4 year PhD position, Seville Spain (deadline 25/07/19)
We are looking for students with a Master degree to join our lab for a 4 year PhD position, application deadline 25/07/19. Our laboratory investigates fundamental questions of developmental biology by using mouse embryonic stem cells spheroids known as Embryoids.
The successful candidate will develop a project to investigate the gene regulatory network that control Embryoid self-organization. The project is going to be strongly multidisciplinary and will combine computational modeling and experiments. Students with a theoretical background (Computer Science, Mathematics, Physics) or a biological background are welcome to apply. Experience on any of the following will be beneficial: cell culture, genome editing of stem cell, developmental biology, partial differential equations and multi-cellular simulations.
The PhD will be carried at the Gene Expression and Morphogenesis Unit (GEM) at the Andalusian Centre for Developmental Biology (CABD), in the charming city of Seville, southern Spain. The research center offers a dynamic environment with close interaction with other groups working on Mouse, Zebrafish, Xenopus, Drosophila and C. Elegans development.
Candidates should send their CV to lmarcon [at] upo.es by the 25th of July 2019. The successful candidate will be employed with a FPI scholarship starting in 2020.
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Dr. Luciano Marcon
Self-Organization of Biological Systems
Centro Andaluz de Biología del Desarrollo – CSIC marconlab.org
Development recently published a bumper Special Issue devoted to single cell approaches to developmental biology. A multitude of model systems featured – from Dicty to Drosophila to mouse to zebrafish – and the issue’s Reviews, Spotlight and Hypothesis gave an overview of the field’s current challenges and opportunities.
The cover was chosen by guest editors Allon Klein andBarbara Treutlein from entries to a cover competition we ran while the issue was being compiled. The beautiful artwork was done by Martin Estermann from Monash University in Australia:
Recently, two iconic developmental biology models entered into the single cell genomics era: chick and zebrafish. In this image, line art was traced using real embryo images for reference and filled with individual dots to represent the reduction of the whole embryo to its smallest structural, functional and biological unit: the cell.
The Guest Editors also surveyed the field and the issue in their Editorial, which we reprint here:
Single cell analyses of development in the modern era
Allon M. Klein, Barbara Treutlein
Single cell analyses encompass multiple approaches that, we suggest, can be summarized by two unifying goals: to explain the cellular composition of tissues; and to characterize the dynamic processes of cells. Both forms of investigation have an old history, but have undergone rapid transformation in the past decade. This Special Issue of Development offers us an opportunity to reflect on the state of this rapidly evolving field.
Arguably, single cell analysis as we recognize it today became established after the broad acceptance of cell theory in the late 19th century. Cells were first recognized much earlier by Robert Hooke and Anton van Leeuwenhoek in the 17th century, enabled by technological development (the microscope) and by their curiosity about how a macroscopic biological system could be understood in terms of its constituent parts. Since the early studies of Hooke and van Leeuwenhoek, the tools of single cell analysis have been continuously evolving, driven by innovations in technology, sample preparation and new questions. By the end of the 19th century, cell theory was firmly established following significant improvements in microscopy and in biochemical techniques that could distinguish between morphologically similar cells and separate them into distinct states by fractionation or staining. By the late 20th century, the development of monoclonal antibodies had rapidly expanded the repertoire of tools by which biologists could distinguish cellular states. Live imaging methods, and the development of fluorescent proteins, extended the study of dynamic molecular processes in cells. By the start of the 21st century, differences between cells could be measured with single molecule accuracy, allowing the study of stochastic chemistry within single cells, and accelerating a new field that aimed to understand information processing and noise in biological systems. In parallel, molecular methods developed in the 1990s allowed the labeling of subsets of cells using transgenic approaches, establishing the fate mapping of cells as an important gold standard technique for determining developmental relationships. Thus, single cell techniques have driven biological discovery for centuries.
