Research position investigating the mechanisms underlying cardiac morphogenesis
The Bloomekatz laboratory in the Department of Biology at the University of Mississippi in Oxford, MS is seeking a researcher to assist in our investigations of cardiac morphogenesis and disease using zebrafish. Please see our website https://thebloomekatzlaboratory.org for details on our research. The successful candidate will have the opportunity to be involved in all aspects of the research and publication process, from conducting developmental biology experiments and zebrafish husbandry, to analyzing imaging data to writing and publication.
-Interested in joining our dynamic group apply online: https://careers.olemiss.edu, search zebrafish. Salary dependent on experience. This position is eligible for benefits. Anticipated start date Jan 2020.
-Further questions can be directed to Dr. Bloomekatz at josh@olemiss.edu. The University of Mississippi is an EOE/AA/Minorities/Females/ Vet/Disability/Sexual Orientation/Gender Identity/Title VI/Title VII/Title IX/ADA/ADEA employer.
Department of Biological Sciences, College of Sciences and Mathematics
Auburn University
The Department of Biological Sciences at Auburn University invites applications for a tenure-track faculty position beginning Fall 2021 at the rank of Assistant or Associate Professor in Plant Developmental Biology.
We seek a highly collaborative candidate who will examine fundamental mechanisms governing developmental processes in plants. A successful candidate is expected to establish an extramurally funded, internationally recognized research program focused on plant developmental biology. Instructional responsibilities include development of graduate and/or undergraduate courses in plant developmental biology related to their area of emphasis. Faculty will join existing Plant Biologists as well as recent Developmental hires in Marine and Terrestrial systems as an emerging group of Developmental Biologists in the department.
Review of applications will begin December 1, 2020 and will continue until a suitable individual is hired. Applicants should submit curriculum vitae, a description of research interests, a statement of teaching philosophy and experience, and contact information of three professional references. Applicants should endeavor to describe how your past and/or potential contributions in teaching, research, and/or service will serve to advance the College of Sciences and Mathematics’s mission of creating an inclusive environment. This should include the following: Statements of values as they relate to your understanding and commitment to diversity, inclusion, and equity in STEM fields; examples of experiences that demonstrate your commitment to fostering the success of traditionally underrepresented groups in STEM (students, staff, and/or peers) and supporting a diversity of perspectives in the classroom, lab, campus, and/or community; and Future plans for continuing to advance inclusive excellence, diversity, or equity in your research, teaching, and service.
Apply your developmental biology / neurobiology skills to the problem of brain cancer.
The lab of Dr. Jennifer Chan is seeking to recruit a motivated postdoctoral fellow to investigate cell fate decisions during the process of brain tumour development and progression. Research activities in the lab focus on growth factor signalling and transcriptional regulation as determinants of neural precursor identity and fate. We use model systems that include patient-derived glioma cultures, xenografts, and engineered mouse models generated from in utero and post-natal electroporation to address our research questions.
The successful candidate will collaborate with investigators in bioinformatics to apply to apply tools of genomics, epigenomics, and transcriptomics to further define important alterations during neoplastic transformation, including interactions of tumour cells with other constituents in the microenvironment. Early career-stage candidates (within 3 years of receiving PhD or equivalent) with experience in advanced immunohistochemistry / fluorescence microscopy; gene editing, and molecular biology; mouse modeling of disease; and/or experience in genomic approaches like RNA-seq, ChIP-seq, ATAC-seq will be preferentially considered.
The position is available immediately.
Other information
Located in Calgary, Alberta, Canada, the Chan Lab is part of the Charbonneau Cancer Institute at the University of Calgary’s Cumming School of Medicine. Within the Charbonneau Institute, we are part vibrant multidisciplinary research groups focused on childhood cancers and brain cancers. Calgary is a very ‘livable’ and family-friendly city located less than an hour’s drive from the Canadian Rocky Mountains – a haven for outdoor enthusiasts.
Application details:
Submit a brief letter of interest, your academic CV, and the names and contact information of at least three references.
