We are excited to announce that the UK South West Zebrafish Meeting 2020 will be hosted by the University of Exeter as a virtual meeting to take place on Friday 11th September 2020.
The aim of the meeting is to bring together zebrafish researchers and technical staff from research institutions from the South West of the UK to share exciting cutting-edge research, knowledge, and zebrafish related expertise. We hope the meeting will forge new collaborations and networks across the South West and we hope you will be able to ‘join’ us! Registration and abstract submission are now open!
Due to the uncertain times regarding COVID-19 and possible long-term travel restrictions, we have decided to host our meeting online. We are in the process of working out the online format and logistics – so that we can host the best meeting possible – and we will inform participants of further details in due course.
We are also pleased to announce that we have 3 confirmed keynote speakers: Prof. Catherina Becker (University of Edinburgh), Dr. Isaac Bianco, (University College London), & Prof. Charles Tyler (University of Exeter).
Please pass the exciting news on to anyone you think may be interested and feel free to tweet about the event using #SWZM20 and follow us on Twitter @swzm20!
Looking forward to hearing from you all,
Steffen, Lucy, Holly, Chengting, Josh, Yosuke, and Michael
The Edmond and Lily Safra Center for Brain Sciences (ELSC) builds upon Hebrew University‘s record of excellence and innovation in its multidisciplinary approach to brain sciences.
ELSC invites applications for postdoctoral fellows in the following fields: theoretical and computational neuroscience, systems neuroscience, molecular and cellular mechanisms, cognitive neuroscience, and neuronal circuits. Postdoctoral fellows receive a competitive stipend for a period of up to two years.
Established ties and frequent collaborations with world renowned labs
Opportunities to audit advanced courses
Rich student and postdoctoral environments
Postdoctoral support staff
Eligibility:
The candidate must be (or have been) a student in an accredited institution of higher education and whose PhD training and post-doctoral projects are in the field of Brain Sciences.
The candidate’s doctoral degree has been submitted in the current year of applying or will be approved by the following year.
Candidates Commitments:
A recipient of an ELSC Fellowship must commence his/her post doctoral training no later than 5 years after completion of the PhD.
A recipient of an ELSC Fellowship must provide written approval from the authority of PhD students in his/her institute, confirming that his/her PhD has been submitted before they begin their post-doctoral training. If PhD was not yet awarded, the candidate must provide approval of a PhD during the first academic year of the post doctoral studies
A letter from the host is mandatory in order to commence the post doctoral studies
A recipient of an ELSC Fellowship must begin the postdoc training within 6 months after receiving the acceptance letter
Terms of Fellowship:
The fellowship can be extended up to 2 years, given availability of funds and the scientific achievements of the candidate. ELSC is not committed to prolong the fellowship in advance.
Preference will be given to students who completed their PhD abroad
We are looking for a motivated PhD student to join our lab recently established at the PMC in Utrecht. The position is funded for 4 years with a full-time employment. The project will deal with developing new (3D) culture systems and to use them to model cancer and study the effect of mutations, as well as organ development. We use state of the art tools, like CRISPR-Cas systems, single cell sequencing, mouse genetics and human organoids derived from both iPS cells and tissue stem cells.
The Prinses Maxima Centrum is a research institute dedicated to basic and applied research for different aspects related to paediatric cancer (https://research.prinsesmaximacentrum.nl/en/).
Ideal candidates have recently completed their master education, have a background in molecular and cellular biology, and preferably with a knowledge of bioinformatic tools, but this is not a must.
The candidate should be talented and highly motivated, and willing to work as part of a team. The group and the institute are international and the work language is English.
To have more detailed information about the project, the position and the lab please send a full CV and a brief cover letter to:
Welcome to our monthly trawl for developmental biology (and related) preprints.
With COVID-19 having shuttered labs around the world, it might be a surprise that April saw the highest ever monthly number of preprints deposited to bioRxiv: 3413, according to Rxivist. Though maybe not much of a surprise, with researchers at home and writing rather than pipetting.
In that 3413 we found the following couple of hundred developmental biology and adjacent picks (plus a handful from arXiv) – let us know if we missed anything. Use these links to get to the section you want:
Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons
Jim Berg, Staci A. Sorensen, Jonathan T. Ting, Jeremy A. Miller, Thomas Chartrand, Anatoly Buchin, Trygve E. Bakken, Agata Budzillo, Nick Dee, Song-Lin Ding, Nathan W. Gouwens, Rebecca D. Hodge, Brian Kalmbach, Changkyu Lee, Brian R. Lee, Lauren Alfiler, Katherine Baker, Eliza Barkan, Allison Beller, Kyla Berry, Darren Bertagnolli, Kris Bickley, Jasmine Bomben, Thomas Braun, Krissy Brouner, Tamara Casper, Peter Chong, Kirsten Crichton, Rachel Dalley, Rebecca de Frates, Tsega Desta, Samuel Dingman Lee, Florence D’Orazi, Nadezhda Dotson, Tom Egdorf, Rachel Enstrom, Colin Farrell, David Feng, Olivia Fong, Szabina Furdan, Anna A. Galakhova, Clare Gamlin, Amanda Gary, Alexandra Glandon, Jeff Goldy, Melissa Gorham, Natalia A. Goriounova, Sergey Gratiy, Lucas Graybuck, Hong Gu, Kristen Hadley, Nathan Hansen, Tim S. Heistek, Alex M. Henry, Djai B. Heyer, DiJon Hill, Chris Hill, Madie Hupp, Tim Jarsky, Sara Kebede, Lisa Keene, Lisa Kim, Mean-Hwan Kim, Matthew Kroll, Caitlin Latimer, Boaz P. Levi, Katherine E. Link, Matthew Mallory, Rusty Mann, Desiree Marshall, Michelle Maxwell, Medea McGraw, Delissa McMillen, Erica Melief, Eline J. Mertens, Leona Mezei, Norbert Mihut, Stephanie Mok, Gabor Molnar, Alice Mukora, Lindsay Ng, Kiet Ngo, Philip R. Nicovich, Julie Nyhus, Gaspar Olah, Aaron Oldre, Victoria Omstead, Attila Ozsvar, Daniel Park, Hanchuan Peng, Trangthanh Pham, Christina A. Pom, Lydia Potekhina, Ramkumar Rajanbabu, Shea Ransford, David Reid, Christine Rimorin, Augustin Ruiz, David Sandman, Josef Sulc, Susan M. Sunkin, Aaron Szafer, Viktor Szemenyei, Elliot R. Thomsen, Michael Tieu, Amy Torkelson, Jessica Trinh, Herman Tung, Wayne Wakeman, Katelyn Ward, René Wilbers, Grace Williams, Zizhen Yao, Jae-Geun Yoon, Costas Anastassiou, Anton Arkhipov, Pal Barzo, Amy Bernard, Charles Cobbs, Philip C. de Witt Hamer, Richard G. Ellenbogen, Luke Esposito, Manuel Ferreira, Ryder P. Gwinn, Michael J. Hawrylycz, Patrick R. Hof, Sander Idema, Allan R. Jones, C.Dirk Keene, Andrew L. Ko, Gabe J. Murphy, Lydia Ng, Jeffrey G. Ojemann, Anoop P. Patel, John W. Phillips, Daniel L. Silbergeld, Kimberly Smith, Bosiljka Tasic, Rafael Yuste, Idan Segev, Christiaan P.J. de Kock, Huibert D. Mansvelder, Gabor Tamas, Hongkui Zeng, Christof Koch, Ed S. Lein
Connectomes across development reveal principles of brain maturation in C. elegans
Daniel Witvliet, Ben Mulcahy, James K. Mitchell, Yaron Meirovitch, Daniel K. Berger, Yuelong Wu, Yufang Liu, Wan Xian Koh, Rajeev Parvathala, Douglas Holmyard, Richard L. Schalek, Nir Shavit, Andrew D. Chisholm, Jeff W. Lichtman, Aravinthan D.T. Samuel, Mei Zhen
Spatial Transcriptional Mapping of the Human Nephrogenic Program
Nils O. Lindström, Rachel Sealfon, Xi Chen, Riana Parvez, Andrew Ransick, Guilherme De Sena Brandine, Jinjin Guo, Bill Hill, Tracy Tran, Albert D. Kim, Jian Zhou, Alicja Tadych, Aaron Watters, Aaron Wong, Elizabeth Lovero, Brendan H. Grubbs, Matthew E. Thornton, Jill A. McMahon, Andrew D. Smith, Seth W. Ruffins, Chris Armit, Olga G. Troyanskaya, Andrew P. McMahon
Atypical neurogenesis in induced pluripotent stem cell (iPSC) from autistic individuals
Dwaipayan Adhya, Vivek Swarup, Roland Nagy, Lucia Dutan, Carole Shum, Eva P. Valencia-Alarcón, Kamila Maria Jozwik, Maria Andreina Mendez, Jamie Horder, Eva Loth, Paulina Nowosiad, Irene Lee, David Skuse, Frances A. Flinter, Declan Murphy, Grainne McAlonan, Daniel H. Geschwind, Jack Price, Jason Carroll, Deepak P. Srivastava, Simon Baron-Cohen
The enhancement of activity rescues the establishment of Mecp2 null neuronal phenotypes
Linda Scaramuzza, Giuseppina De Rocco, Genni Desiato, Clementina Cobolli Gigli, Martina Chiacchiaretta, Filippo Mirabella, Davide Pozzi, Marco De Simone, Paola Conforti, Massimiliano Pagani, Fabio Benfenati, Fabrizia Cesca, Francesco Bedogni, Nicoletta Landsberger
Differentiated neural cells in Romero-Morales, et al.
Pod indehiscence in common bean is associated to the fine regulation of PvMYB26 and a non-functional abscission layer
Valerio Di Vittori, Elena Bitocchi, Monica Rodriguez, Saleh Alseekh, Elisa Bellucci, Laura Nanni, Tania Gioia, Stefania Marzario, Giuseppina Logozzo, Marzia Rossato, Concetta De Quattro, Maria L. Murgia, Juan José Ferreira, Ana Campa, Chunming Xu, Fabio Fiorani, Arun Sampathkumar, Anja Fröhlich, Giovanna Attene, Massimo Delledonne, Björn Usadel, Alisdair R. Fernie, Domenico Rau, Roberto Papa
Nuclear myosin VI regulates the spatial organization of mammalian transcription initiation
Yukti Hari-Gupta, Natalia Fili, Ália dos Santos, Alexander W. Cook, Rosemarie E. Gough, Hannah C. W. Reed, Lin Wang, Jesse Aaron, Tomas Venit, Eric Wait, Andreas Grosse-Berkenbusch, J. Christof M. Gebhardt, Piergiorgio Percipalle, Teng-Leong Chew, Marisa Martin-Fernandez, Christopher P. Toseland
Drosophila Sex Peptide Controls the Assembly of Lipid Microcarriers in Seminal Fluid
S. Mark Wainwright, Cláudia C. Mendes, Aashika Sekar, Benjamin Kroeger, Josephine E.E.U. Hellberg, Shih-Jung Fan, Abigail Pavey, Pauline Marie, Aaron Leiblich, Carina Gandy, Laura Corrigan, Rachel Patel, Stuart Wigby, John F. Morris, Deborah C.I. Goberdhan, Clive Wilson
Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics
S Basu, O Shukron, A Ponjavic, P Parruto, W Boucher, W Zhang, N Reynolds, D Lando, D Shah, LH Sober, A Jartseva, R Ragheb, J Cramard, R Floyd, G Brown, K Gor, J Balmer, TA Drury, AR Carr, L-M Needham, A Aubert, G Communie, L Morey, E Blanco, MA Barber, I Mohorianu, T Bartke, L Di Croce, I Berger, C Schaffitzel, SF Lee, TJ Stevens, D Klenerman, BD Hendrich, D Holcman, ED Laue
Adipose-tissue derived signals control bone remodelling
He Fu, Maria-Bernadette Madel, Dominique D. Pierroz, Mariano Schiffrin, Carine Winkler, Anne Wilson, Cécile Pochon, Barbara Toffoli, Jean-Yves Jouzeau, Federica Gilardi, Serge Ferrari, Nicolas Bonnet, Claudine Blin-Wakkach, Béatrice Desvergne, David Moulin
Fluorogenic probe for fast 3D whole-cell DNA-PAINT
Kenny Kwok Hin Chung, Zhao Zhang, Phylicia Kidd, Yongdeng Zhang, Nathan D Williams, Bennett Rollins, Yang Yang, Chenxiang Lin, David Baddeley, Joerg Bewersdorf
Cell division in the early C. elegans embryo. Plasma membrane, green; chromosomes, magenta.