Over the past two decades, however, technological advances have revolutionized the scale and complexity of single cell analyses. Starting in a few labs and then spreading rapidly, single cell investigation merged with genome-scale analytical methods. The most mature of these technologies today is single cell RNA-sequencing, which can measure the expression profile of thousands of genes simultaneously in thousands of cells (and more) in a single experiment. In parallel, innovations in microscopy now allow us to track single cells in complex tissues with minute-by-minute time resolution and with minimal phototoxicity, spherical aberration or signal attenuation. Some of these technologies are now widely accessible and are being implemented across developmental biology. The new resolution afforded by these methods has led to multiple discoveries in a short period of time, including the discovery of novel cell types, revisions to established differentiation hierarchies and identification of novel regulators of fate choice. In stem cell biology, these measurements allow the analysis of in vitro differentiation products, and the benchmarking of stem cell-derived cells against their natural counterparts. In evolutionary biology, they allow orthologous cell types to be compared across species. In regenerative biology, they allow the stem and progenitor cells driving tissue recovery, as well as the behavior of supporting immune and stromal cells, to be identified. Across different fields, single cell genomic atlases of tissues offer new perspectives on cell types and cell states. In parallel, single cell live-imaging approaches have challenged established mechanistic perspectives of molecular signal transduction, chromatin modification and transcription factor dynamics.
While modern single cell analyses are accelerating biological discovery, we note that they have also imposed a new demand on researchers seeking to benefit from these tools. Unlike single cell innovations of the previous century, modern single cell analytical methods produce high-dimensional data, or ‘big data’, in the sense that raw data obtained using these methods cannot be inspected without the aid of computational algorithms for dimensionality reduction. Although data of a statistical nature is not new to developmental biology, the examination of cell states over tens of thousands of genes cannot be analyzed using basic visualization methods such as histograms. Even seemingly ‘simple’ representations using heatmaps often undergo multiple steps of normalization and hierarchical clustering prior to visualization. Similar challenges occur in visualizing cell behaviors across space and time, in relation to complex spatial neighborhoods or patterns of protein dynamics. Fortunately, there are now many algorithms available to visualize and interpret single cell data. Yet each makes particular assumptions that may skew interpretation of the data, and each is dependent on parameters that can alter the results. Furthermore, many algorithms are non-deterministic, leading to variable representations of the same data. We propose that a unique aspect of modern single cell analysis is its demand for computational methods. These methods offer opportunities for collaboration and immersion in computational biology, and may be altering the training of developmental biologists.
With this background, we are excited to present several review-based articles in this Special Issue that survey the ways in which modern single cell analytical techniques and computational methods are driving advances in developmental biology. We are also delighted by a strong representation of primary research papers, which provide examples of many of the reviewed concepts and how they drive discovery.
Our Reviews broadly cover the conceptual challenges resulting from single cell analysis, the new methods that are available and some of the successes of single cell analyses to date. Two separate articles challenge us to consider how we should understand the notion of cell identity and cell type. Bo Xia and Itai Yanai (Xia and Yanai, 2019) propose that differences between cell types in an organism follow an understandable pattern that allows them to be organized into a ‘periodic table’ that reveals the logic of their underlying structure. Samantha Morris (Morris, 2019) proposes a complementary view that defines cells in terms of their lineage, molecular state and functional phenotypes. In doing so, she importantly clears up some of the nomenclature in the field. Both perspectives highlight the new opportunities that have emerged from the unifying, quantitative language of single cell analyses that force us to confront definitions that have emerged in various isolated studies of distinct tissues. Two additional Reviews survey the use of single cell analyses to reconstruct developmental dynamics. Fabian Theis and colleagues (Tritschler et al., 2019) review the methods available to infer dynamic trajectories from high-dimensional single cell data, while Aaron McKenna and James Gagnon (McKenna and Gagnon, 2019) survey cutting-edge technologies that combine single cell analyses with lineage tracing, thus building bona fide dynamic information into static snapshots. Then three further Reviews provide insights into the future beyond the mature techniques of single cell transcriptomics. Connor Ludwig and Lacramioara Bintu (Ludwig and Bintu, 2019) survey the multiple modalities of measurements beyond RNA-seq, focusing on single cell analyses of chromatin state. Prisca Liberali and colleagues (Mayr et al., 2019) discuss spatially resolved single cell analyses. Finally, Pulin Li and Michael Elowitz (Li and Elowitz, 2019) discuss the use of single cell live imaging to learn about information processing by cells.
