The 2nd NEUBIAS school for Bioimage Analysts will be organized in Jan. 2018 in Szeged, Hungary, and the registration is now open (Organizers: Jean-Yves Tinevez & Kota Miura). Please visit the linked URL below for more details. This school is the most advanced among three levels of NEUBIAS school. Deadline for the registration is Nov. 9th.
The school is part of one week-conference, and there will be another school in parallel: “Early Career Investigator (ECI) school” In this school, you can learn how to program ImageJ macro and MATLAB script for bioimage analysis.
After these schools, there is 3-days symposium. Anyone can join and there is no selection for this meeting. School participants are free to attend this symposium.
The lab of Savraj Grewal (University of Calgary, Canada) is looking to recruit new postdocs and grad students.
Our lab investigates how growth is controlled during animal development. We use a combination of molecular and genetic approaches to investigate the cell-cell signalling pathways and the genetic mechanisms that govern the control of cell, tissue and body growth in Drosophila. Our main focus to-date has been the conserved insulin and TOR kinase pathways, and understanding how they regulate cellular and animal metabolism to drive growth. Further information on our research can be found here. Recent publications can be found here.
POSTDOCS: applicants with a Ph.D. and strong background in developmental biology, genetics, or molecular biology are encouraged to apply. Interested individuals should send a CV and a short statement of research interests to grewalss@ucalgary.
GRAD STUDENTS: applicants with a strong undergraduate degree in any area related to the biological sciences are encouraged to apply. Interested individuals should send a CV and a short statement of research interests to grewalss@ucalgary.
The Marine Biological Laboratory seeks a motivated Postdoctoral Scientist to join the laboratories of Kristin Gribble and David Mark Welch in the Josephine Bay Paul Center. The successful candidate will develop genome editing techniques, including CRISPR/Cas9, in rotifers, a novel aquatic invertebrate model system for studies of aging, neurobiology, developmental biology, ecology, and evolution. Specific goals of the project include designing guide RNAs, optimizing microinjection methodologies, phenotyping and genotyping mutant strains, and screening genes of interest.
Basic Qualifications:
Applicants should have a Ph.D. in biology, cell/molecular biology, biochemistry, or a related field. This position requires proficiency in basic molecular biology techniques, microscopy, microinjection, and CRISPR/Cas9 methodology. We are seeking an independent, organized, enthusiastic, and productive individual with robust problem solving skills. Excellent written, verbal and interpersonal skills, attention to detail, and a strong work ethic are essential. Position level and salary will depend upon education and experience.
Preferred Qualifications:
The ideal candidate will have working familiarity with RNAi techniques, transgenic protocols, and confocal microscopy. Proficiency in bioinformatics is a plus. Previous experience in established animal model or in non-model systems is preferred.
Special Instructions to Applicants:
Please submit the following three items with your application:
Cover letter describing your research goals, specific interest in joining our group, and what you would contribute to the project
Established by the British Society for Developmental Biology in 2014, The Gurdon/The Company of Biologists Summer Studentship scheme provides financial support to allow highly motivated undergraduate students an opportunity to engage in practical research during their summer vacation. Each year, ten successful applicants spend eight weeks in the research laboratories of their choices, and the feedback we receive is outstanding. Our second report from the 2017 group of student awardees comes from Jack O’Shea(student at University College London), who undertook his studentship with Richard Poole at the Division of Biosciences in UCL.
glia to neuron transitions occurring simultaneously in the MCM (top)and PHDs (bottom) of a single animal
When I tell my friends that I spent my summer looking down a microscope at worms they often give a snigger. My enthusiasm on the subject quickly earned me the affectionate (I hope) nickname, ‘Wormboy’. Yet the Wormboys and girls of Richard Poole’s lab instilled in me a great thirst for scientific study over the 8 weeks I spent with them, which I will certainly carry forward in my career. The lab studies the nematode worm C. elegans, and my job was to help characterise a glia-to-neuron transition they discovered in the male tail that occurs during sexual maturation. During my time, I learned how to handle worms, keep them healthy, perform crosses, use a fluorescent microscope and present my data to an audience. All of this as part of my first lab experience was not only invaluable, but very enjoyable, and I came away wanting more.
Worm death was a regular part of lab life. Saving them from starvation and disease was a constant uphill battle, one that at first I found insurmountable. Along with those natural causes of death, they also had to contend me, often crushing them clumsily under my pick and purging potentially contaminative stragglers on said pick in the Bunsen. Happily for the worms, such fates became less and less frequent, and I was eventually able to sustain healthy populations from which I selected young males to dunk in the intensely toxic chemical sodium azide, all the better to view them under fluorescent microscopy. A necessary sacrifice.