Project Description
Cell division is fundamental to life and errors can result in abnormal chromosomal numbers, developmental defects, and cancers. Similarities in the structural and molecular organization of the division apparatus gives the textbook picture, that mechanisms underlying division, including formation and constriction of an actomyosin contractile ring, do not vary between cell and organism types. However, recent research and clinical findings suggest that there is a previously un-appreciated variation in the molecular requirement for cytokinesis to occur, as depletion or mutation of several ‘essential’ proteins only disrupt division in specific cell-types and lineages.
During C. elegans development each cell has a specific identity and gives rise to different cell lineages. Furthermore, the factors that control cell identity have been well mapped by decades of detailed developmental biology. Therefore, it is an excellent multicellular system for observing the interaction between cell identity and cytokinetic perturbation in genetically identical, but functionally variable cells.
This PhD project will use the C. elegans model system and state of the art confocal microscopy to image cytokinesis, tracking the outcome of this rapid and dynamic cellular process, and quantifying localisation of fluorescently labelled cytokinetic proteins, while perturbing different aspects of cell identity. During the PhD, the student will receive training in live-cell fluorescence microscopy and image analysis, as well as general molecular and cell biology techniques and C. elegans genetics and transgenesis (via MosSCI and CRISPR). Furthermore, they will have the opportunity to take part in DTP-wide training and networking events, an external research placement, and attend conferences.
NOTE: Application details are below, however it is strongly recommended to contact the primary supervisor prior to applying.
Applications should be made by emailing bbsrcdtp@liverpool.ac.uk with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project and at the selected University. Applications not meeting these criteria will be rejected.
Please note that the closing date for applications is Monday 18th May at 12noon.
Funding Notes
This is a 4 year BBSRC studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.
2) FLIRT: Fast Local InfraRed Thermogenetics for subcellular control of protein function. 2018 Nature Methods (15) 921–923
3) Using fast-acting temperature sensitive temperature sensitive mutants to study cell division in Caenorhabditis elegans. 2017 Methods in Cell Biology (137) 283-306
4) Cortical PAR polarity proteins promote robust cytokinesis during asymmetric cell division. 2016 Journal of Cell Biology (212) 39 – 49
5) High-Resolution Temporal Analysis Reveals a Functional Timeline for the Molecular Regulation of Cytokinesis. 2014 Developmental Cell (30) 209 – 223
6) aPKC cycles between functionally distinct PAR protein assemblies to drive cell polarity. 2017 Developmental Cell (4):400-415.e9
In the early fly embryo, information encoded in a handful of maternally deposited protein gradients is fed forward through increasingly intricate layers of interacting genes, culminating in the differentiation of the embryo into functional body segments with a high degree of spatial and temporal precision[1],[2]. Short segments of regulatory DNA known as enhancers lie at the heart of this developmental cascade. Enhancers contain binding sites for transcription factor proteins and are thought to act like computational units that “read” input concentrations of relevant transcription factors and “compute” a corresponding level of output gene expression[3]. But while we know quite a bit about what enhancers do, the how remains a mystery: we still lack a quantitative physical understanding of the chain of molecular events that connect transcription factor binding at enhancer DNA to the activation or inhibition of transcription.
Our recent work was aimed at filling this gap through a combination of live imaging experiments and theoretical modeling that allowed us to investigate transcriptional regulation not only across space, but also over time[4]. We focused on the even-skipped (eve) stripe 2 enhancer, which drives a sharp stripe of pattern formation in developing embryos of the fruit fly Drosophila melanogaster. Nearly three decades ago, a seminal study by Steve Small and Michael Levine established the basic principles of eve stripe 2 regulation: two activators, Hunchback and Bicoid, initially establish a broad domain of expression that is then refined into a sharp stripe by the action of the repressors Giant and Krüppel on the anterior and posterior sides of the stripe, respectively[5]. Dozens of papers have followed in their footsteps, making eve stripe 2 one of the most widely studied enhancers in developmental biology.
In 2014, the dynamics of eve stripe 2 expression in living embryos were examined for the first time using the MS2 system[6],[7]. These experiments revealed that the rate of transcription at individual eve loci was highly stochastic, with periodic “bursts” of rapid transcription that were separated by periods with little to no activity. This transcriptional bursting has been observed across a wide variety of model organisms, suggesting that it is the rule, rather than the exception[8],[9],[10],[11],[12],[13]. Because these single-locus fluctuations reflect the molecular processes that drive transcription, the authors speculated that it might be possible to learn more about the molecular mechanisms that underpin transcriptional regulation by taking a quantitative look at how the characteristics of transcriptional bursts varied across different regions of the eve stripe 2 pattern. Yet at that point there was no rigorous way to quantify how transcriptional bursting changed as a function of space and time. The challenge we faced was that rather than reporting on the instantaneous state of the promoter, the fluorescence readout from MS2 experiments at each time point corresponded to the aggregate promoter activity coming from all RNA polymerases actively transcribing the gene and elongating nascent RNA (see Figure 1C). To overcome this challenge, we worked with Hernan Garcia and Chris Wiggins to develop a new computational tool that could systematically dissect burst dynamics at individual loci across a pattern of gene expression.
cpHMM inference
Coined “compound state hidden Markov model” (cpHMM), our new computational technique is conceptually similar to an approach that was recently developed in the Chubb lab[14] and earlier HMM-based approaches[15],[16]. It allowed us to deconvolve the MS2 traces and obtain information about the instantaneous promoter activity at individual eve loci, which we described using a simple “telegraph” model with one active and one inactive state (Figure 1A & C, Video 1). This model has three parameters: the kinetic on- and off-rates that control the switching between transcriptionally active and inactive promoter states, and the rate of RNA polymerase initiation. Thus, in the model, there are three different “knobs” that transcription factors can tune to increase or decrease the average rate of mRNA production at a locus. With this technique in hand, we then set out to infer how these parameters were controlled across space and time from individual MS2 traces obtained from live imaging.
