PREreview of "Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation"
This is a review of the preprint "Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation" by Ethan Edward Ford, Matthew R. Grimmer, Sabine Stolzenburg, Ozren Bogdanovic, Alex de Mendoza, Peggy J. Farnham, Pilar Blancafort, and Ryan Lister.The preprint was originally posted on bioRxiv on September 20, 2017 (DOI: https://doi.org/10.1101/170506).
Journal Club EcoEvol #02 - 06.07.2018
and 2 collaborators
This is a review of the preprint entitled " On the overlap between scientific and societal taxonomic attention - insights for conservation", by Ivan Jarić, Ricardo A. Correia, David L. Roberts, Jörn Gessner, Yves Meinard, and Franck Courchamp. The preprint was originally posted on bioRxiv on June 3, 2018 (http://dx.doi.org/10.1101/334573). Our journal club reviewed this preprint in the meeting of July 6, 2018.
UIUC preprint journal club : 2018-07-30
Steven Burgess (0000-0003-2353-7794), Samuel Fernandes, Antony Digrado, Charles Pignon, Elsa de Becker, Naomi Housego Day, Lusya Manukyan, Stephanie Cullum, Isla Causon, Iulia Floristeanu, Young Cho, Freya Way, Judy Savitskya, Robert Collison, Aoife Sweeney, Pietro Hughes, Cindy Chan
Abstract
This review is compiled from notes taken by the UIUC Plant Physiology preprint journal club during a one hour session on 2018-07-30. The review refers to the preprint "Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana" by Hannes Dittberner, Arthur Korte, Tabea Mettler-Altmann, Andreas Weber, Grey Monroe, and Juliette de Meaux ( doi: https://doi.org/10.1101/253021) published on BioRxiv.
Review
In the paper “Natural variation in stomata size contributes to the local adaptation of Water use efficiency in Arabidopsis thaliana” Dittberner et al. (2018) investigated the genetic basis of water use efficiency using genome wide association analysis. Findings included (1) that there is substantial variation in stomatal size and patterning in A. thaliana accessions (2) decreased stomata size correlates with increased water use efficiency (3) two novel QTL affecting WUE independently of stomatal patterning (4) water use efficiency is a polygenic trait and (5) natural selection contributed to the establishment of variation in WUE in accordance with climatic conditions.
The findings are in accordance with previous studies looking at genetic variation in stomatal size and patterning in A. thaliana (Delgado et al. 2011; Monda et al. 2016), the role of natural selection in WUE of tomato (Muir et al. 2014), analysis of genomic variation in WUE in A. thaliana (Easlon et al. 2014; Aliniaeifard and van Meeteren 2014) and the extensive literature correlating a decrease in stomatal size with increased water use efficiency in many species.
We were impressed by the significant technical advance presented in the form of automated stomatal counting and suggest more could be made of this aspect of the paper. For example the we suggest inclusion of the term ‘high-throughput’ in the title, and think it would be helpful to include a picture of how the screening system works in the introduction.
Further, we found the conclusion that water use efficiency is a polygenic trait very interesting. The implications are important for studies aimed at the improvement of photosynthesis/WUE through conventional breeding or genetic manipulation. We wonder if there are other papers which have already discussed the potential polygenic nature of stomatal traits? Yoo et al. (2011) mentions different genes involved in WUE and stomatal patterning. This kind of paper could have been worth-mentioning in the discussion.
The identification of two novel QTL, not otherwise known to influence water use efficiency or to be related to stomatal patterning and regulation was particularly intriguing, and these two genes provide a great starting point for further analysis in future publications.
Major comments
We believe the kinship matrix accounts for relatedness, and is usually called the k model. To account for population structure one could use principal components, combining these two approaches is known as the Q+K model. It would be helpful to include a citation for calculating the kinship matrix as there are multiple methods available. It might also be worth providing QQplots to show whether including population structure is necessary or not for this study.
