Kamberov Laboratory, Department of Genetics in the Perelman School of Medicine at the University of Pennsylvania, USA.
We are seeking creative and exceptionally motivated candidates to fill a post-doctoral position in the field of evolutionary and developmental genetics.
Research in our lab is directed at uncovering the genetic basis of human adaptive traits, with a core focus on the evolution of skin appendages, namely sweat glands and hair follicles. Taking a highly interdisciplinary approach that combines mouse and human genetics with developmental biology and genomics, our research is making strides at not only enhancing our understanding of human evolution but also applying that knowledge to the improvement of human health. Projects include: dissection of molecular pathways and epigenetic regulation of skin appendage development and regeneration; discovery and modeling of human adaptive variants using transgenic mice; high throughput screening for genetic elements controlling the development and uniqueness of human skin appendages.
The position provides an exciting opportunity to work at the interface of basic and translational research in a collaborative and stimulating environment, and gain experience in a diverse set of technical approaches at the cutting edge of evolutionary and developmental biology.
A doctorate in biology or related field is required. Applicants with a strong background in developmental biology, genetics, genomics or molecular biology are encouraged to apply. Prior experience with mouse genetics and husbandry is preferred.
Interested candidates should provide: 1) your CV 2) A brief letter detailing your interest in the lab and relevant past research experience 3) The contact information for three references who can comment on your research. Application materials and any questions regarding the position should be sent to Yana Kamberov: yana2@mail.med.upenn.edu
Online link to job posting: https://www.med.upenn.edu/apps/my/bpp_postings/index.php?pid=19391
I’m happy to introduce myself as the Node’s new Community Manager, taking up the reins from Cat Vicente, who said goodbye recently, and left this unique site in great shape. I’ve come to the Node from the lab bench, recently as a postdoc with Nick Brown in Cambridge, and before that as PhD student with Rob Ray in Sussex. Like all developmental biologists I was tackling various aspects of the same broad question: how do you go from a genome to an organism?
I spent last week saying goodbye to my flies (one by one), and throwing away redundant tubes of DNA I’d accumulated over the last few years. Turning off the lights in the lab one last time, listening to that constant hum from the incubators…all quite bittersweet, but mixed with a lot of excitement for the Node.
This site is all about the developmental biology community, as readers, writers, and commenters. Anyone can register, and anyone can write. If there’s anything you’d like us to do, or you have any questions or comments or suggestions, just use the Contact Us button on the right, or leave a reply underneath the post.
Otherwise I look forward to getting to know you all, and promoting the brilliant work that comes out of this exciting field. Happy reading!
Here are the highlights from the current issue of Development:
A distinct cartilage programme for bone regeneration
Bone healing, for example fracture repair in humans, often involves a cartilage intermediate but how this tissue is induced and contributes to healing is unclear. Here, Gage Crump and co-workers show that regeneration of the zebrafish jawbone involves cells of a hybrid cartilage-bone nature (p. 2066). They first report that the lower jawbone of adult zebrafish regenerates via a cartilage intermediate. The analysis of cells within this injury-induced cartilage reveals that they express both chondrocyte- and osteoblast-associated genes and can undergo mineralization. This is in contrast to the situation observed in developmental chondrocytes of zebrafish, which do not express osteoblast genes and do not mineralize. The researchers further report that these repair chondrocytes likely arise from the periosteum – a tissue that usually gives rise to osteoblasts. Finally, they demonstrate that the induction of repair chondrocytes from the periosteum involves an unexpected role for Indian hedgehog signalling, which is normally involved in chondrocyte proliferation during development. Thus, while it has generally been assumed that regeneration involves the same processes that are employed during development, this study suggests that regeneration induces a unique cartilage differentiation and repair programme.