Our inference results showed that regulation of bursting took place primarily through the spatiotemporal modulation of on-rates (bursting frequency), with eve loci in the stripe center bursting with about twice the frequency of those at the stripe boundaries (Figure 1B). This finding suggests that the transcription factors responsible for modulating eve activity act by speeding up or slowing down one or more of the molecular steps leading to the initiation of transcriptional bursts, but do not affect the rate of RNA polymerase loading within a burst or the duration of the burst (inverse of the off-rate). Thus, although we did not have single-molecule resolution, we were able to use our computational method to infer the transcriptional state of individual promoters and to make headway towards a molecular understanding of the mechanisms driving transcriptional control.
Figure 1: cpHMM inference based on a kinetic model of promoter activity. (A) Random telegraph model of gene activity with three kinetic rate parameters. (B) Inferred spatial modulation of the burst frequency. (C) MS2 traces, representing aggregate signals from all elongating polymerases, deconvolved to yield the hidden promoter state dynamics.
Temporal, not spatial regulation explains the majority of stripe formation
Our cpHMM inference provided a prediction for the shape of the eve stripe 2 pattern, assuming that it was formed entirely through the spatial control of the burst frequency (green profile in Figure 2B). To our surprise, this “bursting only” prediction significantly underestimated the true dynamic range of the stripe pattern as revealed by our live imaging data (red profile in Figure 2B).
Going back to the raw data, we realized what was happening: the most striking aspect of eve stripe 2 expression is not the control of the average rate of mRNA production (via the control of transcriptional bursting), but, instead, the simple fact that the period of time over which gene loci engaged in bursty transcription was sharply controlled across the stripe. Eve loci in the stripe center were active for >40 minutes, while those on the stripe flanks were active for only 10-15 minutes. This indicated that the stripe pattern was being driven by the joint action of two distinct regulatory strategies, the control of the mean rate and the control of the transcriptional time window (Figure 2A).
We developed a simple quantitative model to connect observed control of the transcriptional time window activity over time with the predicted corresponding pattern of eve mRNA concentration. The model indicated that, indeed, this simple control of the duration of the period of transcriptional activity amongst nuclei on the stripe flanks accounted for the majority of stripe formation (blue profile, Figure 2A), while the control of the rate of mRNA production during the active window–the modality that had been the focus of most studies to date–only served to refine and sharpen this stripe. Thus, while transcriptional bursting certainly provides a window into the molecular nature of transcriptional control, the regulation of the period of time over which transcription occurs is the key strategy employed by the fly to realize the sharp eve stripe 2.
Figure 2: Two regulatory strategies driving stripe formation. (A) Our analysis revealed that eve stripe 2 is generated through the interplay between two different regulatory strategies: the control of the transcription rate while loci are active, and the control of the amount of time that loci are active. (B) A simple model indicated that the control of the transcriptional time window plays the dominant role in driving stripe formation.
We hypothesized that these two “control strategies” for stripe formation (control of average mRNA production rate and control of the transcriptional time window) might result from two different underlying molecular mechanisms. To test this hypothesis, we developed a simple model that used logistic regressions to relate the fraction of nuclei that had ceased transcribing at a given time and location to the concentrations of the four known eve stripe 2 regulators. We applied this framework to our live imaging data, along with a time series of transcription factor concentrations derived from fixed tissue experiments that was previously published by the Gregor Lab at Princeton[17]. The results indicated that the timing with which eve loci on the stripe boundaries stopped transcribing could be explained entirely by the progressive increase in the levels of Giant and Krüppel over time, and–surprisingly–was insensitive to the concentration dynamics of the activators Bicoid and Hunchback. These results suggest that the repressors act to turn off eve loci in nuclei on the stripe edges via a molecular pathway that is orthogonal to the one that controls transcriptional bursting and the mean rate of transcription.
Video 1: Decoding instantaneous promoter state dynamics inferred from MS2 imaging using the cpHMM method. Green and red nuclear coloring corresponds to ON and OFF promoter states in transcriptionally engaged loci, respectively.
Future directions
While our study focused on the pattern driven by the eve stripe 2 enhancer in developing Drosophila embryos, the quantitative techniques we developed to dissect transcriptional bursting and to connect output transcription dynamics to input transcription factor concentrations are quite general. It is our hope that these tools can be used by researchers to gain insight into the transcriptional regulation of other genes both in Drosophila and in other organisms. To facilitate this, we are making the code for cpHMM publicly available at https://github.com/GarciaLab/cpHMM. With respect to new research directions, we have recently collaborated with the Eisen Lab at Berkeley to study the transcriptional dynamics of the full eve locus. There, we found that despite being created by the largely independent activity of five discrete enhancers, the seven eve stripes are sculpted by the same basic regulatory strategies[18].
In addition to inferring the kinetic parameters of promoter activity, our methodology also allows us to decode individual activity traces and find the most likely promoter state sequences (Figure 1C, Video 1). In future work, we hope to utilize this feature of our methodology to dissect the temporal interplay between the fluctuations in the local concentration of transcription factors at a transcriptional locus and the initiation of transcriptional bursts. Specifically, we plan to correlate the inferred promoter state sequence information with real-time measurements of transcription factor concentrations in individual nuclei, which is now possible due to the LlamaTag technology that was recently developed by our colleague Jacques Bothma[19]. Combining these computational and live imaging techniques will allow us to examine the concentration of transcription factors at the start and end of transcriptional bursts, shedding light on how individual transcription factors act within the transcriptional cycle.
Written by Nick Lammers, Vahe Galstyan and Hernan Garcia
I wrote to several colleagues in the process of highlighting (preLight here) a recent preprint on conference reform by Sarabipour et al., some involved in organising conferences, others invested in ECR career development, publishing, and publishing reform. Here are their comments (I will update this resource as I hear back from more people):
“I am really intrigued by the local hub model… [though] it’s often challenging to be a virtual participant when much of the meeting is happening in person.”
