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Professor and Head of Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia

Posted by , on 8 September 2016

Closing Date: 15 March 2021

Monash University is seeking an outstanding candidate to manage and lead the Department of Anatomy and Developmental Biology within the Faculty of Medicine Nursing and Health Sciences. The Department of Anatomy and Developmental Biology is one of six departments of the School of Biomedical Sciences and a leader within its discipline. Areas of research expertise include renal and lung biology, epithelial and reproductive biology, inflammation, embryology, cancer, stem cell biology and regenerative medicine.

The successful candidate will capitalise and build on existing educational and research strengths to create a high-performing team of academics and professional staff who not only provide outstanding educational opportunities to the students in the school but also, through membership of the Monash Biomedicine Discovery Institute, contribute to the research strategy and output of the institute.

To be successful in this role you will have a proven track record of individual research excellence and evidence of leadership through building and developing capability in an academic or research environment.

Applications close 30th September, 2016.

Details can be found at:

http://careersmanager.pageuppeople.com/513/cw/en/job/551205/professor-and-head-of-department-of-anatomy-and-developmental-biology

A position description can be found at:

aug-pd-professor-and-head-of-department-of-anatomy-and-developmental-biology-551205-1

 

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Postdoctoral Position in Zebrafish Functional Genomics

Posted by , on 7 September 2016

Closing Date: 15 March 2021

The Varshney lab is recruiting a highly motivated, passionate and independent individual with excellent interpersonal skills to play a key role in advancing the mission of the lab.

We are focused on tackling the huge challenge of systematically validating the flood of human candidate disease genes identified in various genome- wide association (GWAS) and whole-exome sequencing studies by developing disease models in zebrafish.

The successful applicant will use zebrafish and the emerging genomic technologies to understand the disease pathology of human non-syndromic hearing loss. Our research interests span multiple disciplines: genetics, genomics, molecular biology, and developmental biology.

A recent doctorate in Biological Sciences or related field with experience in Molecular Biology, Cell & Developmental Biology, and Genetics is required. Experience with zebrafish is desirable, but not essential.

Please send a curriculum vitae and summary of research interests to:

Gaurav Varshney, Ph.D.,

Assistant Member,

Functional & Chemical Genomics Program,

Oklahoma Medical Research Foundation.

Email: Gaurav-Varshney AT omrf.org

The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) in Oklahoma City. OMRF investigators enjoy close scientific interactions with OUHSC faculty and participate in OUHSC graduate programs. OMRF has been selected as one of the best research institutions for post-docs from 2011 to 2013 in the USA by The Scientist journal. Additional information about OMRF can be found at the Oklahoma Medical Research Foundation web site: http://omrf.org

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Research Associate (Laurenti Lab)

Posted by , on 7 September 2016

Closing Date: 15 March 2021

Department/Location: Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge

Salary: £28,982-£37,768

Reference: PS10005

Closing date: 04 October 2016

Post-doctoral fellow: healthy ageing of human haematopoietic stem cells.

Fixed-term: The funds for this post are available until 31 October 2019 in the first instance.

The Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute is an international centre of excellence for stem cell research and regenerative medicine. Scientists in the Institute collaborate to advance our knowledge of various stem cell types and to perform pioneering work in translational research areas, providing the foundation for new medical treatments. The Institute currently comprises 29 research groups based across 6 sites in Cambridge. In 2018 all researchers will move to a new building on the Cambridge Biomedical Campus.

Applications are invited for a research associate to join Dr Laurenti’s group. We combine state-of-the-art experimental and computational methods to study the unique biological and molecular properties of human Haematopoietic Stem Cells (HSCs).

The post holder will join a new multidisciplinary project funded by the BBSRC. This collaboration between Dr Laurenti and Prof. Göttgens laboratories has as principal aim the investigation of the functional and molecular heterogeneity of HSCs throughout a human lifetime, with a particular focus on the effects of healthy ageing. The project will combine single cell, transcriptomics, epigenomics, flow cytometry, single cell functional assays in vitro and in vivo.

The successful candidate is expected to creatively and independently carry out their own research project, while collaborating on a regular basis with a team of experimentalists and computational biologists. They will also effectively communicate their work in writing and oral presentations at internal meetings and international conferences.

Candidates should hold a PhD in a relevant field. In particular, they will have a strong background either in stem cell biology, haematology, immunology or ageing. Extensive experience with flow cytometry, mouse models and tissue culture is required. The candidate should also possess molecular biology skills. Additional expertise with high-throughput sequencing data and the R programming language would be desirable. Finally, they will have demonstrated scientific achievement with an excellent publication record.

The start date is flexible but can be as early as November 2016.

Once an offer of employment has been accepted, the successful candidate will be required to undergo a health assessment and a security check.