Putting these ideas into play, the research papers in this Special Issue demonstrate a range of single cell techniques and the discoveries that they enable. Two papers apply live imaging to demonstrate the role of a signal transduction pathway in differentiation (Deathridge et al., 2019) or to demonstrate stochasticity in fate choice (Antolović et al., 2019); several papers build transcriptomic maps of specific developing tissues that will prove useful resources and reveal new hypotheses for developmental regulation (Combes et al., 2019; Martin et al., 2019; Hulin et al., 2019; Li et al., 2019a,b); several studies computationally reconstruct developmental dynamics (Bastidas-Ponce et al., 2019; Delile et al., 2019; Guo and Li, 2019; Prior et al., 2019; van Gurp et al., 2019); and one study benchmarks in vitro differentiation to in vivo development and develops new computational tools to do so (Edri et al., 2019). Taking a slightly different approach, other papers use single cell analyses to characterize cell behaviors during morphogenesis (Amini et al., 2019; Yang et al., 2019), to investigate how cells respond to DNA or tissue damage (Miermont et al., 2019; Dell’Orso et al., 2019), and to understand how heterogeneities in gene and protein concentration influence development (Papadopoulos et al., 2019; Reznik et al., 2019; Velte et al., 2019).
Approaches to single cell analysis began three and a half centuries ago with improvements in microscopy. Today’s modern approaches, although hard to relate to those of 17th century Europe, echo this first revolution. Then, as now, continuous innovations in technology have led to sudden and widespread acceleration in biological inquiry. As this Special Issue illustrates, methods that once required specialized expertise are becoming widely accessible. Yet rapid innovation still continues. Will the tools and concepts surveyed in this Special Issue still be relevant 5 years from today? As you consider this question, we would very much like to thank the authors and referees of the articles in this Special Issue for their contributions, and we hope you enjoy reading it!
Marie Curie fellowship to develop ATAC-seq in Parhyale and study genome-wide regulatory responses during leg regeneration. Project supported by the Marie Curie EvoCell network. euraxess.ec.europa.eu/jobs/425603
A post-doctoral position is available to study transcriptional regulation of lineage fidelity during fate specification and differentiation of ES cells. This project focuses on uncovering epigenetic and co-factor-dependent mechanisms underlying these processes.
The Philpott lab has broad interests in understanding the fundamental mechanisms that determine cell fate choice and differentiation during embryonic development and in cancers, as well as how these processes are co-ordinated with cell cycle progression.
Within the laboratory, we use several experimental systems including mammalian embryonic stem cells, cancer cell culture, organoid systems as well as embryos of the frog Xenopus. We use many techniques including genome-wide analysis of gene expression in single and multiple cells, chromatin binding and accessibility studies and crispr genome editing, alongside diverse biochemical approaches.
The successful candidate will have a PhD, considerable experience in stem cell biology, epigenetics, molecular biology, developmental biology, or a similar field, and a proven track record in scientific publication. Prior experience in mammalian cell culture is essential. Experience of epigenetics and/or transcriptional regulation are essential, while experience of genome-wide transcriptional analysis, and in particular analysis at the single cell level, would also be an advantage. Applicants must display an ability to undertake project management, work within a multi-disciplinary team environment, have excellent presentation and communication skills and the ability to contribute to an environment supporting researchers at all stages of their careers.
The Wellcome – MRC Cambridge Stem Cell Institute (CSCI) is a world-leading centre for stem cell research with the mission to transform human health through a deep understanding of stem cell biology. https://www.stemcells.cam.ac.uk/
CSCI is due to move to the brand new, state of the art Jeffrey Cheah Biomedical Centre building on the Cambridge Biomedical Campus in summer 2019.
Fixed Term: The funds for this post are available for 3 years in the first instance. Deadline: July 28th, 2019.
Informal enquiries should be directed to Prof. Anna Philpott, ap113@cam.ac.uk. recent line manager.
The University values diversity and is committed to equality of opportunity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK.