This microscopy work was the first step in characterising the glia-to-neuron transition of phasmid socket 1 (PhSo1) into the neuron PHD, which occurs in the male tail during sexual maturation. The lab had previously identified a similar transition of the amphid socket to MCM neuron in the head of the male (Sammut et al., 2015), though the PHD transition differs in how the neuron is formed. Where the amphid socket divides asymmetrically to generate the MCM, the PHD derives from PHso1 by direct trans-differentiation, without a division, while its sister- PHso2- remains glial. This new neuron’s activity was found to be linked to initiation of a novel behaviour employed by males during mating thought to improve their chance of spicule insertion. To track the changing identity of PHso1, I compared its expression of glial and neuronal markers linked to GFP and RFP respectively with that of PHso2. The two glial markers I used were grl-2 (socket specific protein) and mir-228 (pan-glial microRNA), and the neuronal marker a nuclear synaptic fusion protein, rab-3.
The glia-to-neuron transition appears to start in males of larval instar 4 (L4), while the gonad is taking shape. Through picking many, many worms, I showed a clear gradient of change of marker expression in PhSo1 compared with PhSo2:
In late L3/early L4 GFP brightness is equal in the two sockets
By mid/late L4, GFP is dimmer in PHso1
The PHso1 of day 1 adults is beginning to express neuronal marker, displaying coexpression of GFP and RFP
By day 2, all GFP has dissipated from the newly formed PHD
Both glial markers displayed the same trend (fig.1 and 2)
Some animals classified mid/late L4 displayed coexpression of markers, but these were all on the cusp of adulthood, undergoing moult at the at the time of imaging (fig. 3)
Of course, fluorescent proteins do not perfectly match levels of the markers they represent, rather they give a general overview of the transformation. At the very least, this result shows PhSo1 might partially dedifferentiate before it eventually acquires neuronal characteristics when the worm becomes an adult. Understanding trans-differentiation events such as this is key to understanding how nature itself reassigns cell fate. And if you’re trying to do something yourself in cell biology, it often pays to learn how nature beat you to it. To determine the mechanics of this trans-differentiation would require a more quantitative technique: single molecule fluorescent in situ hybridisation (smFISH).
SmFISH employs fluorescently tagged RNA oligomers, antisense to an mRNA (or miRNA) of interest. Combined, these oligos fluoresce strongly enough that individual RNAs can be resolved and counted within PHso1. Tracking change in RNA quantity rather than GFP fluorescence would tell you whether or not glial expression stops before neuronal expression begins. Does the cell become completely naive? Perhaps only partially? Or maybe there’s no dedifferentiation at all, and the cell passes through a totally novel identity- part glia, part neuron. Though I didn’t have time to perform these experiments, I did create the necessary strains. By crossing a markerless strain with my GFP/RFP animals, and then selecting against RFP over a couple of generations I rendered worms expressing only one of the two GFP markers so that the RFP reporter used in smFISH would be visible.
Though the work I was doing represented a project in its early stages and was at times very laborious, I quickly got an appetite for it. There was a thrill to it, knowing that no one had ever done what I was doing. I felt that buzz again when I arranged the prettiest pictures I could muster into figures to show to the lab, and then again when they ceremoniously scoured my findings with the same level of scrutiny I had seen them exact on each other. Alongside my data, I showed off a particularly pretty picture of both the worm’s glia-to-neuron transitions occurring at once in the same animal, which I think will remain my crowning achievement in science for a long time (Richard even kindly offered to steal it for his presentations). The BSDB’s grant has allowed me a taste of what a career in academia can offer. Straightforward experiments fraught with unforeseen difficulties. Working on weekends when, infuriatingly, age-specific experiments simply weren’t possible on Friday. Enough money to live off (just). But above all, the enormous reward in discovering something new. And getting to work with some really, really great people. Thanks guys.
Fig 1.1 – Percentages of observed expression patterns of grl-2 and rab-3 in PHD neurons
Fig. 1.2 – progression of grl-2 and rab-3 expression in the PHD and PHso2
Fig 2.1 – Percentages of observed expression patterns of mir-228 and rab-3 in PHD neurons
Fig. 2.2 – progression of mir-228 and rab-3 expression in the PHD and PHso2
Fig. 3 – examples of maulting animals with glial and neuronal marker coexpression
A ERC funded postdoctoral position is available in the laboratory of Julien Courchet at the NeuroMyoGene Institute within the University of Lyon, France.
