Systems Biology

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

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

Exploiting fluctuations in gene expression to detect causal interactions between genes

1. Euan Joly-Smith
2. Mir Mikdad Talpur
3. Paige Allard
4. Fotini Papazotos
5. Laurent Potvin-Trottier
6. Andreas Hilfinger

• Curated by eLife

  eLife assessment

  By taking advantage of noise in gene expression, this important study introduces a new approach for detecting directed causal interactions between two genes without perturbing either. The main theoretical result is supported by a proof, although clearer statements are needed to ensure that there are no edge cases that can violate the theorem. Preliminary simulations and experiments on small circuits are presented, but the evidence remains incomplete because further investigations are needed to demonstrate the broad applicability and scalability of the method.

Reviewed by eLife

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

A kinase to cytokine explorer to identify molecular regulators and potential therapeutic opportunities

1. Marina Chan
2. Yuqi Kang
3. Shannon Osborne
4. Michael Zager
5. Taranjit S Gujral

• Curated by eLife

  eLife assessment

  This manuscript describes an important web resource for kinases connected to cytokines. The compelling information will be used by researchers across a number of fields including analysts, modelers, wet lab experimentalists and clinician-researchers, who are looking to improve our understanding of pathologies and means to correct them through modulating the immune response.

Reviewed by eLife

Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

1. Tae-Yun Kang
2. Federico Bocci
3. Qing Nie
4. José N Onuchic
5. Andre Levchenko

• Curated by eLife

  eLife assessment

  The authors used an appropriate micro-engineered experimental model of angiogenesis coupled to mathematical model to study the early steps of the angiogenic sprouting. To this end, the authors developed a convincing model to predict how VEGF activates Delta-Notch signaling. The work affords important new insight into the complex processes involved in the onset of angiogenesis.

Reviewed by eLife

The genetic and dietary landscape of the muscle insulin signalling network

1. Julian van Gerwen
2. Stewart WC Masson
3. Harry B Cutler
4. Alexis Diaz Vegas
5. Meg Potter
6. Jacqueline Stöckli
7. Søren Madsen
8. Marin E Nelson
9. Sean J Humphrey
10. David E James

• Curated by eLife

  eLife assessment

  This fundamental study provides a unique tool for assessing the range of phosphorylation in insulin reactions due to genetic variation and dietary influence through the utilization of genetically distinct mouse strains. The discoveries of this study hold substantial importance, as they shed light on the interplay between genetic attributes and environmental conditions in shaping the insulin-signaling network within skeletal muscle, a crucial regulator of metabolism. The supporting evidence presented is compelling, and the work is anticipated to captivate a wide audience within the metabolism discipline due to its extensive appeal and by providing inspiration for further hypothesis-driven research.

Reviewed by eLife

Emergence of planar cell polarity from the interplay of local interactions and global gradients

1. Divyoj Singh
2. Sriram Ramaswamy
3. Mohit Kumar Jolly
4. Mohd. Suhail Rizvi

• Curated by eLife

  eLife assessment

  This study presents a valuable model for the emergence of planar cell polarity from the interplay of local interactions and global gradient. The framework of this model is solid, although the appreciation of its result should in places be more quantitative. A quality of this model is its simplicity and its convenience for experimental testing.

Reviewed by eLife