ASAPbio is planning to move our meetings online for the foreseeable future, so we will definitely be using some of these ideas. Replicating the “hallway track” seems to be one of the most significant challenges, so I’m excited to play with Zoom breakout rooms and other ways to promote 1:1 interaction.
I am really intrigued by the local hub model, though this raises the question of what people can do if they can’t travel to a hub or if connections between hubs are as important as interactions within them. This stems from my previous personal experience with hybrid events: it’s often challenging to be a virtual participant when much of the meeting is happening in person. It may be that, with better A/V tools, this problem will diminish (for example, the Meeting Owl enables virtual attendees to feel more like they’re in a room of speakers).
“My thoughts are that the bar for conferences needs to be MUCH higher. We shouldn’t just fight the rich-get richer-factor, we should obliterate it.”
My thoughts are that the bar for conferences needs to be MUCH higher. If we are going to incur the expense and carbon cost of an in person meeting, it should be a complete complement of what’s missing elsewhere. It shouldn’t be a place to showcase work and people we already know and see elsewhere, it should be a way to highlight things we otherwise would never have seen or meet others we never would have met. We shouldn’t just fight the rich-get richer-factor, we should obliterate it.
Second, one of the reasons people don’t like the current iteration of virtual conferences is that we’re trying too hard to make it the SAME as an in person conference might be and make weak substitutes for the real thing. This is why I’m less excited about virtual video conference format in general (though I realize they’re an important piece of this and others likely prefer it). Not only is it a poor substitute, but mainly, I can’t get the protection needed from my work and home life needed to participate in a virtual conference. Instead, we should completely reinvent a conference experience that takes a lot of the elements suggested in the preprint (preprints, Slack etc) and maybe other ways of promoting asynchronous discussion and commenting. Maybe we could finally have the robust comment culture you all have going on at prelights for conference preprints. Actually, conferences are where the bulk/all of my preprint feedback comes from. So having some framework to post preprints and have a dedicated period of time to read/comment asynchronously would be awesome. Along with maybe some incentives to comment/contribute in a timely way (maybe comments or aggregated feedback could get highlighted in journals and comprehensive reports of collected preprints could be another research product people could get credit for).
Maybe there are other ways where people could introduce/brand themselves that are even BETTER than relying upon cold approaching people in a virtual chat room or in person. An ORCID-linked virtual calling card with standardized photo/information in a Slack profile or another item like that attached to preprints so we could get to know all the authors of any preprint better.
“Thanks for highlighting this preprint. I had overlooked it, what with everything going on! I couldn’t agree more with the points raised and – like you and others – I was feeling this way before COVID-19.”
Sally Lowell (Meetings Officer BSDB, Board of Directors, The Company of Biologists) and Kate Storey (Board of Directors, The Company of Biologists), Cambridge, UK
“The problem is that there are considerable logistical and financial barriers to setting up hub conferences. The Company of Biologists is looking at ways to help the community overcome these barriers…”
The ‘hub’ conference model – where regional groups meet and then connect and share with others to make a larger meeting – seems a promising way forward. It maintains the all-important social aspect of conferences while limiting environmentally-damaging international travel. The problem is that there are considerable logistical and financial barriers to setting up hub conferences. The Company of Biologists is looking at ways to help the community overcome these barriers and plan to recruit a ‘Sustainable Conferencing’ officer whose aim would be to develop and oversee a series of measures to support conference organisers with exactly the type of initiatives laid out in this paper, including logistical and technical support for hub conferences. You’ll be hearing more about this in the months to come.
“I’m left thinking that TAGC 2020 did an amazing job in going virtual – a credit to their organisation – and that e-conferences can be a fun and valuable substitute for the real event.”
I’ve been part of two very different online conferences in the last few weeks – the first one as co-organiser. The BSDB meeting was five days before it was meant to start – very deflating but certainly the right decision by the organisers (we were pre-lockdown but the situation was very tense and uncertain, and things were obviously escalating). We got in touch with the organisers about putting some things online and ended up asking participants to provide slides, posters and pre-recorded talks where they could (uploaded to figshare or Youtube, and then collated on the Node). We had a lot of great posters and I think the ‘Tweetorials’ worked very well as a substitute for giving a talk. We also got to chat to some of the housebound plenary speakers in video interviews. I enjoyed being a part of it especially at that uncertain time. In a way it was an act of rebellion against the virus – you took away the meeting but we’ll keep going! Given that we only had a few days to organise I’m happy with the way it turned out – we didn’t have time for instance to organise live video talks, but allowing many ECRs to share their work and seeing the interactions on Twitter was gratifying.
The TAGC 2020 online experience (which is actually still going with poster sessions this week and workshops going on till June) was a different beast entirely. I was very impressed with the set up – all done via Zoom, with chairs introducing the speakers and relaying questions through the Q&A functionality, and everyone speaking via their homes. In all the sessions I attended, the only technical hitches seemed to stem from slow internet speeds in speakers’ houses – this is something to consider if, for instance, you want to globalise conferences and extend opportunities to countries where good internet is not guaranteed. I’ve encountered more technical hitches in normal conferences (switching adapters, scratchy microphones, overheating projectors etc.), and more distractions too when sitting in the audience (loud typers, whispered conversations, humming air conditioners etc.).
The Q&A format seems much more inclusive than at a normal conference, presumably because asking a question in a room full of people can be very daunting. Moreover, the Q&A chat room extended after the speaker had finished speaking, so even if your question wasn’t read out, it could be answered later. This could presumably be rolled out to in-person conferences. There was also a lot of interaction on Slack, but, at least for me I would have interacted with more people at an in-person event – perhaps this reflects my personality or the need for e-conference organisers to think about ways to be creative in getting people together (e.g. in a speed dating style).
I’m left thinking that TAGC 2020 did an amazing job in going virtual – a credit to their organisation – and that e-conferences can be a fun and valuable substitute for the real event.
“The local hub idea sounds great… the only scenario where I foresee some difficulties for early career researchers is while networking for one’s next position…”
I am wondering what will happen to “unpublished data” – you know, the kind of new and exciting things you would hear at a Gordon conference – I think many people will be concerned with confidentiality in an online format. Are students going to be allowed to upload their posters online, accessible to thousands of people with little control (anyone can take screenshots, for example). I know quite a few paranoid PIs who probably would not allow this… yet it can be really useful as a PhD student to get early feedback on projects at conferences.
