Evaluated articles

A whole-organism landscape of X-inactivation in humans

1. Bjorn Gylemo
2. Maike Bensberg
3. Colm E Nestor

• Curated by eLife

  eLife Assessment

  The study provides a valuable analysis of escape from X-inactivation based on three rare female GTEX-donors with non-mosaic X-inactivation. The methods and analyses are solid and broadly support the authors' claims. Their data are more comprehensive than those presented previously and add significant weight to evidence for which genes are inactivated or escape from X inactivation in humans.

Reviewed by eLife

NR2F2 is required in the embryonic testis for fetal Leydig cell development

1. Aitana Perea-Gomez
2. Natividad Bellido Carreras
3. Magali Dhellemmes
4. Furong Tang
5. Coralie Le Gallo
6. Marie-Christine Chaboissier

Reviewed by eLife

Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics

1. Leonid Peshkin
2. Enrico maria Daldello
3. Elizabeth S Van Itallie
4. Matthew Sonnett
5. Johannes Kreuzer
6. Wilhelm Haas
7. Marc W Kirschner
8. Catherine Jessus

• Curated by eLife

  eLife Assessment

  This important paper describes a comprehensive quantitative phospho-proteomic analysis of the meiotic progression of Xenopus oocytes. Using time-resolved proteomic analyses, the authors provide insights into changes in protein levels and phosphorylation states to an unprecedented depth, quality, and quantitative detail. The key findings are compelling and offer a helpful resource for the scientific community.

Reviewed by eLife

Upstream open reading frames buffer translational variability during Drosophila evolution and development

1. Yuanqiang Sun
2. Yuange Duan
3. Peixiang Gao
4. Chenlu Liu
5. Kaichun Jin
6. Shengqian Dou
7. Wenxiong Tang
8. Hong Zhang
9. Jian Lu

• Curated by eLife

  eLife Assessment

  This study reveals the important role of upstream open reading frames (uORFs) in limiting the translational variability of downstream coding sequences. Through a combination of computational simulations, comparative analyses of translation efficiency across different developmental stages in two closely related Drosophila species, and manipulative, experimental validation of translation buffering by an uORF for a gene, the authors provide convincing evidence supporting their conclusions. This work will be of broad interest to molecular biologists and geneticists.

Reviewed by eLife

A green lifetime biosensor for calcium that remains bright over its full dynamic range

1. Franka H van der Linden
2. Stephen C Thornquist
3. Rick M ter Beek
4. Jelle Y Huijts
5. Mark A Hink
6. Theodorus W J Gadella
7. Gaby Maimon
8. Joachim Goedhart

• Curated by eLife

  eLife Assessment

  This manuscript reports on an FLIM-based calcium biosensor, G-CaFLITS. It represents an important contribution to the field of genetically-encoded fluorescent biosensors, and will serve as a practical tool for the FLIM imaging community. The paper provides convincing evidence of G-CaFLITS's photophysical properties and its advantages over previous biosensors such as Tq-Ca-FLITS. Although the benefits of G-Ca-FLITS over Tq-Ca-FLITS are limited by the relatively small wavelength shift, it presents some advantages in terms of compatibility with available instrumentation and brightness consistency.

Reviewed by eLife

Reconstruction of functional olfactory sensory tissue from embryonic nasal stem cells

1. Kazuya Suzuki
2. Fumi Wagai
3. Mototsugu Eiraku

• Curated by eLife

  eLife Assessment

  This manuscript presents a valuable study utilizing an in vitro organoid system to recapitulate the developmental process of the olfactory epithelium. The authors provided solid evidence indicating that a combination of niche factors can induce organoid development and give rise to multiple cell types. However, the calcium imaging part of the study could be seen as a limitation.

Reviewed by eLife

p53 engagement is a hallmark of an unfolded protein response in the nucleus of mammalian cells

1. Joseph H Park
2. Thomas J Wandless

• Curated by eLife

  eLife Assessment

  This paper presents useful findings that misfolded proteins in the nucleus can impair proteasomal degradation and activate p53. The results supporting the findings are largely solid, but incomplete. The manuscript could be strengthened by including more quantitative data analyses and additional experimentation/discussions on the mechanism of p53 activation by misfolded nuclear proteins. The work will be interesting primarily to scientists studying protein homeostasis.

Reviewed by eLife

ACVR2A facilitates trophoblast cell invasion through TCF7/c-JUN pathway in pre-eclampsia progression

1. Shujing Yang
2. Huanyao Liu
3. Jieshi Hu
4. Binjun Chen
5. Wanlu An
6. Xuwen Song
7. Yi Yang
8. Fang He

• Curated by eLife

  eLife Assessment

  The role of ACVR2A is potentially of importance to both the biology of trophoblast cells and to the pathogenesis of preeclampsia. In this manuscript, the authors have taken a useful first step towards better understanding this protein using a loss of function model in trophoblast cell lines and then examining invasion, proliferation, and transcription in these cells. The study is solid and further in vivo evidence on how target factors participate in the occurrence of placental structural disorders and diseases through potential downstream pathways will be invaluable in the future.

