to (1) a lack of clarity regarding how different data sets were used for different steps during algorithm development and validation, resulting in concerns of circularity, (2) a lack of detail regarding the settings for competitor programs during benchmarking, and (3) method development, data simulation for method validation, and empirical analyses all based on the B cell repertoire of a single subject. With clarity around these issues and application to a more diverse set of real samples, this paper could be fundamental to immunologists and important to any researcher or clinician utilizing B cell receptor repertoires in their field (e.g., cancer immunology).

   Reviewed by eLife

2. CYRI-B-mediated macropinocytosis drives metastasis via lysophosphatidic acid receptor uptake

   This article has 9 authors:

   1. Savvas Nikolaou
   2. Amelie Juin
   3. Jamie A Whitelaw
   4. Nikki R Paul
   5. Loic Fort
   6. Colin Nixon
   7. Heather J Spence
   8. Sheila Bryson
   9. Laura M Machesky

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study combines in vivo and in vitro models to characterise the role of CYRI-B, an interactor of the small GTPase Rac1, in controlling pancreatic cancer progression towards a higher proliferative and metastatic stage. The evidence supporting the claims of the authors is convincing in characterizing a novel Rac1 binding protein, CYRI-B, as a regulator of metastatic potential in vivo, with distinct functions at different stages of tumour progression. CYRI-B reduces the typical hyperactivation of Rac1 in the early stages of tumour progression; subsequently, CYRI-B mediates internalization of lysophosphatidic acid receptor 1 (LPAR1) uptake through macropinocytosis, thus regulating chemotactic migration of cancer cells towards lysophosphatidic acid (LPA). Although the inclusion of human pancreatic cancer cell lines would have strengthened the study, the work will be of broad interest to cell biologists and the signalling research communities.

   Reviewed by eLife

3. Perceptual learning improves discrimination while distorting appearance

   This article has 4 authors:

   1. Sarit F.A. Szpiro
   2. Charlie S. Burlingham
   3. Eero P. Simoncelli
   4. Marisa Carrasco

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This work presents a potentially important behavioral finding: that perceptual learning may not only improve but also distort the appearance of visual stimuli. The strength of the presented evidence in support of the main claim is however incomplete, and requires further analyses to confirm that perceptual learning does increase overestimation bias, and clarify why a very large baseline overestimation bias is present in the data.

   Reviewed by eLife

4. RETRACTED: Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights

   This article has 2 authors:

   1. Nima Mohseni
   2. Eran Elhaik

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors present a critique of current usage of principal component analysis in geometric morphometrics, making a compelling case with benchmark data that standard techniques perform poorly. The work is an important contribution to the field and will hopefully lead to a reassessment of the methodology most scientists in morphometrics currently use. This work challenges a very commonly used analytical approach and is bound to raise some controversy in the community, but the authors' critique is based on a well-founded and well-thought out analysis.

   Reviewed by eLife

5. A ‘torn bag mechanism’ of small extracellular vesicle release via limiting membrane rupture of en bloc released amphisomes (amphiectosomes)

   This article has 15 authors:

   1. Tamás Visnovitz
   2. Dorina Lenzinger
   3. Anna Koncz
   4. Péter M Vizi
   5. Tünde Bárkai
   6. Krisztina V Vukman
   7. Alicia Galinsoga
   8. Krisztina Németh
   9. Kelsey Fletcher
   10. Zsolt I Komlósi
   11. Csaba Cserép
   12. Ádám Dénes
   13. Péter Lőrincz
   14. Gábor Valcz
   15. Edit I Buzas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this study, the authors present compelling data illustrating a potential mechanism for a hitherto not described form of extracellular vesicle biogenesis. Their model suggests that small extracellular vesicles are secreted from cells within larger vesicles, termed amphiectosomes, which subsequently rupture to release their smaller vesicle contents. This discovery represents an important advancement in the field.

