I wanted to take a couple of minutes to update you on how things are going at Development. I imagine many of you will be reading this on a laptop in your home office/kitchen/bedroom in between Zoom calls, homeschooling and/or sourdough baking. In much of Europe and North America, as well as other parts of the world, it’s been like this for the best part of 2 months and will continue for at least the next few weeks. Even when quarantine measures begin to be eased and our labs and institutes start to open up, it won’t be straight back to how it was before. Physical distancing requirements, travel restrictions, disrupted supply chains, and potentially new financial constraints will affect us for months to come and might permanently change how we do science.
New colleagues settling into a Development home office
At Development, we’re more fortunate than most. As Academic Editors, although our labs are affected, we’re already used to doing our editorial work remotely and communicating with each other electronically. The professional staff based in the Company of Biologists offices in Cambridge have been able to adapt quickly to working from home and you can see some of their new locations on our Instagram. Regular electronic meetings between Development staff and regular seminars involving all Company staff have kept communication going and morale high. It’s been great to see the team pull together despite the difficulties and I’m pleased that Development has continued to run smoothly.
As the lockdowns and shelter-in-place orders spread around the globe the Development editorial team discussed the effects it might have on our community and what we could do to support researchers. We put together a statement. This included asking reviewers or authors unable to meet journal deadlines to contact us for extensions. We’ve been able to do this for everyone that has been in touch. Of course, our scoop protection policy means that authors do not have to worry about being scooped once a manuscript is submitted. Moreover, we do not necessarily reject a new submission if a similar paper has recently been published: if this happens, please contact us to discuss the case.
We also emphasised that reviewers should limit requests for revisions to those that are essential to support the conclusions of the paper. This has always been the case at Development, but it’s even more important in these times when the ability to conduct experiments is severely restricted. We want to ensure that papers meet the high standards our readers expect, but we do not want to see publication delayed unnecessarily. As editors we try to provide guidance on the revisions that are necessary when we send the reviewers reports and we encourage authors to discuss revision plans with us, if that would be helpful, before embarking on extensive new experiments. More generally, we’re conscious that – with opportunities to meet the community severely restricted this year – there won’t be the occasions to talk about your science or the journal that we normally have. So if you’ve got anything you’d like to discuss, please feel free to drop us a line.
Katherine Brown, our Executive Editor, has been keeping a close eye on any changes in the rate or type of submissions we’ve received. We’re pleasantly surprised that we haven’t noticed any obvious change in the number of research papers submitted, at least not yet. The numbers in both March and April were in line with previous years. As there have been concerns that working from home disproportionately disadvantages women, we’ve also tried to gauge whether there has been a decrease in number of papers submitted with female corresponding authors. This doesn’t seem to be the case for Development, at least from our very preliminary assessment. Approximately 40% of submissions in the last couple of months have a female corresponding author, similar to previous months. Nevertheless, it is something we will continue to monitor and something that will need a more thorough analysis once the immediate crisis is over.
Seema Grewal, our Senior Editor, and Alex Eve, Reviews Editor, have been receiving more proposals for review articles than normal and they have been busy assessing these and advising potential authors. So it looks as if some researchers are using time away from lab to take a deep dive into the literature and write the review they’ve been meaning to. We’re not able to consider all the proposals we receive, but are always happy to discuss ideas. If this is something you’re thinking about, don’t forget to check out Seema’s Introduction to Writing Review Articles. Alternatively, if you want to communicate your thoughts more immediately or practice a different style of writing, take a look at Node Editor Aidan Maartens’ suggestions for Writing for the Node.
I’m also pleased to say that reviewers are continuing to support Development and all the editors are very grateful for this. Understandably, some reviewers are finding it’s taking longer than normal to return their reports, if this happens to you please let us know so that we can keep authors informed. In their reports, many reviewers are acknowledging the difficulty that proposed revisions pose to authors and the discussion amongst reviewers, using cross-referee commenting, can help establish what is really essential for the authors to address. It’s good to see reviewers adopting this constructive approach and I hope this becomes the new normal from now on.
