Looking to conduct research in molecular biology and genetics? We are looking for a lab technician to assist in research on muscle stem cells, development, regeneration, disease, and evolution. More details about our research can be found at http://www.kardonlab.org/. Technician will assist in management of a mouse colony as well as conduct supervised research (leading to publications). Technician must be reliable, well organized, detail-oriented, excited about research and committed to working in our lab for at least two years. Prior lab experience is preferred (although not necessarily required), and class work in biology and enthusiasm for science is essential. Lab is located at the University of Utah in Salt Lake City, affording amazing opportunities for science and outdoor recreation. Looking for someone to start June-July 2018.
Please contact Gabrielle Kardon (gkardon@genetics.utah.edu) with CV, list of references, and a brief statement about why you are interested in the position. BS or BA required.
the GOEvol consortium proudly presents its 6th meeting #Sensation @GOEEvolution 2018 taking place in Göttingen from September 27th to 28th 2018.
The perception of environmental stimuli, their processing and integration is essential for any organism. Apart from the more familiar senses like hearing, seeing or tasting, there are sensory tasks performed by highly specialized animals, such as echolocation in bats or the perception of polarized light in insects. Sensory processing consequently also differs strongly between species. However, at the same time there are astonishing similarities between sensory modalities of phylogenetically distant animal groups, such as the shared cellular structure of light-sensitive organs or the genetic control and developmental origin of sensory cells. With methodological innovation, more and more species can be used for detailed analyses, which further expand the understanding of the evolution of sensation.
Because of the diversity of research and various methodologies in multiple (emerging) model organisms in the field of evolution of sensation we want to bring together scientists from a broad range of fields to reveal commonalities across disciplines.
Following the GOEvol tradition, we aim for an interdisciplinary symposium with an informal atmosphere with plenty of possibilities for social networking. If you enjoy small interactive meetings and the topic suits you, come along!
There are several slots for contributing talks and poster presentations. We strongly encourage interested students and researchers from all levels (Bachelor, Master, PhD and above) to register and apply for talks and poster presentations.
Moreover, we want to support parents to participate. Therefore, depending on the demand, we will be able to provide childcare as well as designated rooms for nursing.
Costs to register are 10€ for students, 20€ for Postdocs and PIs.
Invited speakers:
Sally Leys (University of Alberta, Canada)
Michael Bok (University of Bristol, UK)
Tobias Kaiser (MPI for Evolutionary Biology, Plön, Germany)
Robert Barton (University of Durham, UK)
Mirjam Knörnschild (Free University of Berlin, Germany)
Brigitte Schoenemann (University of Cologne, Germany)
Welcome to our monthly trawl for preprints in developmental biology (plus those hopefully relevant for developmental biologists).
May featured the usual catch of fascinating and beautiful work across the spectrum in the field, from Hox in mice and beetles, doublesex in beetles and bees, and three spinal cord regeneration preprints (incuding one using lampreys!). Our most prolific preprinter was Didier Stainier with four – a productive month for the Bad Nauheim-based biologist.
The preprints were hosted on bioRxiv, PeerJ, andarXiv. Use these links to get to the section you want:
Genome-Scale CRISPR Screening Identifies Novel Human Pluripotent Gene Networks
Robert J Ihry, Max R Salick, Daniel Ho, Marie Sondey, Sravya Kommineni, Steven Paula, Joe Raymond, Elizabeth Frias, Kathleen A Worringer, Carsten Russ, John Reece-Hoyes, Bob Altshuler, Ranjit Randhawa, Zinger Yang, Gregory McAllister, Gregory R Hoffman, Ricardo Dolmetsch, Ajamete Kaykas
Long-term expanding human airway organoids for disease modelling.
