PREreview beta testing phase – Here is how you can help!
Hello everyone! In this post we will detail our beta testing phase, hopefully clarifying what it means to be a beta tester for PREreview and guiding you on how to best contribute. Thank you for taking the time to help us in our mission to make journal clubs worth any researchers' time!
How to start a PREreview journal club: tips & email templates
The following guidelines and email templates are meant to help you start a PREreview journal club at your institution. The first two email templates are for you to send to your department to invite colleagues to your journal club; the last one is for you to send to the authors to let them know you have reviewed their preprint on PREreview. Please let us know if these materials helped you, or suggest changes by emailing us at firstname.lastname@example.org. Thank you!
UIUC Plant Physiology JC (2019/08/12): α-carboxysome formation
The UIUC Plant Physiology journal club reviewed the preprint “α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2” (doi: https://doi.org/10.1101/708164) by Oltrogge et al. 2019. The paper describes the biochemical characterization of the CsoS2 protein involved in carboxysome assembly, identifying a repeat peptide region that makes weak electrostatic interactions with rubisco through the use of bio-layer interferometry (BLI) and x-ray crystallography. The authors identified evolutionary conserved residues through protein sequence comparisons and the sites of interaction between these residues and rubisco through protein X-ray crystallography. We found the paper to be very well written, well presented and valuable addition to knowledge about alpha carboxysome assembly. Our journal club assessed the paper as part of a learning exercise about how to make work accessible to a wide audience. Participants first learned about the “and-but-therefore (ABT)” model of paper writing popularized by Randy Olsen in his freely available book "Huston, we have a narrative", that can be used throughout the manuscript to help maintain the reader’s interest. Focusing on the abstract we found it to contain many of aspects of the ABT model. We also thought it could potentially be strengthened by including a stronger “but” phrase which generally represents the question under consideration. It was suggested that this phrase would start with the fact that there is little knowledge about how the carboxysome is assembled, and some members of the club questioned if the ongoing carboxysome engineering efforts might be mentioned as relevant to the wider importance of the work (either in the abstract or the discussion).One aspect we found particularly interesting was the similarities between CsoS2 and the algal protein EPYC which has been implicated in aggregation of rubisco in the pyrenoid. These appeared to us to an important point, and the reason to include information about CsoS2 as an intrinsically disordered protein (IDP) that could perhaps be emphasized more. As we were not familiar with the PONDR-FIT disorder score, we would have found it helpful to have a little more explanation as to its importance and interpretation. Overall we liked the approach for analyzing IDPs and thought it was an impressive effort to successfully crystallize the CsoS2 peptide with rubisco. In addition, we assessed the presentation of figures, we particularly liked the use of consistent colouring throughout, the choice of clearly legible font sizes on all graphs and the helpful diagrams to illustrate biochemical procedures, such as the BLI procedure in Fig 2b. One consideration is whether the choice of colors is colorblind friendly, using the app color oracle, several of the colors are indistinguishable in all the figures analysed. We also thought inclusion of legend titles would help guide readers on how best to interpret the data. We thought the X-ray crystallography data was presented in a clear and helpful manner, displaying what the individual residue interactions were between the bpeptide and rubisco. If it could be improved further it may be by inclusion of a label of rubisco for non-experts who may not immediately associate CbbL and CbbS as subunits. Finally, we particularly liked Figure 5 as it neatly summarized the proposed role of CsoS2 in carboxysome assembly.Other thoughts included:It would be interesting to include discussion of why the full length CsoS2 peptide does not appear to bind rubisco.The paper tied up loose ends and did a good job of using multiple approaches to build evidence for the direct interaction of CsoS2 and rubisco.
Present and past LivePREJCs: PREreview's community live-streamed preprint journal clubs
Below is a list of upcoming live-streamed preprint journal clubs (LivePREJCs) as well as those hosted in the past. To learn more about what to expect and how to solicit our help to organize one, please read here
Science is dynamic. Academic publishing should be too.
I argue that the academic publishing process as it currently exists is fundamentally antithetical to the advancement of science. Specifically, the way science is supposed to work is that the methods and conclusions of previous research can be scrutinized and improved upon. However, the static nature of articles published in academic journals under the current publication system creates the inaccurate impression that the article exists in its best possible state, without any changes that need to be made to it. It should be possible to publish a much smaller number of articles that can continually be updated and refined as new discoveries are made, instead of an unmanageably and bewilderingly large number of articles on the same topic. This would make it easier to point out and correct errors in a paper and to add results of new experiments as they become available. We no longer need to rely on a system centered around the enshrining of articles in academic journals in the same form forever. Now that such journals do not have to be published in print form, and collaborative scientific platforms like this one are becoming more popular, this is how all science should be conducted.