Insights into cadherin function in the neocortex
Development of the mammalian neocortex involves the radial migration of neurons, which move from their place of birth to their final position in the appropriate neocortical cell layer. This migration is known to involve cadherins but the specific cadherins implicated and the mechanisms by which they act are unclear. Now, on p. 2121, Ulrich Mueller and colleagues report that cadherin 2 (CDH2) and cadherin 4 (CDH4) play crucial roles during radial neuronal migration in the mouse neocortex. The researchers first demonstrate that both CDH2 and CDH4 are expressed in the developing mouse neocortex. The inactivation ofCdh2 or Cdh4 specifically in migrating neurons reveals that both are required for radial migration. The authors further report that CDH2 and CDH4 act via protein tyrosine phosphatase 1B (PTP1B) and α- and β-catenins to control migration. Finally, they show that the perturbation of cadherin-mediated signalling has no effect on the formation or extension of neuronal leading processes but instead disrupts nucleokinesis – the process by which the nucleus translocates forward during migration. These and other findings suggest that cadherin-mediated signalling to the cytoskeleton is crucial for radial migration in the neocortex.
Germ cell migration: as easy as ABC?
The development of the Drosophila embryonic gonad requires the migration of primordial germ cells (PGCs) towards somatic gonadal precursors (SGPs). Previous studies have implicated a role for the ATP-binding cassette (ABC) transporter Mdr49 during this event, suggesting that it functions in the export of a PGC attractant. Here, Girish Deshpande and co-workers further explore the function of Mdr49 in flies (p. 2111). They report that Mdr49 mutant embryos exhibit PGC migration defects but that these can be alleviated by a cholesterol-rich diet. Given that cholesterol is known to be involved in Hedgehog (Hh) precursor protein processing, the authors explore the potential link between Hh signalling and PGC migration. Their studies demonstrate genetic interactions between Mdr49 and genes encoding Hh pathway components, both during PGC migration and wing development. Importantly, the authors reveal that Hh release from hh-expressing cells is compromised in Mdr49 mutant embryos. Overall, these findings highlight a role for Mdr49 in the Hh pathway and lead the authors to propose that Mdr49 functions to allow SGPs to produce sufficient amounts of processed Hh that, in turn, signals to guide migrating PGCs.
PLUS…
Ten years of induced pluripotency: from basic mechanisms to therapeutic applications
Ten years ago, the discovery that mature somatic cells could be reprogrammed into induced pluripotent stem cells (iPSCs) redefined the stem cell field and brought about a wealth of opportunities for both basic research and clinical applications. To celebrate the tenth anniversary of the discovery, the International Society for Stem Cell Research (ISSCR) and Center for iPS Cell Research and Application (CiRA), Kyoto University, together held the symposium ‘Pluripotency: From Basic Science to Therapeutic Applications’ in Kyoto, Japan. Here, Peter Karagiannis andKoji Etosummarize the main findings reported as well as the enormous potential that iPSCs hold for the future. See the Meeting Review on p. 2039
Phosphoinositide signaling in plant development
The membranes of eukaryotic cells create hydrophobic barriers that control substance and information exchange between the inside and outside of cells and between cellular compartments. Besides their roles as membrane building blocks, some membrane lipids, such as phosphoinositides (PIs), also exert regulatory effects. Indeed, emerging evidence indicates that PIs play crucial roles in controlling polarity and growth in plants. Here, Ingo Heilmann highlights the key roles of PIs as important regulatory membrane lipids in plant development and function. See the Primer article on p. 2044
Extracellular matrix motion and early morphogenesis
For over a century, embryologists who studied cellular motion in early amniotes generally assumed that morphogenetic movement reflected migration relative to a static extracellular matrix (ECM) scaffold. However, as Charles Little and colleagues discuss here, recent investigations reveal that the ECM is also moving during morphogenesis. See the Review article on p. 2056
We have money from our grant to fund a PhD studentship including fees. But there is only a little time left to apply, so if you are interested in our project please look at this advertisement
Alexa Burger, Mosimann lab, Institute of Molecular Life Sciences, University of Zürich, Switzerland.
When I first heard about the “new” genome editing method in early 2013 called CRISPR-Cas9, I thought: “Never ever again will I work with targeted nucleases!” Now it’s mid-2016, we published our approaches to maximize Cas9 effectiveness in zebrafish with Development (Burger et al. 2016), and I happily changed my take to: “Never ever have I seen a system work better than this!” But in all earnest, it was a long (and sometimes bumpy) journey to establish CRISPR-Cas9 in our zebrafish laboratory with its current efficiency and wide-spread applicability. In this blog post, I want to share with you some of our experiences with this method especially for those who are still struggling with getting CRISPR-Cas9 set up in their lab. I want to encourage you to continue working on it – it will work eventually, and we had encountered every possible and impossible problem along the way!
