Biophysics

How to assemble a scale-invariant gradient

1. Arnab Datta
2. Sagnik Ghosh
3. Jane Kondev

• Curated by eLife

  Evaluation Summary:

  How biological patterns such as concentration gradient scale with the size of the cell or organism is a long-standing question in developmental and cell biology. In this study, Datta et al show theoretically that directed membrane transport of biomolecules and their release at the cell pole results in a cytoplasmic gradient that scales with cell size if two requirements are met: the cell grows while maintaining its spheroid proportions, (i.e. not by elongation), and the binding of the cytoplasmic fraction of the biomolecule to the membrane should be close to irreversible. A strength of this manuscript is that it invokes a realistic cellular mechanism that could be achieved through several biochemical implementations and can inspire experimental studies. Stronger biological examples and a deeper search in the literature or change in some of the simulation parameters would improve the study, and give the "impetus for experiments" the authors wish to provide.

  (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

A Possible Way to Relate the Effects of SARS-CoV-2-Induced Changes in Transferrin to Severe COVID-19-Associated Diseases

1. Elek Telek
2. Zoltán Ujfalusi
3. Gábor Kemenesi
4. Brigitta Zana
5. Ferenc Jakab
6. Gabriella Hild
7. András Lukács
8. Gábor Hild

Reviewed by ScreenIT

Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility

1. Anacleto Silva de Souza
2. Vitor Martins de Freitas Amorim
3. Robson Francisco de Souza
4. Cristiane Rodrigues Guzzo

Reviewed by ScreenIT

Contingency and selection in mitochondrial genome dynamics

1. Christopher J Nunn
2. Sidhartha Goyal

• Curated by eLife

  Evaluation Summary:

  This study uses long-read sequencing to investigate the origin of spontaneous petite mutants in S. cerevisiae. The results illustrate how the S. cerevisiae mitochondrial genome is prone to recombination events that lead to the formation of complex concatemers of fragments of the mitochondrial DNA that contain a high density of replication origins and, as a result, may outcompete the full mitochondrial genome. Apart from confirming existing hypotheses about the nature of petite mutants and revealing the structural diversity of rho-mitochondrial DNA, the results also allow drawing parallels to the origins of mitochondrial mutations in other organisms.

  (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 name with the authors.)

Reviewed by eLife

Distinctive mechanisms of epilepsy-causing mutants discovered by measuring S4 movement in KCNQ2 channels

1. Michaela A Edmond
2. Andy Hinojo-Perez
3. Xiaoan Wu
4. Marta E Perez Rodriguez
5. Rene Barro-Soria

• Curated by eLife

  Evaluation Summary:

  This study investigates the mechanism of voltage-dependent activation of the KCNQ class of potassium channels that regulate neuronal firing, and are mutated in monogenic forms of epilepsy. This study makes an important technical step forward by reporting measurements of voltage-dependent conformational changes of KCNQ2/Kv7.2 channels, measurements which are known to be extremely difficult for this biologically important channel. Understanding these conformational changes allows the authors to investigate models of how voltage-dependent changes are coupled to opening of the channel pore, and also identify diverse mechanisms by which disease-linked mutations of KCNQ2/Kv7.2 may alter channel function.

  (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

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein

1. Huaying Zhao
2. Ai Nguyen
3. Di Wu
4. Yan Li
5. Sergio A Hassan
6. Jiji Chen
7. Hari Shroff
8. Grzegorz Piszczek
9. Peter Schuck

Reviewed by ScreenIT

Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids

1. Debdeep Chatterjee
2. Reeba S Jacob
3. Soumik Ray
4. Ambuja Navalkar
5. Namrata Singh
6. Shinjinee Sengupta
7. Laxmikant Gadhe
8. Pradeep Kadu
9. Debalina Datta
10. Ajoy Paul
11. Sakunthala Arunima
12. Surabhi Mehra
13. Chinmai Pindi
14. Santosh Kumar
15. Praful Singru
16. Sanjib Senapati
17. Samir K Maji

• Curated by eLife

  Evaluation Summary:

  This study sheds light on the formation of Prolactin/Galanin functional amyloids and their storage in secretory granules of the anterior pituitary gland. This study sharpens our understanding of the regulation of hormonal release from the pituitary gland. It will be of interest to the fields of endocrinology, neurobiology and cancer.

  (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

Bayesian machine learning analysis of single-molecule fluorescence colocalization images

1. Yerdos A Ordabayev
2. Larry J Friedman
3. Jeff Gelles
4. Douglas L Theobald

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to researchers who perform single-molecule fluorescence imaging experiments as well as those who want to include machine learning in their data analyses. The authors have developed a machine learning algorithm that addresses some of the data analysis challenges in the field of single-molecule fluorescence imaging. The methods are rigorously benchmarked using simulated data and tested using real data. There are some concerns whether Tapqir is general enough for use by the broader community of single-molecule fluorescence researchers.

  (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 #2 agreed to share their name with the authors.)

Reviewed by eLife

Mutations of Omicron Variant at the Interface of the Receptor Domain Motif and Human Angiotensin-Converting Enzyme-2

1. Puja Adhikari
2. Bahaa Jawad
3. Rudolf Podgornik
4. Wai-Yim Ching

Reviewed by ScreenIT

Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2

1. Zhi-Bi Zhang
2. Yuan-Ling Xia
3. Jian-Xin Shen
4. Wen-Wen Du
5. Yun-Xin Fu
6. Shu-Qun Liu

Reviewed by ScreenIT