Here are the highlights from the current issue of Development:

Eye’s got rhythm

In zebrafish, the circadian clock, which is the internal timekeeper that coordinates multiple cellular, physiological and behavioural processes with the external rhythmic environment, begins cycling very early in development. However, the functional relevance for embryonic and larval development of these early circadian oscillations is unclear. Here (p. 2644), Ricardo Laranjeiro and David Whitmore find that a number of important developmental regulators show rhythmic expression in a manner consistent with circadian regulation. In particular, they uncover strong circadian expression of the neural transcription factor Neurod, whose levels oscillate specifically in the photoreceptor layer of the retina. They further show that a number of other key regulators of retinal photoreceptor differentiation oscillate, but only after differentiation itself is essentially complete, implying that this rhythmic expression is unrelated to the known functions of these factors in cell fate specification. Instead, the authors propose that certain components of the phototransduction pathway – which also show cyclic expression – may be controlled by these developmental transcriptional regulators, suggesting an intriguing interplay between the circadian clock and key regulators of retinal differentiation and function.

Keeping dendrites in check

A key question in developmental biology is how different tissues maintain proportional growth during development. A striking example of this is the tiling of sensory dendrites across the body wall of theDrosophila larva: during early larval life, the neuronal dendrites extend to cover the entire body wall, without overlapping. As the larva grows further, tiling is maintained – meaning that the dendrites and the overlying epithelium grow proportionally (dendrite-substrate coupling). On p. 2657 Jay Parrish and colleagues investigate the mechanistic basis of this coupling, finding that the microRNA bantam (which they previously showed to be required in the epithelial body wall for proper scaling) regulates endoreplication of these epithelial cells. Inhibiting endoreplication by multiple means disrupts dendrite-substrate coupling such that dendrites overgrow. Moreover, they show that integrin expression in the epithelium is controlled by bantam and other regulators of endoreplication, and is in turn important for appropriate dendrite-epithelial contacts to be made and maintained for proportional growth. Thus, by coordinating cell growth (endoreplication) with epithelial cell-dendrite adhesion, coupled tissue growth can efficiently be achieved.

Sampling the SAM

The shoot apical meristem (SAM) is the growing tip of the plant stem, from which a population of pluripotent stem cells generates all above-ground organs. The SAM is organised both in a central-to-peripheral manner, with the central zone containing the stem cells while their progeny differentiate in the peripheral zone, and in outer-to-inner layers that generate different cell types. These different zones and layers of the SAM are presumably defined and regulated by distinct (if overlapping) gene regulatory networks, and G. Venugopala Reddy and co-workers (p. 2735) set out to define the gene expression landscape of theArabidopsis SAM. They isolate multiple different cell populations from the SAM and perform a detailed transcriptomic analysis to compare the gene expression profiles of the various populations. From these data, the authors are able to identify specific characteristics of particular cell populations, which might provide insight into functional differences between different regions of the SAM. Importantly, the datasets provide a valuable resource for the community and should stimulate further research to better understand the complexity of cell states within SAMs.

Characterising developmental ‘super-repressors’

DNA and histone methylation patterns correlate with – and define – transcriptional activity of the genome. In particular, DNA hypomethylation is associated with active chromatin and generally thought to be permissive for gene transcription. However, this rule is not globally applicable, and Shinichi Morishita, Hiroyuki Takeda and colleagues (p. 2568) now identify a particular class of hypomethylated domains (HMDs) in pluripotent cells of the medaka fish that are associated with strong gene repression. These HMDs are characterised by their large size and strong H3K27me3 deposition, and are referred to as large K27HMDs. Notably, they are most commonly found surrounding promoters of key developmental transcription factors that are under strong transcriptional repression. These HMDs shorten in mature cells, where the genes are expressed, due to DNA hypermethylation in these regions. Importantly, the authors find that a significant proportion of large K27HMDs are conserved between medaka and human stem cells. Together, these data define a genomic feature – the large K27HMD – that may be responsible for ensuring that key developmental transcription factors are kept strongly repressed in pluripotent cells.

Plus…

Amyloid precursor protein and neural development

Interest in the amyloid precursor protein (APP) has increased in recent years due to its involvement in Alzheimer’s disease. Understanding the basic biology of APP and its physiological role during development thus will provide a better comprehension of Alzheimer’s disease.  Here, Nicolas and Hassan present an overview of some of the key studies performed in various model organisms that have revealed roles for APP at different stages of neuronal development. See the Primer on p. 2543

The roles and regulation of multicellular rosette structures during morphogenesis

Multicellular rosettes have recently been appreciated as important cellular intermediates that are observed during the formation of diverse organ systems. Here, Nechiporuk and colleagues review recent studies of the genetic regulation and cellular transitions involved in rosette formation. They discuss and compare specific models for rosette formation and highlight outstanding questions in the field. See the Review on p. 2549

Heterogeneity and plasticity of epidermal stem cells

The epidermis is an integral part of our largest organ, the skin, and protects us against the hostile environment. Here, Jensen and co-workers discuss stem cell behaviour during normal tissue homeostasis, regeneration and disease within the pilosebaceous unit, an integral structure of the epidermis that is responsible for hair growth and lubrication of the epithelium. See the Review on p. 2559

(No Ratings Yet)

Loading...