We’ve also begun to think about how scientific life will change beyond the next month or two. Travel is likely to be greatly restricted for a long time and may never return in quite the same way. This will of course have a major effect on conferences and workshops. It is likely to accelerate changes that were already underway because of the contribution of international travel to Climate Change. We’ve seen conferences switch to online (including TAGC and SDB) as an immediate response to the crisis and this trend is set to continue. As an organiser of conferences and workshops, Development and the Company of Biologists have started to consider how we can adapt formats and use new technology to continue to get most of the benefits of conferences without the travel – we’re currently considering options for our upcoming ‘From stem cells to human development’ meeting and expect to have more news on this in the next few weeks. This is not straightforward as conferences are more than a series of talks. They also provide the opportunity for spontaneous encounters that spark unexpected conversations, ideas, collaborations; for early career researchers to present posters and talk informally with each other as well as leaders in a field; for social interactions that result in new friendships as well as new science. It is these less obvious ingredients of a good conference that builds a field, supports the careers of junior colleagues and enhances scientific dialogue. How we replicate or replace these features is a challenge we need to take on. Nevertheless, the developmental biology community has always been innovative and we’d love to hear your thoughts on what can be done.
Anyway, I have a Zoom meeting scheduled and I can smell my banana bread cooking so let me finish by thanking you all – authors, reviewers and readers – for your continuing support of Development. Your suggestions and opinions are always welcome and I look forward to hearing from you, and one day seeing you again in person.
Hello! Recently, I’ve been tweeting writer’s advice from @jbwallingford using the hashtag: #DevBiolWriteClub. I’m psyched that The Node is now letting me add a little depth to this venture. In this first post, I’ll start by managing some expectations.
If you’ve followed #DevBiolWriteClub on Twitter, you might recall that one of my earliest tweets said: “For now, I will focus on how to be a better writer. This is different from how to write better.” Personally, I like that sentence. I think it’s clever, and it conveys some crucial information. That said, one could also make the argument that it sucks. After all, it’s kind of confusing, and by forcing the reader to think hard about just a few words, it risks failing to convey any information at all.
Regardless, the details of well-written and poorly written passages is NOT the point of #DevBiolWriteClub. Rather, I want to use this forum to address one of the most common and intractable misconceptions in writing, especially among busy scientists. The issue is this: If you are serious about better writing, DO NOT start by thinking harder about sentence structure and grammar. Instead, start right now by focusing on your practice of being a writer.
Writing is like a sport. You only get good at it if you practice, with intent, every day. When I’m not doing science, I’m a rock climber, and one of my favorite coaches is Steve Bechtel (Climbstrong.com.), and he once lamented that he always wanted to write an article titled “500 weeks to stronger fingers,” but that no one would read it. I fear the same for these blog posts, because he’s exactly right. No one likes to hear that there are no shortcuts.
The difference, of course, is that most scientists relate to sports (or art, or baking) as a hobby, as this other thing we do sometimes, and we hope to get better at. Ultimately, though, if we don’t get better, it’s not that big a deal. The problem is that many scientists take the same view of writing. But not improving as a writer is a big deal in science. It’s a very big deal, actually. If you are a scientist and you want to succeed, you mustbecome a writer. And the only way to do that is to practice, day in and day out. For years.
So, that’s the bad news. The good news is that the process for becoming a writer is pretty simple, and you can start today. There are only five rules:
Do the work.
Do the work.
Revise and edit. Again, and again, and again.
Read with intent.
You can’t do it alone.
Now, it’s essential that you understand these rules, especially #1 and #2:
Of course, writers need to write, but what I mean by “do the work” is broader. I want you to create a new habit of mind. Take time out of every workday to practice the craft of being a writer by following any one of the five rules. What you do in each session is less important than doing something each workday.
Maybe you will actually write new words in a session, but if you don’t, that’s OK! Some days are stacked with experiments, so maybe you can only find a few minutes to revise something you’re working on (#3). Or maybe all you can manage is to spell-check something you wrote yesterday (also #3). Or maybe you just read (#4). Or maybe today’s the day you have the courage to show what you’ve written to a friend and get their feedback (#5). All of these examples can fall under Rules #1 and #2. But here’s the thing: You need to approach every session intent. Set aside time to do it; try hard; and when you’re done, reflect on your performance. This is the work. Let’s get to it.
In the coming posts, I’ll write more about each of these rules and I’ll provide advice on how to follow them.
In the latest episode of Genetics Unzipped, Kat Arney sits down with leading evolutionary geneticist Professor Sarah Tishkoff from the University of Pennsylvania to talk about her work mapping the genetic diversity of African populations. Sarah talks about the challenges of carrying out ethical fieldwork in Africa and explains why its so important to us more genetically diverse data to inform the development of precision medicine.
We also hear from Garrett Hellenthal and Lucy van Dorp from the UCL Genetics Institute, who are unearthing hidden histories and cultural complexities hidden within DNA. From the mighty Kuba Kingdom to the curiously exclusionary Ethiopian Ari people, the genomes of these populations tell rich, detailed stories about people and places.
