Systems Biology

A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs

1. Michi Miura
2. Naho Kiuchi
3. Siu-Ying Lau
4. Bobo Wing-Yee Mok
5. Hiroshi Ushirogawa
6. Tadasuke Naito
7. Honglin Chen
8. Mineki Saito

• Curated by eLife

  eLife Assessment

  This important study combines virology experiments and mathematical modeling to determine the nuclear export rate of each of the eight RNA segments of the influenza A virus, leading to the proposal that a specific retention of mRNA within the nucleus delays the expression of antigenic viral proteins. The proposed model for explaining the differential rate of export is compelling, going beyond the state of the art, but the experimental setup is only in partial support and further studies will be needed to confirm the proposed mechanism.

Reviewed by eLife

Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression

1. Nadine Tuechler
2. Mira Lea Burtscher
3. Martin Garrido-Rodriguez
4. Muzamil Majid Khan
5. Dénes Türei
6. Christian Tischer
7. Sarah Kaspar
8. Jennifer Jasmin Schwarz
9. Frank Stein
10. Mandy Rettel
11. Rafael Kramann
12. Mikhail M Savitski
13. Julio Saez-Rodriguez
14. Rainer Pepperkok

Reviewed by Review Commons

Evaluating Study Design Rigor in Preclinical Cardiovascular Research: A Replication Study

1. Isaiah C Jimenez
2. Gabrielle C Montenegro
3. Keyana Zahiri
4. Damini Patel
5. Adrienne Mueller

• Curated by eLife

  eLife Assessment

  The objective of this important study is to assess the study design and rigor, enhance the quality of clinical research studies, and emphasize crucial design elements in basic science research. It specifically tackles the ongoing problem of experimental design deficiencies that obstruct the effective translation of research findings into clinical applications. This paper is particularly convincing as it highlights the lack of progress in addressing these issues over the past decade, despite a substantial body of existing research. It serves as a strong call to action for the broader scientific community to improve research practices.

Reviewed by eLife

CausalXtract, a flexible pipeline to extract causal effects from live-cell time-lapse imaging data

1. Franck Simon
2. Maria Colomba Comes
3. Tiziana Tocci
4. Louise Dupuis
5. Vincent Cabeli
6. Nikita Lagrange
7. Arianna Mencattini
8. Maria Carla Parrini
9. Eugenio Martinelli
10. Herve Isambert

• Curated by eLife

  eLife Assessment

  This important study represents a data processing pipeline to discover causal interactions from time-lapse imaging data, and convincingly illustrates it on a challenging application for the analysis of tumor-on-chip ecosystem data. The authors describe the raw data they used (imaging data), go through a step-by-step description on how to extract the features they are interested in from the raw data, and how to perform the causal discovery process. This paper tackles the problem of learning causal interactions from temporal data, which is applicable to many biological applications.

Reviewed by eLife

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

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

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