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Developing Future Biologists (DFB) is a student-led organization at University of Michigan dedicated to ensure that the next generation of biologists regardless of race, gender, or socioeconomic status have the opportunity to learn the core concepts of developmental biology. During the last week of May, DFB held its 2^nd successful week-long short course aiming to inform students from diverse backgrounds about developmental biology and career opportunities in science.

DFB is a graduate student-founded and led initiative that seeks to introduce the core concepts of developmental biology to students from a diverse set of backgrounds. The idea of bringing this course to Puerto Rico was conceived by a former University of Michigan (UM) graduate student, Andrea Ramos, who attended the University Puerto Rico at Ponce for her undergraduate studies. With four additional UM graduate students and three faculty members planning began and within a year the first iteration of DFB was held in Ponce.

This year, thanks to funding from sources such as The Society for Developmental Biology and a number of sources at the University of Michigan, the course was able to extend its reach to undergraduate students from different campuses of the University of Puerto Rico across the island. Throughout the week, 24 Puerto Rican undergraduate students were exposed to various key topics in developmental biology through lectures and hands on lab activities using different model organisms and research techniques.

Our developmental biology course is designed to ensure that students understand how an organism develops from a single cell to a fully developed organism, and what happens when developmental processes are disrupted. During the week we covered topics such as: vertebrate embryogenesis, cell signaling, gene expression, organogenesis, and developmental defects. The lectures led by UM faculty and laboratory sessions led by UM graduate students are highly interactive in order to capture the interest and enthusiasm of the students. For example, the gene expression lecture included a Wnt dance and labs included activities ranging from staging Xenopus embryos to observing limb structures in various mouse mutants.

Learning about developmental biology was however only half of what we aimed to achieve. Another component of our program is based in establishing long term mentoring relationships with the students to help them learn about careers and educational opportunities in science. This year students were also able to attend sessions on career development topics including mock interviewing, a CV workshop, a panel discussion on grad school, and a session on presentation design. In addition, to these informative sessions, there were also several social events throughout the week, such as an ice cream social, and a bowling night, where the graduate student instructors from UM and the DFB students could network.

Currently the mentoring from both the first and second iterations of DFB has continued, with some students already inquiring about application formatting and some alumni from the first DFB attending summer programs at various school in the states including UM. In the future, DFB aims to organize a local iteration of the course in the Detroit and at other institutions with underrepresented minorities. The group further aspires to continue having the weeklong course at the end of May in Puerto Rico.

However, whatever the future of DFB, one thing is for certain: the memories and excitement made thought the week will never be forgotten, and lives on through the mentoring and networking that is still ongoing between the DFB alumni and the graduate student instructor of the course.

Article Contributors: Eden A. Dulka, Martha Echevarria Andino, Samhitha Raj, & David Lorberbaum of the 2016 DFB Team

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My name is Martin Minařík and I am a PhD student in Robert Cerny’s lab at Charles University in Prague, Czech Republic. Our lab focuses mostly on the development of non-teleost fishes, namely bichirs, sturgeons, and gars. The advantage of having these animals as model organisms is that their breeding seasons alternate throughout the year, so that we can always focus on one species at a time. Thus, while bichirs and sturgeons keep us busy during winter and spring, respectively, the gar season spans throughout the summer.

Unlike zebrafish and medaka, gars did not undergo the teleost-specific genome duplication, rendering them a suitable model for approximating the ancestral ray-finned genome. The same holds true for a variety of phenotypic traits that have been lost in teleosts, ranging from the amphibian-like mode of gastrulation through the thick, enamel-covered ganoid scales to the asymmetric tailfin. Recent years have therefore seen a revival of gar research, with the genome of the spotted gar (Lepisosteus oculatus) being available since 2011. While the spotted gar is reasonably accessible both in the wild and in the pet trade, it has rather slow generation time with females starting to spawn in their fourth year of life. The tropical gar (Atractosteus tropicus), on the other hand, reaches sexual maturity within the first (males) or second (females) year. Moreover, for some reason the tropical gar meat is popular in one particular place in the world – the swampy state of Tabasco, Mexico. The local aquaculture facilities produce millions of eggs each year to sustain the wild stocks thriving in the lakes around the city of Villahermosa, making it the ideal place to reach vast quantities of embryos suitable for wide variety of experiments.

The fact that gars are being bred down in the Mexican tropics is a mixed blessing. Of course travelling each summer to the land of cocoa and iguanas is extremely exciting for a Central European. On the other hand, it brings some difficulties, too. The first is the working temperature, with the spawning room heated up to 40°C. It gets better in the lab, where the temperature is set to 28°C, which represents a compromise between the long-term survival of the researcher and the embryos.

