Evaluated articles

Frontal cortical regions associated with attention connect more strongly to central than peripheral V1

1. Sara A. Sims
2. Pinar Demirayak
3. Simone Cedotal
4. Kristina M. Visscher

• Curated by eLife

  Summary: The manuscript is a replication of findings from Griffis et al., 2017, and it seeks to validate those findings using a different modality (diffusion-weighted imaging; DWI). While the questions asked in this manuscript are of considerable interest to the field, the findings' focus and implications are relatively narrow. Further, the study does not reveal new conclusions about brain function or organization. Authors may be cautious about interpreting the findings as representing direct structural connections between the occipital and frontal cortex -- as the reported structural and functional connectivity values may not be strong enough to support such a strong interpretation. The reviewers also agree that the methods are not presented clearly, in a manner that is straightforward to follow and critique.

Reviewed by eLife

Structural characterization of the ANTAR antiterminator domain bound to RNA

1. James L Walshe
2. Rezwan Siddiquee
3. Karishma Patel
4. Sandro F Ataide

• Curated by eLife

  Summary: The reviewers were excited by the structural data, and felt that the structure represents an important advance in our understanding of ANTAR domain proteins. Nonetheless, while the reviewers found the proposed model of ANTAR regulation to be interesting, they raised concerns about the limited evidence in support of this model. In addition to the suggestions in the individual reviews, the authors thought the model could be tested using mutagenesis together with an in vivo or in vitro reporter system, and/or by structural studies of nascent transcripts in transcription complexes with EutV.

Reviewed by eLife

Starburst amacrine cells amplify optogenetic visual restoration through gap junctions

1. Yusaku Katada
2. Hiromitsu Kunimi
3. Naho Serizawa
4. Deokho Lee
5. Kenta Kobayashi
6. Kazuno Negishi
7. Hideyuki Okano
8. Kenji F. Tanaka
9. Kazuo Tsubota
10. Toshihide Kurihara

Reviewed by eLife

Adaptive evolution of nontransitive fitness in yeast

1. Sean W Buskirk
2. Alecia B Rokes
3. Gregory I Lang

• Curated by eLife

  Summary: The findings presented in this manuscript are interesting. They show that selection is happening at multiple scales - among viruses within a cell - and between their host cells within a population. The conflict between these levels of selection results in evolved populations that are less fit than the ancestors. This work demonstrates that evolution may not be a simple linear march of progress. Rather, progress over short time scales can sometimes lead to a reduction of fitness over the longer time scale due to the evolution of ecological interactions.

Reviewed by eLife

DRAXIN regulates interhemispheric fissure remodelling to influence the extent of corpus callosum formation

1. Laura Morcom
2. Timothy J Edwards
3. Eric Rider
4. Dorothy Jones-Davis
5. Jonathan WC Lim
6. Kok-Siong Chen
7. Ryan J Dean
8. Jens Bunt
9. Yunan Ye
10. Ilan Gobius
11. Rodrigo Suárez
12. Simone Mandelstam
13. Elliott H Sherr
14. Linda J Richards

• Curated by eLife

  Summary: Your manuscript is an excellent account of the cellular and genetic mechanisms involved in the diversity of corpus callosum dysgenesis (CCD) phenotypes in humans and in a mouse model. Your work over the years has revealed that interhemispheric fissure (IHF) fusion is critical for proper formation of the callosum and its failure is the main cause of complete CCD. Here you nicely show that the extent of aberrant interhemispheric fissure (IHF) remodeling does in fact correlate with commissure dysgenesis severity, in inbred and outcrossed BTBR mouse strains, as well as in humans with partial CCD. The phenotypes in the mouse are very similar to what is found in humans, and also variable, perhaps related to stochasticity on the mechanisms involved, or to the dependency on other allelic variants.

  You also identify an eight base pair deletion in Draxin and misregulated astroglial and leptomeningeal proliferation as genetic and cellular factors for variable IHF remodelling and CCD in BTBR acallosal strains. The Draxin mutations interrupt the normal remodeling (closing) of interhemispheric fissure necessary for callosal axons to cross. Your study thus places the focus on midline cellular populations and away from axonal navigation as the main source of corpus callosum dysgenesis. The findings are important to understand what mutations cause CCD in humans and how, mechanistically, it occurs.