We found the use of a Bonferroni correction in the analysis quite conservative, there are other options such as Benjamini-Hochberg adjusted p-values that could lead to declaring other SNPs as significant. Also, from the GWAS results, there seem to be other SNPs popping up - although, not significant. It might be worth using an alternative to p-values when investigating the possible biological significance of outstanding SNPs on a Manhattan plot - such as selecting the top 10 hits for investigation.
Minor comments:
- Keywords: Consider revisiting, as many of the keywords are already on the title. Additionally, it would be helpful to include terms rather than acronyms which are not familiar to non-experts.
- Introduction: Would be good to include examples of some of the limitations to automated confocal microscopy approaches to orientate readers.
- Line 143: (Atwell et al., 2010). This citation doesn't seem to be right. If the author is referring to genomic heritability it could cite de los Campos et al. (2015).
- Methods: Would like to see further information on the methodology used for carbon isotope discrimination in the main text
- Results: Might consider using the term ‘genetic-heritability’ rather than ‘pseudo-heritability’
- Results: Direct comparison with previously reported dC13 values for accessions that have been demonstrated to differing WUE would be helpful.
- Figure 4: the text on the figure is likely to be too small to see properly
- Line 505: “soil composition...” This is a really interesting point about the complexity of environmental effects on plant physiology. It might be helpful to provide some explanation for readers less familiar with soil content. (e.g. water holding content and effect on root structure - e.g.https://doi.org/10.1073/pnas.1721749115)
- Line 499-500. Repetition of text on 498-499
- Results: It would be helpful to share where the functional annotation for genes come from. This gene appears to be involved in mRNA decapping. There is only one publication, which found it is involved in PAMP triggered immunity, plants were dwarf in stature. TAIR does not annotate a role in cell differentiation (10.15252/embj.201488645)
- Discussion: It is interesting to see a comparison with a related species and how the observed pattern is consistent between the two.
- Data accessibility: This is excellent. Great to see that all data and code will be made available and deposited in a permanent repository!
References
Aliniaeifard and van Meeteren (2014) J Exp Bot. 65(22): 6529–6542.
de los Campos et al. (2015) PLoS Genet 11(5): e1005048. doi:10.1371/journal.pgen.1005048
Delgado et al. (2011) Ann Bot.; 107(8): 1247–1258
Easlon et al. (2014) Photosynth Res 119: 119. https://doi.org/10.1007/s11120-013-9891-5
Monda et al. (2016) Plant Physiol, 170: 1435–1444
Muir et al. (2016) Genetics. 2014 Dec; 198(4): 1629–1643.
Preprint Journal Club Review of: "Diurnal active photolocation enhances predator detection in a marine fish"
and 4 collaborators
Diurnal active photolocation enhances predator detection in a marine fish
Matteo Santon, Pierre-Paul Bitton, Jasha Dehm, Roland Fritsch, Ulrike K. Harant, Nils Anthes, Nico K. Michiels
Who we are:
We are a group of zoologists at different career stages with a diverse background. We have started a preprint review journal club in order to discuss topics across our different areas of concentration to stay up-to-date with the latest research and get practice writing reviews. We selected this preprint, “Diurnal active photolocation enhances predator detection in a marine fish,” by Matteo Santon et al. due to the interesting experimental design and general interest of the topic.
This manuscript built upon a body of previous work in a logical, easy-to-read way. The authors demonstrate experimentally that diurnal active photolocation exists in diurnal fish and that it aids in predator detection. We were generally impressed by the experimental design and the thorough treatment of the topic. We do, however, have a few questions that we could not answer by reading the manuscript and also some comments on the presentation of the information.
Questions:
- For the lab experiment:
a. What kind of glass was used for the partition between the triplet and the predator? This is explicitly stated for the field experiment (spectrally neutral Evotron Plexiglas), but we were wondering if the same glass was used in the laboratory experiments?b. What is the purpose of the “sub-optimal substrate” strip of gravel along the long side of the tank and why is it not included in the schematic drawing of the setup?c. In lines 200-201, the authors state, “Both stimuli were simultaneously present in the tank, but only one was visible to the triplefins.” Here we would like to know how they prevented visibility of one stimulus and suggest that the spatial relationship be stated or illustrated more clearly.