Norman Sachs, Domenique D. Zomer-van Ommen, Angelos Papaspyropoulos, Inha Heo, Lena Bottinger, Dymph Klay, Fleur Weeber, Guizela Huelsz-Prince, Nino Iakobachvili, Marco C. Viveen, Anna Lyubimova, Luc Teeven, Sepideh Derakhshan, Jeroen Korving, Harry Begthel, Kuldeep Kumawat, Emilio Ramos, Matthijs F.M. van Oosterhout, Eduardo P. Olimpio, Joep de Ligt, Krijn K. Dijkstra, Egbert F. Smit, Maarten van der Linden, Emile E. Voest, Coline H.M. van Moorsel, Cornelis K. van der Ent, Edwin Cuppen, Alexander van Oudenaarden, Frank E. Coenjaerts, Linde Meyaard, Louis J. Bont, Peter J. Peters, Sander J. Tans, Jeroen S. van Zon, Sylvia F. Boj, Robert G. Vries, Jeffrey M. Beekman, Hans Clevers
Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development
Ashley L. Lennox, Ruiji Jiang, Lindsey Suit, Brieana Fregeau, Charles J. Sheehan, Kimberly A. Aldinger, Ching Moey, Iryna Lobach, Ghayda Mirzaa, Alexandra Afenjar, Dusica Babovic-Vuksanovic, Stéphane Bézieau, Patrick R. Blackburn, Jens Bunt, Lydie Burglen, Perrine Charles, Brian H.Y. Chung, Benjamin Cogné, Suzanne DeBrosse, Nataliya Di Donato, Laurence Faivre, Delphine Héron, A. Micheil Innes, Bertrand Isidor, Bethany L. Johnson-Kerner, Boris Keren, Amy Kimball, Eric W. Klee, Paul Kuentz, Sébastien Küry, Dominique Martin-Coignard, Cyril Mignot, Noriko Miyake, Caroline Nava, Mathilde Nizon, Diana Rodriguez, Lot Snijders Blok, Christel Thauvin, Julien Thevenon, Marie Vincent, Alban Ziegler, William Dobyns, Linda J. Richards, A. James Barkovich, Stephen N. Floor, Debra L. Silver, Elliott H. Sherr
The phylogenetically distinct early human embryo
Manvendra Singh, Thomas J Widmann, Jose L Cortes, Gerald G Schumann, Stephanie Wunderlich, Ulrich Martin, Jose L Garcia-Perez, Laurence D Hurst, Zsuzsanna Izsvak
Automating multimodal microscopy with NanoJ-Fluidics
Pedro Almada, Pedro Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Romain F. Laine, Guillaume Charras, Buzz Baum, Christophe Leterrier, Ricardo Henriques
NmeCas9 is an intrinsically high-fidelity genome editing platform
Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Paul D. Donohoue, Alexander H. Settle, Alexandra M. Lied, Kyle McGovern, Chris K. Fuller, Peter Cameron, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
Tsukasa Kouno, Jonathan Moody, Andrew Kwon, Youtaro Shibayama, Sachi Kato, Yi Huang, Michael Böttcher, Efthymios Motakis, Mickaël Mendez, Jessica Severin, Joachim Luginbühl, Imad Abugessaisa, Akira Hasegawa, Satoshi Takizawa, Takahiro Arakawa, Masaaki Furuno, Naveen Ramalingam, Jay West, Harukazu Suzuki, Takeya Kasukawa, Timo Lassmann, Chung-Chau Hon, Erik Arner, Piero Carninci, Charles Plessy, Jay W Shin
Postdoctoral positions are available in the Parichy lab at University of Virginia. The lab studies development using zebrafish and related species. Current emphases include hormonal control over post-embryonic neural crest stem cells, plasticity in cell state, evolution of novel cell types, and mechanisms of pattern formation and cell–cell communication within zebrafish and across Danio species.
Methods include super-resolution time-lapse imaging on lab-dedicated microscopes, single cell RNA-sequencing, forward and reverse genetics, conditional manipulation of gene activity, and others.
The Parichy lab is situated in a highly interactive department with state-of-the-art facilities and UVA has outstanding current and historical strengths in morphogenesis and pattern formation. Training environment is excellent.
Applicants must have or be pursuing a Ph.D. and must have experience with modern methods of developmental biology. Prior experience with zebrafish is not required.
Applicants should submit the following to Dr. David Parichy (dparichy@virginia.edu):
• CV
• contact information for three references
• brief description of interests, experience and career goals
At the 2018 Spring Meeting in Warwick, the PhD and PostDoc representatives organises a series of events for young researchers. These ranged from asking questions such as “What is the secret to success?” through to some crafty synthetic biology and ending with the award of the 2018 BSDB writing competition.