Reviewed by eLife

Mechanical imbalance between normal and transformed cells drives epithelial homeostasis through cell competition

1. Praver Gupta
2. Sayantani Kayal
3. Nobuyuki Tanimura
4. Shilpa P Pothapragada
5. Harish K Senapati
6. Padmashree Devendran
7. Yasuyuki Fujita
8. Dapeng Bi
9. Tamal Das

• Curated by eLife

  eLife Assessment

  In this important study, the authors combine innovative experimental approaches, including direct compressibility measurements and traction force analyses, with theoretical modeling to propose that wild-type cells exert compressive forces on softer HRasV12-transformed cells, influencing competition outcomes. The data generally provide solid evidence that transformed epithelial cells exhibit higher compressibility than wild-type cells, a property linked to their compaction during mechanical cell competition. However, the study would benefit from further characterization of how compression affects the behavior of HRasV12 cells and clearer causal links between compressibility and competition outcomes.

Reviewed by eLife

Cluster size determines morphology of transcription factories in human cells

1. Massimiliano Semeraro
2. Giuseppe Negro
3. Giada Forte
4. Antonio Suma
5. Giuseppe Gonnella
6. Peter R Cook
7. Davide Marenduzzo

• Curated by eLife

  eLife Assessment

  This is a valuable polymer model that provides insight into the origin of macromolecular mixed and demixed states within transcription clusters. The well-performed and clearly presented simulations will be of interest to those studying gene expression in the context of chromatin. While the study is generally solid, it could benefit from a more direct comparison with existing experimental data sets as well as further discussion of the limits of the underlying model assumptions.

Reviewed by eLife

Axonal injury signaling is restrained by a spared synaptic branch

1. Laura J Smithson
2. Juliana L Zang
3. Lucas Junginger
4. Thomas J Waller
5. Lauren Reilly-Jankowiak
6. Sophia A Khan
7. Ye Li
8. Dawen Cai
9. Catherine A Collins

• Curated by eLife

  eLife Assessment

  This important study leverages the power of Drosophila genetics and sparsely-labeled neurons to propose an intriguing new model for neuronal injury signaling. The authors present convincing evidence to show that the somatic response to axonal injury can be suppressed if the injury is not complete, suggesting the presence of a new mode of injury 'integration.' While the underlying mechanism of this fascinating observation has yet to be determined, the phenomenon itself will be of broad significance in the field.

Reviewed by eLife

Acetylcholine modulates prefrontal outcome coding during threat learning under uncertainty

1. Gaqi Tu
2. Peiying Wen
3. Adel Halawa
4. Kaori Takehara-Nishiuchi

• Curated by eLife

  eLife Assessment

  This is an important study using a combination of optogenetics and calcium imaging to provide insight into the function of the cholinergic input to the prelimbic cortex in probabilistic spatial learning as it relates to threat. These data are timely in contributing to an ongoing discussion in the field about the role of phasic cholinergic signaling to the cortex, about which relatively little is known. The strength of the evidence is incomplete and could be improved by changes in task design and analyses, cross-validation of the conditions in calcium imaging, as well as the incorporation of control experiments to more definitively show it is indeed acetylcholine working in this circuit.

Reviewed by eLife

Otoacoustic emissions but not behavioral measurements predict cochlear nerve frequency tuning in an avian vocal communication specialist

1. Diana M Karosas
2. Leslie Gonzales
3. Yingxuan Wang
4. Christopher Bergevin
5. Laurel H Carney
6. Kenneth S Henry

• Curated by eLife

  eLife Assessment

  In contrast with mammals, measures of cochlear tuning in budgerigars do not match the frequency dependence of behavioral tuning. Earlier behavioral data in the budgerigar had shown good selectivity at around 3-4 kHz, but it was unknown whether this unusual selectivity arose in the inner ear or was a more central adaptation. The authors measured both auditory-nerve tuning curves and stimulus-frequency otoacoustic emissions and found fairly normal-looking cochlear tuning in the budgerigar. These important findings imply that any behavioral/perceptual differences in frequency selectivity are likely more central in original. These solid new data also provide significant support for the utility of otoacoustic estimates of cochlear tuning.

Reviewed by eLife

Diverse calcium dynamics underlie place field formation in hippocampal CA1 pyramidal cells

1. Mate Sumegi
2. Gaspar Olah
3. Istvan Paul Lukacs
4. Martin Blazsek
5. Judit K Makara
6. Zoltan Nusser

• Curated by eLife

  eLife Assessment

  This fundamental study provides new insights into the plasticity mechanisms underlying the formation of spatial maps in the hippocampus. Supported by a large and comprehensive dataset, the evidence is convincing. This study will be of interest to neuroscientists focusing on spatial navigation, learning, and memory.