Applications should be submitted as a single PDF file and sent as an email with the subject line “Post-Doctoral Fellowship, Glioma Biology” to: jawchan@ucalgary.ca
Royal Society Publishing has recently published a special issue from Philosophical Transactions B – Contemporary morphogenesis, organized and edited by Kyra Campbell, Emily S Noël, Alexander G Fletcher and Natalia A Bulgakova.
Our brain is immersed in a clear, colourless, nutrient-rich fluid called the cerebrospinal fluid (CSF), which provides mechanical support to the brain and helps to circulate important molecules for brain development and function. Within the interconnected cavities of our brain, the CSF flows in and out constantly. The CSF is actively produced by the choroid plexus (ChP), a highly secretory tissue present at different locations inside the brain cavities.
The ChP-CSF system plays a number of central roles in our brain, such as actively secreting and transporting hormones and nutrients to different brain regions and maintaining the physiological balance of ions and salts. In addition, the ChP is implicated in circadian cycle regulation, influencing the master clock regulation in the brain, and during sleep, CSF flow has been proposed to remove toxic protein aggregates and waste from the brain. Another key function of the ChP is the formation of a selectively permeable barrier, the blood-CSF-barrier, which separates the CSF from the blood, protecting the brain from toxic substances and certain drugs, similar to the blood-brain-barrier.
Despite all these important functions, the ChP and the CSF have long been ignored or dismissed simply as a waste disposal system of the brain, therefore for a long time little was known about these fascinating components of our brain. We now understand a lot more of the development and function of this tissue thanks to research on animal models such as mice, however, the study of human ChP and CSF is still complicated by technical and ethical challenges to obtain biopsies of ChP, particularly at early developmental stages. Studying human CSF is also particularly challenging due to the fact that extraction of this fluid requires painful lumbar punctures which run the risk of blood contamination.
In Madeline Lancaster’s lab at the MRC-LMB in Cambridge, we routinely generate cerebral organoids from human pluripotent stem cells. Cerebral organoids develop neural tissue which expands and matures forming structures that resemble early developmental stages of our brain’s dorsal cortex. Organoids are placed in a supporting media that contains only the essential nutrients and key ingredients that help and sustain brain development. This essential media allows for the spontaneous development of the brain tissue as it would normally develop in vivo, so sometimes we observe the generation of other brain identities other than the desired cerebral cortex. It was in this way that we initially observed the presence of ChP-like tissue adjacent to part of the cerebral cortex. It was this initial observation that prompted us to reproducibly generate ChP tissue. In our recent study entitled “Human CNS barrier-forming organoids with cerebrospinal fluid production” (Pellegrini et al., 2020), we developed a new in vitro model to study early development of human ChP in a dish.
Confocal image of a convoluted ChP organoid sectioned and stained for specific tissue markers
We started using patterning molecules secreted in vivo and previously shown to model ChP development in vitro (Sakaguchi et al., 2015; Watanabe et al., 2012). By adding these molecules at certain timepoint and for a certain duration, the organoids became entirely enriched in ChP tissue. To our surprise we noticed that these organoids would develop various-shaped, clear looking cysts that appeared completely isolated from the pink media surrounding the organoid. Initially, because of the unknown identity of these mysterious cysts, many of these organoids were discarded or considered “failed organoids”. One day, instead of throwing these organoids away we decided to look more carefully at them. By sectioning and staining the tissue with specific markers we came to understand that indeed the cyst was entirely surrounded by ChP.
The first question we had was: are these fluid compartments filled with human CSF? We were able to extract several millilitres of this clear fluid from different organoids. We then decided to perform mass spectrometry analysis to investigate the overall protein composition of the fluid. Together with the fluid extracted from organoids, we also analysed the media as a “negative control” and human in vivo CSF from healthy donors as a “positive control”. The results were quite surprising. The first observation was that this intriguing organoid fluid was not a mere ultrafiltrate of the surrounding media, but a fluid that contained proteins secreted de novo by the ChP. Second, looking at the proteins secreted de novo by the organoid we could find several human CSF proteins, including specific signalling molecules secreted during development, such as Insulin Growth Factor 2 (IGF2), and disease-relevant biomarker such as Serpin Family F Member 1 (SERPINF1) and clusterin (CLU) were indeed present in the organoid fluid, but not in the media. Comparing CSF extracted from organoids at different stages, we could notice a difference in the protein composition, with an enrichment in extracellular matrix proteins at early stages, compared to later stages in which we detected several apolipoproteins involved in lipid metabolism. When we compared our dataset with published proteomic databases of CSF in vivo, we realised that these differences in CSF composition reflected what is reported in embryonic CSF compared to older post-natal CSF stages, matching different stages of maturation.