A huge thanks to Michelle Ware and Alexandra Ashcroft for all their work in organising BSDB events for young researchers over the years. Learn more about the incoming PhD and PostDoc representatives of the BSDB here.
Career workshop
The career workshop kicked off the BSDB 70th birthday celebrations, with a topic focused on ‘building resilience and overcoming obstacles’. The idea was to utilise the knowledge and experience of the successful developmental biologists attending the meeting to give plenary and session talks. In total we had 18 tables, lead by Ottoline Leyser, Jordan Raff, Robb Krumlauf, Maria Leptin, Steve Wilson, Matthew Freeman, Fiona Watt, Magdalena Zernicka-Goetz, Jan Traas, Judith Kimble, Henrik Semb, Anne Ferguson-Smith, Patrick Lamaire, Jean Paul Vincent, Kate Storey, Austin Smith and Yohanns Belliache.
We wanted to have honest and open discussions about how to succeed in academia. ‘What is the secret to success, if there is any?!’. It is not very often you get to have opportunity to pick the brains of the leaders in your area of interests. This led to an afternoon of lively discussions.
Student/postdoc social
The format of the last couple of student/postdoc socials have been designed to get people to interact with people other than their lab mates! This year was no exception. This year’s activity was for randomly assigned teams to build models, within 1 hour, of any one of the following themes: fertilisation, plant development, somitogenesis, cell-fate determination and evo-devo.
We will let the pictures do the talking, but we were blown away by how amazing the models were and how much effort people put into making them. Megan Davey and Rita Sousa-Nunes judged the competition but had a hard time choosing winners since the models were excellent.
We are grateful to all the exhibitors who kindly donated prizes: Abcam, Class Learning, Proteintech, Philosophical Transactions B and Biographical Memoirs, The Company of Biologists, Stratech, 2BScientific and Indigo Scientific.
2018 BSDB Writing Competition
Finally, the student/postdoc events ended with the announcement of the 2018 Writing Competition. As part of the BSDB 70th anniversary celebrations, we initiated a writing competition where first prize was
a trip to the 77th Annual Society of Developmental Biology meeting (Portland, Oregon, USA). Katherine Brown, Aidan Maartens, Ottoline Leyser and Jonathan Slack judged the competition, selecting Daniyal Jafree as the winner.
So this year, is the final year for us organising these events. It has been a blast. Thank you all for making it such a wonderful and memorable experience. Please don’t forget to contact your future student (students@bsdb.org) or postdoc (postdocs@bsdb.org) reps for any comments or suggestions regarding the British developmental biology community.
See here for more pictures of the student/postdoc events.
The visualization of temporal data by line graphs has been documented and popularized by William Playfair in the 18th century (Aigner et al, 2011; Beniger and Robyn, 1978). Today, time-dependent changes are still depicted by line graphs and ideally accompanied by a measure of uncertainty (Marx, 2013). Below, I provide a ‘walk-through’ for generating such a plot with R/ggplot2 to visualize data from time-series. For convenience, example data and an R-script that performs all steps is available here. The data that I used is from Mastop et al (2017). After the make-over with ggplot2, the graph looks like this:
Some time ago, my favorite (commercial) software package for making graphs was no longer supported due to a system upgrade. So I was looking for a powerful and flexible alternative for data visualization. I ended up with R and ggplot2. First of all, the elegant data visualization delivered by the ggplot2 package is hard to beat. On top of that, it is completely free and it has a large user base. The biggest obstacle (in my experience) was getting used to the tidy data format that is needed as input. The conversion of ordinary, spreadsheet type data into long, tidy data is dealt with in a previous blog, and again briefly explained below. Before we start, we need to load two packages (these need to be installed first):
>require(tidyr)
>require(ggplot2)
The example data (available here) is read from a file in csv format into a dataframe (you need to set the “working directory” to match the location of the file):
The first column defines time and the other columns have data of individual cells corresponding to each of the timepoints. This data has a spreadsheet format, which is also named a ‘wide’ format. The first step is to convert it into a tidy data format, which is ‘long’. For details see my previous blog. The command to convert the df_wide dataframe into a tidy dataframe, df_tidy, is:
>df_tidy <- gather(df_wide, Cell, Ratio, -Time)
You can have a look at the first six rows of the dataframe to see what has changed:
>head(df_tidy)
Generating a basic graph
Once the data in the df_tidy dataframe is in long/tidy format, it can be used to generate a graph. The minimal instructions needed to display a graph are:
The dataframe that is used as input: df_tidy
The data used for the x-axis: Time
The data used for the y-axis: Ratio
To plot the data with minimal instructions use the function qplot():
>qplot(data=df_tidy, x=Time, y=Ratio)
Points/dots are used by default, but for these data lines are more appropriate:
The ‘qplot’ command provides a quick way to plot the data. To have a bit more control we turn to ggplot2(). The syntax is slightly more complex, but it allows to plot multiple layers. To reproduce what was done with qplot we need:
The aes() function is used for mapping “aesthetics”. The aesthetics specify how the variables from the dataframe are used to visualise those variables. In this case ‘Time’ is used for mapping the data onto the x-axis and ‘Ratio’ is used to map the data onto the y-axis. The geom_line() function specifies that the data is shown as a line. Inside geom_line(), aes(color=Cell) specifies that the line of each cell is mapped to a unique color. For more information on aesthetics and examples see this book chapter.