This year will mark the 6^th year since I have been assisting in the Marine Biological Laboratory (MBL) course in Embryology. Each year I am excited at the prospect of meeting students and postdocs from around the world, as well as the outstanding faculty and old friends that offer their time to continue a long tradition of teaching in the village of Woods Hole in Cape Cod. My involvement in the course began when I was postdoctoral fellow and continues after I obtained my first faculty position at Dalhousie University in Halifax, Canada, where I set up my own lab in the study of neural development. To recover from grant writing, administrative duties and teaching, each summer I escape to Woods Hole to re-invigorate my joy of discovery and sharing that with a new class of eager students. The Embryology course has been given almost every summer in one form or another for over 125 years. Several generations of eminent embryologists have passed through the wind swept and sun bleached buildings of MBL. Few courses can boast such a tradition.

The pages of The Node attest to the exhilarating and often life changing experience afforded by the Embryology course. Most hail from around the world to learn the secrets of embryos. Beautiful little animals floating, spherical or misshapen, pigmented or transparent, in seawater, representing potential. During 6 weeks in the summer, these embryos will be poked, sliced, grafted, transfected, stained, and photographed to reveal their astonishing molecular and cellular organization. It is a privilege to be a developmental biologist and be able to study what has occupied our thoughts from the beginning of recorded wisdom: the story of origins; how do fantastic and amazing creatures each with their own unique ways of experiencing the world come to be? From this broad question, our field has shattered into many sub-disciplines and specialties. But as developmental biologists, we remain unified in our pursuits of how form and function arise in life. At the embryology course, students and postdocs learn to address this from a variety of different angles. They burn the midnight oil studying gastrulation and pattern formation in arthropods, nematodes, vertebrates, planarian, mollusks, and whatever they dredge up from the cold waters on the Atlantic. Like the embryo, as the course unfolds, so too will the students acquire new characteristics and reveal their potential. They will make lifelong friends, and perhaps a newfound direction of research. They will remember the experience for the rest of their lives.

This year, the FIFA World Cup of Football (as it is called in the rest of the world!) will add a festive international flair to a diverse student body that hail from Argentina, Spain, USA, Croatia, Germany, England, Canada, Japan, Taiwan, and China. Games will be broadcast across laptop screens and on the overhead projection screen in the main teaching lab. Some hearts will be broken, others will triumph! Ole, ole! But embryos are indifferent as they float translucently in the petri dish. Revealing their secrets only reluctantly to those who ask the right questions and probe with the right tools.

Basic scientific discoveries at places like MBL have lead to fundamental insights into the role of oceans in biogenic cycling and climate, diversity of ocean life, neurobiology and embryology. They all affect how we will cope with the changes of climate, and contribute to our understanding of diseases such as neurdegeneration and cancer. Perhaps there is something in the sea air that stimulates the minds of MBL fellows and scientists. One thing is certain however, without government support for basic research, these discoveries would not have been made. It is not hyperbole to say that our future, and the life forms we share our planet with, depends on a thorough understanding of the world in which we live in. We need places like MBL to lead in discovery and train the next generation of scientists in curiosity-driven research. That is the team I am rooting for.

– Angelo Iulianella (http://iulianella.medicine.dal.ca/).

(1 votes)

Loading...

When adenomas appear in the colon, the same cells of the tissue produce a molecule that neutralizes its progression.

Adenomas, which are highly prevalent in the population, provide the substrate on which carcinomas develop.

Barcelona, Monday 23 June 2014.- Colon cancer development starts with the formation of benign tumours called adenomas. It is estimated that between 30% and 50% of people over 50 will develop one of these tumours. These adenomas or polyps are the pre-cancerous lesions that, once they accumulate further genetic mutations over many years, can progress to colon cancer. A team headed by scientists at the Institute for Research in Biomedicine (IRB Barcelona) and headed by the ICREA researcher Eduard Batlle has discovered that the colon has a safety mechanism to restrict the formation and growth of adenomas. The study was published on Sunday in the advanced online edition of the journal Nature Cell Biology and will be the cover of the July issue.

The scientists have observed that the formation of an adenoma in the colon is accompanied by an increase in the production of a molecule called BMP (bone morphogenetic protein). The study explains that BMP limits the self-renewal capacity of adenoma stem cells, thus impeding the rapid development of the lesion. “Colon epithelial cells respond to the presence of these tumours and attempt to suppress them or at least control them through the BMP pathway. Without this safety circuit, we would have many more polyps showing rapid growth. Colon cancer is a disease that develops slowly and this slowness may be caused by this safety mechanism,” says Eduard Batlle, head of the Colorectal Cancer Laboratory at IRB Barcelona whose research interests include the study of how colon cancers arise and how they become malignant.

