Systems Biology

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.

Reviewed by eLife

Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns

1. Ken-ichiro F Kamei
2. Koseki J Kobayashi-Kirschvink
3. Takashi Nozoe
4. Hidenori Nakaoka
5. Miki Umetani
6. Yuichi Wakamoto

• Curated by eLife

  eLife Assessment

  This paper reports the fundamental finding of how Raman spectral patterns correlate with proteome profiles. The authors then go further to show that this can be used to infer global stochiometric regulation of the proteomes. These findings are likely general and the authors provide compelling evidence by analyzing bacterial and human cells but there are some suggestions provided below to make the work clearer and more accessible for it to reach a broader audience.

Reviewed by eLife, Arcadia Science

Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

1. David Dierks
2. Ran Shachar
3. Ronit Nir
4. Miguel Angel Garcia-Campos
5. Anna Uzonyi
6. David Wiener
7. Ursula Toth
8. Walter Rossmanith
9. Lior Lasman
10. Boris Slobodin
11. Jacob H Hanna
12. Yaron Antebi
13. Ruth Scherz-Shouval
14. Schraga Schwartz

• Curated by eLife

  eLife Assessment

  This study presents a fundamental finding on how levels of m6A levels are controlled, invoking a consolidated model where degradation of modified RNAs in the cytoplasm plays a primary role in shaping m6A patterns and dynamics, rather than needing active regulation by m6A erasers and other related processes. The evidence is compelling through its use of transcriptome-wide data and mechanistic modeling. Relevant for any reader with an interest in RNA metabolism, this new framework consolidates previous observations and highlights the importance of careful experimentation for evaluation m6A levels.

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 convincing 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 higher levels 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

The Product neutrality function defining genetic interactions emerges from mechanistic models of cell growth

1. Lucas Fuentes Valenzuela
2. Paul Francois
3. Jan Skotheim

• Curated by eLife

  eLife Assessment

  The paper addresses the question of gene epistasis and asks what is the correct null model for which we should declare no epistasis. By reanalyzing synthetic gene array datasets regarding single and double-knockout yeast mutants, and considering two theoretical models of cell growth, the authors reach the valuable conclusion that the product function is a good null model. The analysis is still incomplete, as some assumptions and hypotheses are not fully justified. However, once verified, the results have the potential to be of value to the field of gene epistasis.

Reviewed by eLife

Regulation of replication timing in Saccharomyces cerevisiae

1. Rosie Berners-Lee
2. Eamonn Gilmore
3. Francisco Berkemeier
4. Michael A. Boemo

Reviewed by Review Commons

Transplantation of exogenous mitochondria mitigates myocardial dysfunction after cardiac arrest

1. Zhen Wang
2. Jie Zhu
3. Mengda Xu
4. Xuyuan Ma
5. Maozheng Shen
6. Jingyu Yan
7. Guosheng Gan
8. Xiang Zhou

• Curated by eLife

  eLife Assessment

  In this valuable report, the authors investigated the effect of mitochondrial transplantation on post-cardiac arrest myocardial dysfunction (PAMD), which is associated with mitochondrial dysfunction. They convincingly demonstrated that mitochondrial transplantation enhanced cardiac function and increased survival rates after the return of spontaneous circulation (ROSC). They have also shown that myocardial tissues with transplanted mitochondria exhibited increased mitochondrial complex activity, higher ATP levels, reduced cardiomyocyte apoptosis, and lower myocardial oxidative stress post-ROSC.

Reviewed by eLife

Systems genomics of salinity stress response in rice

1. Sonal Gupta
2. Simon Niels Groen
3. Maricris L Zaidem
4. Andres Godwin C Sajise
5. Irina Calic
6. Mignon Natividad
7. Kenneth McNally
8. Georgina V Vergara
9. Rahul Satija
10. Steven J Franks
11. Rakesh K Singh
12. Zoé Joly-Lopez
13. Michael D Purugganan

• Curated by eLife

  eLife Assessment

  Working with a diverse panel of rice accessions grown in field conditions, this valuable study measures changes in transcript abundance, tests for patterns of selection on gene expression, and maps the genetic basic of variation in gene expression in normal and elevated salinity treatments. The manuscript provides solid evidence that mean gene expression levels are further from the optimum abundance for more genes under the elevated salinity treatment compared to normal treatment, and that a relatively small number of genes are hotspots that harbor genetic variants which affect broader genome-wide patterns of natural variation in gene expression under high salinity conditions. However, the design, clarity, and interpretation of several statistical analyses can be improved, some opportunities for integration among datasets and analyses could yet be realized, and genetic manipulation is required to confirm functional involvement of any specific genes in regulatory networks or organismal traits that confer adaptation to higher salinity conditions. The manuscript will be of interest to evolutionary biologists studying the genetics of complex traits and a resource for plant biologists studying mechanisms of abiotic stress tolerance.

Reviewed by eLife

Hormone circuit analysis explains why most HPA drugs fail for mood disorders and predicts the few that work

1. Tomer Milo
2. Shiraz Nir Halber
3. Moriya Raz
4. Avi Mayo
5. Uri Alon

Reviewed by Review Commons

Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer

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

• Curated by eLife

  eLife Assessment

  This manuscript offers valuable theoretical predictions on how horizontal gene transfer (HGT) can lead to alternative stable states in microbial communities. Using a modeling framework, solid theoretical evidence is provided to support the claimed role of HGT. However, given that the model has many degrees of freedom, a more comprehensive analysis of the role of different parameters could strengthen the study. Additionally, potential interactions between plasmids that carry out HGT are not discussed in the model. This paper would be of interest to researchers in microbiology, ecology, and evolutionary biology.

Reviewed by eLife