Roles of metabolism in the developmental origins of health and longevity
A postdoctoral research position funded by the Wellcome Trust is available in the laboratory of Dr. Alex Gould at the Francis Crick Institute in London. The lab works on the mechanisms by which dietary nutrients during development can have profound long-term effects upon adult metabolism and lifespan. We are looking for a highly motivated researcher with experience in molecular biology and/or metabolism. The successful applicant will be able to choose from several Drosophila and mouse models that have been established in our lab (PMID: 21816278, PMID: 26451484, PMID: 29123106, PMID: 29515102 and unpublished). They will be exposed to a range of techniques including genetics, molecular biology, confocal microscopy, biochemistry, metabolomics as well as mass spectrometry imaging (PMID: 22246326, PMID: 26451484). Access will be provided to state-of-the-art facilities in advanced light and electron microscopy, metabolomics and single-cell sequencing. Examples of other projects ongoing in the lab can be seen at: www.agouldlab.com www.crick.ac.uk/research/labs/alex-gould
Applications are now open for this year’s Gene Regulatory Networks for Development at The Marine Biological Laboratory in Woods Hole, USA from October 13-26. The application deadline is July 17th. The course is for graduate students, postdoctoral researchers, staff scientists and faculty members. It focuses on using experimental data and computational modeling to analyze gene regulatory networks controlling development.
This unique course is an intense and always interesting experience and has had great reviews in all of the previous years. Students will meet with renowned experts in the field for an in-depth treatment of experimental and computational approaches to GRN science. Through lectures, highly interactive discussions, and group projects we will explore the GRN concept and how it can be applied to solve developmental mechanisms in various systems and contexts. Topics include structural and functional properties of networks, GRN evolution, cis-regulatory logic, experimental analysis of GRNs, examples of solved GRNs in a variety of developmental contexts, and the computational analysis of network behaviour by continuous and discrete modelling approaches.
Scott Barolo – U. of Michigan (co-director)
James Briscoe – Francis Crick Institute
Martha Bulyk – Harvard U.
Ken Cho – UC Irvine
Doug Erwin – Smithsonian Institution
Robb Krumlauf – Stowers Institute
Arthur Lander – UC Irvine
Bill Longabaugh – Institute for Systems Biology
Lee Niswander – U. of Colorado
Isabelle Peter – Caltech (co-director)
Alexander Stark – IMP Vienna
Zeba Wunderlich – UC Irvine
We are looking to appoint a Research Technician who will provide support to a one-year Neuroblastoma UK-funded project entitled “Establishment of an in vitro model of neuroblastoma initiation using pluripotent stem cell differentiation”. The project aims to dissect the cellular and molecular basis of neuroblastoma initiation using human pluripotent stem cell (hPSCs) differentiation and hPSC lines engineered to ectopically overexpress common neuroblastoma-associated oncogenes.
You will join a research team under the guidance of Dr Anestis Tsakiridis, providing support for routine hPSC culture and differentiation, preparation of samples/analysis and carrying out molecular cloning/genetic modification of hPSCs. Appropriate training will be provided. This is an excellent opportunity to gain hands-on laboratory experience and to be part of a leading research team. Our group’s research aims to define the molecular basis of cell fate decisions during human embryonic development and determine how “altered” embryonic multipotent states drive tumourigenesis (https://www.tsakiridislab.com/).
Applicants must have a good honours degree or equivalent experience in a developmental/stem cell biology-related subject along with previous experience of working in a research laboratory. Familiarity with some/all of the following techniques is desirable: hPSC culture; RNA isolation; molecular cloning; mammalian cell transfection; quantitative real time PCR; immunostaining; fluorescence microscopy; flow cytometry. Applicants should also have an interest in stem cell and developmental biology.
To apply: visit the University of Sheffield job portal (https://www.sheffield.ac.uk/jobs/index)
Closing date: 7th August 2019
Expected start date: 1st September 2019
For more details/questions contact: a.tsakiridis@sheffield.ac.uk
The Company of Biologists Workshops provide leading experts and early-career researchers from a diverse range of scientific backgrounds with a stimulating environment for the cross-fertilisation of interdisciplinary ideas. In November, experts will gather in the beautiful surroundings of Wiston House in West Sussex with the aim of ‘Understanding Human Birth Defects in the Genomic Age‘. Organised by Mustafa Khokha, Karen Liu and John Wallingford, the Workshop is an amazing opportunity to explore applied developmental biology.