Do we all have the same capacity to deal with polyps?

One hypothesis that has arisen from the study is that we are not equally protected and that there are genetic variations in the population that determine that some people have more robust safety mechanisms to respond to polyp formation than others.

This hypothesis is supported by the fact that the scientists have identified a genomic region through which BMP protein production is controlled, that is to say, the specific site that regulates the safety circuit triggered when adenomas are detected. It is the same site that holds certain genomic variations in the population that are associated with susceptibility to colon cancer. These genomic variations have been revealed by studies in the population and by analysis of the genomes of colon cancer patients that are available in data bases such as that of the 1000 Genomes Project Data.

“We provide a plausible explanation of why certain genomic variations (called snip – SNP-) are associated with a greater risk of colon cancer and we believe it is because these variations affect this safety system that protects us from adenomas,” explain the scientists.

“This basic study will allow more defined research into the genomic variations associated with colon cancer that are in the region where BMP is regulated.” A better understanding of the mechanism that accelerates or restricts the development of cancer may allow, for example, the discovery of new biomarkers to better identify the population at greatest risk of colon cancer and even the current degree of risk.
Colon cancer is one of the four most prevalent cancers, together with breast, prostate and lung cancer, and it has a global incidence of 1,600,000 cases per year with a mortality rate of 50%. The researchers highlight that if those over 50 underwent preventive tests such as colonoscopies then 80% of the deaths from this disease would be averted.

The study has involved the participation of groups from the “Centro Nacional de Investigaciones Oncológicas”, the “Hospital Clínico de Barcelona-IDIBAPS-UB”, and the Centre for Genomic Regulation. Funding was provided by an ERC Grant from the European Research Council awarded to Eduard Batlle, from the Josep Steiner Foundation of Switzerland, and from the Spanish Ministry of the Economy and Competitiveness.

Reference article:
The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression
Gavin Whissell, Elisa Montagni, Paola Martinelli, Xavier Hernando-Momblona, Marta Sevillano, Peter Jung, Carme Cortina, Alexandre Calon, Anna Abuli, Antoni Castells, Sergi Castellvi-Bel, Ana Silvina Nacht, Elena Sancho, Camille Stephan-Otto Attolini, Guillermo P. Vicent, Francisco X. Real and Eduard Batlle
Nature Cell Biology (2014) Doi: 10.1038/ncb2992

IMAGE: Image of a benign colon tumour. In green, adenoma stem cells. The scientists have discovered that the colon has a safety mechanism to prevent the self-renewal of adenoma stem cells.

More information:
Sònia Armengou. Press Officer. IRB Barcelona
+34 93 403 72 55/ 618 294 070
Twitter: @IRBBarcelona

This article was first published on the 23rd of June 2014 in the news section of the IRB Barcelona website

(No Ratings Yet)

Loading...

It is our birthday today! It is exactly 4 years since the Node was launched, and since then we have grown in users and readers every year! Thank you all for writing, commenting, rating and reading the Node! We hope you will join us in another year of great discussions, research, meetings, competitions, etc, etc, etc…

Birthday also means cake, so it is an appropriate time to share the video below. It shows how to cut a cake in the most scientific way, according to a 1906 paper in Nature by Francis Galton!

(1 votes)

Loading...

We have a lectureship available in Cell and Developmental Biology at the University of Bath, UK. Please share with anybody who you think might be interested.

http://www.bath.ac.uk/jobs/Vacancy.aspx?ref=BK2506

(No Ratings Yet)

Loading...

Registration is now open for the Queenstown Molecular Biology meeting, Queenstown, New Zealand including the Developmental Biology and Reproduction satellite meeting.

August 28-29^th 2014, Rydges Hotel, Queenstown, New Zealand

Sessions include: Reproduction, Infertility, Fate determination, Organ development, Developmental pathways in human disease and cancer, Neurodevelopment, Stem cells, Germ cells and Pluripotency.

Student speaker and poster prizes on offer thanks to Australia and New Zealand Society for Cellular and Developmental Biology (ANZSCDB) and Genetics Otago

For a further details and registration go to http://www.qmb.org.nz/

(No Ratings Yet)

Loading...

The heat started to increase in Japan, as the rainy season approached and with it the high levels of temperature and humidity. But this was not an obstacle for scientists from all over Japan (and also some scientists from abroad) to meet in the great and beautiful city of Nagoya, in Aichi prefecture. Here took place the 47^th Meeting of the Japanese Society of Developmental Biologists (27th-30th May 2014). The meeting was greatly organized by Masahiko Hibi-sensei, a professor in the University of Nagoya, who, as it happens, was a previous PI in my current institute, RIKEN Center for Developmental Biology.