The geom_line() function defines that the data are displayed as lines. We can add another layer with a different geometric shape, geom_point(), to show the individual data as dots (in this example the dots will not have a color, since no aesthetic mapping is specified for geom_point):
The appearance of the plot depends on the sequence in which the layers are added. This is defined by the sequence in which the objects are added, i.e. the first object defines the first layer and next object is added on top. For instance, this code will generate a plot in which the lines are on top of the points:
The option of adding layers allows the addition of a summary of the data, for instance the average, or data for various types of error bars. To achieve this, a dataframe is defined to store the summary statistics:
We add the 95% confidence interval (95%CI) as a measure of uncertainty. Here we employ geom_ribbon() to draw a band that captures the 95%CI. To this end, we employ aes() inside geom_ribbon() to specify that the upper and lower limits of the confidence interval from df_summary define the borders of the ribbon. (Note that alternative methods that display uncertainty may be considered.)
The resulting figure only shows the data summary. Since it can be valuable to show the underlying data we will plot the data from individual cells as well. These data are present in another dataframe, yet it is possible to add these data to another layer. To demonstrate this, the original data from the individual measurements (from df_tidy) is added:
Improving the presentation and annotation of the graph
The graph shown above displays all the data of interest, but it looks cluttered. In the final session the lay-out and annotation will be changed to improve the visualization and communication of the results (see also ‘Graphics for Communication’).
To make the individual data less pronounced, the lines are plotted in grey. Also, the graph looks better if the ribbon of the 95%CI is drawn on top, so we move the grey lines to the first layer and plot the average and 95%CI on top of that:
To indicate where we performed a manipulation of the system another layer can be added. In this experiment a stimulus was added at t=44 and inhibited at t=146. To reflect this, we add a grey box with the function annotate():
The end results is a nice and clean visualization of the data, which is an improvement over the original visualization (made with commercial software, see insets of figure 6 from Mastop et al (2017)). The instruction to plot graphs with ggplot() usually consists of several different functions and may be daunting at first sight. I hope that providing this ‘walk-through’ that shows how to build a graph layer-by-layer lowers the barrier to start using R/ggplot2 for visualization of (temporal) data.
Acknowledgments: Thanks to Franka van der Linden, Eike Mahlandt and Jenny Olins for testing and debugging the code.
Applications are invited for a four year PhD studentship funded by The Royal Society to conduct research under the supervision of Dr Amanda Sferruzzi-Perri at the Department of Physiology, Development and Neuroscience.
Title: Role of placental endocrine malfunction in the programming of disease in offspring
Closing date: 17th June 2018
For more details about the project and application process please see the following webpage:
DanStem is looking for a postdoctoral candidate with a strong cell biological and cell signaling background in directed differentiation of human pluripotent stem cell biology.
The candidate is expected to work on the engineering of human pluripotent stem cell-derived islet of Langerhans-like aggregates with functional properties close to human islets. The functionality and therapeutic potential of the aggregates will be tested in vitro and in vivo in mice.