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
Flight feathers are amazing evolutionary innovations that allowed birds to conquer the sky. A study led by Matthew Towers (University of Sheffield, UK) and Marian Ros (University of Cantabria, Spain) and published in the journal Developmentnow reveals that flight feather identity is established thanks to Sonic hedgehog – a signalling molecule well-known for giving the digits of the limb their different identities (so that your thumb is different from your pinky, for example). These findings suggest the pre-existing digit identity mechanism was co-opted during the evolution of flight feathers, allowing birds take to the air.
Feathers and the flight they support have long fascinated humans. In the bird embryo, feathers begin as buds—thickenings of the epidermis—that then develop into follicles, from which the keratin-based feathers are produced. Not all feathers are equal, however—compare for instance the downy feathers on the breast of a robin with the flight feathers of its wing. Classical embryological experiments in the 1950s, which involved grafting one part of the embryo on to another, suggested that feather identity (e.g. the choice to become a down versus a flight feather) is established at the earliest stages of development, even before the feather buds form. But in the seventy-odd years since then, we still don’t know much about which signals regulate feather identity.
The new study, carried out with Lara Busby as first author, reveals that flight feather identity is specified by Sonic hedgehog (Shh), a famous signalling molecule known to be involved in the development of limb digits, including human fingers. (And yes, Shh is named after the computer game character, but that’s another story.) Using chicken embryos, the scientists found that Shh is required in the earliest stages of wing development for the mature birds to develop flight feathers. They also defined a set of genes that are likely to be involved in this process. Importantly, they discovered that Shh works in a defined temporal sequence to specify the different flight feather identities, mirroring how it specifies the different digit identities. This similarity suggests that the digit identity network was co-opted for flight feather development during evolution.
Sonic hedgehog is normally produced at the posterior margin of the embryonic chicken wing bud. Grafts of Sonic hedgehog-producing cells were made to the anterior side of a wing bud of another chicken embryo. This operation duplicates the tissues of the mature wing, including the black-pigmented feather buds as shown in the image. The flight feathers buds are the ones protruding from the left and right margins of the wing. Duplicated tissues are on the anterior side of the image (left), and normal tissues are on the posterior side (right)
Dr. Towers said: “Flight feathers are one of the most important evolutionary adaptations that allowed birds to take to the air. Our unexpected findings, showing that the digits and flight feathers share remarkably similar developmental programmes, provide important insights into how the bird wing evolved to permit flight.”
The researchers hope to extend this work by trying to understand how the early exposure of embryonic chick wing bud cells to Shh is ‘memorised’ to allow flight feather formation at a much later stage of development.
Contact: Dr. Matthew Towers, Reader of Developmental Biology and Wellcome Senior Fellow in Basic Biomedical Science at the University of Sheffield, UK.
In a previous blog I explained how animated plots can be made to illustrate the dynamics of data. Animated plots go nicely together with the movies from which the data was extracted. Here, I explain how to display a movie and plot side-by-side, starting from a stack of images and using only open source software. I will use ImageJ/FIJI for image analysis and for creating the movie. Then, R/Rstudio is used for data processing, generating the animated plots and for adding the plot to the movie. A basic understanding of the software is assumed and necessary to complete the tutorial. The steps that are involved are 1) creating a movie, 2) quantification of signal over time, 3) labeling the movie, 4) creating an animated plot and 5) combining the plot with the movie.
The data
First, let’s discuss where the data came from. I acquired the data with TIRF microscopy, which is a technique that detects fluorescence at the basal plasma membrane of cells. TIRF imaging of cells expressing a GFP-tagged Protein Kinase C (GFP-PKC) was used to study the dynamic association of PKC with the plasma membrane, after stimulating the cells. The fluorescence intensity follows an oscillatory pattern that was triggered by adding UTP and that reflects calcium oscillations (Oancea and Meyer, 1998). The raw data, processed data and an R-scripts to generate the movie is available in a file archive at Zenodo.org, doi: 10.5281/zenodo.3785592
Step 1: Creating a movie
The data is astack of images named ‘EGFP-PKCbetaII_100uMUTP_16bit.tif’ which can be downloaded from the archive at Zenodo, or directly through this link. The TIF file can be opened with FIJI or ImageJ. To play the image stack as a movie press backslash [\] and again to stop it.