  This manuscript was co-submitted with https://www.biorxiv.org/content/10.1101/2020.08.03.233593v1

Reviewed by eLife

Flagellar energetics from high-resolution imaging of beating patterns in tethered mouse sperm

1. Ashwin Nandagiri
2. Avinash Satish Gaikwad
3. David L Potter
4. Reza Nosrati
5. Julio Soria
6. Moira K O'Bryan
7. Sameer Jadhav
8. Ranganathan Prabhakar

Reviewed by eLife

Phasic oxygen dynamics confounds fast choline-sensitive biosensor signals in the brain of behaving rodents

1. Ricardo M Santos
2. Anton Sirota

Reviewed by eLife

Trading mental effort for confidence in the metacognitive control of value-based decision-making

1. Douglas G Lee
2. Jean Daunizeau

• Curated by eLife

  Summary: This manuscript addresses a timely subject: the role of cognitive control (or mental effort) in value-based decision making. While there are plenty of models explaining value-based choice, and there is a growing number of computational accounts concerning effort-allocation, little theoretical work has been done to relate the two literatures. This manuscript contributes a novel and interesting step in this direction, by introducing a computational account of meta-control in value-based decision making. According to this account, meta-control can be described as a cost-benefit analysis that weighs the benefits of allocating mental effort against associated costs. The benefits of mental effort pertain to the integration of value-relevant information to form posterior beliefs about option values. Given a small set of parameters, as well as pre-choice value ratings and pre-choice uncertainty ratings as inputs to the model, it can predict relevant decision variables as outputs, such as choice accuracy, choice confidence, choice induced preference changes, response time and subjective effort ratings. The study fits the model to data from a behavioral experiment involving value-based decisions between food items. The resulting behavioral fits reproduce a number of predictions derived from the model. Finally, the article describes how the model relates to established accumulator models of decision-making.

  The (relatively simple) model is impressive in its apparent ability to reproduce qualitative patterns across diverse data including choices, RTs, choice confidence ratings, subjective effort, and choice-induced changes in relative preferences successfully. The model also appears well-motivated, well-reasoned, and well-formulated. While all reviewers agreed that the manuscript is of potential interest, they also all felt that a stronger case needs to be made for the explanatory power of the model, and that the model should be embedded more thoroughly in the existing literature on this topic.

Reviewed by eLife

Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants—An exemplar of how human disturbance impacts group-living species

1. Maggie Wiśniewska
2. Ivan Puga-Gonzalez
3. Phyllis Lee
4. Cynthia Moss
5. Gareth Russell
6. Simon Garnier
7. Cédric Sueur

• Curated by eLife

  Summary: Your study used simulated elephant poaching to investigate the impact of selective individual removal on the functional resilience of animal social networks to human-induced disturbance. This topic is interesting and timely, because understanding how threatened animal populations are impacted by humans is of critical importance and requires more study -- especially for species/processes with limited real-world data, but with a potentially strong impact on ecosystem functioning. However, the reviewers unanimously agreed that the logic and assumptions underlying the study are problematic and, thus, limit the insights that can be drawn from the simulation results. They highlighted specifically that the network metrics used to infer functionality are not supported by field data on elephants, or indeed any other study systems. Please find more detailed comments from all three reviewers appended below.

Reviewed by eLife

BAP1/ASXL complex modulation regulates epithelial-mesenchymal transition during trophoblast differentiation and invasion

1. Vicente Perez-Garcia
2. Georgia Lea
3. Pablo Lopez-Jimenez
4. Hanneke Okkenhaug
5. Graham J Burton
6. Ashley Moffett
7. Margherita Y Turco
8. Myriam Hemberger

Reviewed by eLife

Fine-Tuning of Piezo1 Expression and Activity Ensures Efficient Myoblast Fusion during Skeletal Myogenesis

1. Huascar Pedro Ortuste Quiroga
2. Massimo Ganassi
3. Shingo Yokoyama
4. Kodai Nakamura
5. Tomohiro Yamashita
6. Daniel Raimbach
7. Arisa Hagiwara
8. Oscar Harrington
9. Jodie Breach-Teji
10. Atsushi Asakura
11. Yoshiro Suzuki
12. Makoto Tominaga
13. Peter S. Zammit
14. Katsumasa Goto

Reviewed by eLife

De novo learning versus adaptation of continuous control in a manual tracking task

1. Christopher S Yang
2. Noah J Cowan
3. Adrian M Haith

Reviewed by eLife

LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior

1. Nana Naetar
2. Konstantina Georgiou
3. Christian Knapp
4. Irena Bronshtein
5. Elisabeth Zier
6. Petra Fichtinger
7. Thomas Dechat
8. Yuval Garini
9. Roland Foisner