The meeting embraced developmental biologists from a high variety of fields, and thus it was not that small albeit being a national meeting. So, it was organized in several parallel sessions, including some main Symposia, a couple of technical Workshops, and several sessions of contributed oral presentations (each about a common topic). Therefore, it was impossible attending to everything. I hope the reader forgives me if I focus mainly in what I’m interested in.

The meeting opened a day before the official date (28th), with a satellite meeting in Japanese in the morning (to which I did not attend for obvious reasons) and three oral sessions in the afternoon (in English), one of them mixing topics on neural development, system biology, technological and theoretical approaches. For a start, and given that it was not the official day 1 (but day 0…), the room was not full, but still there were some discussion and even a cute picture of a hibernating hamster (see below), presented by Torsten Bullmann, of RIKEN QBiC, about his work on the protein tau and its role on the plasticity of dendrites.

It was a surprise for some of the audience, since it seemed that tau is a very well known marker for axons… but Bullmann explained that it depends on its phosphorylation state and thus you can use different antibodies against tau to mark either axons or dendrites. Other quite interesting talk was that of Kenneth Ho et al., also from RIKEN QBiC, about the Systems Science of Biological Dynamics (SSBD) database that they have created and to which any scientist can upload published data or download them, so that everyone can use them. You can find the database and more information about it here. This database looks quite good, and is distinct from other databases that contain just sequence information. A set of tools to work with the images is also integrated into the database, such as ImageJ utilities. You can have a look at the database also in this video:

On the second day (official 1^st day), I attended to the joint symposium between the Spanish Society for Developmental Biology (SEBD, standing for the Spanish name of the society) and the Japanese one. This was the first time that the JSDB held a joint symposium with a society from abroad, and I would say that it was a success. Great scientists from Spain joined the meeting, both senior and young. The talk by Ángela Nieto, from the Institute for Neurosciences in Alicante and president of the SEBD, on the role of snail and other transcription factors in epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions, not only during development but also during the metastatic process of cancer, woke up the curiosity of the audience in the early morning. Have a look to this great review by Nieto about this topic here. Of much interest was also the talk by Miguel Torres, from the National Center for Cardiovascular Research (CNIC) in Madrid, on how cells compete with each other to contribute to the embryonic development of mammals; and that of María Abad, from the Spanish National Cancer Research Centre (CNIO), also in Madrid, who talked about the in vivo generation of iPS cells. You can check the work by Torres here, and that of Abad, here. Ana Gradilla, a Mexican researcher who belongs to the SEBD, presented her work done at the Center for Molecular Biology Severo Ochoa (Madrid) about the very hot topic of the distribution of morphogens within exovesicles through cytonemes in Drosophila. The discussion on this work (check it out here) was also continued during a nice nijikai (Japanese word for after-party), the second day after the reception.

One important feature of this meeting was the high number of talks. Masahiko Hibi, the organizer of the meeting, said that the aim of the meeting was to give as many chances as possible to young researchers to give a talk. In this regard, there were two sessions of flash talks, one on each of the first two days, of 3 minutes of duration where the presenters had to introduce their work, and later on continue the discussions with those interested in the poster session. It was actually a success, since I haven’t seen such a lively poster session in any meeting so far. I’d like to highlight that of Yuichiro Hara, from RIKEN CDB, who presented about transcriptomic and genomic resources of the Madagascar ground gecko, a very interesting emerging model organism. They are now constructing a database, Reptiliomix, which contains these transcriptomics resources. Keep an eye on their lab website  about the anticipated release of the web server.

After the flash talks I attended one of the workshops scheduled in the meeting (at the same time that two very nice oral presentation sessions, about Early Embryogenesis and Evo-Devo, and about Morphology – I wish I could have cloned myself to attend those-). I attended the workshop because I had to give a contributed talk there. This workshop was entitled “New Genome Technologies in Developmental Biology” and was organized by Atsuo Kawahara, from Yamanashi University and RIKEN QBiC, and by Takashi Yamamoto, from Hiroshima University. The workshop was basically focused in the most recent genome editing technology, such as the CRISPR/Cas9 system, a topic that was very present during the whole meeting, highlighting the importance of these very new techniques. However, my talk was about a comparative transcriptomics analysis between turtle and chicken tissues, including the carapacial ridge, the embryo’s structure controlling the shell formation.

The second day started with the two plenary lectures of the meeting. The first one, by Alex Schier from Harvard University, was about the role of a newly described gene, toddler, in the early embryogenesis of zebrafish. The second talk was by Hans Clevers, from the Hubrecht Institute in the Netherlands who described Lgr5 as a marker for stem cells in the crypts of the intestinal epithelium. Clevers’ team could also generate intestinal organoids by controlling the expression of Lgr5, technology developed by this postdoctoral fellow Toshiro Sato. Clevers delighted the audience with beautiful animations, including those that represented clonal crypts from cells expressing different fluorescent proteins… eventually resulting in colorful intestinal epithelia. Both plenary talks were followed by many questions from the audience.