The first processing step is to convert the 16-bit stack to 8-bit (the line below refers to a ‘menu path’ like this: menubar > submenu > command):
Image > Type > 8-bit
A false color or lookup table (LUT) can be added to improve the visualization of the intensity changes:
Image > Lookup Tables > Fire
The ‘Fire’ LUT works well for this data, but other LUTs can be selected as well. To get the best result, several different LUTs should be tried. Here, I’ll use one of my favorites: the Parrot LUT, reported in this blog. The stack can be saved as gif to generate a movie:
The analysis should be done on the original data (not on converted 8-bit data). After opening the original TIF stack, regions of interest (ROIs) can be drawn to select individual cells. In this example I have drawn three ROIs in the center of the image. The ROIs are available here as a file called ‘RoiSet.zip’’ and can be added to the image stack by dropping the zip file on the ImageJ/FIJI menu bar. The ROIs are now available in the ROI manager that can be activated by selecting it under ‘Window’:
Menu > ROI Manager
Select all three ROIs in the ROI manager. Next, quantify the intensity of all stacks by selecting on the ROI manager window:
More>> Multi Measure
Make sure to activate the checkboxes ‘Measure all 100 slices’ and deselect ‘One row per slice’ and hit OK. A screenshot of the window and the Results window is shown below:
To indicate the cells that are used for the quantification, I have added labels to the GIF that was created in step 1. This can be done in ImageJ/FIJI:
Image > Stacks > Label…
An example of the settings and the result is shown in the screenshots below. Note that I have indicated that the label is only shown in the first 5 frames by setting ‘Range: 1-5’:
After adding the three labels, the image is saved again as a GIF. The result is available as ‘EGFP-PKC-labeled.gif’. I took note that the image has a height of 529 pixels, a number that we need later on.
Step 4: Animated Plots
For the next steps we switch to R/Rstudio. The complete script that I used is available as ‘Movie-with-plot.R’. Below, I will explain every step of the code. Running the code from the command line in Rstudio requires a bit of knowledge of R and it requires several packages that need to be installed and loaded (The ‘>’ sign indicates the prompt of the command line):
Now we are ready to load the data that was generated in ImageJ/FIJI:
>df_results <- read.csv("Results.csv")
The CSV file has a column named ‘Label’ that we need to split in three different columns based on a colon as a delimiter. The relevant column that we need later on is ‘Sample’:
I rename the column ‘Slice’ to ‘Frame’, since I think that is more appropriate.
>df_tidy <- df_tidy %>% rename(Frame = Slice)
To compare intensities, it makes sense to perform a normalization (also explained in another blog). Here, I normalize the intensity data by dividing the data (per Sample) by the average of the first 5 datapoints, reflecting a baseline. The data is stored in a new column, ‘Normalized Intensity’:
To synchronize the movie with the animated plot, it is essential to keep the number of frames (timepoints) the same. This number is determined from the data and we will use it later on:
>nframes <- length(unique(df_tidy$Frame))
Tweaking the layout
The appearance of the default plot can be fine-tuned in many ways. Below are a few of my favorite adjustments to the standard layout. The result of each step can be inspected in Rstudio by calling the object (note that it will take some time to render the animation):
When both the animated plot and the movie are ready, they can be combined. We will adjust the dimensions of the animated plot (size and number of frames) to that of the movie. The number of frames (nframes) has already been determined. The size of the movie can be assessed in ImageJ or FIJI. In this example, we combine the movie and plot horizontally, so we need to know the height of the movie (which is 529 pixels). With these parameters we can correctly render the animated plot and assign the result to object panel_b:
This object can be displayed by entering ‘combined_gif’ in the command line:
>combined_gif
Subsequently, we add all the other frames to the new object:
>for (i in 2:nframes) {
combined_panel <- image_append(c(panel_a[i], panel_b[i]))
combined_gif <- c(combined_gif, combined_panel)
}
Finally, we can save the object combined_gif as a GIF:
>image_write_gif(combined_gif, 'Combined.gif')
The resulting GIF is shown below:
Final Words
The combination of a movie and plot is an attractive and informative way to visualize data from timelapse imaging. This walk-through discusses the basics and lots of additional tweaking and annotations can be done. For instance, labeling of the images can be done in R instead of ImageJ, but I haven’t really figured out how to do that. A potential improvement would be to generate a script for the entire workflow (including the labeling), since it will make it simpler to generate movies in the long run.
I hope that this tutorial is useful and I’m curious how it works for you. I’d appreciate any feedback or suggestions for improvements and I’m looking forward to watch your movies and their plot!
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
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