Our group studies the molecular mechanisms underlying axon outgrowth and neural circuits formation in the mouse cerebral cortex. Our current research is supported by an ERC Starting Grant and funds from AFM-telethon to explore how a dynamic regulation of the energy metabolism is involved in axon morphogenesis and cortex development. We focus on a previously identified kinase pathway controlling terminal axon branching through the regulation of mitochondria trafficking and distributing in developing axons (Cell 2013). Building on this previous research, the proposed project will use a combination of whole cell metabolomics, real-time fluorescent videomicroscopy and live 2-photon imaging to characterize some of the molecular mechanisms involved in the local regulation of mitochondria function in developing axon in vivo.
The selected candidate will join a young research team within a dynamic and collaborative scientific environment at the newly created NeuroMyoGene Institute (INMG). The candidate will have access to state-of-the-art facilities for imaging and metabolic analyses, including high quality confocal and 2-photon microscopes, animal phenotyping centers and a seahorse analyzer. Our institute is located in a newly renovated laboratory space in the Rockefeller faculty of Medicine in close proximity to the Neuroscience and the Cancer Research Centers.
Applicants should have a PhD degree or equivalent with a strong background and practical experience in neurobiology, confocal microscopy and/or real-time imaging. Previous experience working with rodent models is required. Training in techniques relevant to cell signaling, metabolic regulation and optogenetics would be an asset. We are looking for a highly motivated candidate with a strong attitude towards independent work and good interpersonal and communication skills. Excellent written and spoken English skills are essential. Ability to speak French in not mandatory.
The initial appointment is one year and can be renewed for 2 additional years. Salary including benefits will depend on previous experience according to guidelines at the University of Lyon. Applications will be reviewed on a rolling basis until position is filled. Selected candidates will be invited for an interview early 2018. Project start date is expected during the first semester of 2018.
Interested candidates should contact Dr Julien Courchet (julien.courchet@inserm.fr) with their CV, a summary of their previous research (< 1 page), a brief statement of their research interests and career goals, as well as the contact information for at least 3 references.
The MRC Weatherall Institute of Molecular Medicine (WIMM) has fully funded 4-year Prize PhD (DPhil) Studentships available to start in October 2018. These Studentships are open to outstanding students of any nationality who wish to train in experimental and/or computational biology.
The Institute is a world leading molecular and cell biology centre that focuses on research with application to human disease. It includes the recently opened MRC WIMM Centre for Computational Biology and houses over 500 research and support staff in 50 research groups working on a range of fields in Haematology, Gene Regulation & Epigenetics, Stem Cell Biology, Computational Biology, Cancer Biology, Human Genetics, Infection & Immunity. The Institute is committed to training the next generation of scientists in these fields through its Prize PhD Studentship Programme.
The fully funded studentships include a stipend of £18,000 per annum and cover University and College fees.
Further information on the studentships, how to apply, and the projects available can be found at:
The Karam Teixeira laboratory (https://www.gen.cam.ac.uk/research-groups/karam-teixeira) at the University of Cambridge (Department of Genetics) is looking to recruit an outstanding Postdoctoral scientist to investigate the molecular mechanisms sheltering totipotency and controlling germline stem cell behavior in vivo. Using the Drosophila germline as a model for studying stem cells, we employ an integrated approach, combining high-throughput molecular analysis (next-generation sequencing) and computational investigation with developmental, microscopy, and genetic analyses (including CRISPR-Cas9 gene editing, tissue-specific RNAi knockdown, etc). We were previously able to assemble the complete genetic framework controlling germline stem cell self-renewal and differentiation in vivo, revealing conserved new aspects of stem cell biology (Teixeira et al, Nature Cell Biology, 2015; Sanchez et al, Cell Stem Cell, 2016). Moving forward, our goal is to build a refined molecular understanding of how protein synthesis control – a new frontier in gene regulation – governs stem cell fate transitions in vivo. Our lab is generously funded by the Wellcome Trust.
Candidates must have experience in a wide range of molecular biology techniques, and prior expertise in next generation sequencing would be an advantage. Experience working with fly genetics is a plus but not required. The successful candidate will be highly motivated, willing to join a young and dynamic research group, have good communication skills, and possess strong problem solving capacities.
How do phenotypic differences between cells of the same clonal origin emerge? How exactly does the transition between the initial and final phenotypes occur? What happens in the cell during the transition? When there are two or more options, how is the choice made between them? How long does it take to acquire a new phenotype? What is the minimal difference required to consider two cells as phenotypically different? To define a cell type, should we consider only morphological, molecular differences or both simultaneously?