The afternoon of the second day was also followed by flash talks presentations, and after that the second workshop (“Frontiers in Developmental Biology by Unique Approaches”) and two parallel oral presentation sessions. In this case I decided to attend one of the oral sessions, about the Gene Expression and Epigenetics, where I attended an interesting talk about the differences in Shh regulation between chicken and mouse, by Takanori Amano, from the National Institute of Genetics of Japan.

Since a meeting does not consist only of science, but also of socializing events among scientists, the second day was finished by a very nice reception in a hotel near the meeting venue. It was a very relaxing time, and I could finally enjoy some time with my Spanish colleagues and discuss, among other things, about the situation of science in our country (not a very hopeful future, I would say). Some announcements that you might be interested in were about the next year’s JSDB meeting, to be held in Tsukuba, and organized by Hiroshi Wada, from the Tsukuba University; Ángela Nieto, as the president of the SEBD, announced the next meeting of the Spanish Society (together with the Portuguese Society of Developmental Biology) will be held in Madrid this year from October 13^th to 15^th, and it will be in association with the JSDB (there will be a couple of fellowships for young researchers to attend, so don’t forget to apply if you plan to attend!). Also, the next year’s JSDB meeting will hold a joint symposium with the Dutch Society for Developmental Biology (see this past post in the Node), in the same way that this year was with the Spanish counterpart.

The last day had 6 symposia, 3 in the morning and 3 in the afternoon. In the morning, I attended the symposium of the Asia-Pacific Developmental Biology Network, to have a glimpse of what is done in the region. I attended the talk of Xinhua Lin, at the Institute of Zoology from the Chinese Academy of Science, about tissue homeostasis by gut stem cells in Drosophila. And, finally, in the afternoon I went to the talk given by Benny Shilo, from the Weizmann Institute of Science in Israel, about the dorso-ventral patterning of the Drosophila embryo.

Overall, it was a nice meeting, not too small, and not too big. In my case, I have been working for almost four years in Japan, and it has been my first national meeting, what have allowed me to get an idea of what Japan is up to. Given the fact that I am actually thinking about continuing my scientific career here, I could learn about different institutes, universities and researchers with whom I can collaborate in the future. However, the atmosphere is much more international than I expected, and thus even if you are not working in Japan, attending this meeting is definitely worthy. So, keep an eye on the upcoming meeting in 2015 in Tsukuba, and come if you have the chance. You will not regret it!

(1 votes)

Loading...

Last month 39 people from around the world gathered together in the flagship European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany to take part in the Master Course on Bioimage Data Analysis. This was the third edition of the course that had previously been held in Heidelberg and Barcelona, and is aimed at training scientists to meet the growing need to extract measurable and quantitative data from biological images. In this latest incarnation there was a meeting component (invited speaker talks, short talks selected from abstracts and a poster session), a practical component, and a strong “community building” component.

Takeo Kanade from the robotics institute at Carnegie Mellon University started off the course with a fascinating keynote lecture that not only explained some technical aspects of segmentation of biological images, he also gave a great review of the key elements that make a computer capable of “seeing”. In addition, lectures were presented by pioneering researchers such as Fred Hemprecht from the Heidelberg Collaboratory for Image Processing (HCI), Ivo Sbalzarini from the Max Plank Institute of Molecular Cell Biology and Genetics, Nadine Peyriéras from the CNRS, France and Christophe Zimmer from the Institut Pasteur. Diverse aspects of imaging were presented in these lectures, as well as radically different approaches to image analysis. However, all of them had a common thread; how do we teach a computer to “see” the information contained in digital image so that we can quantify this information in a way that is biologically meaningful.

Two underlying themes emerged from these talks. The first focused on how scientists can more easily make computers “understand” what is that they are “seeing” by providing the computers with models of both, the world, and how it appears on the other side of a microscope. Giving computers both of these models as well as the laws that rule them (-i.e. a cell can only divide into two or a nucleus cannot leave a cell-) allows computers to “see” better, requiring less human intervention and data curation. The second theme focused on how to make software designed to quantify images more user friendly. These talks focused on how tool creators (those that design the software) are minimizing the need to change a variety of parameters inside the different tools (known as parameterize) in order to obtain the desired outcome. This is important because unless the user really understands how the tool was implemented, using an application resembles more a leap of faith than a scientific decision. By incorporating computer learning with representative training sets, programmers and tool developers are simplifying the way in which the user applies a given tool, having full control of the quantification process.

The classroom component of the course consisted of structured exercises in which the students learned how to apply the different strategies for segmentation and data analysis using real biological data. Students used the image analysis platform Fiji (ImageJ) and Matlab, and R for part of the analysis. With these tools, students implemented workflows that exemplify some of the most common tasks in image analysis such as the segmentation and visualization of complex 3D structures, tracking particles and cell movements, and analysis of the speed and directionality of biological movements big and small, among others. In addition, students got “insider information” from the experts in the field, regarding how and why they use different strategies (plugins, tools and macros) to accomplish the desired image restoration and segmentation required to quantify a given feature.