The local hub idea sounds great, I think participation from home would make the experience quite different. The only scenario where I foresee some difficulties for early career researchers is while networking for one’s next position – for example German PhD students wanting to move to the US for a postdoc. How would one network in such a case? Or do we expect these will be the few people still travelling overseas, applying for specific funding to do so?
I would also stress the idea of no printed materials and less gadgets (I think this is also in the preprint maybe). It’s one thing which has often bothered me – people come back with so much junk from conferences!
“I would agree that there are too many meetings right now – the same people travelling everywhere to deliver the same talks again and again. Promoting the idea of small workshops could help, but this holds the danger of further disadvantaging communities that already have little access to such meetings. The way forward, for in-person meetings, is to work closely with the scientific societies that host regional and local conferences – perhaps via the hub option discussed in the preprint.”
“A model with mainly virtual conferences can also end up discriminating against disadvantaged groups, and I didn’t really see that addressed in the paper.”
I think the arguments put forward in the preprint make a lot of sense, but I have a few concerns:
1) I fear that fully open virtual conferences could kill the sharing of unpublished data. Conferences that end up as a boring highlight of published data might be one of the reasons why “44% mentioned that these conferences had “no perceptible impacts” on their research projects, programmes or policies”. We all know that if people do not engage, conferences are basically useless and virtual conferences open to all might make that a more common problem. My suggestion is that, rather than having all conferences open to all people, you could have non-profit pay-per-view based conference attendance where you can only watch if you register with an institutional email and pay a small fee that covers organisational costs (like softwares that detect is the talk is being filmed and things like that, or more if they fund travel grants, see point 2). Hence, people would have to register beforehand, you would have an attendance registry, and, like the GRC, you would have to sign a non-disclosure form.
2) A model with mainly virtual conferences can also end up discriminating against disadvantaged groups, and I didn’t really see that addressed in the paper. Virtual conferences do not have the valuable bonus of allowing people to approach other people and talk in person, that’s obvious, and the local “in person” gatherings are not a solution because once again they can discriminate massively against people from less wealthy countries. A workshop in London with people from UCL, FCI, Imperial and so on is not the same as a workshop in Lisbon (I talk about London and Lisbon as cities that I’ve worked in, but it’s easy to find more striking examples). Further, the advantage of in person conferences is that, regardless of where you are from, you can easily approach someone. I imagine that might be a bit harder to achieve virtually. Hence, I think a compromise has to be reached, where we retain smaller international conferences, no bigger than your average GRC (~150 people), organised in a very similar way to the GRCs, namely prioritising unpublished data and social activities so that people know each other and increase travel grants considerably with priority for ECR from less rich countries. This would be funded by people paying to attend the conference virtually. A way to make people keen on this could be to give priority in the questions to virtual attendees.
“Coffee breaks, lunch queues, walking to a talk, taking the lift, catching the conference coach, even waiting in the airport/at the train station – this is when a lot of conversations start and can lead to lasting relationships. I am interested to see what the future holds for conferences, and accept that we can’t go on how we have in the past, but I will mourn the loss of personal interactions!”
As someone who both attends and hosts conferences, I can’t see that any of the suggestions come close to addressing what I think of as the biggest benefit of attending conferences: the ‘in between’ interactions. Coffee breaks, lunch queues, walking to a talk, taking the lift, catching the conference coach, even waiting in the airport/at the train station – this is when a lot of conversations start and can lead to lasting relationships.
I think other things are easier to achieve. I like the idea of a ‘scores on the doors’ approach to gender balance for meetings. Every conference should make it clear what the split is. At the last JCS meeting we tried a number of initiatives to promote ECRs. We did ask for questions from them first, but as I’ve seen at other meetings, they often find it too daunting to be the first ones to speak. We had lots of slots for short talks, and reduced the number of long talks to fit them in. But the most popular and successful was ‘speed dating’, where people talked to someone for a few minutes, then switched when we rang a bell. We had fantastic feedback on that – ECRs and PIs who might not have spoken, and reports of collaborations being formed from that.
I am interested to see what the future holds for conferences, and accept that we can’t go on how we have in the past, but I will mourn the loss of personal interactions!
While [increasing the capacity for giving remote presentations] helps groups such as female professors, group leaders, and senior postdocs who may be invited to speak, this still does not help amplify the voices of junior postdocs and PhD students. These are groups that could very much benefit from more of a shift in conference format and especially conference ‘culture’.
Most researchers are familiar with the concept of the ‘leaky pipeline’: the phenomenon whereby the proportion of female researchers relative to male researchers decreases with seniority. Within the constraints of the most commonly-used conference structures – e.g. keynote speakers, invited speakers, accepted oral presentations, accepted poster presentations – conference organisers often struggle to secure a gender-balanced group of invited speakers, especially for fields in the physical sciences. This can be for several reasons, including unconscious bias against women and a lack of awareness of appropriate female scientists in the field. However, one major problem is that in fields with a small pool of female researchers possessing the traditional requirements for an ‘invited speaker’, there is often a collection of women who get invited to speak at a large number of conferences. This puts enormous pressure on these researchers – should they reject these invitations, many feel that they are contributing to the problem of under-representation of women at conferences, but should they accept these invitations this can put large strains on their personal and professional lives due to the amount of travelling required. The role of many female researchers in caring roles for family members (not just limited to children, but also elderly and disabled relatives, which is often overlooked) frequently exacerbates this.
One way of ensuring more gender-balanced line-ups of invited speakers is to cast the net wider e.g. invite women from earlier career stages to speak. However, this may be perceived as unfair on more senior male researchers who feel ‘overlooked’ for invited speaker opportunities. A straightforward solution to this would be specifically allocating some invited speaker slots only to early career researchers, so that career stage diversity becomes more integrated within conference structures, thus opening another avenue to allow women and other under-represented groups to present.