The typical day starts in the hatchery by injecting the fishes with hormones. Once spawning behaviour is detected in females, they have to be anaesthetized and spawned manually to avoid releasing the adhesive eggs to the artificial vegetation. It means that sometimes we have to wake up every hour or two during the following night and check the tanks. This gets particularly annoying at the beginning of rainy season, as the ten-metre passage from the lab building to the hatchery is enough to turn your skin into a mosquito banquet. Nowadays this is especially unpleasant, with dengue, chikungunya and zika hiding in mosquitoes’ salivary glands (a thick layer of repellent helps, but one has to be careful to not contaminate the tanks).

Once we get the embryos, the work paces up. We have 24 hours until the neurula stage; the experiments have to be set up and the embryos dechorionated, which is kind of tricky in this fish. The outer membrane is soft and sticky, and it tends to bend inwards when broken so that it adheres to the embryo and tears it apart. To prevent this, one can steal some dried milk from the office and wash the eggs in a milky water to saturate the adhesive layer. Lenin, the lab PI, helps us a lot to get things ready on time. The easiest thing to do in a lab which is not equipped for a serious embryological work is to soak the embryos in selected inhibitors of key signalling pathways. They can also be easily injected with cell tracking dyes – there is no need for micromanipulator as the eggs are double the diameter of Xenopus’s. But if you are loading your needle from a drop of DiI in a saccharose solution, be careful to prevent ants from finding it. The smallest ones, called lelitas in Villahermosa, are difficult to notice, but when they spot the piece of parafilm, they immediately form a swarming highway to the sweet, fluorescent drop. You can run out of your cell tracking dye really quickly this way!

For someone who is used to working with teleosts, the gar eggs are really different and fascinating. The embryo is sitting on a huge, empty archenteric cavity, which you can easily inject and visualise, simply with pen ink to start with. Soon it starts to develop prominent attachment glands which the larvae use to adhere to the surface of the water. They tend to aggregate in thousands, forming rafts in the tanks spanning tens of centimeters in diameter – it might sound counterintuitive, but their yolk is fairly poisonous so the clusters of larvae are probably less tempting for predators than it might seem at first glance. As the development proceeds, they grow large opercula, which make them look like tiny umbrellas. Living in extremely warm waters low in oxygen, they use this to generate a flow of water to the gills.

The adult gars are kept in outdoor tanks together with tilapias on which they feed occasionally. The largest tilapias, however, are too big for them to catch, so from time to time it is necessary to eliminate them. The best way apparently is to make a tilapia barbecue. With loads of chilli and limes, of course. Meanwhile, our embryos develop to the desired stage. Thanks to the high temperatures it takes only four days until they hatch in the lab, or two days in the hatchery, respectively. Unfortunately, we have to wait with the analyses until we get back to Prague with our samples, so it might be hard to adjust the experiments sometimes, as we can only have a superficial look at the results in the aquaculture lab. However, working in tropical gar in the middle of Mexican swamps is indeed worth all the difficulties.

Finding ways to combine the study of gar embryology with the culture of keeping this traditional fish species in Mexican aquaculture might be challenging sometimes, but the exchange of skills and ideas is beneficial for both parties. It is so refreshing to get out of the lab in Prague and jump into the warm fish tanks in Villahermosa to catch fishes for your own experiments! And as the collaboration tightens, we have also our first Mexican students visiting Prague, using sturgeon embryos to adopt techniques they could later use in their own gar projects. So hopefully this intercultural and interspecific enrichment will successfully continue.

The whole process of the artificial fertilization in the Mexican gar in two minutes.

This post is part of a series on a day in the life of developmental biology labs working on different model organisms. You can read the introduction to the series here and read other posts in this series here.

(15 votes)

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Epithelial Cell and Developmental Biology – Mechanotransduction at tight junctions

Applications are invited for the posts of two postdoctoral research fellows. One will be based in the Laboratory for Epithelial Cell Biology (with Karl Matter and Maria Balda) of the UCL Institute of Ophthalmology and the other in the Zebrafish Group of the Department of Cell & Developmental Biology (with Masazumi Tada).

The successful applicants will join a collaborative research programme that focuses on the role of mechanotransduction at epithelial tight junctions in epithelial differentiation and dynamics, and early development. The aim is to analyze the molecular mechanisms of how tension at tight junctions is transmitted between adhesion proteins and the cytoskeleton, and the roles such processes play during epithelial cell dynamics and differentiation in vitro and during zebrafish gastrulation. (J Cell Biol 208, 821-838, 2015; J Cell Biol 204, 111-127, 2014; Nat Cell Biol 13, 150-166, 2011; Development 136, 383-392, 2009; Development 139, 3897-3904, 2012; Nat Rev Mol Cell Biol 2016).

The positions are funded by the BBSRC and require a PhD in Cell/Molecular/ Developmental Biology, Biophysics, or another related discipline. The persons appointed will have experience in developmental biology, biophysical approaches, molecular cell biology and/or advanced microscopy. Good communication skills and interest in collaborative research are essential.