Despite the plethora of studies, these simple questions remain unanswered. Most of the studies focus on identifying the essential genes or environmental factors usually at the level of cell populations. The huge amount of molecular data accumulated over the past decades gave us the illusion of knowledge. Knowing the players is obviously essential, but this is only the starting point for the understanding. Unfortunately, our understanding of the process of differentiation remains desperately scarce, as the lack of clear responses to the above listed simple questions shows.
Recently, two important challenges came to modify the perception of differentiation. The first comes from the spectacular development of single-cell technologies. The second is that we have to come to realize how much phenotypic plasticity is a genuine characteristic of cells. The main lesson from the rapid development of single-cell detection techniques is the unambiguous demonstration of how different individual cells are and how poorly population-level averages represent them. The bulk of our knowledge on differentiation comes from studies of cell populations. Perhaps unconsciously, we took for granted that individual cells all follow with small variation the same sequence of events as what we could see at the level of cell populations. The unexpectedly high variation of individual cell phenotypes in populations that were believed to be homogenous (because of the morphological similarity of the cells, their clonal origin, their expression of some markers etc.) draw the attention to the phenotypic plasticity of the cells and to the fact that fate decisions are “taken” by individual cells.
Clearly, a coherent, systemic level explicative frame is needed that can account for the coherent population-level behaviour emerging from highly variable individual cell phenotypes and behaviour.
Our recently published work [1] was motivated by the wish to contribute to this effort. Although we used the extensively studied hematopoietic stem cell model, we were surprised how much these general questions fit to the model. The definition of the hematopoietic stem cell is widely debated, no precise description of the earliest events of differentiation and only very scarce information on the morphological changes during the same period were available. The study of hematopoietic stem cells is made difficult by the lack of exact criteria to identify them. Nonetheless, there is a consensus that CD34+ cell fraction in the umbilical cord blood contains high number of these cells. We decided therefore to privilege an integrated view and work on the whole population of CD34+ cells. Individual cells were randomly sorted from the population at different fixed time-points and their gene expression profile was analysed by single-cell RT-PCR. The structure of the population and its components were identified on the basis of the collected single-cell gene expression data. Parallelly, we set up a time-lapse system that allowed the continuous monitoring of the cells and their progeny during the first 96hrs after stimulation. Adding the continuous observations of the morphological changes and cell division timing of individual cells to the single time-point single-cell molecular analysis sampling of the same population provided a glimpse of the true dynamic nature of cellular fate decision.
The CD34+ cell fraction is traditionally considered as heterogeneous. Indeed, before cytokine stimulation every cell displayed a unique gene expression profile. However, no groups could be identified on the basis of their statistical similarity, this population is not a mixture of a limited number of “cell types”. When cytokines were added to the culture, every cell responded in a unique way. Again, every cell displayed a unique gene expression pattern that was different of the previous seen at t=0 hours. It was characterized by the simultaneous expression of different lineage-specific genes. This state is known as a multi-lineage primed pattern [2, 3]. A second round of change occurred during the second 24 hours. Two days after the stimulation of the cells two distinct transcription patterns emerged. One pattern was typical for myelo-erythroid progenitors, while the second was reminiscent of multipotent cells. Until now, the results overall confirmed the previous studies; the main novelty was the apparent rapidity of transition from the initial to a multilineage primed gene expression pattern and, just 24 hours later, to two distinct profiles. However, these snapshots did not allow us to deduce on the dynamics of the changes.
Time-lapse video of a cell clone with cells conserving polarized morphologies. GIF made from from Movie S1 in the paper
The real surprise came from the analysis of the time-lapse records. Individual CD34+ cells were placed in microwells and imaged for a week at 1 image/min. The resulting time-lapse records allowed us to record cell cycle lengths and morphological changes of each individual cell within individual clones. After stimulation, the cells usually displayed a polarized shape with a strong protrusion on one side called uropod. The first unexpected observation was to see that the unusual length of the first cell cycle. The cells made more than 50 hours on average to divide. This means, that the first major transcriptional change occurred during the first cell cycle and the second around the end of the first or the very beginning of the second cell cycle. After the first division, we could see two different morphologies; one was strongly polarized with a uropod, the second is spherical. The daughter cells usually inherited the morphology of their mothers. Polarized cells gave two polarized and round cells two round daughters. However, we were surprised to observe that a significant proportion of the cells did not conserve a stable morphology; they switched from one morphology to another and back many times during the cell cycle. The majority of their daughter cells also conserved the fluctuating phenotype
Red color: CD133; Green: actin; Blue: DNA
We called these cells “hesitant”. The overall picture suggest that stimulated CD34+ cells, after a brief passage through a multilineage primed state reach (without cell division!) one of the two alternative states characterized by a typical transcription pattern and cellular morphology. However, a significant proportion of cells fluctuate between the two morphologies. Does this morphological instability reflect transcriptome fluctuations? To answer this question, we have isolated individual cells with the three different – stable round, polarized or “hesitant” – behaviours and analysed their gene expression pattern. It appeared that the cells with stable morphology displayed one of the two expression patterns first observed at the 48 hors time point. The “hesitant” cells were characterized by an intermediate profile. The molecular analysis correlated to the time-lapse data suggests therefore that these cells are in an unstable state; their transcriptome undergoes fluctuations that are reflected in their fluctuating morphology also.