   Reviewed by eLife

6. Malaria parasite resistance to azithromycin is not readily transmitted by mosquitoes

   This article has 7 authors:

   1. Hayley D. Buchanan
   2. Robyn McConville
   3. Lee M. Yeoh
   4. Michael F. Duffy
   5. Justin A. Boddey
   6. Geoffrey I. McFadden
   7. Christopher D. Goodman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important work addressed the identifcation of antimalarial drug resistance mutations that do not readily transmit to new human hosts, focusing on azithromycin resistance. The technically challenging analyses of azithromycin-resistant parasites as they traverse the mosquito host and human liver are conducted using state-of-the-art tools, including humanized mice. While the claim regarding the lack of transmission by atovaquone-resistant P. berghei is convincing, the evidence for the lack of transmission by atovaquone-resistant P. falciparum is insufficient. This work will appeal to biologists and biomedical scientists in parasitology and drug discovery, offering insights into combating antimalarial drug resistance and understanding the fitness costs associated with drug-resistant parasites.

   Reviewed by eLife, Rapid Reviews Infectious Diseases

7. Modulation of α-synuclein aggregation amid diverse environmental perturbation

   This article has 3 authors:

   1. Abdul Wasim
   2. Sneha Menon
   3. Jagannath Mondal

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides important biophysical insights into the molecular mechanism underlying the association of alpha-synuclein chains, which is essential for understanding the pathogenesis of Parkinson's disease. The data analysis is solid, and the methodology can help investigate other molecular processes involving intrinsically disordered proteins.

   Reviewed by eLife

8. Root cap cell corpse clearance limits microbial colonization in Arabidopsis thaliana

   This article has 6 authors:

   1. Nyasha Charura
   2. Ernesto Llamas
   3. Concetta De Quattro
   4. David Vilchez
   5. Moritz K Nowack
   6. Alga Zuccaro

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study investigated the involvement of programmed cell death (PCD) in Arabidopsis thaliana root cap cells and its effect on microbial colonization. The authors have reported the importance of timely corpse clearance in the root cap and a root cap-specific transcription factor in controlling microbial colonization by beneficial fungi. By demonstrating the connection between transcriptional control of PCD and microbial colonization, this study provides fundamental insights into how relationships are established and regulated at the root-microbiome interface. The strength of the evidence presented is convincing, providing a foundation for further research concerning the spatial and temporal dynamics of microbiome recruitment along the root axis.

   Reviewed by eLife

9. Human induced pluripotent stem cell-derived cardiomyocytes to study inflammation-induced aberrant calcium transient

   This article has 11 authors:

   1. Yuki Tatekoshi
   2. Chunlei Chen
   3. Jason Solomon Shapiro
   4. Hsiang-Chun Chang
   5. Malorie Blancard
   6. Davi M Lyra-Leite
   7. Paul W Burridge
   8. Matthew Feinstein
   9. Richard D'Aquila
   10. Priscilla Hsue
   11. Hossein Ardehali

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This useful study focuses on heart failure with preserved ejection fraction (HFpFE), common in patients with HIV. Researchers used induced human pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to stimulate HEFpEF) and found that inflammatory cytokines alter Ca2+ transients. SGLT2 inhibitors and mitochondrial antioxidants reversed this effect. While the study is incomplete and preliminary, its strength lies in introducing hiPSC-CMs as a tool for investigating HFpEF mechanisms. A major weakness was found to be limited functional assessment relevant to HFpEF.

   Reviewed by eLife

10. An in vitro approach reveals molecular mechanisms underlying endocrine disruptor-induced epimutagenesis

    This article has 5 authors:

    1. Jake D Lehle
    2. Yu-Huey Lin
    3. Amanda Gomez
    4. Laura Chavez
    5. John R McCarrey

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This important study, characterizing the epigenetic and transcriptomic response of a variety of cell types representative of somatic, germline, and pluripotent cells to BPS, reveals the cell type-specific changes in DNA methylation and the relationship with the genome sequence. The findings are convincing and provide a basis for future analyses in vivo. This work should be of interest to biomedical researchers who work on epigenetic reprogramming and epigenetic inheritance.

    Reviewed by eLife