PrePrint Journal Club Review: Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
and 8 collaborators
Title: Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.
Authors: Gerard Minuesa, Steven K Albanese, Arthur Chow, Alexandra Schurer, Sun-Mi Park, Christina Z. Rotsides, James Taggart, Andrea Rizzi, Levi N. Naden, Timothy Chou, Saroj Gourkanti, Daniel Cappel, Maria C Passarelli, Lauren Fairchild, Carolina Adura, Fraser J Glickman, Jessica Schulman, Christopher Famulare, Minal Patel, Joseph K Eibl, Gregory M Ross, Derek S Tan, Christina S Leslie, Thijs Beuming, Yehuda Goldgur, John D Chodera, Michael G Kharas
Date of submission to bioRxiv: May 14, 2018
__________________________________________________________________________________
Dear Authors,
Thank you for posting your manuscript titled Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia as a preprint on bioRxiv! We reviewed this work at our journal club at the Structural Genomics Consortium, University of Toronto. Compiled comments from the attendants are below. To structure the feedback, we used the quick worksheet guidelines published on PREreview.
We hope this feedback will be useful to improve the manuscript.
Kind regards,
PreReview Journal Club Members, Structural Genomics Consortium, University of Toronto
__________________________________________________________________________________
What is the main question the study attempts to answer?
- Can chemical inhibition of Musashi2’s RNA-binding function be used to selectively target myeloid leukemia cells?
- How does Ro 08-2750 inhibit MSI RNA-binding activity?
What is (are) the hypothesis?
Small molecule antagonism of the RNA binding domain of MSI2 has therapeutic potential in the treatment of acute myeloid leukemia. Ro-08-2750 binds at an RNA-interacting site and competitively inhibits RNA binding of MSI2.
What techniques/analyses do the researchers adopt to test their hypothesis(es)?
The authors use biophysical assays, computational structural biology, cell biology techniques, and an animal model. These methods are all common to preclinical drug development and are appropriate to address the outlined hypothesis and in most cases adequately address the question being asked.
Why is this study relevant?
Understanding of RNA biology and its importance in human health has expanded greatly in recent years. While proteins with RNA binding domains have been implicated in disease, they are typically thought of as “undruggable” as they often lack defined pockets. MSI2 overexpression is common in AML patients with poor clinical prognosis. This study highlights that (1) RRM domains can be targeted by a small molecule antagonist and (2) that this approach may have therapeutic value in the treatment of AML.
Write here any general comments you might have about the research approach.
Structural studies
- The structure-activity-relationship was clearly described considering a lack of a co-crystal structure.
- Given that residues F66, F97 and R100 of MSI2 are also conserved in MSI1, it would have been interesting to see how Ro 08-2750 compares between both proteins.
Biophysical Assays
- It would be interesting to see measurements of compound binding to MSI2, for example ITC or thermal shift assays.
Cell Biology
- The assays used appeared to be well thought out and provided good evidence for target engagement and therapeutic potential in cellular models of AML. However, given the genetic diversity of AML, it would be informative to include a sentence to describe why MOLM13 and K562 cells were selected for these studies.
Write here any specific comment you might have about experimental approaches and methods used in the study.
- In the discussion the authors state that Ro 08-2750 is the first “selective MSI inhibitor”. MSI2 was compared to SYNCRIP for selectivity; however, given the extensive repertoire of RNA binding domains found in the human genome, we feel that a more extensive characterization is warranted to make a definitive statement. This could be accomplished by either utilizing a biotinylated compound for pulldowns and MS-id or by measuring binding to a panel of RRMs.
- It would be interesting to see KD/KO studies alongside compound treatment to evaluate to what degree this compound may phenocopy genetic perturbation of MSI2 in AML. In addition, it would also be cool to see how the mutants deficient in Ro binding are functional in cells, which may hint at potential mechanisms of resistance.