These are the key observations and the immediate conclusions of this work. However, these observations may contribute to the current tendency to reframe the issue of cell differentiation and stem cells in general. Cell differentiation can be approached using the concepts of stability and change – two complementary concepts widely used in biology. Stem cells may represent a highly unstable cell fraction contrary to the cells with stable differentiated phenotype. Unstable stem cells are actively exploring the space of available phenotypes before getting trapped by one of them. This is a kind of trial-and-error process. Under normal conditions, the unstable period is relatively short lasting; this is why the unstable cells we consider as stem cells are so rare in a normal tissue. However, a substantial change in the environment can destabilize many cells at the same time. This is what we see when CD34+ cells are stressed by the sudden addition of a cytokine cocktail. Due to the progressive adaptation to the new environment, the proportion of the “hesitant” stem cells decreases gradually as they attracted to the more adapted phenotypes. Importantly, this process seems to depend only indirectly on cell divisions. This interpretation is in remarkable agreement with earlier theoretical predictions and experimental work [4-8] and supported by recent experimental observations also [9-12].
Our paper was initially submitted to a well-known journal in stem cell biology. Beyond the disappointment of the rejections (every scientist is used to that), we were surprised by the poor quality of the reviews. The referees raised some technical concerns about the single-cell RT-PCR versus single-cell RNA sequencing, but not a single word about the time-lapse experiments that represented the major part of the paper, nor about the coupling the molecular and cellular scales, which is the true originality of the work. The reviews were very different when the manuscript was submitted to PloS Biology. The comments concerned all aspects of the work and the suggestions truly helped to improve the final version.
It would be naïve to think that a single paper can answer the fundamental questions raised at the beginning of this text. Clearly, we need a fresh view on cell differentiation that goes beyond the simple gathering and classification of molecular data and takes into account the true dynamics.
Mojtahedi M, Skupin A, Zhou J, Castano IG, Leong-Quong RY, Chang H, et al. Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biol. 2016;14(12):e2000640. doi: 10.1371/journal.pbio.2000640. PubMed PMID: 28027308; PubMed Central PMCID: PMC5189937.
Doing a PhD is tough, the data from surveys supports that. However it is not insurmountable, and here we have a collection of some guidance from the Twitter community. Let us know in the comments if you have any thoughts to add.
The Department of Biology within the College of Natural and Health Sciences at The University of Tampa invites applications for a tenure track position in developmental biology at the rank of Assistant Professor starting in August 2018.
The University of Tampa is a medium-sized, comprehensive, residentially-based private institution of 8,913 undergraduate and graduate students. The University is ideally situated on a beautiful 110-acre campus next to the Hillsborough River, adjacent to Tampa’s dynamic central business district, which is a growing, vibrant, diverse metropolitan area. UT reflects this vibrancy; with 20 consecutive years of enrollment growth UT boasts 229 student organizations, a multicultural student body from 50 states and 140 countries, and “Top Tier” ranking in U.S. News and World Report.
Primary responsibilities will include an undergraduate teaching load of 12 contact hours per semester. The candidate is expected to teach introductory biology for majors, an upper division course in developmental biology, and other courses as needed.
Secondarily, the candidate is expected to engage in scholarly and research activity that involves undergraduates, advise students, and provide service to the department, college, university and broader community. Research activities must yield peer-reviewed publications.
PhD preferred (advanced ABD candidates considered), prior teaching and research experience with undergraduates is desirable.
Salary for this position is competitive and commensurate with experience.
Review of applications will begin January 2, 2018, and continue until the position is filled. Limited start-up packages and modest research space are available for tenure-track positions.
The 2nd NEUBIAS school for Bioimage Analysts will be organized in Jan. 2018 in Szeged, Hungary, and the registration is now open (Organizers: Jean-Yves Tinevez & Kota Miura). Please visit the linked URL below for more details. This school is the most advanced among three levels of NEUBIAS school. Deadline for the registration is Nov. 9th.
