Systems Biology

Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age

1. Dylan C Sarver
2. Muzna Saqib
3. Fangluo Chen
4. G William Wong

• Curated by eLife

  eLife Assessment

  This important study provides a comprehensive assessment of mitochondrial function across age and sex in mice. The strength of evidence supporting this resource is compelling, given the exhaustive number of tissues profiled and in-depth analyses performed.

Reviewed by eLife

Genome-wide consensus transcriptional signatures identify synaptic pruning linking Alzheimer’s disease and epilepsy

1. Huihong Li
2. Zhiran Xie
3. Yuxuan Tian
4. Yaxi Yang
5. Bingying Lin
6. Si Chen
7. Jianwei Li
8. Jie Wu
9. Mingjie Chen
10. Xueke Liu
11. Yushan Sun
12. Zihan Deng
13. Mengqi Hong
14. Bing Huang
15. Naili Wei
16. Xiaoyu Ji

Reviewed by PREreview

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

1. Yuzhen Liu
2. Christopher D McGann
3. Mary Krebs
4. Thomas A Perkins
5. Rose Fields
6. Conor K Camplisson
7. David Z Nwizugbo
8. Chris Hsu
9. Shayan C Avanessian
10. Ashley F Tsue
11. Evan E Kania
12. David M Shechner
13. Brian J Beliveau
14. Devin K Schweppe

• Curated by eLife

  eLife Assessment

  This study presents a valuable new method for probing the DNA and proteins associated with targeted genomic elements in cells. The authors present solid evidence that the method can map DNA-DNA interactions for individual loci and can detect enriched proteins at repetitive DNA loci such as telomeres, but benchmarks of the method's resolution and specificity remain incomplete. The methodological details of this study will be of particular interest and utility to chromatin biologists.

Reviewed by eLife

PhysiMeSS - a new physiCell addon for extracellular matrix modelling

1. Vincent Noël
2. Marco Ruscone
3. Robyn Shuttleworth
4. Cicely K. Macnamara

• Curated by GigaByte

  Editors Assessment:

  PhysiCell is an open source multicellular systems simulator for studying many interacting cells in dynamic tissue microenvironments. As part of the PhysiCell ecosystem of tools and modules this paper presents a PhysiCell addon, PhysiMeSS (MicroEnvironment Structures Simulation) which allows the user to accurately represent the extracellular matrix (ECM) as a network of fibres. This can specify rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM, allowing the PhysiCell user the ability to investigate physical interactions with cells and other fibres. Reviewers asked for additional clarification on a number of features. And the paper now clear future releases will provide full 3D compatibility and include working on fibrogenesis, i.e. the creation of new ECM fibres by cells.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

1. Jie Luo
2. Jeff Ranish

• Curated by eLife

  eLife Assessment

  This manuscript presents a valuable new quantitative crosslinking mass spectrometry approach using novel isobaric crosslinkers. The data are solid and the method has potential for a broad application in structural biology if more isobaric crosslinking channels are available and the quantitative information of the approach is exploited in more depth.

Reviewed by eLife

Diversity in Notch ligand-receptor signaling interactions

1. Rachael Kuintzle
2. Leah A Santat
3. Michael B Elowitz

• Curated by eLife

  eLife Assessment

  This valuable study significantly enhances our understanding of how various ligands and receptors interact within the Notch signaling pathway. By developing novel cell-based assay systems, the authors systematically analyzed the effects of different ligand-receptor combinations on pathway activation. The convincing data reveal intriguing and unexpected differences and provide a foundation for interpreting Notch signalling in both normal and disease-related contexts.

Reviewed by eLife

Ribosome demand links transcriptional bursts to protein expression noise

1. Sampriti Pal
2. Upasana Ray
3. Riddhiman Dhar

• Curated by eLife

  eLife Assessment

  This interesting study focuses on a previously reported positive correlation between translational efficiency and protein noise. This is unexpected as typically noise is inversely related to expression and increasing translation efficiency would increase the protein expression and thus be expected to reduce noise in gene expression. Using mathematical modeling and analysis of experimental data the authors argue that this phenomenon arises due to ribosomal demand. However, the work appears incomplete, with the reviewers having raised questions regarding the validity of the assumptions used in the mathematical model as well as the clarity of the presentation.

Reviewed by eLife

Proteomic and functional comparison between human induced and embryonic stem cells

1. Alejandro J Brenes
2. Eva Griesser
3. Linda V Sinclair
4. Lindsay Davidson
5. Alan R Prescott
6. Francois Singh
7. Elizabeth KJ Hogg
8. Carmen Espejo-Serrano
9. Hao Jiang
10. Harunori Yoshikawa
11. Melpomeni Platani
12. Jason R Swedlow
13. Greg M Findlay
14. Doreen A Cantrell
15. Angus I Lamond

• Curated by eLife

  eLife Assessment

  This study reports differences in proteomic profiles of embryonic versus induced pluripotent stem cells. This important finding cautions against the interchangeable use of both types of cells in biomedical research, although the mechanisms responsible for these differences remains unknown. The proteomic evidence is convincing, even though there is limited validation with other methods.

Reviewed by eLife

DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

1. Vincent Gardeux
2. Roel PJ Bevers
3. Fabrice PA David
4. Emily Rosschaert
5. Romain Rochepeau
6. Bart Deplancke

• Curated by eLife

  eLife Assessment

  Genetic analysis of complex traits in Drosophila provides a resource for exploring the relationship between genetic and phenotypic variation. The web tool DGRPool presented in this paper makes data and results from the Drosophila Genetic Reference Panel accessible that will enable downstream analyses of genetic association. The findings of this paper are considered to be important, with practical implications beyond a single subfield, supported by convincing evidence using appropriate and validated methodology in line with current state of the art.

Reviewed by eLife

A mathematical model for ketosis-prone diabetes suggests the existence of multiple pancreatic β-cell inactivation mechanisms

1. Sean A Ridout
2. Priyathama Vellanki
3. Ilya Nemenman

• Curated by eLife

  eLife assessment:

  This theoretical study makes a useful contribution to our understanding of a subtype of type 2 diabetes – ketosis-prone diabetes mellitus (KPD) – with a potential impact on our broader understanding of diabetes and glucose regulation. The article presents an ordinary differential equation-based model for KPD that incorporates a number of distinct timescales – fast, slow, as well as intermediate, incorporating a key hypothesis of reversible beta cell deactivation. The presented evidence is solid and shows that observed clinical disease trajectories may be explained by a simple mathematical model in a particular parameter regime.

Reviewed by eLife