To apply online for this vacancy and to view further information about the role, please visit: http://www.jobs.cam.ac.uk/job/11327. This will take you to the role on the University’s Job Opportunities pages. There you will need to click on the ‘Apply online’ button and register an account with the University’s Web Recruitment System (if you have not already) and log in before completing the online application form.

The closing date for all applications is the Tuesday 04 October 2016.

Informal enquiries are also welcome via email to: jobs@stemcells.cam.ac.uk.

Interviews will be held 13-14 October 2016.

Please quote reference PS10005 on your application and in any correspondence about this vacancy.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

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From our sister journals – August 2016

Posted by , on 6 September 2016

Here we highlight some developmental biology related content from other journals published by The Company of Biologists.


Journal typography

inline-graphic-1

Meritxell Huch, Wellcome Trust Sir Henry Dale Fellow at the Gurdon Institute in Cambridge, was interviewed as a Cell Scientist to Watch (she’s certainly one for developmental biologists to watch too!).

 

GuyThe Tanentzapf lab assayed the effects of outside-in integrin activation in the Drosophila embryo, and found that this form of activation is crucial for developmental transitions.

 

RA

Kang-Yell Choi and colleagues found that retinoic acid stabilisation of HRas is required for neuronal differentiation during brain development

 

AurA

The Gönczy lab identified Aurora-A kinases as crucial regulators of spindle positioning from worms to humans.


CoB_BioOpen_AW

Bsg25

Paul Lasko and colleagues identified the centrosomal protein Bsg25 as a crucial regulator of mitosis and embryonic development.

 

Shh

Pamela Yao and colleagues investigated a pool of Sonic Hedgehog contained in extracellular vesicles around neurons.

 

genome

Takashi Yamamoto and colleagues presented a super-ovulation method paired with genome engineering in mice.


CoB_DisModMech_AW_RGB

DMM1

Judith West-Mays and colleagues showed that loss of the transcription factor AP-2β in neural crest cells leads to multiple eye defects, providing a model for early-onset glaucoma

 

DMM2

Using patient-derived stem cells, Mylène Hervé and El Chérif Ibrahim implicated miRNAs and the splicing factor NOVA-1 in familial dysautonomia


Journal typography

SEB

Kathryn Knight reported from ‘Improving Experimental Approaches in Animal Biology: Implementing the 3Rs’, a conference held in June that showcased the various ways researchers can change their habits to ensure  the ethical use of animals in research.

 

jeb

Glen Watson and colleagues found that repair of adult murine hair cells – which is normally only minimal –  is enhanced by sea anemone repair proteins.

 

butterfly

Adriana Briscoe and colleagues identified an expanded number of photoreceptor classes and sexual dimorphism in their expression in a species of nymphalid butterflies

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Postdoctoral Position in behavioral neuroscience at the Novartis Institutes for Biomedical Research

Posted by , on 5 September 2016

Closing Date: 15 March 2021

We are seeking a postdoctoral fellow interested in studying social behavior using zebrafish models at the Novartis Institutes for Biomedical Research (NIBR), Cambridge, USA. The goal of the study is to identify genetic and neural basis of social behavior in zebrafish.

Education and preferred qualifications: Ph.D. (completed or near completion) in behavioral neuroscience or related fields; experience in quantitative, large-scale analysis of behavior is a plus; prior experience in zebrafish is not required.

Interested candidates may send their CV, and contact address of three potential referees to ajeet.singh[at]novartis.com. For general information regarding postdoctoral fellowships at the NIBR, please look at http://postdoc.nibr.com/.

 

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August in preprints

Posted by , on 5 September 2016

Our latest monthly trawl for developmental biology (and other cool) preprints. See June’s post for background, and let us know if we missed anything


It was another bumper month for preprints, as bioRxiv’s Richard Sever celebrated:

 

bioarxiv

 

This month we found three pieces on the development of the spinal cord, three investigations into gene expression networks in the early fly embryo, some in vivo cell biology featuring centrosomes and kinesins, as well as a lot of evolutionary content and some very cool sounding tools, perhaps the most striking of which is a hand-powered centrifuge modelled on a whirligig! bioRxiv provided the bulk of the preprints, with one coming from PeerJ.