By now, you must have heard of CRISPR-Cas9 for genome editing. In this system, the endonuclease Cas9 is guided to its target location via a short guide RNA (sgRNA or just gRNA, which is the part modified from the original CRISPR repeats) that binds 20 bp of complementary sequence in the genome with its 5’ end and is bound by Cas9 on its 3’ end. By forming this ribonucleoprotein complex (RNP), Cas9 can efficiently cut DNA at your desired locus in the genome of your preferred model organism.
In Spring 2013, I had just moved with my family to Zurich, Switzerland. I had been a postdoc at Massachusetts General Hospital Cancer Center in Boston; as part of the larger Harvard Medical School, I experienced both myself and through collaborators and friends all the ups and downs of using the more complex zincfinger nucleases and later TALENs in zebrafish (so I hope you will relate to my first reaction when hearing about yet another nuclease-based gene editing toy!). Jonas Zaugg, who performed his master thesis in the Mosimann lab, and myself first started looking into CRISPR-Cas9 in autumn 2013 to generate first mutants. As other approaches published at the time (Chang et al., 2013; Hwang et al., 2013; Jao et al., 2013), we injected in vitro-made, capped Cas9 mRNA together with one of the published gRNAs for the zebrafish gene scl24a5, mutants of which are called “golden” due to their resulting yellow-ish pigmentation (Lamason et al., 2005). To be honest, we initially obtained rather lousy results, struggled with the long Cas9 mRNA and the tiny sgRNAs, and I thought to myself “here we go again…”.
Our genome editing game changed completely once we teamed up with Martin Jinek’s laboratory: Martin had done key work on the Cas9 protein itself during his postdoc in Jennifer Doudna’s laboratory at Berkley (Jinek et al., 2012; Jinek et al., 2013), and he had started his lab on-campus around the same time as our PI Christian Mosimann. The two PIs met at a lunch event, and started chatting about their mutual interest in electric string instruments and science. This led to Martin and his graduate student Carolin Anders dropping by our lab with a liquid nitrogen container containing small tubes of (what we call) crystal-grade Cas9 protein that was either GFP- or mCherry-tagged.
Previous accounts of Cas9 protein use in zebrafish were highly encouraging (Gagnon et al., 2014). Using Carolin and Martin’s input on how they treated Cas9-sgRNA complexes in vitro and for structure analysis, we assembled 850-1000 nanograms per microliter of Cas9 with sgRNA into ready-to-use RNP complexes (mixing and incubating at 37°C for 5min, then kept at room temperature) and injected those into zebrafish embryos. A key ingredient turned out to be sufficient KCl salt to keep Cas9 happy with at least 300mM. As documented in our paper, leaving out this crucial step causes the Cas9 RNPs to clump up quickly in the injection needle, so we highly recommend checking for sufficient salt in your final injection mix! The resulting solubilization is applicable to any Cas9 source and should also work with commercial protein stocks (given it is sufficiently concentrated and has an NLS, which is not always the case…).
The subsequent first experiments were, in retrospect, quite funny. We attempted to mutagenize EGFP, which we have abundantly available in our lab’s many transgenics. After the first EGFP targeting injection into homozygous ubi:EGFP embryos, we didn’t see any fluorescence in the embryos the next day. Thinking we messed up the cross, we repeated the experiment and this time we kept some uninjected controls – these were glowing green as usual the next day, but almost none of the Cas9 RNP-injected embryos showed any fluorescence. That’s when it dawned to us that we had mutated the EGFP ORF with such efficiency that there was no functional EGFP protein whatsoever.