PREreview of bioRxiv article "A generalist pathogen view of diverse host evolutionary histories through polygenic virulence"
This is a review of Caseys et al. bioRxiv doi: https://doi.org/10.1101/507491 posted on June 25, 2019. This study aims at addressing whether coevolutionary models of host-pathogen interactions apply to a generalist pathogen that exhibits quantitative virulence across a broad range of plants. They generated an exhaustive virulence matrix for the nectrophic fungus Botrytis cinerea on 90 genotypes of 8 plant species. They conclude that this pathosystem doesn’t fit traditional arms-race coevolution models with quantitative variation in susceptibility distinct from the phylogenetic relationships between the examined plants.
PREreview of bioRxiv article “Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity”
This is a review of Baudin, Schreiber, Martin et al. bioRxiv doi: https://doi.org/10.1101/592824 posted on March 29, 2019. The authors used structural modelling to identify elements required for self-association of the NLR immune receptor ZAR1, specifically its N-terminal CC-domain ZAR1CC. They discovered that the N-terminal α1 helix and EDVID motif in ZAR1CC are important for oligomerization and function of ZAR1. This complements recent findings by Wang et al. (2019) based on cryo-EM structures, highlighting the importance of the α1 helix for the activity of ZAR1 although some differences were noted that could reflect the different experimental set ups (CC domain vs full-length protein) as discussed in the paper.
PREreview of bioRxiv article “Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans”
This is a review of Knaus et al. bioRxiv doi: https://doi.org/10.1101/633701 posted on May 16, 2019. In this paper, the authors studied variations in ploidy in a wide range of isolates of the potato blight pathogen Phytophthora infestans.
Bio 200C Assignment Bhumil Patel
Review: Optimized FRET pairs and quantification approaches to detect the activation of Aurora kinase A at mitosis.In this manuscript, Bertolin et al. improve on their original Aurora Kinase A biosensor to produce a second generation that would help follow AURKA activation in regions where it is extremely low in concentration and undetectable with the original AURKA biosensor. The authors develop two independent strategies to improve on their previous work. First, they develop a single-color AURKA biosensor for multiplex FRET and second, a method to observe and quantify FRET efficiency in areas with very low AURKA abundance. The authors show that dark acceptors ShadowG and ShadowY allow for single-color FRET/FLIM measurements while first generation tandem GFP isn’t suitable due to low concentration of AURKA. They also show the inability of the original construct to measure FRET by 2c-FCCS and thus develop a novel method by replacing the donor-acceptor pair with a mTurquoise2 and novel superYFP. The experiments allowed the authors to develop guidelines when making new FRET biosensors such as characterizing the nature of the protein and making sure the conformational changes of the protein fall within the Forster’s radius of the donor-acceptor pair.The improvements to AURKA biosensors represent a novel way for studying the function of this kinase. While fluorescence anisotropy has been used in the past to study FRET in different kinases such as PKA, ERK, and cAMP, it has not been known to work with AURKA due to the nature of the protein and it’s function. Also, given the fact that levels of AURKA is regulated throughout the cell cycle, the ability to detect it at low levels will help understand it’s function in diverse contexts.The authors provide good explanations with regards to the anomalies seen in their data and point out any results that deviate from their expected hypothesis. However, experiments with regards to characterizing the effects of inserting a novel superYFP on the cell and AURKA’s function need to be seen. The author’s also fail to provide clear explanations for discrepancies between the inactivated kinases in Fig. 1B and 1C. The author’s work is systematic, giving context when constructing new strains, and provides clear explanations when talking about new methods of quantifying FRET. One thing that I did have a hard time understanding was the use of anisotropy to measure FRET, and I think the authors could have done a better job introducing the concept.In terms of experiments that need to be done in order to further validate the results. As mentioned previously, the differences observed in Δlifetime for inactivated ShG-AURKA-mTurq2 and ShY-AURKA-mTurq2 need to be investigated or explained better. Similarly, effects of inserting flanking donor-acceptor pairs on the function of the kinase need to be quantified. It would be relevant to see how insertion of the flanking pairs affect AURKA localization to the spindle poles and morphology of the cell compared to wildtype. It would also be interesting to see if normal, non-arrested cells can function properly for multiple generations with the inserted constructs.There are minor spelling mistakes that can be attributed to continental differences. But for the most part, the article is easy to read and well written, however, explaining the thresholds in Fig. 1 and 2 will help the readers. As someone who is not familiar with analyzing fluorescence data, I did have a tough time understanding Fig. 3 and 4C, but the data and the author’s interpretation are clear and convincing.