Another interesting observation is that our organoid-generated CSF lacked blood proteins, such as haemoglobin, which were instead detected in CSF from humans. This is because organoids lack vasculature. We suspect that the presence of these proteins in human CSF is due to contamination from the lumbar punctures used to extract the fluid. Lacking these potential contaminants, the organoid-CSF represents a “cleaner” version of the ChP secretome. These results meant that we were able to generate a close to authentic CSF in a dish, from human cells. Compared to the small amount of CSF one can obtain from mouse embryos, we could extract several millilitres and we could look at the composition of this fluid without any other contaminants.
As mentioned above the ChP forms the blood-CSF-barrier, which regulates the exchange of nutrients and signals from the blood to the CSF, blocking entry of different compounds such as therapeutics. This brain barrier is less studied than the blood-brain-barrier, but it could provide an alternative way to access the brain if appropriately targeted. We therefore wondered: does the ChP in these organoids form a selectively permeable barrier?
Initially, we had a hint that the answer was yes because the liquid inside these cysts is clear, meaning that even the small molecule of phenol red, usually present in our media, is not able to freely cross the barrier. Since we could extract significant amount of fluid from these organoids, the first experiment was simply to add fluorescently labelled molecules of different sizes to the media and observe, after 2 hours of incubation, whether we could detect any fluorescence in the inside of the fluid-filled organoid compartment. Even the smallest of these molecules tested was undetectable inside of the organoid, indicating that the ChP in vitro was indeed forming a barrier. We then wanted to know whether the ChP forming the barrier could select certain molecules instead of others.
While having a coffee with brilliant chemist and friend Dr. Claudia Bonfio, who also works at the MRC-LMB in the completely unrelated field of prebiotic chemistry, we discussed possible ways to detect small molecules in their native state, in a system like the ChP organoids. This unusual meeting between chemistry and biology resulted in the idea of using Nuclear Magnetic Resonance (NMR). Using this technique, we were able to demonstrate the selective permeability of the ChP barrier by challenging the system with two highly similar small molecules with opposite permeabilities such as L-dopa and dopamine. We indeed observed that only L-dopa, and not dopamine, was able to cross the ChP barrier, exactly recapitulating the selectivity observed in vivo. This initial proof of principle experiment was fundamental for us to trust the system and then challenge it with other drugs.
With this experimental approach we were able to show that organoids can qualitatively but also quantitatively predict the permeability of new drugs. When we tested the new drug Sephin 1, a compound that prevents protein misfolding that has recently entered clinical trials, we noticed that the permeability data were slightly lower in the organoids compared to the available data in animals, in this case mice. This indicates that the system could recapitulate permeability of drugs in human, but the levels of transporters expressed in the ChP can be different in other species, reflecting differences in permeability. Finally, we decided to use our method to reveal why the drug BIA 10-2474, which failed clinical trials for multiple conditions including chronic pain and multiple sclerosis, was toxic only in humans. We indeed observed an unusual accumulation of this compound inside the organoid fluid. This observation was consistent with the hypothesis of an accumulation in the CSF of these patients. Together with other toxic effects reported for this drug, the use of ChP organoids could have perhaps have raised some flags during preclinical testing. We think that ChP organoids potentially represent a preclinical in vitro human model to validate safe entry of therapeutics to the brain, with the potential to reduce the number of drugs that fail during clinical trials.