 

Happy preprinting…

 

Developmental Biology

Unraveling the differential dynamics of developmental fate in central and peripheral nervous systems. Dola Sengupta, Sandip Kar

 

PAPC couples the Segmentation Clock to somite morphogenesis by regulating N-cadherin dependent adhesion. Jerome Chal, Charlene Guillot, Olivier Pourquie

 

Eph/ephrin signaling controls progenitor identities in the ventral spinal cordJulien Laussu, Christophe Audouard, Anthony Kischel, Poincyane Assis-Nascimento, Nathalie Escalas, Daniel Liebl, Cathy Soula, Alice Davy

 

Evo-engineering and the Cellular and Molecular Origins of the Vertebrate Spinal Cord. Benjamin Steventon, Alfonso Martinez Arias

 

Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls. Fabian Rost, Aida Rodrigo Albors, Vladimir Mazurov, Lutz Brusch, Andreas Deutsch, Elly M Tanaka, Osvaldo Chara

 

Transcriptomic Signatures for Ovulation in Vertebrates. Dongteng Liu, Michael Brewer, Shixi Chen, Wanshu Hong, Yong Zhu

 

A conceptual view at microtubule plus end dynamics in neuronal axons. André Voelzmann, Ines Hahn, Simon Pearce, Natalia P Sánchez-Soriano, Andreas Prokop

 

Activated Ras expression in eye discs with altered levels of hsrω lncRNA causes JNK-induced Dilp8 secretion and reduces post-pupal ecdysone leading to early pupal death in Drosophila. Mukulika Ray, Subhash C. Lakhotia

 

Dynamic Maternal Gradients Control Timing and Shift-Rates for Gap Gene Expression. Berta Verd, Anton Crombach, Johannes Jaeger

 

A damped oscillator imposes temporal order on posterior gap gene expression in DrosophilaBerta Verd, Erik Clark, Anton Crombach, Johannes Jaeger

 

Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network. Erik Clark, Michael Akam

 

Different combinations of ErbB receptor dimers generate opposing signals that regulate cell proliferation in cardiac valve development. Ryo Iwamoto, Naoki Mine, Hiroto Mizushima, Eisuke Mekada

 

An RNA-binding tropomyosin recruits kinesin-1 dynamically to oskar mRNPs. Imre Gaspar, Vasily Sysoev, Artem Komissarov,Anne Ephrussi

 

Polo kinase phosphorylation determines C. elegans centrosome size and density by biasing SPD-5 toward an assembly-competent conformation. Oliver Wueseke, David Zwicker, Anne Schwager, Yao Liang Wong, Karen Oegema, Frank Julicher, Anthony A Hyman, Jeffrey Woodruff

 

Divergence of gene regulatory network linkages during specification of ectoderm and mesoderm in early development of sea urchins. Eric M Erkenbrack, Eric H Davidson

 

Hypergravity hinders axonal development of motor neurons in Caenorhabditis elegans. Saraswathi Subbammal Kalichamy, Tong Young Lee, Kyoung-hye Yoon, Jin Il Lee

 

Evaluating the Stability and Flexibility of DNA Methylation Patterns from Stem to Differentiated Cells. Minseung Choi, Diane P Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stoger, Charles D. Laird

 

Stem Cell Plasticity and Niche Dynamics in Cancer Progression. Noemi Picco, Robert Gatenby, Alexander Anderson

 

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells. Stefan Semrau, Johanna Goldmann, Magali Soumillon, Tarjei S. Mikkelsen, Rudolf Jaenisch, Alexander van Oudenaarden

 

Strigolactone regulates shoot development through a core signalling pathway. Tom Bennett, Yueyang Liang, Madeleine Seale, Sally P Ward, Dorte Mueller, Ottoline Leyser

 

Modifications to a LATE MERISTEM IDENTITY-1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Ryan J Andres, Viktoriya Coneva, Margaret Frank, John R Tuttle, Sang-Won Han, Luis F Samayoa, Baljinder Kaur, Linglong Zhu, Hui Fang, Daryl T Bowman, Marcela Rojas-Pierce, Candace H Haigler, Don C Jones, James B Holland, Daniel H Chitwood, Vasu Kuraparth


 

Evolution etc

Promoter architecture and sex-specific gene expression in Daphnia pulex. R. Taylor Raborn, Ken Spitze, Volker P Brendel, Michael Lynch

 

Increased taxon sampling reveals thousands of hidden orthologs in flatworms. Jose M Martin-Duran, Joseph F Ryan, Bruno Cossermelli Vellutini, Kevin Pang, Andreas Hejnol

 

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties. Sabrina M. Schiemann, Jose M. M. Martin-Duran, Aina Borve, Bruno C. Vellutini, Yale J. Passamaneck, Andreas Hejnol

 

Expression of segment polarity genes in brachiopods supports a non-segmental ancestral role of engrailed for bilaterians. Bruno Cossermelli Vellutini, Andreas Hejnol

 

Conserved traits of spiralian development in the bryozoan Membranipora membranacea. Bruno Cossermelli Vellutini, Jose M Martin-Duran, Andreas Hejnol

 

Comparative transcriptomics reveals candidate genes involved in the adaptation to non-marine habitats in panpulmonate mollusks. Pedro Eduardo Romero, Barbara Feldmeyer, Markus Pfenninger

 