Finally, but not less importantly, the attendees got to present their work in short talks and a poster session. This component of the course had a dual goal. On one hand it exemplified how diverse problems in biology are converging in the need to generate quantitative data and how the use of quantitative microscopy will clearly be a first line tool for biologists in years to come. On the other, it generated a sense of community amongst the course participants, imparting the philosophy of the course: to foment and energize the next generation of Image Analysts as members of a growing community that not only applies but also generates tools and research that will propel the specialty well into the future.

(5 votes)

Loading...

After serving on some academic selection committees recently, I’m worried about the future of some of our young scientists. Especially concerning are the number of applications where the candidate, pursuing a academic or research career, does not seem to have a understanding of what is required to put together a stand-out application for a position, and it in some cases may even be to late for them to be competitive for such positions.
It is getting tough out there on the academic job front; each position may receive well over 50-100 applications (even getting into the hundreds at larger high profile Universities).

How can we help our PhD students who want a career in academia? They need to get on top of things early on and learn what they need to achieve to be considered for research and group leader positions.

Job applications are becoming like grant applications – in a pool of excellent candidates the selection committee will look for a reason not to put you through to the short list. How are you going to make your CV and application stand out in a competitive field?

Below I have listed a few tips to get the discussion started.

“The post-doc position”

Outline your Research expertise and interests
An overview of your research interests (what about this research excites you?), can also (briefly) outline your previous research projects and their outcomes

Publications – vital
This could be split into manuscripts in preparation, manuscripts under review and accepted/published. It is critical to publish during your PhD. Your PI is likely to be very busy so it may be up to you to push to get the first drafts of the manuscript together. Plus those employers that are looking for post-doc want to see evidence that you can write!

Qualifications and Employment record
Include expected date of thesis completion or examination.

Presentations:
Contributed and invited talks at meetings/conferences and at departmental level. Never turn down opportunities to speak, it is your best shot at getting you and your research noticed. As they say, every talk is a job talk.

Laboratory skills
Describe the skills/techniques that you are proficient in and have experience with. The employer may be looking for new skills you can bring to the group as well as experience required for the project.

Teaching and mentoring experience
Evidence of teaching and mentorship can be important.
This may include student demonstrating and guest lectures. List the students that you helped to supervise and the relevant output (eg thesis or if their data ended up in your publication).

Grants, awards, scholarships
List any travel awards, PhD scholarship, anything you applied for $ and got it. Any prizes at conferences and meetings = Peer esteem.

Professional activities and skill development
Workshops, reviewing grant applications, committee work, outreach activities. Take the opportunities to be involved all these activities when they are offered or seek them out yourself.
Professional memberships – Membership to societies. Join up – it is often very cheap for students and early career researchers plus they offer travel grants and awards.
The COVERLETTER – Please write one and address the advertised project, otherwise it looks like you are just applying for everything. Be enthusiastic about the proposed project/research area and address how your skill sets met the selection criteria. If you don’t have all the skills listed (and it is rare to have them all), then you can address this to say why you aren’t proficient in this area, and refer to your ability to quickly pick up new skills.

“Lecturership position”

Publications (vital):
The number of publications since PhD is often used as a marker of research output (often around 2 publications per year is considered great but this will vary depending upon the research field). Impact factor is also taken into consideration eg a fewer number of high impact papers can be weighted similarly to a CV with an overall higher number of publications. Where possible you might want to include impact factor,  number of citations of each paper, H-index, ranking of the journal within your field of research (Eg this journal is ranked 2nd out of 50 journals in the field of developmental biology) = essentially showing the measure of the impact of your work in the field of research.
For multi-author publications – what was your contribution? (this can be important if you aren’t the first or last author in a long list of authors, even if it is a Nature or Science paper).

Previous grant funding
Provide evidence of research grant success – this proves you have ideas and they are fundable. It is expensive to do research, you need to show you can fund your research (and bring some extra income into the department). These don’t have to be large grants; keep an eye out for smaller funding opportunities to get you your first grants as PI.

Research interests and projects
You need to outline the research directions for the programme of research you will establish in your new group. Include how they fit with the department (and existing facilities) and other members of the university. What funds will you apply for? Do you have any established collaborations?

Leader qualities
Examples of how you have lead research projects/programmes in the past.
Supervision of research students – what was the outcome (eg did they contribute to publications?)

Teaching
Develop a teaching profile or teaching philosophy. Why do you want to teach, what kind of teacher do you want to be? Include any evidence of teaching experience. Look at the courses within the department you are applying, discuss what courses can you contribute too.