Finally, we were curious to explore in more detail the cellular architecture of the choroid plexus in order to better characterise the different cell populations present in the system. We took advantage of this isolated nature of ChP organoids, not attached to other tissues, to identify cell populations unique to this region of the brain. We looked closely at the ChP and by merging our single cell and proteomic data we were able to learn which specific cell types secrete the biomarkers detected in the organoid CSF fluid. In addition, we identified these obscure “dark” and “light” cells that were first reported in electron micrographs from the ‘70s, but we were also able to discover a new cell type, previously unidentified in the ChP: the myoepithelial cells. These cells have been reported in other secretory tissues such as salivary and mammary glands, and they are enriched in contractile fibres which could potentially help to “squeeze” the secretory epithelial cells to help CSF production.
Artwork by L. Pellegrini representing a section of a brain organoid with both cortical and ChP tissue.
In summary, we learnt that ChP organoids could secrete CSF and form a selectively permeable barrier that can be used to select drugs in a human-specific system in vitro. We also learnt that if you notice something unusual in your experiments, don’t just throw it away!
The BFSCI serves as a hub for basic and translational research in stem cell biology and regenerative medicine across the medical school campus and is located in state-of-the-art research space.
The CDRB Department ranks as one of the top cell/developmental biology departments in the country, with a focus on cell biology of developmental proesses and epithelial organ development, utilizing multiple model systems to delve into fundamental questions of biology and disease pathogenesis.
We seek highly interactive and collaborative investigators whose research interests will complement and enhance those of the Department and/or the Institute.
Faculty positions in CDRB: Assistant or Associate Professor focusing on vertebrate niche stem cell biology, cell biology, epithelial biology, and/or developmental biology
Faculty positions in BFSCI: Assistant or Associate Professor focusing on basic or translational mammalian stem cell biology, tissue homeostasis and/or regenerative medicine
Candidates should hold a Ph.D., M.D., V.M.D., M.D./Ph.D. or equivalent degree and are expected to participate in research and graduate student mentoring and teaching. The Icahn School of Medicine provides an exceptional intellectual environment with outstanding facilities; generous start-up packages are available.
Applicants should submit a single PDF file containing a cover letter, CV, and a 2-3 page statement of research interests. Please name the file as: Applicant’sLastName.Applicant’sFirstName.pdf.
Applicants should also arrange to have three individuals send confidential letters of reference. Please have the letters named as: Applicant’sLastName.Applicant’sFirstName_Referee’sLastName.pdf.
Please indicate in your cover letter whether you are applying for a position in CDRB, BFSCI, or both.
Completed applications and letters of reference should be submitted via email to Taylor Stokelin: taylor.stokelin@mssm.edu and will be reviewed on a rolling basis with an initial deadline of November 1, 2020.
The Icahn School of Medicine at Mount Sinai is an Equal Opportunity and Affirmative Action Educational Institution and Employer. Women and members of underrepresented minority groups are strongly encouraged to apply.
We seek a Lab Manager. Our laboratory uses genomics, organoids and mouse models to study mammalian kidney in health and disease. We possess substantial expertise in single cell omic and multi-omic approaches including all aspects of informatic analysis. Examples of our recent work can be found here:
Our supportive environment values team work. We seek a lab manager to oversee and coordinate lab functioning and compliance but also to design, conduct and oversee research projects. We are located in recently renovated space in the McDonnell Medical Science Building. The successful applicant will have substantial lab experience and writing skills. This position offers superb opportunities for continued scientific learning in a well-funded laboratory, and continued career development including authorship, and is full time. Salary range $51 – $91k.
The successful applicant will hold the title of Lab Manager. The Humphreys Lab is a collaborative, highly productive and supportive scientific work environment.
Humphreys Laboratory:
The Humphreys lab consists of eight post-doctoral fellows, three graduate students and a lab manager. An overview of the Humphreys Lab research can be found at: http://humphreyslab.com/ and on Twitter @HumphreysLab
To apply for this position, please submit a letter explaining your interest, a CV and contact information for references to Benjamin Humphreys MD, PhD (humphreysbd@wustl.edu)
Please, always run specificity controls with Morpholinos. Morpholinos can reveal gene functions that can be concealed by genetic compensation in a mutant, but rigorous specificity controls are essential to determining whether a morphant phenotype is due to knockdown of the oligo target or an unexpected interaction with a different RNA. The Morpholino-in-a-mutant approach described in Jiang et al. 2020 (linked below) is an excellent approach when a mutant is available.