There are around 10 funded places for early-career researchers available – a fantastic opportunity to share your research with leading scientists in an intimate setting.
Transcriptional autoregulation occurs when transcription factors bind their own cis-regulatory sequences, ensuring their own continuous expression along with expression of other targets. During development, continued expression of identity-specifying transcription factors can be achieved by autoregulation, but until now formal evidence for a developmental requirement of autoregulation has been lacking. A new paper in Development provides this proof with the help of CRISPR/Cas9 gene editing in the C. elegans nervous system. We caught up with the paper’s two authors: postdoc Eduardo Leyva-Díaz and his supervisor Oliver Hobert, Professor of Biological Sciences and HHMI Investigator at Columbia University, New York, to find out more about the work.
Oliver Hobert (L) and Eduardo Leyva-Díaz (R).
Oliver, can you give us your scientific biography and the questions your lab is trying to answer?
OH I started out investigating signal transduction for my PhD with Axel Ullrich and Gerhard Krauss in Germany, and then moved to the USA for my postdoc with Gary Ruvkun. In Gary’s lab, I started working with C. elegans on transcription factor regulation and specification of neuronal fates. In my own lab, we have continued to pursue our interest in understanding the molecular mechanisms that control the generation of diverse cell types in the nervous system. More recently, we are also becoming more and more interested in understanding how neuronal identity features are modulated by certain factors, such as environmental conditions or sexual identity.
And Eduardo, how did you come to work in the Hobert lab, and what drives your research today?
EL-D My fascination with science began in biology laboratory classes in high school, with a very dedicated and passionate teacher. Since then, I’ve been always attracted to genetics and molecular biology, and my first research experience as an undergraduate student was in Prof. Jose Luis Micol’s lab working on Arabidopsis thalianagenetics. Towards the time of my graduation, I became interested in the nervous system, specifically in learning and memory, although I have never really worked on that field. The one thing I was not interested in at all at that time was developmental neurobiology, but funnily enough, after my rotation in different labs at the Instituto de Neurociencias de Alicante, I was totally captivated by it, and devoted my next 6 years to studying mouse brain development in Guillermina Lopez-Bendito’s lab. After my thesis defense, I stayed for a few months in the lab and worked on a new research line aimed at reprogramming endogenous astrocytes into different projection neurons. With this experience in identity reprogramming and transcriptional regulation, I developed a deep interest in neuronal identity specification, particularly regarding the maintenance of neuronal features. The Hobert lab was then a clear perfect match, with C. elegans representing an excellent model system to study neuronal identity specification and maintenance.
When did you first become interested in transcriptional autoregulation? And given it has been known about for decades, why do you think it has taken so long to formally test its functional requirement?
OH & EL-D A key characteristic of several terminal selectors, identity-specifying transcription factors, is their role in the maintenance of neuronal identity, which is thought to be achieved by transcriptional autoregulation. However we, as well as others, had only inferred transcriptional autoregulation from the presence of binding sites of a transcription factor in its own genomic locus, and from genetic loss-of-function studies in which the activity of a transcription factor is removed and a loss of transcription of this locus is consequently observed. Formal proof for the functional relevance of autoregulation has been sparse, however. The advent of CRISPR/Cas9 technologies has been key to providing formal proof for this requirement, because it enabled us to disrupt autoregulation, but not other functions of a specific transcription factor. We could therefore precisely ask what it is that autoregulation actually does – and we came up with a surprise that we had not anticipated.
C. elegans embryo in which the che-1 locus has been tagged with gfp through CRISPR/Cas9 genome engineering. che-1::gfp expression can be observed in the bilaterally symmetric ASE neuron pair (ASEL + ASER) and their sister cells, which are in the process of undergoing apoptotic cell death.
Can you give us the key results of the paper in a paragraph?
OH & EL-D In this paper, we use CRISPR/Cas9 to remove a cis-regulatory motif from a cell identity-specifying transcription factor, showing that the disruption of transcriptional autoregulation leads to a failure to maintain the differentiated state of the cell. Upon regulatory motif mutation, we observe a gradual decrease in neuronal function and cell identity marker expression. This was an expected result that provided formal proof for the importance of identity-triggering transcription factors in maintaining the identity state of a cell. However, we also found that transcriptional autoregulation is not only required to maintain a specific cellular state, but is also required during development to amplify the expression levels of the autoregulating transcription factor to a critical threshold level in order to allow it to initiate expression of its target genes, which will define the differentiated state of the cell.