Evolution of simple multicellularity increases environmental complexity. Maria Rebolleda-Gomez, William C. Ratcliff, Fankhauser Jonathon, Michael Travisano


 

Tools and resources

Assembly of Radically Recoded E. coli Genome Segments. Julie E. Norville, Cameron L. Gardner, Eduardo Aponte, Conor K. Camplisson, Alexandra Gonzales, David K. Barclay, Katerina A. Turner, Victoria Longe, Maria Mincheva, Jun Teramoto, Kento Tominaga, Ryota Sugimoto, James E. DiCarlo, Marc Guell, Eriona Hysolli, John Aach, Christopher J. Gregg, Barry L. Wanner, George M. Church

 

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-Seq data. Peijie Lin, Michael Troup, Joshua W. K. Ho

 

Highly parallel direct RNA sequencing on an array of nanopores. Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Andrew J Heron, Mark Bruce, Joseph Lloyd, Anthony Warland, Nadia Pantic, Tigist Admassu, Jonah Ciccone, Sabrina Serra, Jemma Keenan, Samuel Martin, Luke McNeill, Jayne Wallace, Lakmal Jayasinghe, Chris Wright, Javier Blasco, Botond Sipos, Stephen Young, Sissel Juul, James Clarke, Daniel J Turner

 

Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy. M. Saad Bhamla, Brandon Benson, Chew Chai, Georgios Katsikis, Aanchal Johri, Manu Prakash

 

Genetically targeted 3D visualisation of Drosophila neurons under Electron Microscopy and X-Ray Microscopy using miniSOG. Julian Ng, Alyssa Browning, Lorenz Lechner, Masako Terada, Gillian Howard, Gregory Jefferis

 

Direct determination of diploid genome sequences. Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna Church, David B Jaffe

 

Biotinylation by antibody recognition – A novel method for proximity labeling. Daniel Zvi Bar, Kathleen Atkatsh, Urraca Tavarez, Michael R Erdos, Yosef Gruenbaum, Francis S. Collins

 

The impact of chromatin dynamics on Cas9-mediated genome editing in human cells. Rene M. Daer, Josh P. Cutts, David A. Brafman, Karmella Haynes

 

DNAmod: the DNA modification database. Ankur Jai Sood, Coby Viner, Michael M. Hoffman

 

The ExAC Browser: Displaying reference data information from over 60,000 exomes. Konrad J Karczewski, Ben Weisburd, Brett Thomas, Douglas M Ruderfer, David Kavanagh, Tymor Hamamsy, Monkol Lek, Kaitlin E Samocha, Beryl B Cummings, Daniel Birnbaum, The Exome Aggregation Consortium, Mark J Daly, Daniel G MacArthur

 

Bright photoactivatable fluorophores for single-molecule imaging. Luke D Lavis, Jonathan B Grimm, Brian P English, Anand K Muthusamy, Brian P Mehl, Peng Dong, Timothy A Brown, Zhe Liu, Timothée Lionnet

 

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life. Soeren M Karst, Morten S Dueholm, Simon J McIlroy, Rasmus H Kirkegaard, Per H Nielsen, Mads Albertsen

 

Is there anything we missed for August? Anything in the list that catches your eye? Let us know in the comments section

 

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This month on the Node

Posted by , on 5 September 2016

August was meant to be a quiet month, with researchers (in Europe, at least)  leaving the lab for a well earned break and winding down before the start of the academic year…but here on the Node we’ve had another bumper month full of diverse content. Happy reading!

 

Meetings

IMG_5198

 

We had a wonderful report from Joaquín Navajas Acedo, Aleisha Symon and Tsai-Ming Lu from the Woods Hole Embryology Course. They really managed to capture the intense excitement and slight mania of the course, and I’m sure made a lot of readers eager to sign up for next year. I reported from the BSD-ISD in Boston: a fantastic conference, and a wonderful city. I also got to meet Yusuff and Mathew who carried on the SDB-BSDB interview chain (long may it continue!).

 

Research

Fig31280px-Praia_do_Porto_da_Barra_1

We found out about how mechanical signals influence stem cell fate, the link between sex, hormones and stem cells, the genomic changes that accompany multicellularity, the effects of aging on stem cell niches, and, in our latest ‘Day in the life…’ post, what it’s like to work on sponges in Brazil.  I also had the pleasure of revisiting a forgotten classic: Maria de la Cruz’s lineage tracing in the heart.

 

Meeting people is easy…

back et al

 

We started a new series to complement our usual research posts: The People Behind the Papers, highlighting the faces behind recent exciting developmental biology papers. We started with an interdisciplinary team from Heidelberg who uncovered how nuclear pore complexes get into the nuclear envelope, and then featured Thomas Lozito, author of a recent Development paper on lizard tail regeneration.