For those using Morpholinos, these three papers provide important perspective on the need for and good design of specificity controls.
On the mechanism behind many differing phenotypes of morphants and mutants:
Sztal TE, Stainier DYR. Transcriptional adaptation: a mechanism underlying genetic robustness. Development. 2020 Aug 14;147(15):dev186452. doi: 10.1242/dev.186452.
https://dev.biologists.org/content/147/15/dev186452
Describing a case where the mutant – morphant phenotypic difference is not caused by transcriptional adaptation:
Jiang Z, Carlantoni C, Allanki S, Ebersberger I, Stainier DYR. Tek/Tie2 is not required for cardiovascular development in zebrafish. Development. 2020 Sep 14:dev.193029. doi: 10.1242/dev.193029.
https://dev.biologists.org/content/early/2020/09/12/dev.193029
On Morpholino controls:
Stainier DYR, Raz E, Lawson ND, Ekker SC, Burdine RD, Eisen JS, Ingham PW, Schulte-Merker S, Yelon D, Weinstein BM, Mullins MC, Wilson SW, Ramakrishnan L, Amacher SL, Neuhauss SCF, Meng A, Mochizuki N, Panula P, Moens CB. Guidelines for morpholino use in zebrafish. PLoS Genet. 2017 Oct 19;13(10):e1007000. doi: 10.1371/journal.pgen.1007000. eCollection 2017 Oct.
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007000
Our body consists of a multitude of highly specialized tissues: the neurons in our retina seem to have little in common with the glandular cells in the intestine or our muscle fibers. Yet nothing hints at that complexity at the time of conception, when the genomes of sperm and egg fuse to define the blueprint of a new individual. Indeed, how an entire organism arises from a single cell truly is one of the most fascinating questions of biology. As the embryo develops, its building blocks (cells) gradually assume specialized functions and coordinately go through transient states that serve as intermediate steps wherefrom more complex structures will be molded as time progresses. Throughout this process, cells dynamically receive and send information to instruct their neighbors to assume specific fates. This cell-to-cell communication ensures all parts working together perfectly to create a self-organizing system that will eventually give rise to an entire body. Embryonic development thus follows a delicate choreography wherein every cell has to fulfill a precise role depending on its relative position in space and time. Unraveling the blueprint of the making of an embryo is a daunting endeavor that has fascinated developmental biologists for decades.
This study started with two physicists-turned-biologists (Pierre Neveu and Lars Hufnagel) marveling at SPIM (selective plane illumination microscopy) movies of developing Phallusia mammillata embryos, an ascidian species that is an ideal model for advanced imaging approaches due to the high optical transparency of early embryos. Our ambition was ignited to take a quantitative systems approach to decipher the molecular mechanisms underpinning the marvelous unfolding of embryonic complexity captured in those movies. We set out to employ high resolution single-cell RNA sequencing (scRNA-Seq) to decipher the complete transcriptome of every single cell in the developing embryo from zygote to gastrulation.
We quickly came to realize that the choice of an appropriate model system would be critical for the success of this highly ambitious project. Neither of us had previously worked on ascidian development but we embraced Phallusia mammillata for its many advantageous properties. Ascidian embryos are made up of a very small number of cells and their development is stereotypical. This means that the developmental history of any given cell is known but it also means that its future fate can be predicted and all individuals develop according to that same invariable blueprint. However, ascidians have a genetic makeup that resembles the ones of vertebrates (albeit less complex as genome duplication has not occurred).
We thought that possessing the complete (or near complete) collection of cells of individual embryos would enable us to ask two fundamental questions (Figure 1): could one actually determine the physical position of a given cell from its gene expression? How variable is gene expression during development?
Figure 1. A: Both the lineage history of a cell and its spatial position will influence its gene expression. B: The bilateral symmetry of Phallusia mammillata embryos allows to compare the reproducibility of gene expression in bilaterally symmetric cell pairs within one embryo and across embryos.