Increasing the capacity for giving remote presentations should definitely help to alleviate the pressure on senior female researchers to undertake frequent travelling. While these options help groups such as female professors, group leaders, and senior postdocs who may be invited to speak, this still does not help amplify the voices of junior postdocs and PhD students. These are groups that could very much benefit from more of a shift in conference format and especially conference ‘culture’. This would involve a greater number of discussion and networking sessions that don’t rely on the presence of ‘prestigious’ senior speakers, allowing more junior female researchers to engage more actively in scientific meetings without worrying that they have been invited to participate due to tokenism. Furthermore, it is important that such sessions are not implicitly associated with drinking; while alcohol at ‘networking’ sessions can help people relax and talk more, it can also unfortunately make women quite vulnerable. Alcohol-free networking events during core hours should be encouraged to widen participation from all members of the community, irrespective of carer responsibilities, personal or religious beliefs.
Finally, even though I enjoyed the flexibility of tuning in to talks on demand [during the massive TAGC online conference] from the comfort of my home and at my chosen hour, I did miss the ability to excuse myself from all other professional and domestic commitments for a few days and immerse myself in the meeting. A relatively small tradeoff, I guess!
The preprint by Sarabipour et al. does a commendable job at analyzing what’s broken in the existing scientific conference system and provides comprehensive suggestions about reinventing it. As a woman, an ECR and also having been a graduate student in a developing nation, I can personally (and painfully) relate to the challenges highlighted by the authors. The recent online avatar of TAGC organized by the Genetics Society of America (GSA) served as the perfect pilot experiment that tested a number of these recommendations on a scale possibly unlike anything before this. Although spurred by the ongoing global crisis rather than by design, for many researchers across the world including myself, this was the first taste of a fully online major scientific conference. I wasn’t even planning to attend the original TAGC this year, so the online version definitely opened up a possibility that didn’t exist before, regardless of the pandemic. I greatly appreciated the flexibility of being able to attend talks in parallel sessions without the ‘fear of missing out’, as well as the ability to visit recorded talks later. It is remarkable that GSA pulled this off so successfully with so little time for preparation.
While I am in complete agreement with the authors about the pressing need for reforms and the guidelines that they provide, I have a few concerns:
First, an issue with future meetings relying very heavily on the preprint culture for dialogue is that preprints are still not mainstream enough, outside of a handful of countries (another important preprint by Abdill et al.). Therefore, the use of preprints to facilitate discussion and feedback could continue to disproportionately benefit only researchers from certain geographic locations. The disparity in preprinting also likely differs between scientific communities (specific model organisms versus the general cell biology community, for example). Changing this will require a more extensive change in mindset globally and broader acceptance of preprints as a valid form of scholarly communication.
Also, sharing entire posters online for anyone to access and potentially save could be likely perceived as a threat by many labs, pushing people away from sharing unpublished work.
Second, the networking aspect of meetings is undoubtedly the most valuable for any ECR attendee. Many strategies have been laid out to at least partially recreate these opportunities in the vision for future meetings, but they cannot really stand in for many aspects of these interactions. Again, I think the suggestions are just the initial steps and there is a long road ahead of us. Maybe we will eventually just accept it as the new normal, as we have with so many other things.
Finally, even though I enjoyed the flexibility of tuning in to talks on demand from the comfort of my home and at my chosen hour, I did miss the ability to excuse myself from all other professional and domestic commitments for a few days and immerse myself in the meeting. A relatively small tradeoff, I guess!
Without these [interacting with, and learning from people from elsewhere] diverse interactions and the friendships and collaborations that form from them, are we at risk of research, particularly in smaller and more poorly-resourced communities, becoming even more regionally silo’d than it already can be, based on distribution of resources and local policies etc?
Stable high-bandwidth internet is not uniformly available across many regions of developing countries – the infrastructure is often unreliable and data can be very expensive. The use of hubs, as opposed to fully-digital meetings where everyone attends from their home (so, after COVID and global lockdown) solves this problem partly – institutions should be able to provide bandwidth, if not always stability. But yes, I agree completely with you that internet access should be a human right – not just for conferencing, but for education at all stages of life, innovation and commerce, and freedom of speech and communication.
I’m not sure how to get around two things that physically travelling to a meeting provide you: (1) A break from your daily routine and responsibilities, so you can focus on the science and connecting with people. We already know that attending a big conference in your home city is a very different experience to attending one that you travelled to get to – life seems to intrude much more! This might be even more so for those with teaching and family responsibilities – as we are already seeing with diverse WFH struggles. And (2) those in-person connections – which as you say are often so serendipitous, and not necessarily directly related to the content of the conference, but can nevertheless be important for career and personal development. I acknowledge that that’s already a privileged position – so many who don’t have the chance to go to conferences, or have other responsibilities, don’t experience those things anyway. So then, it’s a sort of levelling of the playing field, and the expectation is that democratisation of the conference content makes up for that loss to the smaller number of researchers and their science.
The hybrid approach – gathering at hubs and then virtual conferencing between those hubs, partly provides some of that mentioned above. But I still feel like it’s missing the massive value that is gleaned from interacting with, and learning from people from elsewhere, who are different and have had distinct experiences, especially for students and ECRs.
Without these diverse interactions and the friendships and collaborations that form from them, are we at risk of research, particularly in smaller and more poorly-resourced communities, becoming even more regionally silo’d than it already can be, based on distribution of resources and local policies etc?
I think the post-pandemic future will hold a mixture of virtual and modified in-person meetings. Perhaps some rationing of how many meetings one can travel to, and how far, in a given period will be recommended for researchers in the future, but I have no idea how that can be enforced. You also mentioned making meetings longer, to justify the commitment and carbon-cost. It makes sense, but the introvert in me recoils – there will need to be programmed down time as much as programmed social engagement and networking, or us introverts will leave broken and hesitant to attend too often!
This whole discussion has been about conferences, but many of the same problems could be highlighted about workshops and courses – with the exception that they are usually a bit longer, smaller, and have a higher ECR:PI ratio. If these can be preserved at a larger proportion for travel and IRL participation, then the opportunity for in-person engagement and relationship building, which is reduced for ECRs with a switch to virtual meetings, will at least be partly preserved through these valuable events (although more for students and early-stage post-docs than for those in the job market).