 

Research aides

facebase

The folks from DMDD told us about their latest batch of data, and we found out about FaceBase, a free online resource for craniofacial researchers. At the end of the month, Helena Jambor told us why we should never, ever use bar plots for statistical data.

 

 

 

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Assistant Professor Tenure Track Faculty, Division of Developmental Biology (DB) at Cincinnati Children’s Hospital Medical Center (CCHMC)

Posted by , on 2 September 2016

Closing Date: 15 March 2021

Applications are invited for a tenure track Assistant Professor faculty position in the Division of Developmental Biology (DB) at Cincinnati Children’s Hospital Medical Center (CCHMC). 

DB is home to a large community of developmental biologists (please visit our web site at: http://www.cincinnatichildrens.org/research/divisions/d/dev-biology/default/). We are a highly collaborative interdisciplinary group of basic scientists and clinicians studying fundamental questions in developmental biology, the genetic basis of pediatric disease and regenerative medicine.  Being embedded in CCHMC, one of the top ranking pediatric research centers in the world, creates a unique environment in which clinical translation of basic science is greatly enhanced. CCHMC is making a major long-term investment in basic and translational research and developmental biology is one of the pillars in this effort.
 
DB faculty have access to state of the art subsidized cores, to high-quality graduate and MD/PhD programs, and to training programs for postdoctoral fellows, clinical fellows, residents and clinical faculty. Successful candidates must hold the PhD, MD, or MD/PhD degrees, have recently completed postdoctoral training, have published significant original work and have a mature research plan.

Applicants should submit their curriculum vitae, two to three page research statement focused on future plans, and contact information for three people who will provide letters of recommendation to DB_devbiologists@cchmc.org. Applications must be submitted by December 2, 2016.

The Cincinnati Children’s Hospital Medical Center, and the University of Cincinnati are Affirmative Action/Equal Opportunity Employers. Qualified women and minority candidates are especially encouraged to apply.

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The people behind the papers: Kristen Koenig & Jeffrey Gross

Posted by , on 2 September 2016

Today’s paper is from the latest issue of Development and  introduces the squid Doryteuthis pealeii as a lophotrochozoan model for eye development. And the people are PI Jeffrey Gross, Director of the Louis J. Fox Center for Vision Restoration and Professor of Ophthalmology and Developmental Biology at the University of Pittsburgh, and lead author Kristen Koenig, who has recently started her own lab at the FAS Centre for Systems Biology at Harvard University.

 

Jeff and Kristen Balanced

 

So Jeffrey, can you give us the brief history of the Gross lab, and what key questions your group is trying to answer?

JG I started the lab 11 years ago at the University of Texas at Austin, and we moved about a year ago to the University of Pittsburgh Medical School.  We’re broadly interested in eye development and diseases.  Major questions in the lab focus on optic cup morphogenesis, the epigenetic regulation of retinal and retinal pigment epithelium development and regeneration.

To be honest, we’re rather unfocused, which I think is great! I encourage the students and postdocs in the lab to come up with their own questions and interests and then to go for them; this is the way I was trained as a Ph.D. student with Dave McClay, and I think it is the best way for Ph.D. students and postdocs to learn how to do science.  As a result, we’ve worked on a fairly diverse set of questions over the time I’ve had the lab and it really makes this is a fun job.

 

“I encourage the students and postdocs in the lab to come up with their own questions and interests and then to go for them; this is the way I was trained as a Ph.D. student with Dave McClay, and I think it is the best way for Ph.D. students and postdocs to learn how to do science.”

 

And Kristen: how did you come to join the Gross lab?

KK I decided to go to the University of Texas for graduate school because it seemed like an exciting research environment that had all the scientific resources one could want but was not a competitive or negative place to work. When choosing the Gross lab, I knew I wanted to study evolutionary questions but I was also concerned with generating a positive relationship with my advisor.  The eye is an excellent system to study the evolution and development of complexity and Jeff was amazingly supportive of crazy ideas so it was a good fit.  Also, the developmental biology community at UT was and still is a really exciting and supportive group of researchers.

 

Figure1
Stages 20-23 embryos stained with Sytox Green, from Fig. 1 in the paper.

 

While your lab usually works on zebrafish, your Development paper focuses on eye development and photoreceptor differentiation in the longfin inshore squid (Doryteuthis paeleii). So why cephalopods, and this squid in particular, for this project?

JG I’ve always been interested in evo-devo work and wanted us to do some work on eye evolution, but this project really didn’t start until Kristen Koenig joined the lab as a Ph.D. student.  The squid project was her idea and I just provided some advice on getting it started – she’s really the brains of the operation!

There is a long history of research using Doryteuthis pealeii at the Marine Biological Laboratory (MBL) in Woods Hole, MA and there is terrific infrastructure for collecting adults and obtaining gametes at the Marine Resources Center at the MBL.  Moreover, Kristen and I have spent a significant amount of time at the MBL, which is truly a magical place, so it made a lot of sense to use the resources there and our connections to build Doryteuthis pealeii as a model.  There are also worse places in the world than Woods Hole to have to spend a summer working in the lab!