The small number of cells that make up a Phallusia embryo at gastrulation brings a crucial advantage. It allowed us to sample a large number of individuals at moderate costs in order to compare how different the gene expression is between individual embryos of the same stage.
Moreover, ascidian embryos are bilaterally symmetric so in theory there should be two copies of every cell in a given embryo (one for the left part and one for the right part of the embryo). This solves a fundamental conundrum of any single-cell approach: How to get hold of a suitable biological replicate?
Cell type identification in individual embryos
Dissociating single embryos up to gastrulation, we performed RNA-Seq at very high depth. However, a first obstacle we had to tackle was the lack of a published annotated transcriptome for Phallusia. After performing the de novo assembly of the Phallusia transcriptome, it turned out that we could capture quantitatively in single cells the expression levels of as many genes as for bulk mRNA-Seq on pools of embryos.
Figure 2. A. Strategy to capture expression profiles of cells from individual embryos. B: The expression of only four genes is sufficient to classify cells into the 8 cell types present in 32-cell embryos.
Due to potential variability between embryos, we thought it might be simpler to classify cells within a given embryo (and then compare cell types across embryos of the same stage, Figure 2). Relying on an iterative classification scheme, we identified 18 cell types in a 64-cell embryo. This diversity is striking despite the small number of cells. Another interesting point is the low dimensionality of the classification: the number of gene groups that can classify cell types is smaller than the number of cell types. It means that cell fate specification relies on the modular expression of genes (and not only on genes that would be exclusively expressed in individual cell types as what would be commonly assumed).
Reconstructing lineage trajectories from scRNA-Seq data
Equipped with the exact cell type composition of the embryo after each round of cell divisions, we then asked what is the mother-daughter relationship between cell types. When matching cell types across stages, correct accounting must factor in cell divisions, in other words there should be twice as many cells in the daughter cell types of a given mother cell type. Indeed, if one does not keep track of cell divisions, one would fail to capture offshoots of the germ cell lineage (which is itself transcriptionally silent up to the 64-cell stage and therefore stands out compared to other cell lineages).
Two findings stand out from the lineage reconstruction. First, we only found asymmetric mRNA inheritance between daughter cells in the germ cell lineage. Our dataset thus dispels the notion of mosaic development (at least relying on RNA-based factors) for all the somatic lineages. Second, specification is driven by three successive waves of upregulation of transcription factors. This stepwise cascading principle of transcription factors was valid for all somatic lineages.
Reconstructing the spatial organization of the embryo from scRNA-Seq data
Development is a dynamical process in which time and space are fundamentally linked. The gene expression of a given cell will adapt to the signals it receives from its surroundings in a history-dependent manner. Reversing the above statement, the spatial and temporal identity of every cell should be encoded in its gene expression signature. This is a crucial point as we had not kept track of the spatial origin of cells during the dissociation of the embryos. Thus, the next logical step was to see if we could reconstruct the physical organization of the embryo directly from the expression profiles of all its cells.
A perfect starting point is when the embryo activates its genome. Cells are a blank slate (except the ones that inherit maternal determinants, the future germ cells in the case of Phallusia) and will respond to the morphogenetic cues present in their environment. Expression profiles of the cells of 16-cell embryos define two axes: one separates the two embryo poles and the other one corresponds to the anteroposterior axis. Remarkably, the expression profiles of the different cells project in a way that mirrors the cells’ physical positions in the embryo. It thus appears that the future germ cells (through the inheritance of maternal determinants, among which a Wnt ligand) act as a signaling center that organizes the initial patterning of the embryo at 16-cell stage. The same map recapitulates the relative positions of the 8 cell types present in 32-cell embryos but can no longer resolve a few sister cell types at the 64-cell stage. In fact, different signaling ligands are upregulated at the 16- and 32-cell stages, changing the morphogenetic cues cells experience. The introduction of new dimensionality reduction axes at the 64-cell stage is thus necessary and theses axes map faithfully the position of the different cell types of the vegetal pole. In practice, one axis corresponds to the anteroposterior axis and the other to the medial-lateral axis.