Other helpful additions to the CV
Any community engagement or outreach activities.
Presentations such as conferences but include others too and note if you were an invited speaker. University service such as work on committees (there will be a lot of this if you get the job!) Evidence that you understand the compliance issues that must be met and administrated by you as a group leader such as animal ethics, lab safety, biological compliance.
Your employment record – if you have any career gaps it may help to explain them.

The Coverletter. Do one!
Why do you want to move to this department/university? Specifically address the selection criteria.

The Final word – It is going to take planning! Start planning early in your career for the position you want in 5 years time. Don’t turn down opportunities and take a few risks.

Dr Megan Wilson (@DrMegsW)

(2 votes)

Loading...

Electroporation: an efficient technique for embryologists

During embryonic development, the specification of different cell types giving rise to the future organs involves a precise spatiotemporal regulation of cell proliferation, migration, and differentiation. Studying these processes requires tools to manipulate gene expression locally in the developing embryo.To this aim, embryologists have widely used the technique of electroporation, consisting in the delivery of exogenous molecules (such as nucleic acids) into targeted cells through electric permeation of the plasma membrane(Calegari et al., 2004; Escoffre et al., 2009; Nakamura and Funahashi, 2012; Swartz et al., 2001). Localised electroporation is achieved by two main approaches depending on the position and the geometry of the targeted tissue (Fig. 1).  If the zone of interest surrounds a natural body cavity, one can generate an electric field with large electrodes and inject locally the exogenous molecule (Fig. 1a; Itasaki et al., 1999; Soares et al., 2008). Otherwise, the electroporation solution is homogeneously applied and the electric field is then spatially restricted by, for instance, using needle-shaped electrodes placed in close proximity to the targeted area (Fig. 1b; Davidson et al., 2003; Momose et al., 1999). One important drawback of this second strategy is that electrolysis occurring at the needles surface during pulse application generates harmful chemical species that may result in cell damage and poor embryo survival (Kim et al., 2008; Wang et al., 2010; Wang and Lee, 2013).

Figure 1. Strategies for localised electroporation in early post-implantation mouse embryos. (a) The first technique involves a uniform electric field and a localized injection of nucleic acids. (b) The second technique relies on a localized electric field and a homogenous nucleic acid solution. (c) Our technique involves dielectric guides where electric field is spatially restricted inside confined channels filled with electroporation buffer. 

When embryology meets microfabrication

To circumvent these problems, we developed a system where the electric field generated by large electrodes is conveyed to the targeted zone by narrow channels, also known as dielectric guides, filled with electrolyte (Fig. 1c; Mazari et al., 2014). In this way, efficient electroporation with reduced cell damage is obtained as the electroporated tissue is exposed to a confined electric field while lying far away from the electrode. Moreover, the sample is immobilized by suction in front of the channel, therefore obviating the need for micromanipulation. Interestingly, dielectric guide-based electroporation devices for single cells in culture had been successfully adapted to the on-chip format, with microfabricated electrodes and fluidic channels (Fox et al., 2006; Wang et al., 2010; Wang and Lee, 2013). To design similar tools able to target small embryos or organ explants, the most important parameters are the dimensions of the dielectric guide. Indeed, transfecting as few as 4 or 5 cells of a specific tissue, which approximately represent an average surface of tens square micrometers, requires the guide aperture to be of a similar size. Derived from the microchip industry, microfabrication techniques are particularly well-suited to create microstructures. Through a straightforward and quite simple process, these microengineering techniques then enable the reproducible production of defined shapes and positions at the micrometer scale.

An optimised and collaborative approach

As a proof of principle, we chose to target small cell populations in the visceral endoderm (VE), the outer epithelium of mouse embryos at embryonic day 5.5 of development (E5.5) (Fig. 2a-b). This is a critical time for the establishment of embryonic polarity, with distal VE (DVE) cells undergoing a stereotypical migration that will define the future anterior side (Takaoka and Hamada, 2012). However, existing electroporation procedures for this stage face poor embryo survival and poor reproducibility. First, we conceived an electrical model of E5.5 embryos and used it in numerical simulations to compare the outcome of different electroporation strategies. This analysis demonstrated that the proposed dielectric guides device would permeabilize a more restricted area than current electroporation systems. In addition, we experimentally and systematically investigated pore generation and cell viability to determine the best electrical conditions for efficient electroporation of DVE cells. Constant optimisation by alternative simulations and experimental tests, resulted in the development of dielectric guide-based devices and associated protocols to locally electroporate E5.5 mouse embryos in an efficient, reproducible, and safe way (Fig. 2a-c).

Figure 2. Use of the dielectric guide-based device on an E5.5 embryo. (a) View of the whole system included between the electrodes. An E5.5 embryo (blue arrow) is positioned with its DVE abutting the dielectric guide connected to the cathode, so as to target precisely this tissue. (b) Close-up view of the same embryo. (c) Image of a transgenic Hex-GFP E5.5 embryo electroporated in the DVE with pCAG-mCherry DNA. (d) Close-up view of migrating mCherry expressing cells. The red arrows show cell projections.  