 

“They are definitely charismatic embryos.  It is a pleasure to look at them for as long as I do.”

 

What’s it like working with squid? They look kind of cute…

KK Doryteuthis pealeii are great to work with.  They are a good size, develop at a reasonable pace, they are abundant and resilient to manipulations. Their eyes are quite large during development so for someone interested in visual systems they are quite exciting organisms. As you mentioned, they are definitely charismatic embryos.  It is a pleasure to look at them for as long as I do.

 

Fig2
Stages 24-29 of Doryteuthis eye development, from Fig. 2 in the paper

 

 

And you get the embryos from Woods Hole?

KK Yes.  During most of my dissertation work I spent every summer at the Marine Biological Labs in Woods Hole.  As Jeff mentioned, the Marine Resources Center there has an excellent capacity to provide access to adult squid and their eggs.  Without the MRC, none of this work would have been possible.  I only have embryos during the summer months so I have to plan my experiments for the year during that time.

 

Could you give us the paper’s key results in a short paragraph?

JG, KK Our research interest is to better understand visual system evolution across the Bilateria from a developmental perspective. We established the squid, Doryteuthis pealeii, as a lophotrochozoan model for complex eye development. Utilizing histological, transcriptomic and molecular assays we characterized eye formation in Doryteuthis pealeii. Through lineage tracing and gene expression analyses, we demonstrated that cells expressing Pax and Six genes incorporate into the lens, cornea and iris tissue, suggesting a convergent involvement in lens formation. We identified the sole source of retinal tissue in the squid and functional assays demonstrated that Notch signaling is required for photoreceptor cell differentiation and retina organization. These assays support a conserved role for notch signaling in neurogenesis in the cephalopod eye.

 

new pax
Pax6 expression in the placode stage, from Fig. 11 in the paper

 

Were there any particularly surprising results that came out of the lineage tracing?

JG, KK Our lineage tracing showed that the cells generating the optic lobe originated from a different place than originally thought.  This ultimately has consequences on how we interpret gene expression at these early stages and also suggests that these cells might be migrating to incorporate into the developing optic lobes.

 

I’m wondering about the question of conservation or convergence (of photoreceptor cell types and the molecular pathways that generate them, in metazoa). What does your work bring to the debate?

JG, KK The photoreceptor cells in the squid retina are rhabdomeric and express r-opsins. There is still a lot to understand about the molecular pathways that generate these cells to enable gene regulatory network comparisons across organisms.  Our work supports a role for notch signalling during neurogenesis within the squid retina.  This may illuminate a conserved function for notch within pseudostratified neuroepithelia.

 

“Just seeing the basics of eye morphogenesis continues to blow my mind.”

 

Was there any part of the work you were most proud of?

KK That’s a tough question because each part of the project presented its own set of unique challenges.  The part I still think about regularly is the staging series of eye formation.  Just seeing the basics of eye morphogenesis continues to blow my mind.  There is so much information in those images and when I look at them it only generates more curiosity and questions.

 

new fig 11
Squid fate map, mapped onto a microCT reconstruction, from Fig. 12 in the paper

 

And any part of the work that was particularly frustrating or intractable?

KK Some parts of the lineage tracing were challenging.  The experiment consisted of hundreds of embryos and had many steps and it was important to keeping track of every individual embryo at each step.  Also, half way through the experiment I had to trust the mail delivery system that my specimens wouldn’t get stalled in transit back to Texas and melt into a sad pool of defeat.  In the end I knew the experiment was possible but it was just very important to stay consistently focused and organized.

 

And you’ve left the Gross lab now? What’s next for you?

KK Yes, I just recently left Texas.  I am now at the FAS Center for Systems Biology at Harvard University.  I am a John Harvard Distinguished Science Fellow and am starting my own lab continuing to study squid eye formation and the evolution and development of visual systems more broadly.

 

Now you have this squid developmental resource, any future plans to carry on with Doryteuthis? What do you want to know now?

JG I hope to, if Kristen doesn’t mind letting me squat in her lab at Harvard from time to time!  The way the lens develops in the squid is fascinating, and I think the cell biology underlying this will be fun to study.  I hope that we’ll be able to take a look at this in more detail over the next few summers, and use some of the molecular and imaging tools that Kristen has developed to drill down to the mechanism.