Instantly, we could see the difference in all our other CRISPR-Cas9 targeting using our new tricks. And what a difference that was! From about 5 percent (tops) with Cas9 mRNA to up to 100 percent mutagenesis efficiency with the RNPs. We went on to scrutinize every single step in our sgRNA production, injection protocols, genotyping procedures, etc. Along the way, we made all the mistakes one can make: degraded RNA due to dirty pipettes, wrong storage of Cas9 protein stocks, wrong primer sequences ordered (beware of the reverse-complement!), miscalculated injection mixes…the list goes on. All this was topped in the sheer load of sequences we accumulated of targeted loci that we initially needed to analyze by hand. Another key enemy became the frequent single-nucleotide polymorphisms (SNPs) in the zebrafish genome: single SNPs in a 20bp stretch for sgRNA targeting usually abolishes all detectable mutagenesis in our hands, so we frequently sequence targeted loci before injections.
As a lab, we got together and defined some ground rules for our mutagenesis work. We developed the policy to test every new sgRNA on a denaturing MOPS gel. We asked our bioinformatics collaborators in Mark Robinson’s lab next door to code a simple online interface to calculate injection mixes that Lukas Weber coined CrispantCal, which Raul Catena subsequently also turned into a smart phone app. We developed a cloning- and purification-free sequence verification strategy for routine mutagenesis analysis and collected samples for a massive deep-sequencing verification of 40+ loci.
Most importantly, Helen Lindsay from the Robinson lab developed the R-based software tool CrispRVariants for rapid sequence analysis of mutation events (Lindsay et al., in press; preprint at http://biorxiv.org/content/early/2016/03/10/034140). In simple terms, CrispRVariants uses a smart procedure to align sequence results to the intended target locus and performs a base-by-base comparison to the wildtype reference sequence. Paired with sequence counts, CrispRVariants spits out so-called panel plots that visualize the mutagenesis results with allele details. Continuously refined through our day-to-day experiences, these panel plots became a daily discussion point in the lab as we now had a standardized visualization of mutagenesis events – and we hope the online version CrispRVariantsLite will help also you to easily grasp your mutation spectra!
Cas9 RNP-injected zebrafish crispant targeting slc24a5 (golden) on the left, wildtype sibling on the right, and CrispRVariants panel plot depicting the somatic mutant alleles resulting from Cas9 mutagenesis below.
CrispRVariants-based analysis rapidly corroborated that our new protocols achieved exceedingly high mutagenesis efficiencies, reaching even complete biallelic mutagenesis in individual zebrafish embryos. We also started to see previously described loss-of-function phenotypes in injected F0 embryos: we call such Cas9-based somatic mutants “crispants” in analogy to morpholino-injected embryos referred to as morphants. While we do frequently use crispants to figure out if a candidate gene is interesting enough to follow-up as stable mutant in the course of our lab’s work on mesoderm cell fates, we quickly became cautious about using this approach for actual loss-of-function analysis: sequence analysis revealed that most mutated loci have a high propensity to be repaired in a stereotypic set of alleles, including in-frame alleles or even other still functional alleles possibly involving also clonal selection during development. Such effects paired with still variable mutagenesis efficiency make crispant phenotypes for most genes too variable for reproducible, reliable phenotype studies, but nonetheless allow a first glance at the full-blown loss-of-function phenotype. We are harnessing this effect now for limited candidate gene screens for novel cardiovascular regulators and tumor modifiers, and (if space permits!) we alwaysgenerate stable germline mutants for each gene with interesting phenotypes. So beyond tool development, the focus of our endeavors was to be able to probe for new, exciting biology, and we are all enthusiastically applying our new tools to our individual projects.
But keep in mind: realistically, how often do you really need complete mutagenesis? High mutation load in injected animals can perturb their proper development, and you consequently never get adult founders. More important is that, once the Cas9 RNP mutagenesis is optimized, the injections can be titrated to allow for proper development and subsequent screening of germline transmission.
Crispant for tbx5a in triple-fluorescent transgenic reporter background, featuring the typical cardiac and pectoral fin phenotypes found in tbx5a (heartstrings) germline mutants (picture by Elena Chiavacci).
My favorite part of this journey was the collaborative work with protein biochemists, biostatisticians, and our lab’s creative team of biologists. Several spin-off projects have developed and are ongoing in the lab, and we have instructed several outside collaborators in our techniques with hands-on demos during lab visits. Technically, our protocols should be directly applicable to any model organism that allows for injection-based delivery of Cas9 RNPs. In the end however, all comes down to understanding your genetics: once the mutagenesis works, you need to be fluent in the language of classic genetics and quirks such as maternal contribution, phenotype expressivity vs penetrance, hypomorphs, etc. CRISPR-Cas9 is only the beginning. Happy crispring!