• Curated by eLife

  Summary: This work builds on prior studies by the Foisner group that investigated the function(s) of the soluble A-type lamin binding protein, LAP2a. One of their prior observations using antibody labeling was that there appeared to be a depletion of the nucleoplasmic pool of A-type lamins in cells lacking LAP2a. In this manuscript, the authors employ CRISPR-Cas9 editing to develop new tools to investigate the attributes specific to nucleoplasmic versus lamina-integrated A-type lamins. Using this new approach (and comparing it with their prior observations), the authors hit upon a new model in which LAP2a influences the conformational state of A-type lamins, which in turn influences its detection by a commonly used antibody. This technical detail explains the new realization that nucleoplasmic lamin A persists in LAP2a-null cells, albeit in a different state. The authors provide evidence that LAP2a antagonizes stable lamin A filament assembly, that is absence leads to stabilized intranuclear lamin A assemblies, and that telomere mobility is negatively influenced by loss of LAP2a in a manner depending on the presence of lamin A/C. The authors' work further identifies two pathways by which nucleoplasmic lamins emerge, namely by 1) initial localization to the lamina followed by relocalization to the nucleoplasm, and 2) from the pool of mitotic lamins which are not associated to the lamina.

  Overall there was enthusiasm for the study, with the reviewers stating their appreciation for the author's mechanistic approach to studying lamin assembly state and the use of complementary cell biology/microscopy and biochemical approaches. The rigor of the science was also lauded, including inclusion of, for example, genome editing quality control measures. Taken together the reviewers felt that the findings provided a new perspective on how LAP2a influences the state of A-type lamins. As the impact of lamins on nuclear organization is critical for nuclear functions and important for nuclear integrity, these results are fundamental for the understanding of both lamin A/C and LAP2a.

Reviewed by eLife

Value Certainty in Drift-Diffusion Models of Preferential Choice

1. Douglas Lee
2. Marius Usher

• Curated by eLife

  Summary: This study investigates how uncertainty about the values of choice alternatives affects decision-making from the perspective of drift-diffusion modeling. Both reviewers agree that this is an interesting question. The authors propose different candidate models for how uncertainty might affect the drift rate or the diffusion variance, and test these candidates on four food-preference datasets. The authors report that the best model is one in which the drift rate scales with the value of the options normalized by their respective uncertainties.

  Despite the relevance of the research question, both reviewers have found the contribution of the findings to existing knowledge to be not sufficiently strong and clear. Several empirical observations reported in the study are already well known, and several of the alternative models are known to be "strawmen" for researchers in value-based decision-making and drift-diffusion modeling. In particular, the reviewers have noted that is not surprising that a lower certainty alone cannot correspond to higher diffusion noise in a drift-diffusion model, and can thus be captured by a lower drift. They agreed, and further amplified in the consultation session amongst reviewers, that the precise computational way by which this drift modulation is implemented would need to be investigated much further. Furthermore, to increase the strength of the conclusions, the authors should explore in more detail the different classes of DDMs, and the ways in which value certainty could affect other parameters of the model than the ones considered in the manuscript.

Reviewed by eLife

A new model of decision processing in instrumental learning tasks

1. Steven Miletić
2. Russell J Boag
3. Anne C Trutti
4. Niek Stevenson
5. Birte U Forstmann
6. Andrew Heathcote

• Curated by eLife

  Summary: This cognitive modeling study on a timely topic investigates the combination of reinforcement learning and decision-making for modeling choice and reaction-time data in sequential reinforcement problems (e.g., bandit tasks). The central claim of the paper is that the often-used combination of reinforcement learning with the drift-diffusion model (which decides based on the difference between option values) does not provide an adequate model of instrumental learning. Instead, the authors propose an "advantage racing" model which provides better fits to choice and reaction-time data in different variants of two-alternative forced-choice tasks. Furthermore, the authors emphasize that their advantage racing model allows for fitting decision problems with more than two alternatives - something which the standard drift-diffusion model cannot do. These findings can be of interest for researchers investigating learning and decision-making.