Reviewed by eLife

Microglia replacement by ER-Hoxb8 conditionally immortalized macrophages provides insight into Aicardi-Goutières Syndrome neuropathology

1. Kelsey M Nemec
2. Genevieve Uy
3. V Sai Chaluvadi
4. Freddy S Purnell
5. Bilal Elfayoumi
6. Leila Byerly
7. Micaela L O’Reilly
8. Carleigh A O’Brien
9. William H Aisenberg
10. Sonia I Lombroso
11. Xinfeng Guo
12. Niklas Blank
13. Chet Huan Oon
14. Fazeela Yaqoob
15. Brian Temsamrit
16. Priyanka Rawat
17. Christoph A Thaiss
18. Will Bailis
19. Adam P Williamson
20. Qingde Wang
21. Mariko L Bennett
22. F Chris Bennett

• Curated by eLife

  eLife Assessment

  This revised study describes an important new model for in vivo manipulation of microglia, exploring how mutations in the Adar1 gene within microglia contribute to Aicardi-Goutières Syndome. The methodology is validated with exceptional data, supporting the authors' conclusions. The paper underscores both the advantages and limitations of using transplanted cells as a surrogate for microglia, making it a resource that is of value for biologists studying macrophages and microglia.

Reviewed by eLife

Neural adaptation to the eye’s optics through phase compensation

1. Antoine Barbot
2. John T Pirog
3. Cherlyn J Ng
4. Geunyoung Yoon

• Curated by eLife

  eLife Assessment

  This paper shows convincingly that the human visual system can recalibrate itself to compensate for phase alterations in an image induced by optical blur. This phenomenon is studied using state-of-the-art adaptive optics approaches that allow the manipulation of the eye's optics while making concurrent psychophysical measurements. The findings are broadly important because they highlight a neural mechanism by which flawed information is used to create seemingly accurate perceptions of the visual environment.

Reviewed by eLife

Female Moths Incorporate Plant Acoustic Emissions into Their Oviposition Decision-Making Process

1. Rya Seltzer
2. Guy Zer Eshel
3. Omer Yinon
4. Ahmed Afani
5. Ofri Eitan
6. Sabina Matveev
7. Galina Levedev
8. Michael Davidovitz
9. Tal Ben Tov
10. Gayl Sharabi
11. Yuval Shapira
12. Neta Shvil
13. Maya Harari Gibli
14. Ireen Atallah
15. Sahar Hadad
16. Dana Ment
17. Lilach Hadany
18. Yossi Yovel

• Curated by eLife

  eLife Assessment

  This study reveals that female moths use ultrasonic sounds emitted by dehydrated plants to guide their oviposition decisions. It highlights sound as an additional sensory modality in host searching, adding an important piece to the puzzle of how insects and plants interact. Through convincing experimental approaches, the authors provide insights that advance our understanding of plant-insect interactions.

Reviewed by eLife

Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodes

1. Stephen A Banse
2. Christine A Sedore
3. Anna Coleman-Hulbert
4. Erik Johnson
5. Brian Onken
6. David Hall
7. Erik Segerdell
8. E Grace Jackson
9. Yuhua Song
10. Haley C Osman
11. Jian Xue
12. Elena Basttistoni
13. Suhzen Guo
14. Anna Foulger
15. Madhuri Achanta
16. Mustafa Sheikh
17. Theresa Fitzgibbon
18. John H Willis
19. Gavin C Woodruff
20. Monica Driscoll
21. Gordon Lithgow
22. Patrick C Phillips

• Curated by eLife

  eLife Assessment

  This important study explores the power of computational methods to predict lifespan-extending small molecules, demonstrating that while these methods significantly increase hit rates, experimental validation remains essential. The study uses all-trans retinoic acid in Caenorhabditis elegans as a model, providing genetic and transcriptomic insights into its longevity effects. The data are compelling in describing a robust, computationally informed screening process for discovering compounds that extend lifespan in this species.

Reviewed by eLife

A sex-specific Mendelian randomization-phenome-wide association study of body mass index

1. Zhu Liduzi Jiesisibieke
2. Io Ieong Chan
3. Jack Chun Man Ng
4. C Mary Schooling

• Curated by eLife

  eLife Assessment

  The study presents valuable findings on Mendelian randomization-phenome-wide association, with BMI associated with health outcomes, and there is a focus on sex differences. The phenotype and genotype data are convincing. The work will be of interest to researchers and clinicians in epidemiology, public health and medicine.

Reviewed by eLife