Cell Biology

APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy

1. James Rae
2. Charles Ferguson
3. Nicholas Ariotti
4. Richard I. Webb
5. Han-Hao Cheng
6. James L. Mead
7. Jamie Riches
8. Dominic J.B. Hunter
9. Nick Martel
10. Joanne Baltos
11. Arthur Christopoulos
12. Nicole S. Bryce
13. Maria Lastra Cagigas
14. Sachini Fonseka
15. Edna C. Hardeman
16. Peter W. Gunning
17. Yann Gambin
18. Thomas Hall
19. Robert G. Parton

• Curated by eLife

  Summary: The manuscript by Rae et al. reports a new protocol for labeling genetically-tagged proteins of interest with heavy atom particles for visualization by electron microscopy. The optimized protocol builds on the use of the enzyme APEX2, fused to the target protein of interest. The contrast enhancement may be useful in diverse 3D EM techniques. Also, reviewers were enthusiastic about the prospects for quantitative studies, even for low-levels of endogenous expression. Semi-quantitative studies may be enabled because the new method appears to improve the proportionality of the signal such that the number of APEX2 tags in a sample correlates with the number of heavy atom particles. The apparent simplicity of the protocol raises the potential for it to become a standard in the field of EM labeling.

  Reviewer #1, Reviewer #2 and Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism

1. Anthony A Ruberto
2. Aline Gréchez-Cassiau
3. Sophie Guérin
4. Luc Martin
5. Johana S Revel
6. Mohamed Mehiri
7. Malayannan Subramaniam
8. Franck Delaunay
9. Michèle Teboul

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest in the fields of circadian biology and metabolic physiology. It provides a molecular mechanism for protection against development of fatty liver in response to high sugar consumption. Quality data support the key claims of the paper in each of the main research areas (circadian biology and metabolism) but additional efforts are needed to integrate the two parts. The current study does not thoroughly connect the in vitro and in vivo findings and misses the opportunity to fully characterize the role of KLF10 in circadian regulation in response to excessive sugar consumption.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Augmenter of Liver Regeneration Regulates Cellular Iron Homeostasis by Modulating Mitochondrial Transport of ATP-Binding Cassette B8

1. Hsiang-Chun Chang
2. Jason S. Shapiro
3. Xinghang Jiang
4. Grant Senyei
5. Teruki Sato
6. Konrad T. Sawicki
7. Hossein Ardehali

• Curated by eLife

  Evaluation Summary:

  This is an interesting manuscript and experiments generally make their point on Alr effects. However, additional data would strengthen the paper with respect to the relative roles of cytoplasmic vs mitochondrial isoforms as would mitochondrial function studies.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Endothelial cell senescence exacerbates pulmonary hypertension through Notch-mediated juxtacrine signaling

1. Risa Ramadhiani
2. Koji Ikeda
3. Kazuya Miyagawa
4. Gusty Rizky Teguh Ryanto
5. Naoki Tamada
6. Yoko Suzuki
7. Ken-ichi Hirata
8. Noriaki Emoto

Reviewed by eLife

Decreasing pdzd8-mediated mitochondrial-ER contacts in neurons improves fitness by increasing mitophagy

1. Victoria L. Hewitt
2. Leonor Miller-Fleming
3. Simonetta Andreazza
4. Francesca Mattedi
5. Julien Prudent
6. Franck Polleux
7. Alessio Vagnoni
8. Alexander J. Whitworth

Reviewed by Review Commons

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast

1. Rachael E. Turner
2. Paul F. Harrison
3. Angavai Swaminathan
4. Calvin A. Kraupner-Taylor
5. Melissa J. Curtis
6. Belinda J. Goldie
7. Michael M. See
8. Amanda L. Peterson
9. Ralf B. Schittenhelm
10. David R. Powell
11. Darren J. Creek
12. Bernhard Dichtl
13. Traude H. Beilharz

• Curated by eLife

  Evaluation Summary:

  This study aims to provide a comprehensive analysis of factors governing polyadenylation site selection in yeast. Overall, the authors reveal that multiple but distinct inputs including polyadenylation machinery integrity, transcription elongation rate, nucleotide availability and chromatin landscape all contribute to controlling cleavage and polyadenylation.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

The recycling endosome protein Rab25 coordinates collective cell movements in the zebrafish surface epithelium

1. Patrick Morley Willoughby
2. Molly Allen
3. Jessica Yu
4. Roman Korytnikov
5. Tianhui Chen
6. Yupeng Liu
7. Isis So
8. Neil Macpherson
9. Jennifer Mitchell
10. Rodrigo Fernandez-Gonzalez
11. Ashley E. E. Bruce

• Curated by eLife

  Evaluation Summary:

  Willoughby et al. examine the role of Rab25 in early embryogenesis in zebrafish. They implicate Rab25 activity in abscission and show various defects including delayed epiboly and altered cell behaviors associated with defective acting dynamics. Overall, this is an interesting and well-written paper. However, there are a number of important controls that are missing and some connections such as the implication of membrane recycling that require stronger experimental validation.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Micronuclei arising due to loss of KIF18A form stable micronuclear envelopes and do not promote tumorigenesis

1. Leslie A. Sepaniac
2. Whitney Martin
3. Louise A. Dionne
4. Timothy M. Stearns
5. Laura G. Reinholdt
6. Jason Stumpff

Reviewed by Review Commons

Human Erbb2-induced Erk activity robustly stimulates cycling and functional remodeling of rat and human cardiomyocytes

1. Nicholas Strash
2. Sophia DeLuca
3. Geovanni L Janer Carattini
4. Soon Chul Heo
5. Ryne Gorsuch
6. Nenad Bursac

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to scientists in the field of regenerative medicine. The authors compare effects of persistent lentiviral expression of various mitogens in cardiomyocytes in vitro. Technically experiments are of a very high standard, but the data are somewhat difficult to translate to the in vivo situation. The statistical analyses would have to be robust and sufficient for the conclusions to be supported by the data.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis

1. Anna Anchimiuk
2. Virginia S Lioy
3. Florian Patrick Bock
4. Anita Minnen
5. Frederic Boccard
6. Stephan Gruber

• Curated by eLife

  Evaluation Summary:

  This manuscript presents some intriguing data to support the notion that B. subtilis cells have tuned a variety of parameters related to SMC loading and translocation to ensure that individual complexes do not collide. This is likely an important but poorly understood aspect of condensins/SMCs, and as such represents a valuable contribution to the field and should be of interest to a broad set of readers.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife