Systems Biology

Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate

1. Diana Széliová
2. Stefan Müller
3. Jürgen Zanghellini

Reviewed by Review Commons

Systematic exploration of bacterial form I rubisco maximal carboxylation rates

1. Benoit de Pins
2. Lior Greenspoon
3. Yinon M. Bar-On
4. Melina Shamshoum
5. Roee Ben-Nissan
6. Eliya Milshtein
7. Dan Davidi
8. Itai Sharon
9. Oliver Mueller-Cajar
10. Elad Noor
11. Ron Milo

Reviewed by Review Commons

Tools and methods for high-throughput single-cell imaging with the mother machine

1. Ryan Thiermann
2. Michael Sandler
3. Gursharan Ahir
4. John T Sauls
5. Jeremy Schroeder
6. Steven Brown
7. Guillaume Le Treut
8. Fangwei Si
9. Dongyang Li
10. Jue D Wang
11. Suckjoon Jun

• Curated by eLife

  eLife assessment

  This article provides a review and test of image-analysis methods for bacteria growing in the 'mother-machine' microfluidic device, introducing also a new graphical user interface for the computational analysis of mother-machine movies based on the 'Napari' environment. The tool allows users to segment cells based on two previously published methods (classical image transformation and thresholding as well as UNet-based analysis), with solid evidence for their robust performance based on comparison with other methods and use of datasets from other labs. While it was difficult to assess the user-friendliness of the new GUI, it appears to be valuable and promising for the field.

Reviewed by eLife

Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability

1. Fabien Duveau
2. Céline Cordier
3. Lionel Chiron
4. Matthias Le Bec
5. Sylvain Pouzet
6. Julie Séguin
7. Artémis Llamosi
8. Benoit Sorre
9. Jean-Marc Di Meglio
10. Pascal Hersen

• Curated by eLife

  eLife assessment

  This study presents important findings on how cells sense and respond to their surroundings, in particular when two environmental signals are presented periodically, in alternation or conjunction. The compelling analyses reveal some unexpected behaviors that could not have been drawn, from simpler experimental designs, related to the dynamic interplay between the starvation and hyper-osmotic stress responses in budding yeast, exemplifying that applying complex signals can unveil new biological insights, even for well-studied systems. The work will be of broad interest to researchers interested in fungal biology, dynamic systems, cell signaling, and cell biology.

Reviewed by eLife

Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model

1. Sergi Llambrich
2. Birger Tielemans
3. Ellen Saliën
4. Marta Atzori
5. Kaat Wouters
6. Vicky Van Bulck
7. Mark Platt
8. Laure Vanherp
9. Nuria Gallego Fernandez
10. Laura Grau de la Fuente
11. Harish Poptani
12. Lieve Verlinden
13. Uwe Himmelreich
14. Anca Croitor
15. Catia Attanasio
16. Zsuzsanna Callaerts-Vegh
17. Willy Gsell
18. Neus Martínez-Abadías
19. Greetje Vande Velde

• Curated by eLife

  eLife assessment

  This study presents valuable findings that examine both how Down syndrome (DS)-related physiological, behavioral, and phenotypic traits track across time, as well as how chronic treatment with green tea extracts 25 enriched in epigallocatechin-3-gallate (GTE-EGCG), administered in drinking water spanning prenatal through 5 months of age, impacts these measures in wild-type and Ts65Dn mice. The strength of the evidence is solid, due to high variability across measures, perhaps in part attributable to a failure to include sex as a factor for measures known to be sexually dimorphic. This study is of interest to scientists interested in Down Syndrome and its treatment, as well as scientists who study disorders that impact multiple organ systems.

Reviewed by eLife

A constraint-based framework to reconstruct interaction networks in microbial communities

1. Omid Oftadeh
2. Asli Sahin
3. Evangelia Vayena
4. Vassily Hatzimanikatis

Reviewed by Arcadia Science

High-volume, label-free imaging for quantifying single-cell dynamics in induced pluripotent stem cell colonies

1. Anthony J. Asmar
2. Zackery A. Benson
3. Adele P. Peskin
4. Joe Chalfoun
5. Mylene Simon
6. Michael Halter
7. Anne L. Plant

Reviewed by Arcadia Science

What fraction of cellular DNA turnover becomes cfDNA?

1. Ron Sender
2. Elad Noor
3. Ron Milo
4. Yuval Dor

• Curated by eLife

  eLife assessment

  This manuscript describes a model to estimate what fraction of DNA from specific human tissues becomes cell-free DNA in plasma. This fundamental study, supported by convincing evidence, will be of great interest to the community, as the amount of DNA from a certain tissue (for example, a tumor) that becomes available for detection in the blood has significant implications for disease detection.

Reviewed by eLife

The type of carbon source not the growth rate it supports can determine diauxie

1. Yu Huo
2. Weronika Danecka
3. Iseabail Farquhar
4. Kim Mailliet
5. Tessa Moses
6. Edward W. J. Wallace
7. Peter S. Swain

Reviewed by Review Commons

Vitamin D constrains inflammation by modulating the expression of key genes on Chr17q12-21.1

1. Ayse Kilic
2. Arda Halu
3. Margherita De Marzio
4. Enrico Maiorino
5. Melody G Duvall
6. Thayse Regina Bruggemann
7. Joselyn J Rojas Quintero
8. Robert Chase
9. Hooman Mirzakhani
10. Ayse Özge Sungur
11. Janine Koepke
12. Taiji Nakano
13. Hong Yong Peh
14. Nandini Krishnamoorthy
15. Raja-Elie Abdulnour
16. Katia Georgopoulos
17. Augusto A Litonjua
18. Marie Demay
19. Harald Renz
20. Bruce D Levy
21. Scott T Weiss

• Curated by eLife

  eLife assessment

  The effect of Vitamin D supplementation in reducing asthma via anti-inflammatory mechanisms is a topic of wide interest, with somewhat conflicting published data. Here, bioinformatic approaches help to identify a role of VDR in inducing the expression of the key regulator Ikzf3, which possibly suppresses the IL-2/STAT5 axis, consequently blunting the Th2 response and mitigating allergic airway inflammation. These are important findings based on convincing evidence.

Reviewed by eLife