Systems Biology

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

1. Saugat Poudel
2. Jason Hyun
3. Ying Hefner
4. Jon Monk
5. Victor Nizet
6. Bernhard O Palsson

• Curated by eLife

  eLife assessment

  This study presents valuable findings on core genome mutations that might have driven the emergence of the Staphylococcus aureus lineage USA300, a frequent cause of community-acquired infections. The authors present a solid novel approach that combines genome-wide association studies and RNA-expression analyses, both applied to extensive publicly available datasets. This approach generated an intriguing hypothesis that should be validated experimentally. The work will interest microbiologists working in genomic epidemiology and phenotype-genotype association studies.

Reviewed by eLife

Dynamic map illuminates Hippo to cMyc module crosstalk driving cardiomyocyte proliferation

1. Bryana N. Harris
2. Laura A. Woo
3. R. Noah Perry
4. Mete Civelek
5. Matthew J. Wolf
6. Jeffrey J. Saucerman

Reviewed by Review Commons

Mining the heparinome for cryptic antimicrobial peptides that selectively kill gram-negative bacteria

1. Daniel Sandín
2. Javier Valle
3. Jordi Gómez
4. Laura Comas
5. María Nieves Larrosa
6. Juan José González-López
7. María Ángeles Jiménez
8. David Andreu
9. Marc Torrent

Reviewed by Review Commons

Diurnal rhythmicity in metabolism and salivary effector expression shapes host colonization by aphids

1. Jinlong Han
2. Daniel Kunk
3. Meihua Cui
4. Yoshiahu Goldstein
5. Vered Tzin
6. Vamsi J. Nalam

• Curated by eLife

  eLife assessment

  In this study, the authors found that a species of aphid that is a known agricultural pest salivated longer and produced more honeydew when feeding at night. The authors identified aphid genes with diurnal expression patterns, including potential saliva-related genes. Silencing these genes reduced aphid performance only on real plants, suggesting a specific role in plant feeding. While this study is valuable for understanding plant-insect interactions in agriculture, it is currently incomplete, as further research is needed to elucidate the function of the identified genes.

Reviewed by eLife

Self-inhibiting percolation and viral spreading in epithelial tissue

1. Xiaochan Xu
2. Bjarke Frost Nielsen
3. Kim Sneppen

• Curated by eLife

  eLife assessment

  This study presents a cellular automaton model to study the dynamics of virus-induced signalling and innate host defense against viruses such as SARS-CoV-2 in epithelial tissue. The simulations and data analysis are convincing and represent a valuable contribution that would be of interest to researchers studying the dynamics of viral propagation.

Reviewed by eLife

An Hfq-dependent post-transcriptional mechanism fine tunes RecB expression in Escherichia coli

1. Irina Kalita
2. Ira Alexandra Iosub
3. Lorna McLaren
4. Louise Goossens
5. Sander Granneman
6. Meriem El Karoui

• Curated by eLife

  eLife assessment

  Combining experimental and computation approaches, this manuscript provides solid evidence for a post-transcriptional mechanism that provides robust control over the protein expression level of RecB in E. coli. In addition to uncovering how DNA damage drives more efficient translation of RecB protein, this work also reveals important tenets for how broader mechanisms that suppress noise and underlie responsive tuning of protein levels can be achieved.

Reviewed by eLife

Agent-based model demonstrates the impact of nonlinear, complex interactions between cytokines on muscle regeneration

1. Megan Haase
2. Tien Comlekoglu
3. Alexa Petrucciani
4. Shayn M Peirce
5. Silvia S Blemker

• Curated by eLife

  eLife assessment

  This is so-far the most comprehensive, spatially resolved in 2D, dynamical, multicellular model of murine muscle regeneration after injury. The work is an attempt to combine many contributors to muscle regeneration into one coherent calibrated framework. The presented analysis is solid and the model has the potential to be a very valuable tool in the areas of tissue morphogenesis, regenerative therapies, quantitative modeling and simulation.

Reviewed by eLife

Expressive modeling and fast simulation for dynamic compartments

1. Till Köster
2. Philipp Henning
3. Tom Warnke
4. Adelinde Uhrmacher

Reviewed by preLights

Heritable epigenetic changes are constrained by the dynamics of regulatory architectures

1. Antony M Jose

• Curated by eLife

  eLife assessment

  This useful manuscript explores conditions for epigenetic inheritance by studying the stability of simple network models to permanent and transient perturbations. A novel aspect of the study is that it unifies non-genetic inheritance phenomena across cell divisions of unicellular organisms and in the germline of multicellular organisms. However, the models studied are more a collection of vignettes of numerical studies than a systematic study, therefore the evidence presented remains incomplete. As a first step towards building a more systematic theoretical framework, this work will be of interest to colleagues in the field of epigenetic inheritance.

Reviewed by eLife

The bistable mitotic switch in fission yeast

1. Béla Novák
2. John J. Tyson

Reviewed by Review Commons