I think fields will benefit from centralised portal(s) where all the online material that will be produced through virtual meetings is collected and curated. The volume of information will be huge!
Data from time-lapse experiments is often displayed in a graph or plot, to visualize the dynamics of biological systems (Goedhart, 2020). Ironically, the perception of the dynamics is largely lost in a static plot. That’s where animated plots come in. Animated plots are a great way to display the dynamics of the underlying data. Below, I provide a walk-through for creating an animated time series using R in Rstudio (footnote 1). The final result looks like this:
Static plot
The basis for the animation is a static plot. So I start with a brief explanation of how to generate a plot from time-series data (a more detailed explanation of plotting timeseries data can be found in a previous blog). First we load the ggplot2 package that is used for plotting:
>require(ggplot2)
Next, we can read the file, which contains the data in a ‘tidy’ format (to transform your own wide, spreadsheet data into tidy format see this blog) and assign it to the dataframe df_tidy:
Animated plots can be generated with the gganimate package and we will be using functions from the magick package for saving GIFs and so both are loaded:
>require(gganimate)
>require(magick)
To turn the static plot into an animated plot, we add the function transition_reveal(Time) to reveal the data over time:
Running this command may take some time (at least a minute on my MacBook). Once it’s ready, the animation is shown in the Viewer panel in RStudio. We will discuss how to save the animation in a bit. But first we will beautify the animation by adding a vertical line that runs along:
One of the advantages of this step is that we can do some styling of this object. For instance, changing the default R/ggplot2 layout to a more neutral look:
Now we can render the animation and assign it to the object animation. The number of frames in the animation can be specified and it makes sense to use the number of time-points (footnote 2).
Saving this as a GIF will give the animation that is shown at the start of this blog.
Final words
I like the animated plot as it elegantly displays the dynamics of the data. The animated plot can be combined with a movie of the process. But that will be a topic for a next blog…
Footnote 2: The default for generating high-quality GIFs is the Gifski renderer, but I had some issues with the rendering. To use the default type and save enter:
We would like to take this opportunity to thank the Node for the chance to write a post about JoVE and how our resources can be beneficial for the research and teaching of developmental biology and multiple other disciplines.
All researchers will be familiar with the challenges of replicating an experiment you’ve read in a paper, or learning a new technique in the lab. Spending hours looking through reference lists or trying to work out exactly what is meant by “shake vigorously” or “aspirate gently”. In an ideal world you ask someone who knows the technique to show you how, but with the global nature of scientific research, time restraints and physical distance means this isn’t always possible. But what if a researcher on the other side of the world could show you how to perform their methodology at any time of day with no travel costs involved? This is where JoVE comes in!
JoVE is dedicated to publishing scientific research in a visual format, capturing the intricate details of life science research and overcoming two of the biggest challenges faced by the scientific community:
1) Poor reproducibility and low transparency of biological experiments
2) The time, labour, and cost intensive nature of learning new experimental techniques
With technology so ubiquitous in our everyday lives, it stands to reason that we should harness its power in scientific research and education.
Since launching in 2006, JoVE Video Journal has published more than 12,000 scientific video demonstrations on experimental methods in 13 discipline specific sections including Developmental Biology. JoVE Video Journal was the first and remains the only peer-reviewed journal of visualised experiments, and today JoVE video articles are viewed by millions of users making scientific research more productive and reproducible.The field of developmental biology employs a multitude of complex and rapidly developing research methodologies. As such, the Developmental Biology section of JoVE Journal, featuring insightful video articles authored by renowned experts in the field, is invaluable for researchers worldwide to learn experimental methods quicker and more precisely.
With more than 500 articles in our developmental biology section, it’s difficult to to highlight just a few examples of the excellent discoveries that have furthered our knowledge in this field. Why not take a look at this selection of some of our more recent additions to the journal that demonstrate the broad range of research:
It’s not just seasoned researchers that can benefit from this video format, we also have visual teaching aids for students at the start of their scientific careers. JoVE’s database of educational videos are designed for educators and students, to better teach and learn key scientific concepts with the aid of animations, and fundamental lab techniques with easy-to-understand video demonstrations. By providing a visual approach to learning basic techniques, JoVE Science Education makes experimentation more accessible to undergraduates in developmental biology classes.
Our Science Education collections cover a range of lab techniques valuable to developmental biologists from very basic skills such as centrifugation, volume measurements, and pipetting, to more advanced developmental biology specific techniques such as culturing embryonic stem cells, explant culture, and genetic engineering of model organisms.
For teaching foundational scientific theory we have JoVE Core Biology, an animated textbook organised into sections including cellular processes, genetics, and human biology. Instead of flicking through hundreds of pages of dry text and confusing diagrams, Core Biology uses concise animated videos to bring the concepts alive.
During the current COVID-19 pandemic, JoVE is aiding universities, colleges and secondary schools in the transition to online teaching by providing free access to all of our educational content until the 15th of June 2020. So now is the perfect time to try it out. Just head to www.jove.com to activate your free trial, and take a look at our faculty resource center for help setting up remote access for your students.
We are constantly adding to our content with new educational resources released all the time, and 150 new journal articles published each month. However, this does not mean that we prize quantity over quality. We believe carefully produced, peer-reviewed scientific videos represent the best way for scientists to share a new technique, and for researchers and students to learn from it. With every video, we aim to drive the next breakthrough in science research and education.
So remember, the next time you are in the lab or want to boost student performance, check JoVE first.
Rebecca Ellerington, Curriculum Specialist UK and Ireland
Like many science enthusiasts, I read the book The Double Helix when I was a student. It’s a dramatic tale of how American geneticist James Watson and British molecular biologist Francis Crick discovered the structure of DNA back in the early 1950s. Of course, being written by Watson himself, it’s no surprise that he’s the dashing hero of the story.
The names of James Watson and Francis Crick are inextricably linked with the discovery of the DNA double helix. And if you’ve been paying attention, you’ll also know that credit is due to Rosalind Franklin, Maurice Wilkins and Ray Gosling too. But what about Elwyn Beighton, Fred Griffith or Rudolf Signer?
In this episode we’re unwinding history to uncover some of the less well-known stories behind the discovery of the structure and function of DNA.
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
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