Systems Biology

Exploration of the Metabolomic Mechanisms of Postmenopausal Hypertension Induced by Low Estrogen State

1. Yao Li
2. Hui Xin
3. Zhexun Lian
4. Wei Zhang

• Curated by eLife

  eLife Assessment

  This useful study provides incomplete evidence regarding the pathophysiological role of low estrogen levels post-menopause in hypertension, focusing on L-AABA as a key mediator. The results describe a novel hypothesis for the pathophysiology of hypertension in this population and are of interest to experts in hypertension and vascular biology.

Reviewed by eLife

Emergence of power-law distributions in protein-protein interaction networks through study bias

1. David B. Blumenthal
2. Marta Lucchetta
3. Linda Kleist
4. Sándor P. Fekete
5. Markus List
6. Martin H. Schaefer

• Curated by eLife

  eLife Assessment

  This manuscript makes an important contribution to the understanding of protein-protein interaction (PPI) networks by challenging the widely held assumption that their degree distributions uniformly follow a power law. The authors present convincing evidence that biases in study design, such as data aggregation and selective research focus, may contribute to the appearance of power-law-like distributions. While the power law assumption has already been questioned in network biology, the methodological rigor and correction procedures introduced here are valuable for advancing our understanding of PPI network structure.

Reviewed by eLife

Emergence of alternative stable states in gene exchange communities

1. Juken Hong
2. Wenzhi Xue
3. Teng Wang

• Curated by eLife

  eLife Assessment

  This manuscript offers a modeling platform in which horizontal gene transfer (HGT) is incorporated into the ecological dynamics of microbial communities. The investigation is valuable as it brings to the forefront a potentially significant process and highlights its implications. However, the investigation in its current form is incomplete because it is based on a narrow range of parameters and assumptions. As a result, the scope and relevance of the findings are not fully clear. A more in-depth description of model assumptions and the formulation structure and a more thorough analysis of the impact of different parameters would strengthen the manuscript. This work will be of interest to microbiologists as well as researchers in ecological and evolutionary biology.

Reviewed by eLife

Abundant clock proteins point to missing molecular regulation in the plant circadian clock

1. Uriel Urquiza-García
2. Nacho Molina
3. Karen J. Halliday
4. Andrew J. Millar

Reviewed by Review Commons

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

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

Perturbation-response analysis of in silico metabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity

1. Yusuke Himeoka
2. Chikara Furusawa

• Curated by eLife

  eLife Assessment

  This valuable study uses dynamic metabolic models to compare perturbation responses in a bacterial system, analyzing whether they return to their steady state or amplify beyond the initial perturbation. The evidence supporting the emergent properties of perturbed metabolic systems to network topology and sensitivity to specific metabolites is solid, although the authors do not explain the origin of some significant inconsistencies between models.

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