  The study asks an important question for understanding the interaction between reinforcement learning and decision-making, the methods appear sound, and the manuscript is clearly written. The superiority of the advantage racing model is key to the novelty of the study, which otherwise relies on a canonical task studied in several recent papers on the same issue. However, the reviewers feel that the framing of the study and its conclusions would require additional analyses and experiments to transform the manuscript from a modest quantitative improvement into a qualitative theoretical advance. In particular, as described in the paragraphs below, the authors should test how their advantage racing model fares in reinforcement problems with more than two alternatives. This is, from their own account throughout the paper, a situation where their model could show most clearly its superiority over standard drift-diffusion models used in the recent literature.

Reviewed by eLife

Basis of specificity for a conserved and promiscuous chromatin remodeling protein

1. Drake A Donovan
2. Johnathan G Crandall
3. Vi N Truong
4. Abigail L Vaaler
5. Thomas B Bailey
6. Devin Dinwiddie
7. Orion GB Banks
8. Laura E McKnight
9. Jeffrey N McKnight

Reviewed by eLife

Disentangling neocortical alpha/beta and hippocampal theta/gamma oscillations in human episodic memory formation

1. Benjamin J. Griffiths
2. María Carmen Martín-Buro
3. Bernhard P. Staresina
4. Simon Hanslmayr

• Curated by eLife

  Summary: All reviewers agree that the study addressed an important question in episodic memory. Yet, the reviewers are not convinced that the experimental design could truly dissociate the perception and binding processes, an assumption the whole work is based on. Moreover, the PAC analysis in the hippocampus using MEG recordings and its comparison to other brain regions need more analyses and confirmation.

Reviewed by eLife

Novel enzyme for dimethyl sulfide-releasing in bacteria reveals a missing route in the marine sulfur cycle

1. Chun-Yang Li
2. Xiu-Juan Wang
3. Xiu-Lan Chen
4. Qi Sheng
5. Shan Zhang
6. Peng Wang
7. Mussa Quareshy
8. Branko Rihtman
9. Xuan Shao
10. Chao Gao
11. Fuchuan Li
12. Shengying Li
13. Yin Chen
14. Yu-Zhong Zhang

Reviewed by eLife

Evolutionary dynamics of transposable elements in bdelloid rotifers

1. Reuben W Nowell
2. Christopher G Wilson
3. Pedro Almeida
4. Philipp H Schiffer
5. Diego Fontaneto
6. Lutz Becks
7. Fernando Rodriguez
8. Irina R Arkhipova
9. Timothy G Barraclough

• Curated by eLife

  Summary: Nowell et. al. present an analysis of transposable elements (TEs) in bdelloid rotifers and compare their dynamics to those in related species. Through this comparative analysis, the authors test various evolutionary hypotheses about asexual genomes, as well as recent suggestions that these ancient asexual organisms may not actually be asexual. Nowell et. al. find no evidence supporting the presence of recombination (and thus, sex) in bdelloid rotifers, and no strong predicted evolutionary signatures of asexuality in TE dynamics in these species. Additionally, they find evidence for expansion of RNAi-related genes, which may play a role in countering the expected TE dynamics in asexual species. Overall, this work is substantial, thorough, and presents some answers to long-standing questions about the genome evolution of long-term asexual species.

Reviewed by eLife

DCC regulates astroglial development essential for telencephalic morphogenesis and corpus callosum formation

1. Laura Morcom
2. Ilan Gobius
3. Ashley PL Marsh
4. Rodrigo Suárez
5. Jonathan WC Lim
6. Caitlin Bridges
7. Yunan Ye
8. Laura R Fenlon
9. Yvrick Zagar
10. Amelia M Douglass
11. Amber-Lee S Donahoo
12. Thomas Fothergill
13. Samreen Shaikh
14. Peter Kozulin
15. Timothy J Edwards
16. Helen M Cooper
17. IRC5 Consortium
18. Elliott H Sherr
19. Alain Chédotal
20. Richard J Leventer
21. Paul J Lockhart
22. Linda J Richards

• Curated by eLife

  Summary: This study is a welcome follow-up to your earlier demonstration that midline zipper glia (MZG) migrate along the interhemispheric fissure (IHF) and intercalate across the hemispheres, and in doing so, remodel the meningeal basement membrane to provide a substrate for callosal axon growth. The authors identify DCC and its ligand Netrin1 to be important for this process, by acting on the distribution and morphology of MZG, in addition to their service as axon guidance signals for callosal axons to be attracted to and across the midline.

  Co-submission with https://www.biorxiv.org/content/10.1101/2020.07.29.227827v1

Reviewed by eLife