- For the mouse data presented it would be informative to the reader to include both survival and tumour volume data. Additionally, have the authors done any experiments to test the suitability of this compound for in vivo use (ex. What is the PK of Ro?).
- Additional biophysical assay to measure direct binding of the compound to MSI2’s RRM domain would be informative, ex. ITC or thermal shift assay.
Structural studies
- We found that the molecular dynamics analysis greatly complemented the structural data and enabled a thorough description of the potential binding mechanism for the Ro compounds. It would be useful to note whether co-crystallization of MSI2 and Ro was attempted, though the mutagenesis experiments provided evidence of the importance of interactions with F66, R100, and F97. It is unclear why YANK was selected to perform alchemical analysis given that the program has not yet been extensively validated and carries a “Use at your own risk!” warning. It would have been reassuring to see these calculations carried out with a more validated software.
Write here any specific comment/note about figures in the paper (this could be related to the way data are displayed and your ability to understand the results just by looking at the figures).
- Extended figure 7 appears to be mislabeled in text and extended figure 8 is missing.
- For figure 3d, we felt it would be easier to interpret if annexin V + cells were normalized to the DMSO control.
- For the RNA-IP experiments, we would suggest that this data be presented as % input, akin to a ChIP experiment. This would account for any changes in gene expression that may confound the interpretation of this result as well as allow the authors to probe RNAs that should not change in response to compound (ie. negative control)
Write here any additional comment you might have (this includes minor concerns such as typos and structure of the manuscript).
- On line 216: what does “proximal” mean here?
- Classically, the term inhibitor would be reserved for a compound disrupting an enzymatic activity. Here, antagonist may be a more appropriate term.
- Any supplementary tables listed in the text should be included for readers/reviewers.
OIST E&E PREreview Journal Club, "Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities"
and 9 collaborators
Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communitiesEzequiel Santillan, Hari Seshan, Florentin Constancias, Daniela I. Drautz-Moses, Stefan Wuertz, May 4th 2018, bioRxiv[doi: https://doi.org/10.1101/313585] Understanding the effects of disturbance on ecosystem function and diversity has many potential applications in microbial ecology and human disease biology. In this paper, the authors tackled the long-standing question of how different disturbance frequencies affect bacterial community diversity and function. To do so, activated-sludge communities within laboratory-scale microcosms were exposed to toxic 3-chloroaniline (3-CA) at varying frequencies. Ecosystem function and community diversity were measured weekly by measuring biomass and organic carbon, ammonia, and toxin removal as proxies for ecosystem function and T-RFLP 16S rRNA gene fingerprinting and shotgun metagenomics were performed to examine variation in bacterial diversity and community composition. This work is an excellent example of integrating genomic and functional analysis, thereby providing a more thorough understanding of the effects of disturbance frequency on microbial community diversity and function. Interestingly, both genetic methods yielded similar results, suggesting that the less expensive gene fingerprinting method could be sufficient when sequencing resources are limited. We particularly commend the use of multiple alpha-diversity measurements and the inclusion of abundance-related indices, which are less method dependent and allow results to be compared between studies. Ultimately, the authors propose the "Intermediate Stochasticity Hypothesis,” which suggests that stochastic processes produce higher diversity assemblages at intermediate disturbance frequencies while deterministic processes produce lower diversity assemblages at low and high disturbance frequencies. Overall, this paper is a fascinating and substantial contribution to microbial ecology. There are, however, a few issues that we feel could be improved in future versions of the manuscript. Major concerns:This comment is unique to the preprint. The manuscript references multiple figures available in the supplementary materials, but these materials were not made available as part of the preprint. This hindered our ability to understand the fine points of the experiments. We encourage the authors to upload the supplementary materials to bioRxiv. 