Burger, A., Lindsay, H., Felker, A., Hess, C., Anders, C., Chiavacci, E., Zaugg, J., Weber, L. M., Catena, R., Jinek, M., et al. (2016). Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 2016 143: 2025-2037.
Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., Xiong, J.-W. W. and Xi, J. J. (2013). Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res23, 465–472.
Gagnon, J. A., Valen, E., Thyme, S. B., Huang, P., Ahkmetova, L., Pauli, A., Montague, T. G., Zimmerman, S., Richter, C. and Schier, A. F. (2014). Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One9, e98186.
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J. R. and Joung, J. K. (2013). Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol31, 227–229.
Jao, L.-E., Wente, S. R. and Chen, W. (2013). Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. U. S. A.110, 13904–9.
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A. and Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (80-. ).337, 816–821.
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E. and Doudna, J. (2013). RNA-programmed genome editing in human cells. Elife2, e00471.
Lamason, R. L., Mohideen, M.-A. P. K., Mest, J. R., Wong, A. C., Norton, H. L., Aros, M. C., Jurynec, M. J., Mao, X., Humphreville, V. R., Humbert, J. E., et al. (2005). SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science310, 1782–6.
Lindsay, H., Burger, A., Felker, A., Hess, C., Zaugg, J., Chiavacci, E., Anders, C., Jinek, M., Mosimann, C. and Robinson, M. D. (2015). CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments. Cold Spring Harbor Labs Journals. http://biorxiv.org/content/early/2016/03/10/034140
Maintaining genome integrity of adult stem cells is important to prevent cancer initiation and stem cell functional decline during aging. Our recent work (Siudeja, Cell Stem Cell, 2015) has demonstrated that a surprising level of genome instability arises during aging in adult intestinal stem cells of Drosophila. Mechanistically, this is caused by frequent loss of heterozygosity due to mitotic recombination as well as gene inactivation through deletion and complex chromosome rearrangements leading to tumor suppressor inactivation. This model provides an excellent system in which to address important fundamental questions of how stem cell genomes are maintained. The postdoctoral project will further investigate the causes and consequences of stem cell genome instability using Drosophila genetics and whole-genome sequencing approaches.
We are seeking enthusiastic, collaborative, and highly motivated post-doctoral candidates with good Ph.D. track records. Both biologists and bioinformaticians are welcome to apply. Experience in genetics and/or whole-genome NGS sequencing analysis would be appreciated.
Our team is situated within a new, dynamic, international department with state-of-the-art imaging, sequencing, and proteomics facilities at the Institut Curie in the heart of downtown Paris. To apply, please send your CV, cover letter, and names of two references to allison.bardin@curie.fr.
The Zika virus is making headlines as a major world health crisis linked to a host of neurological conditions. In the cases of microcephaly and Guillain-Barre, the evidence that Zika Virus is the root of the condition is strong enough to be considered causal. Babies born to infected mothers often have microcephaly, a condition that manifests in smaller than average head size and brain development. According to the most recent estimate, the babies of pregnant women infected in the first trimester have between a 1 and 13 percent risk of microcephaly. Guillain-Barre, a condition that can affect infected individuals themselves, is a disorder where a person’s immune cells attack his or her nerve cells. The list of neurological conditions potentially caused by Zika Virus infection doesn’t stop there: there have been case reports of other brain and spinal cord infections .
A new study examines the Zika infection in the brain on a cellular level. Xuyu Qian and his team at John’s Hopkins University used a 3D model of part of the brain to get a more accurate idea of how and where Zika infection occurs in brain. Their results indicated Zika infects a specific type of brain cell.
Until recently, researchers studied cells in the lab in a flat layer on a dish. However, this method did not provide an accurate representation of the complex 3D systems inside our bodies and the bodies of other organisms. Mini-organs, or organoids in scientific jargon, are 3D models of various organs that have burst onto the research scene in the past several years. To study Zika’s effect on the brain, the researchers made mini-brains, specifically modelling the part of the brain called the ‘forebrain.’ They created this mini-brain using ‘human induced pluripotent stem cells,’ which are cells reversed back into stem cell state from adult cells.