We combined our electroporation technique, transgenic mouse lines, and live imaging to study the behavior of VE cells during DVE migration between E5.5 and E6.0 (Fig. 2c). We were able to specifically label subpopulations of follower DVE cells that so far had been difficult to visualize, and to monitor the production of dynamic cellular projections during their migration (Fig. 2d). Furthermore, we demonstrated that our microdevice can be used to electroporate tissues in a wide range of embryonic contexts just by adapting the guides dimensions. A distinctive feature of our work lies in the proposed interdisciplinary approach that brings together expertise from biology to physics. Our strategy coupling numerical simulations, prototype microfabrication, and in vivo testing, provides an optimized and rigorous framework for the design of other tailor-made electroporation devices (Fig. 3). We hope that this work will provide a stimulating example ofthe electrifying interest of microfabrication approaches to developmental biologists.

Figure 3.  Interdisciplinary and auto-optimised strategy used to conceive a dielectric guide-based tool to electroporate locally, reproducibly, and safely small cells populations from external tissues of embryos or organ explants.    

Bibliography  

Calegari, F., Marzesco, A., Kittler, R., Buchholz, F., & Huttner, W. (2004). Tissue-specific RNA interference in post-implantation mouse embryos using directional electroporation and whole embryo culture Differentiation, 72 (2-3), 92-102 DOI: 10.1111/j.1432-0436.2004.07202002.x

Davidson, B., Tsang, T., Khoo, P., Gad, J., & Tam, P. (2003). Introduction of cell markers into germ layer tissues of the mouse gastrula by whole embryo electroporation genesis, 35 (1), 57-62 DOI: 10.1002/gene.10166

Escoffre, J., Portet, T., Wasungu, L., Teissié, J., Dean, D., & Rols, M. (2009). What is (Still not) Known of the Mechanism by Which Electroporation Mediates Gene Transfer and Expression in Cells and Tissues Molecular Biotechnology, 41 (3), 286-295 DOI: 10.1007/s12033-008-9121-0

Fox, M., Esveld, D., Valero, A., Luttge, R., Mastwijk, H., Bartels, P., Berg, A., & Boom, R. (2006). Electroporation of cells in microfluidic devices: a review Analytical and Bioanalytical Chemistry, 385 (3), 474-485 DOI: 10.1007/s00216-006-0327-3

Itasaki N, Bel-Vialar S, & Krumlauf R (1999). ‘Shocking’ developments in chick embryology: electroporation and in ovo gene expression. Nature cell biology, 1 (8) PMID: 10587659

Kim, J., Cho, K., Shin, M., Lee, W., Jung, N., Chung, C., & Chang, J. (2008). A novel electroporation method using a capillary and wire-type electrode Biosensors and Bioelectronics, 23 (9), 1353-1360 DOI: 10.1016/j.bios.2007.12.009

Mazari, E., Zhao, X., Migeotte, I., Collignon, J., Gosse, C., & Perea-Gomez, A. (2014). A microdevice to locally electroporate embryos with high efficiency and reduced cell damage Development, 141 (11), 2349-2359 DOI: 10.1242/dev.106633

Momose, T., Tonegawa, +., Takeuchi, J., Ogawa, H., Umesono, K., & Yasuda, K. (1999). Efficient targeting of gene expression in chick embryos by microelectroporation Development, Growth and Differentiation, 41 (3), 335-344 DOI: 10.1046/j.1440-169X.1999.413437.x

Nakamura, H., & Funahashi, J. (2013). Electroporation: Past, present and future Development, Growth & Differentiation, 55 (1), 15-19 DOI: 10.1111/dgd.12012

Soares, M., Torres-Padilla, M., & Zernicka-Goetz, M. (2008). Bone morphogenetic protein 4 signaling regulates development of the anterior visceral endoderm in the mouse embryo Development, Growth & Differentiation, 50 (7), 615-621 DOI: 10.1111/j.1440-169X.2008.01059.x

Swartz, M., Eberhart, J., Mastick, G., & Krull, C. (2001). Sparking New Frontiers: Using in Vivo Electroporation for Genetic Manipulations Developmental Biology, 233 (1), 13-21 DOI: 10.1006/dbio.2001.0181

Takaoka, K., & Hamada, H. (2012). Cell fate decisions and axis determination in the early mouse embryo Development, 139 (1), 3-14 DOI: 10.1242/dev.060095

Wang, M., Orwar, O., Olofsson, J., & Weber, S. (2010). Single-cell electroporation Analytical and Bioanalytical Chemistry, 397 (8), 3235-3248 DOI: 10.1007/s00216-010-3744-2

Wang, S., & Lee, L. (2013). Micro-/nanofluidics based cell electroporation Biomicrofluidics, 7 (1) DOI: 10.1063/1.4774071
 

(No Ratings Yet)

Loading...