1. Figure 2 is an integral figure to the manuscript because it showcases the effects of 3-CA disturbance frequencies on community performance, namely organic carbon and toxin removal (plots A, C) and nitrification products (plots B, D). In the Materials and Methods section (lines 353-356), the authors state that these parameters were measure weekly, which leads to the assumption that data is available for days 7, 15, 21, and 35, even though only the data from days 7 and 35 are included in the figure (is there T0 data?). The results section refers to supplementary figures S2 and S3 in addition to Figure 2, so these supplementals may portray the data of interest. However, since these data are so important to the overall conclusions, we believe it should be available in the main text. One way to accomplish this could be to have one plot per variable with time on the x-axis and different colors for each disturbance frequency. The number of plots could be reduced by not including Volatile Suspended Solids (VSS) results in the main text. In Figure 2A, the COD removal and 3-CA removal is not monotonously decreasing relative to the disturbance frequency (specifically, level 2 and 4). We figured that this was due to the number of days since the disturbance being different for each disturbance frequency at measurement time on day 7. We encourage the authors to mention and explain this in the text, as this was a puzzling feature of the results for us for some time. It also calls into question the appropriateness of the weekly measurements, especially given that some disturbance level will be highly correlated to this rhythm of measurement (level 1 disturbance will always happen on the same day of the measurements, while level 2 and others will drift). 2. Along with disturbance frequency, varied intensity and duration of disturbance and differing sampling frequencies (e.g- data collection every two days or bi-weekly, larger spread of intermediate disturbance levels) might produce a different pattern of microbial community diversity and function. Questions we can ask are: would the system reach the observed IDH pattern at an early stage? Would the intermediate levels still follow the IDH model? We would be very interested in the authors opinions on these topics, perhaps in the discussion section.
ITQB Preprint Journal Club: 3 July 2018
and 2 collaborators
This is a review of the preprint "Cell boundary confinement sets the size and position of the E. coli chromosome" by Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Debasish Chaudhuri, Bela Mulder and Cees Dekker. The article was posted on bioRxiv on 15 June 2018 (https://doi.org/10.1101/348052). The ITQB Preprint Journal club reviewed the article on 3 July 2018. This review was written by Dr. Ambre Jousselin, who led the Preprint Journal Club. Dr. Manuel Melo made major contributions to analysis of simulations, and Dr. Zach Hensel helped edit the review for posting on PREreview and commented on microscopy methods.
ITQB Preprint Journal Club: 9 Nov 2017
Metabolic Interactions Between Dynamic Bacterial Subpopulations
Adam Z Rosenthal, Yutao Qi, Sahand Hormoz, Jin Park, Sophia Hsin-Jung Li, Michael Elowitz
Version reviewed: V1. October 25, 2017.
bioRxiv 208686; doi: https://doi.org/10.1101/208686
Note: This review incorporates input from attendees to the ITQB Preprint Journal Club on November 9, 2017.
Overview:
Rosenthal et al. demonstrate that stochastic changes between metabolic gene expression states underlie the population-averaged progression through acetate production to acetoin detoxification during exponential growth of B. subtilis. They show that the probabilities of cells being in the slow-growing, acetate-producing (sucC+) and acetoin-producing (alsS+) states depend upon competence regulators (comK) as well as environmental acetate concentration. The work combines population averaged experiments with single-cell fluorescence snapshot and timelapse microscopy experiments to conclusively prove the claims in the abstract. The work was very interesting for members of our journal club coming from several different fields. We were particularly interested in the the implications of the final gel-pad timelapse experiment and its discussion in the main text—the possibility that competence, toxic-product secretion, and subsequent detoxification could be coupled to give B. subtilis an advantage in a complex environment will be a great problem to investigate in the future.
PREreview Journal Club: "Links between environment, diet, and the hunter-gatherer microbiome"
and 6 collaborators
A review of the Biorxiv preprint entitled: Links between environment, diet, and the hunter-gatherer microbiomeGabriela K Fragiadakis, Samuel A Smits, Erica D Sonnenburg, William Van Treuren, Gregor Reid, Rob Knight, Alphaxard Manjurano, John Changalucha, Maria Gloria Dominguez-Bello, Jeff Leach, Justin L SonnenburgPosted to Bioarxiv on May 15, 2018doi: https://doi.org/10.1101/319673