As our brains mature, cells specify from stem cells, with stages in between, to specific types of brain cells. On this route to specification, there is a middle step called ‘neural progenitor cells.’ Qian and his colleagues’ research showed that Zika infects these neural progenitor cells more than other types.
The image above shows a mini-brain that corresponds to the first trimester of human fetal development. The image on the left is the mini-brain not infected with the Zika virus and it shows the normal defined stripes, or layers of cells. On the right it the Zika-infected mini-brain, overall loss of structure, quantified by the researchers as reduced thickness of layers.
Using a 3D as opposed to a 2D model is specifically important for studying Zika in the brain because it allows us to see the effect of the virus on properties such as the formation of layers of cells, as well as the tendency to infect certain types of brain cells.
Postdoc and PhD positions are currently available in the Gouti Lab at Max Delbrück Centre for Molecular Medicine in the Helmholtz Association (MDC), Berlin.
The Gouti lab uses human and mouse pluripotent stem cells to model embryo development in vitro and unravel the mechanisms that regulate cell fate decisions during neuromuscular system development. During embryonic development spinal cord motor neurons are generated with high precision along the anterior-posterior (AP) axis and establish connections with skeletal muscles to control movement. We seek to understand how these two tissues are generated and interact in space and time during neuromuscular system development.
We have recently succeeded in generating neuromesodermal progenitors (NMP) cells in vitro from mouse and human pluripotent stem cells that can be further differentiated to spinal cord neurons and/or muscle cells. The in vitro generation of NMP cells opens up new opportunities for the study and treatment of neuromuscular diseases as it gives unprecedented access to the simultaneous development of both neural and mesodermal cell types in the “dish” (Gouti et al, Plos Biology 2014; Gouti et al, Trends Genet, 2015;).
We are looking for highly motivated, talented Postdoctoral fellows and Ph.D students to contribute to the research area of neuromuscular system development and disease. Our lab uses, stem cell modeling in parallel with genetic engineering techniques (Crispr/Cas9), next generation sequencing (single cell RNA-seq, ChiP-seq) and live cell imaging.
The MDC provides a state of the art human iPS cell core facility and the opportunity to work in an interdisciplinary environment of research excellence. The Gouti Lab is actively involved in iMed, which includes five other Helmholtz centers in the Research Field Health besides the MDC. The program aims to interlink and coordinate the research activities of the centers in the field of personalized medicine and, through collaboration with local clinical partners, to promote the rapid transfer of research results into clinical practice.
For the Ph.D. positions interested applicants are encouraged to apply through the MDC Ph.D. program. The deadline for the current open Ph.D. call is 1st of July. For more information please visit : Ph.D at MDC
For the Postdoc positions, interested applicants should have previous experience in stem cell biology, muscle biology, developmental biology, live cell imaging and/ or analysis of high-throughput data. Strong publication record and ability to communicate research findings in English are essential.
To apply for a postdoc position, please send a letter of scientific interest along with your CV, publication list and contact information of 2 -3 referees to Mina Gouti (mina.gouti@mdc-berlin.de.). Closing date : 31st of August
This post was originally published as a Newsletter article from ShARM (Shared Ageing Research Models)
Scientists using animals in research have a responsibility to ensure that the studies are appropriately designed, conducted, analysed and reported so that they impartially and robustly answer the question they are intended to, and truly add to the knowledge base. Unfortunately there is a large body of evidence, including from the NC3Rs, to show that many animal studies are flawed and that this has significant implications in terms of reproducibility and the translation of findings into potential clinical benefits.
At the NC3Rs we have developed a new exciting online tool which is designed to tackle the problem – the Experimental Design Assistant (EDA).
The EDA is an online resource to help researchers improve the design and analysis of animal experiments. It complements the ARRIVE guidelines for reporting animal research and was developed in collaboration with an expert working group of in vivo scientists and statisticians from academia and industry, and Certus Technology, a team of software designers specialised in innovative software for the life sciences.