Do you think the early function in initiation of che-1expression is likely to be a general feature of autoregulation?
OH & EL-D In general, we think that if a gene can autoregulate it makes sense that this autoregulation is also used early in development. However, we have found in the literature examples of other autoregulating transcription factors for which maintenance relies on autoregulation, while the initial amplification is achieved by different means. Interestingly, this dual role of autoregulation, early amplification/late maintenance, seems to be modular and context dependent, since in some cases the autoregulation of other factors is only important early in development. Nonetheless, it does not seem far-fetched to propose that the functional duality of transcriptional autoregulation constitutes a widely used gene regulatory principle during animal development.
It does not seem far-fetched to propose that the functional duality of transcriptional autoregulation constitutes a widely used gene regulatory principle during animal development
When doing the research, did you have any particular result or eureka moment that has stuck with you?
EL-D For me, the eureka moment was when we realized about the function of transcriptional autoregulation in early development. We were very satisfied with the close correlation between che-1 expression and neuronal functional performance through the different developmental stages. But when we looked earlier, we were at first surprised by finding already low levels of che-1 expression in the embryo. Then we realized that it would only make sense if autoregulation also contributed to transcription factor initial amplification and, consequently, acquisition of the differentiated state.
And what about the flipside: any moments of frustration or despair?
EL-D Without any doubt, the moments of frustration and despair were at the very beginning of the project. Generating precise motif mutations in the che-1promoter was key for this story, and obtaining some of the cis-regulatory mutations took longer than expected. The application of CRISPR/Cas9 engineering to different projects was just becoming established in the lab at that point, and we were at the initial phase of standardization and protocol set up. Of course, we got our mutants, and the road was mostly paved after that.
So what next for you after this paper?
EL-D I am intensively working on a second project, where we are trying to understand how the expression of pan-neuronal genes is controlled. Neuronal identity is determined by the expression of neuron-type specific genes and pan-neuronal genes, which are shared by all neurons in the nervous system. We now know several examples about neuron-type specific gene regulation, but not that much about pan-neuronal genes. Previous work form the Hobert lab has shed some light into the how, and now I am trying to find the who, identifying key factors controlling pan-neuronal gene expression. And then, job hunting.
Where will this work take the Hobert lab?
OH This work will hopefully not present the endpoint of studying transcriptional autoregulation. While there’s plenty of evidence to suggest that positive autoregulation is a widespread phenomenon, we also know that some identity-specifying terminal selectors do not autoregulate, even though their expression is maintained throughout the life of a neuron. How does this work? In at least one other case, we also have reason to believe that there is negative autoregulation, in which a terminal selector dims down its own expression. We would love to understand how and why this is.
Finally, let’s move outside the lab – what do you like to do in your spare time in New York?
EL-D New York is an amazing place and I love to explore the city and its surroundings with my wife and friends. I especially enjoy discovering all the culinary options, and I try to take advantage of the different cultural activities that the city has to offer. I also like to stay active, running and playing different sports. Finally, I love to travel when possible, to discover new places or back to Spain to enjoy the weather, food, family and friends.
OH I don’t have much to add to this. New York is an amazing, dynamic and constantly changing place that leaves new things to discover even if one has lived in the city for a while.
In this episode we’re celebrating the actual birthday of the society – founded on the 25th June, 100 years ago – with past president, Nobel laureate and winner of the Genetics Society’s first centenary medal, Sir Paul Nurse.
To mark this auspicious day, the Genetics Society held a very special birthday party at the John Innes Centre in Norwich. First we were treated to a wonderful exhibition of artefacts from the society’s history, including co-founder William Bateson’s original microscope and some fascinating photos. Then past president of the society and Nobel prize-winner Sir Paul Nurse unveiled two blue plaques dedicated to each of the founders, followed by the first ever Centenary medal lecture.
If you enjoy the show, please do rate and review and spread the word. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com
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