Hence, the spatial organization of the embryo is reflected in the gene expression of individual cells and it can be reconstructed from it. Cells read out the local signaling environment and adapt their gene expression accordingly.
After assembling the Phallusia transcriptome, it became apparent that Phallusia possesses orthologs for all the transcription factors and signaling molecules expressed during embryogenesis annotated in the Ciona genome. There is a remarkable conservation of the expression territories of ortholog genes between the two species. Thus, there is a strong regulative dimension to ascidian development despite the limited number of cells constituting their embryos.
Assessing the variability and reproducibility of gene expression during development
Our dataset has both high cell coverage of individual embryos but also many embryos of a given stage. We could then study the reproducibility of gene expression within an embryo and across embryos.
How similar are the two sides of the embryo? Here again, the small number of cells in the embryo allows an unambiguous comparison. Some cell types have only two cells per embryo so there is necessarily one coming from the left side of the embryo and one from the right side. In the majority of these cell pairs originating from the same embryo, the expression of marker genes is highly reproducible with a precision comparable to the one of housekeeping genes.
While bilaterally symmetric cells in a given embryo are highly similar, there is an obvious spread in gene expression profiles within particular cell types. What could account for these differences? The most natural explanation would be that they are due to slight differences in staging. In other words, cells with lower expression levels are younger than cells with higher expression levels. An alternative explanation would be that gene expression is noisy and cells have different expression levels that do not influence normal development. However, an analysis called RNA velocity allows to extrapolate the future expression levels of a given gene by looking at the ratio between spliced and unspliced counts. RNA velocity supports the notion that cells are caught at different times along the upregulation trajectory of these genes. The coordinated upregulation of dozens of genes in a given cell type is in fact accurately modeled with a model of linear variation in time. Thus, expression differences between embryos and between cells of the same cell type can be attributed to slight differences in developmental timing. It appears that transcriptional programs guiding cell fate unfold according to a temporally well-choreographed sequence in a given cell type.
Projecting the single cell expression profiles onto a fully segmented movie of embryonic development enabled us to generate a digital embryo, i.e. a 4D representation of embryonic development accounting for every cell and every gene. This data can be explored and visualized at digitalembryo.org, where anyone can generate their own movies of the temporal and spatial gene expression dynamics oftheir genes of interest.
Charting an atlas of a developing embryo at the single-cell and whole genome level would have seemed an impossible mission a mere decade ago. The merge of developmental biology and quantitative approaches from systems biology holds great promise for the future. While traditional studies have focused on the role of individual genes in specific lineages, unraveling the complexity of the making of an entire organism will greatly benefit from the holistic perspective made available by the constant advance of single-cell techniques.
The Rohner Lab at the Stowers Institute for Medical Research has an opening for a Research Specialist to further develop tools for the emerging research organism Astyanax mexicanus. Visit http://research.stowers.org/rohnerlab/ for more information on the research in the lab.
The selected candidate will help with day to day operations of the lab and develop new tools for the cavefish system, such as transplantions, genome editing, viral mediated gene transfer, generation of cell lines, transgenic lines and others. The candidate will receive strong support from the core facilities that provide advice, training and service to enhance the Institute’s interdisciplinary and collaborative research programs. Current core facilities are staffed by over 100 scientists with expertise in bioinformatics, cytometry, histology, imaging, microarray, next generation sequencing, transgenic and ES cell technologies, proteomics and molecular biology. The Stowers Institute offers a highly competitive compensation and benefits package.
The Rohner Lab has a strong commitment for mutual success and is dedicated to providing support for all lab members. Minimum requirements include a doctoral degree in the life sciences, chemistry, or biomedical engineering with significant postdoctoral experience in one or more of the following areas: molecular biology, developmental biology, genetics, genomics, evodevo, physiology.
In addition to excellent verbal and written communication skills, successful candidates must be dynamic and able to motivate others, and being creative and proficient at problem solving.
Application Instructions: To apply, please submit (1) a brief cover letter, (2) a current CV, and (3) contact information for two professional references to Dr. Nicolas Rohner at nro@stowers.org cc: careers@stowers.org. Applications due on October 15th, 2020, after that position will remain open until filled.
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