Informal enquiries about the posts may be made to Karl Matter (email: k.matter@ucl.ac.uk) or Masazumi Tada (m.tada@ucl.ac.uk).
Applications can be be submitted at:
http://www.ucl.ac.uk/hr/jobs/
Ref No: 1559085 and 1557441
Closing date: July 15, 2016

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” the ability to reproduce experimental findings remains essential for the forward movement of science and the application of laboratory findings to the clinic”

This is an extract from a Special Article article that originally appeared in Disease Models and Mechanisms (available here Open Access)

Paul Schofield, Jerrold Ward, John P. Sundberg

Reproducibility of data from experimental investigations using animal models is increasingly under scrutiny because of the potentially negative impact of poor reproducibility on the translation of basic research. Histopathology is a key tool in biomedical research, in particular for the phenotyping of animal models to provide insights into the pathobiology of diseases. Failure to disclose and share crucial histopathological experimental details compromises the validity of the review process and reliability of the conclusions. We discuss factors that affect the interpretation and validation of histopathology data in publications and the importance of making these data accessible to promote replicability in research.

Reproducibility: an age-old quest

“A good physiological experiment … requires that it should present anywhere, at any time, under identical conditions, the same certain and unequivocal phenomena that can always be confirmed.” –

Johannes Peter Müller, German physiologist and comparative anatomist (1801-1858).

Illustrated by this quote from Müller, a formal concept of reproducibility existed even in the beginnings of modern experimental biology. Today, the ability to reproduce experimental findings remains essential for the forward movement of science and the application of laboratory findings to the clinic.

There has been much discussion in recent years about the reported irreproducibility of preclinical data obtained using animal models (Begley and Ioannidis, 2015; Collins and Tabak, 2014; Freedman et al., 2015; Mak et al., 2014) and the cost to the success of both translational research and the public purse. The inability to replicate drug-target discovery studies and to reliably replicate phenotype observations from the literature (Begley and Ellis, 2012) has caused profound concern amongst investigators and funding agencies alike, which has been mirrored in discussions and commentaries in the literature. Several issues are tied up inextricably in these discussions. Reproducibility depends first and foremost on the accurate and comprehensive reporting of key experimental procedures and conditions, but it also depends on the open availability of the data, protocols and reagents (Schofield et al., 2009). Both aspects of reproducibility are crucial, and require distinct solutions.

Read the rest here:  http://dmm.biologists.org/content/9/6/601

(2 votes)

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Applications are invited for a senior research staff position and a postdoc position in the Department of Molecular Evolution and Development at University of Vienna. Both are supported by the European Research Council (ERC) grant lasting for five years, and planned for at least two years starting from August 1^st, 2016 with possible renewal. The successful applicants will work on the epigenomic evolution of Drosophila sex chromosomes. We will be using Drosophila species with recently born sex chromosome (‘neo-sex’) systems to address: How does the Y chromosome become heterochromatic? How does this universal evolution process drive the adaptation of small RNA defense systems? And how does such a male-specific arms race between parasitic transposable elements and small RNAs fuel the changes of the female genome? The candidates are expected to be independent and highly motivated, and are required to have a Ph.D. in molecular biology, genetics or other related fields. Essential qualifications include demonstrated experience in Drosophila transgenics, CRISPR/Cas9 mutagenesis, in situ hybridization, next-gen sequencing library preparation (RNA-seq, ChIP-seq & CLIP-seq). Knowledge and skills in bioinformatics (Unix, perl/python programming etc.) and next-gen sequencing data analyses (genome assembly and annotation, ChIP-seq and RNA-seq data analyses) are desirable but not mandatory. The senior staff is required to have at least 8 years’ postdoctoral research experience.

Successful applicants will receive very competitive salary (staff: €70k/year, postdoc: €64k/year) and benefits, most importantly enjoy the diverse and vibrant research environment of the Department and the University. The group members will have frequent interactions with other neighbor labs of Drosophila neurobiology (Prof. Thomas Hummel) and developmental biology (Prof. Ulrich Technau), and have a chance to develop collaborative research projects. The university is located near the city center of Vienna, which houses numerous other world’s leading research institutes including Gregor Mendel Institute, Institute of Molecular Biotechnology and Institute of Science and Technology. The city has been attracting many outstanding scientists with well-established network in evolutionary biology (http://www.univie.ac.at/evolvienna/?page_id=6), RNA biology (http://www.mfpl.ac.at/rna-biology/) and there is an encouraging plan to move the biology departments of the University near other institutes of Vienna Biocenter to form a research cluster. Vienna has been voted as the world’s most livable city for the seventh time, and is famous for its history and culture, and now also a modern and international lifestyle. Interested candidates please send her/his CV and contact information of three referees to Dr. Qi Zhou (muntjaczhou@gmail.com). We will start reviewing the application immediately until the position is filled.

Qi Zhou, Ph.D.

http://zhqkiz.wix.com/zhouqi

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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

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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!

Aidan

(Follow us @the_Node, and me personally @flatbrained)

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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 and Koji 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

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