 

Eye development and photoreceptor differentiation in the cephalopod Doryteuthis pealeiiKristen M. Koenig, Peter Sun, Eli Meyer, Jeffrey M. Gross. 
Browse the People Behind the Papers archive here
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A Tale of Trunks or Zen and the art of doing a PhD

Posted by , on 1 September 2016

The story of this paper is also the story of my PhD. It begins as most papers and PhDs do: with a distinct and often unrelated starting project or plan. It is great to have a plan. But time and luck and data bend and twist the plan; until it finally breaks and you end up ditching said plan.

Then the real fun can begin.

 

I – Enter the plan

Vertebrates are an incredibly diverse group of organisms, as demonstrated by the wide range of body shapes and sizes animals belonging to this group can exhibit. This remarkable flexibility was likely a decisive factor allowing for the amazing adaptation of vertebrates to almost all habitats throughout the globe. The general body plan of a vertebrate is usually determined in embryonic development during the process of axial extension, in which the embryo elongates in a rostral to caudal progression by the activity of a very particular population of cells located in the posterior embryonic end. These are the axial progenitors, and their job is to proliferate and give rise to all post-cranial structures of the embryo (Wilson et al., 2009). Yet, an in-depth study of this important cell population was – and still is – hindered by the lack of specific molecular markers.

My initial project was then, to do a molecular characterization of axial progenitors in the mouse embryo; and my supervisor, Moisés Mallo, and I had a nice, neat strategy designed to fish these markers out. At the same time – like a responsible and efficient (and somewhat neurotic) PhD student – I had compiled quite a list of candidate genes that might be expressed and/or could potentially be important to axial progenitors just by searching for truncation phenotypes in existing databases. This way I could screen those genes while waiting for the other experiment’s results. One of these candidate genes was Oct4.

 

II – How I met Oct4

Oct4 is the gene equivalent of a rock star. Besides being an integral part of the core pluripotency network, Oct4 is also famously known for being an indispensable part of the reprogramming cocktail able to turn somatic cells back into pluripotent stem cells (Takahashi and Yamanaka, 2006). All vertebrate species studied so far seem to have a functional Oct4 counterpart (Frankenberg et al., 2014). In the mouse embryo, Oct4 is expressed as early as the two-cell stage, becoming gradually down regulated as development progresses until its complete silencing in somatic tissues by mid-gestation stages. However, in 2013, a paper came out by DeVeale and colleagues (DeVeale et al., 2013), which showed that, if Oct4 was inactivated during a very particular window of developmental time, some of the resulting mouse embryos could exhibit significant axial truncations, while others showed dramatically shortened trunks, yet perfectly specified tails. The latter were remarkably similar to a variety of transgenic embryos we had described just a few months before, in which the type I TGF-β receptor Alk5 was constitutively active in axial progenitor-containing areas (Jurberg et al., 2013). This showed that not only Oct4 seemed to be important for trunk development, but also suggested the existence of some sort of inverse functional link between Oct4 expression and TGF-β signalling through Alk5 during mouse axis elongation.

 

But was that really true? At that point, I and my good friend and former labmate Arnon D. Jurberg had been working with this pathway for quite some time, specifically with the Gdf11 mutant. Gdf11 is the main ligand for the Alk5 receptor in vivo, and mutants for both these proteins have characteristically longer trunks due to a delayed trunk to tail transition (Andersson et al., 2006; Jurberg et al., 2013; McPherron et al., 1999). So we definitely knew that these molecules were important for axial progenitors during the extension process. Thus, we decided to put this putative functional connection to the test using our faithful Gdf11 mutant. We reasoned that if premature activation of Alk5 activity was equivalent to the absence of Oct4 during axis formation, and this excess signalling was able to generate shorter trunks, then perhaps the lack of signalling through Alk5 – by absence of Gdf11, for example – could result in an increased expression of Oct4 and that could maybe account for the longer trunks in these mutants. Admittedly, it was a bit of a stretch. But to our vast surprise and amazement, our preliminary results showed us that we might actually be right. 

 

III – Oct4 and the “snakefied” mice

Proving beyond any doubt that Oct4 was really and truly ectopically expressed in Gdf11 mutants took sensibly two years, three different methodologies and a healthy dose of stubbornness. However, in the meantime, we still wanted to know if Oct4 missexpression was responsible for the longer trunks these mutants showcased, which required a way to overcome its progressive downregulation throughout development. Therefore, we chose to take advantage of the Cdx2 promoter, which we had previously demonstrated to be active in axial progenitors, and use it to drive Oct4 expression in transgenic mouse embryos. So it was a dark December day – and a national holiday to boot – when Moisés and I were lucky to dissect together a particularly good batch of E18.5 transgenic embryos courtesy of Ana Nóvoa, transgenic wizard extraordinaire. And the results surpassed even our wildest expectations. Not only were we able to obtain embryos that mimicked the Gdf11 mutant axial phenotype, we also got fetuses that yielded up to 20 or 30 trunk segments (Fig.1). Which meant two things: first, that Oct4 missexpression was most likely the main factor responsible by the longer trunks in Gdf11 mutant embryos; and second, that the trunk to tail transition could be delayed almost indefinitely if you just maintained the right level of Oct4 activity during axial extension.