The resource is aimed at scientists who use animals in their research. Benefits include advice and feedback on the experimental plans, along with a range of functionalities providing support with the randomisation and blinding of the experiment, as well as sample size calculation. It equips researchers with practical information and knowledge, allowing them to determine the most efficient design for their experiment and understand the implications of choosing a particular design.
A central feature of the EDA is the use of a formal, diagrammatic notation to describe experimental plans and analyses. This is an approach that has been adopted by many technical disciplines to improve communications. It allows the design of an experiment to be recorded clearly and unambiguously and EDA diagrams help convey experimental plans efficiently.
The EDA is not designed to replace specialist statistical advice. For researchers who have limited access to statistical support, the feedback and advice provided by the system will be particularly pertinent, as it will provide users with information, which is specific to the experiment they are planning. For all scientists involved in the research process, the EDA is also extremely useful as a communication tool, for example, between students and their supervisors, or with colleagues and collaborators. These visual representations are far more explicit than the cursory text description traditionally included in grant applications, ethical review submissions or journal publications. Our goal is to integrate the EDA into the scientific process to facilitate better peer review of experimental plans.
We look forward to hearing what you think about the EDA. The feedback has been fantastic but this is a very new and novel system, which has to evolve according to the needs of the research community. Please contact us at eda@nc3rs.org.uk, your feedback will help us ensure that the system improves and evolves according to your needs.
We know that cells are the building blocks of our bodies. But they are not like inert wooden blocks. They are complicated tiny machines that communicate with each other to make sure that the many simultaneously occurring processes in our bodies are in order.
Stem cells participate in many of these cellular conversations, and a particularly important dialogue is the one that turns certain stem cells into specific types of cells, while keeping others in stem cell state. Retaining stem cells ensures that our bodies can fix the wear and tear of our organs and tissues in future.
So how exactly do cells talk to each other? They send signals using molecules. Setting up a gradient of a certain molecule is one way cells send signals. With many molecules on the surface of cells in one area, and gradually less molecule across space, cells can receive a range of different messages depending on the density of the molecule.
Researchers from the Hubrecht Institute in Utrecht and UMC Utrecht visualized stem cell signaling in the gut for the first time. Their question was how one of the main growth signals in the gut sets up a gradient.
The image above shows a part of this mini-gut called the crypt, which are the protrusions that give our guts high surface area to allow absorption of nutrients. In panel A, the protrusions are allowed to grow normally. In panels B, C and D, the signal that allows the cells to divide and form the gradient is blocked. Since the signal can’t spread the protrusion can’t grow.
Learning how stem cells signal is important for developing methods to help our bodies regenerate, and to stop this process when it goes awry in the formation of tumours.
Farin, H. F., Jordens, I., Mosa, M. H., Basak, O., Korving, J., Tauriello, D. V., … & Clevers, H. (2016). Visualization of a short-range Wnt gradient in the intestinal stem-cell niche. Nature.
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Ten years ago, the discovery that mature somatic cells could be reprogrammed into induced pluripotent stem cells (iPSCs) redefined the stem cell field and brought about a wealth of opportunities for both basic research and clinical applications. To celebrate the tenth anniversary of the discovery, the International Society for Stem Cell Research (ISSCR) and Center for iPS Cell Research and Application (CiRA), Kyoto University, together held the symposium ‘Pluripotency: From Basic Science to Therapeutic Applications’ in Kyoto, Japan. Here, 
The membranes of eukaryotic cells create hydrophobic barriers that control substance and information exchange between the inside and outside of cells and between cellular compartments. Besides their roles as membrane building blocks, some membrane lipids, such as phosphoinositides (PIs), also exert regulatory effects. Indeed, emerging evidence indicates that PIs play crucial roles in controlling polarity and growth in plants. Here, Ingo Heilmann highlights the key roles of PIs as important regulatory membrane lipids in plant development and function. See the Primer article on p. 
For over a century, embryologists who studied cellular motion in early amniotes generally assumed that morphogenetic movement reflected migration relative to a static extracellular matrix (ECM) scaffold. However, as Charles Little and colleagues discuss here, recent investigations reveal that the ECM is also moving during morphogenesis. See the Review article on p. 
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