The goal of this project is to engineer therapeutically active islet-like aggregates for future cell therapy phase 1 trials in Type 1 Diabetes (T1D).
The candidate is expected to use state-of-the-art genetics, molecular and cell biological, and tissue engineering experimental strategies. The candidate will work together with a dedicated team of scientists and technicians who together will tackle bottle-necks towards implementing the phase 1 clinical trials in T1D.
Qualifications:
The candidate is required to hold a PhD degree in pluripotent stem cell/developmental biology. A few years of postdoctoral experience in the same areas is a merit. The candidate should also have hands on experience in human pluripotent stem cell maintenance and differentiation, 3D culture of pluripotent stem cells, various cell and molecular biological methods, flow cytometry and live-cell imaging. Experience in differentiation towards pancreatic lineages is a merit. Finally, we are looking for applicants with a good record of peer reviewed scientific publications, grant writing skills and an interest in team work.
About our center:
The Novo Nordisk Foundation Center for Stem Cell Biology – DanStem – addresses basic research questions in stem cell and developmental biology and translates results from basic research into new strategies and targets for the development of new therapies for diabetes and cancer. DanStem was established as a result of a series of international recruitments coupled with internationally recognized research groups focused on insulin producing beta cells and cancer research already located at the University of Copenhagen.
The position is for 2 years with a possible extension. The employment is planned to start as soon as possible or upon agreement.
The terms of employment are set according to the Agreement between the Ministry of Finance and The Danish Confederation of Professional Associations or other relevant professional organization. The position will be at the level of postdoctoral fellow and the basic salary according to seniority is 32.700-34.400 DKK/month. A supplement could be negotiated, dependent on the candidate´s experiences and qualifications. In addition, a monthly contribution of 17.1% of the salary is paid into a pension fund.
Applicants recruited from abroad may be eligible for a special researcher taxation scheme. In all cases, the ability to perform the job will be the primary consideration, and thus we encourage all – regardless of their personal background and status – to apply.
The application must be submitted online and in English, by clicking on “Apply online” below.
The closing date for applications is July 15th 2018 at 23.59pm.
The application must include:
Cover letter detailing the basis on which the applicant scientific qualifications meet the requirements for this position.
Curriculum vitae.
List of references (full address, incl. email and phone number)
Diplomas – all relevant certificates.
List of publications.
The further process:
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on his/her assessment. You may read about the recruitment process on
DanStem and The University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates, regardless of personal background
The Laboratory of Early Mammalian Developmental Biology (LEMDB), University of South Bohemia, České Budějovice, Czech Republic (Alexander W. Bruce group).
The LEMDB is currently recruiting both Masters (Mgr) & Ph.D. level studentships to research projects related to cell-fate choice.
Research projects offered in relation to p38 mitogen-activated-kinase’s role in primitive endoderm/ PrE development, the regulation of spatial allocation of cells relevant to first differential cell-fates i.e. outer trophectoderm/TE & inner-cell-mass/ ICM and others…
University provided stipend guaranteed for 4-years (plus grant based salaries and performance related bonuses)
Please send your CV and covering letters to lab head Alexander W. Bruce at: awbruce@prf.jcu.cz
In September, Development is hosting the third of its highly successful series of meetings focusing on human developmental biology. Held in the Wotton House estate near Dorking in Surrey and organised by Paola Arlotta, Ali Brivanlou, Olivier Pourquiéand Jason Spence, the meeting will cover the latest developments and future prospects for this rapidly evolving field.
Looking to conduct research in molecular biology and genetics? We are looking for a lab technician to assist in research on muscle stem cells, development, regeneration, disease, and evolution. More details about our research can be found at http://www.kardonlab.org/. Technician will assist in management of a mouse colony as well as conduct supervised research (leading to publications). Technician must be reliable, well organized, detail-oriented, excited about research and committed to working in our lab for at least two years. Prior lab experience is preferred (although not necessarily required), and class work in biology and enthusiasm for science is essential. Lab is located at the University of Utah in Salt Lake City, affording amazing opportunities for science and outdoor recreation. Looking for someone to start June-July 2018.
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Costs to register are 10€ for students, 20€ for Postdocs and PIs.
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