 

Fig.1: Sustained Oct4 expression in axial progenitors extends the trunks in mouse embryos. Skeletal analysis of a wild type, a Gdf11-/- and three Cdx2-Oct4 transgenic embryos at E18.5 with increasing strengths in their phenotype. The number of thoracic (T) and lumbar (L) vertebrae is shown.

 

IV – How the snake got its curves

Needless to say, if something has long, rib-packed and organ-filled trunks… well, it’s snakes. Could Oct4 have a role in the making of their long trunks too? For that we needed to check its expression during snake embryonic development, which was most definitely not our area of expertise. We decided to ask for help from Francisca Leal and Martin J. Cohn from the University of Florida, proud owners of a lovely snake facility and source of infinite wisdom in all snake-related matters. We hit the jackpot: expression studies revealed that Oct4 was still present in snake embryos long after it was gone in equivalently staged mice embryos (Fig.2). That made for a classic case of gene expression heterochrony, in which the timing of a gene’s activation or silencing changes from one species to another.

 

The node_2
Fig.2: Oct4 expression snake embryos. A. Oct4 expression in a corn snake embryo shortly after it underwent trunk to tail transition. B. Close up of the lower trunk/tail region.

 

What could have possibly happened during evolution for Oct4 to be so differently regulated in these two groups of organisms? Thanks to Francisca and her sequence analysis skills, we found out that the genomic landscape upstream of the snake Oct4 locus had diverged dramatically from mice and even lizards. Yet, this entire region was extremely well conserved among snakes. As sequence conservation generally means conservation in function, we wondered if these conserved non-coding sequences 5’ of snake Oct4 had any regulatory potential by testing them in mice. We found that a tiny, little 250bp region – the only region conserved in both lizard and snake species – was extremely active on its own, whereas when embedded within larger snake-specific sequences it was a lot less able to drive reporter gene expression. But these were only scattered, isolated pieces of a bigger puzzle. When we used a snake BAC containing the whole genomic context around Oct4 – a kind gift from Isabel Guerreiro and Denis Duboule – and got no expression in transgenic mice, we realized that this entire region most likely operated as a complex regulatory module, composed by a 250bp core regulatory enhancer under the additional control of neighbouring sequences. In the end, we think that the remarkable conservation in snake non-coding sequences probably resulted from strong selective pressures over Oct4 expression due to the adaptation to a fossorial lifestyle, which favoured long trunks for burrowing and prey constriction.

 

V – Epilogue

So there you have it: the story of how ditching the initial plan can be a good thing, if you just pay attention and let it happen. Especially when results start acquiring a life, to tell a story of their own. Go with the flow. Get really curious and excited. Talk to people, ask for help, and help out even more. And maybe, just maybe, you might stumble across something that, ultimately, turns out to be your dream Evo-Devo project.

 

 

References

Aires R, Jurberg AD, Leal F, Nóvoa A, Cohn MJ, Mallo M. (2016) Oct4 Is a Key Regulator of Vertebrate Trunk Length DiversityDev Cell. 2016 Aug 8;38(3):262-74

Andersson, O., Reissmann, E. and Ibáñez, C. F. (2006). Growth differentiation factor 11 signals through the transforming growth factor-beta receptor ALK5 to regionalize the anterior-posterior axis. EMBO Rep. 7, 831–7.

DeVeale, B., Brokhman, I., Mohseni, P., Babak, T., Yoon, C., Lin, A., Onishi, K., Tomilin, A., Pevny, L., Zandstra, P. W., et al. (2013). Oct4 Is Required ˜E7.5 for Proliferation in the Primitive Streak. PLoS Genet. 9, e1003957.

Frankenberg, S. R., Frank, D., Harland, R., Johnson, A. D., Nichols, J., Niwa, H., Schöler, H. R., Tanaka, E., Wylie, C. and Brickman, J. M. (2014). The POU-er of gene nomenclature. Development 141, 2921–3.

Jurberg, A. D., Aires, R., Varela-Lasheras, I., Nóvoa, A. and Mallo, M. (2013). Switching Axial Progenitors from Producing Trunk to Tail Tissues in Vertebrate Embryos. Dev. Cell 25, 451–462.

McPherron, A. C., Lawler, A. M. and Lee, S.-J. J. (1999). Regulation of anterior/posterior patterning of the axial skeleton by growth/differentiation factor 11. Nat. Genet. 22, 260–264.

Takahashi, K. and Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676.

Wilson, V., Olivera-Martínez, I. and Storey, K. G. (2009). Stem cells, signals and vertebrate body axis extension. Development 136, 2133–2133.

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