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MSc/PhD Student Position “Using Fruit Flies to Characterize Mechanisms of Nerve Cell Degeneration or Proliferation” University of Alberta, Edmonton, Alberta, Canada

Posted by , on 15 March 2016

Closing Date: 15 March 2021

One MSc or PhD student position is available for a September 2016 start date to study mechanisms determining the degeneration or the proliferation of neurons using the D. melanogaster fruit fly model. The two complementary projects will use common assays to investigate the following questions: i. How does calcium and redox signaling between the Endoplasmic Reticulum (ER) and mitochondria determine neuronal degeneration and inflammation. ii. How does the neurofibromatosis type 2 gene product Merlin determine neuronal proliferation. The project is part of a collaboration between the Simmen and Hughes laboratories that aims to further use the fruit fly model organism for the characterization of the fundamental cell biology behind neurodegeneration and childhood tumors of the nervous system. A publication list and more information about the labs can be found on these two sites

http://www.cellbiology.ualberta.ca/FacultyMembers/ThomasSimmen.aspx

http://www.cellbiology.ualberta.ca/FacultyMembers/SarahHughes.aspx

The location of the research project is at the University of Alberta, the 5th largest University in Canada with world-class biomedical research labs. The University of Alberta Cell Biology graduate program is amongst the best Cell Biology programs worldwide. Edmonton is a culturally vibrant, young city that lies in close proximity to the Rocky Mountains, offering excellent opportunities for sports enthusiasts.

Minimal requirements are competitive grades from an internationally acclaimed University. Applicants need to provide a cover letter that outlines their career objectives and why they would like to enter a PhD program, CV and scanned university grades. Outstanding applicants from Europe are encouraged to apply, but must have excellent English knowledge both spoken and written (high TOEFL/GRE scores or equivalent). Successful applicant will have to enter the University of Alberta Cell Biology graduate program. Detailed instructions for prospective applicants can be found here

http://www.cellbiology.ualberta.ca/~/media/cellbio/Documents/GraduateManualOct2015.pdf

Address further inquiries to Thomas.Simmen@ualberta.ca or Sarah.Hughes@ualberta.ca

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Special Issue on Organoids

Posted by , on 15 March 2016

In vitro organogenesis has exploded onto the stem cell and developmental biology scene. It is now possible to make  miniaturised approximations of many different organs – known as organoids – entirely in vitro, using either pluripotent stem cells or adult tissue stem cells as starting material. Coaxed towards their fate by various signalling molecules and growth factors, these self-organising populations faithfully recapitulate many of the developmental milestones associated with their in vivo counterparts, and can be used to model both developmental and disease processes.

 

To highlight the terrific progress that is being made in this field, and to draw attention to the enormous potential that organoids hold for understanding developmental and regenerative processes, Development is proud to announce a Special Issue on Organoids.

 

MelissaProf. Melissa Little – who recently published a spectacular report on growing kidney organoids – will be Guest Editor of the Special Issue, which is scheduled for publication in early 2017. For more information about the Special Issue, including scope, article types and deadlines, click here. You can read an Editorial from Melissa and discover why she’s excited about the emerging organoid field here, or read Catarina Vicente’s “An interview with Melissa Little” here.

 

Many people share a great enthusiasm for organoid research, especially for how it can be used to study human development. In the video below, Development’s Executive Editor Dr Katherine Brown chats with Dr. Juergen Knoblich, whose report of cerebral organoids (or “minibrains” as they’re known) was heralded as one the major breakthroughs of 2013. In the interview, Juergen talks about why the world was so captivated by his research, whether the minibrains are truly recapitulating development and what the future challenges are for the organoid field.

 

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An interview with Melissa Little

Posted by , on 15 March 2016

This interview first appeared in Development.

 

Melissa Little is a Senior Principal Research Fellow at the Murdoch Childrens Research Institute in Melbourne, Australia. Her lab has studied kidney development and regeneration for over 20 years, recently making notable advances in the generation of kidney organoids from human iPSCs. We chatted with Melissa about her career, her thoughts on the potential of the organoid and stem cell fields, and what she hopes to achieve during her guest editorship with Development.

 

MelissaHow did you first become interested in biology?

As a child I was fascinated by the world around me. I spent a lot of time camping in the Australian outback and found the plants, animals and insects just fascinating.

 

You started your research career as a cancer biologist. How did you eventually move on to studying kidney development?

At university I enrolled in science, assuming I was going to study botany or zoology. But I loved my first-year course in physiology, so my primary degree is actually in this area. Molecular biology was just beginning during my PhD, so I worked on the molecular basis of childhood cancer. I worked on Wilms’ tumour (a childhood kidney cancer), before the WT1 gene was isolated, and later worked on WT1 during my postdoc with Nicholas Hastie in Edinburgh. The paradigm at that time was the two-hit hypothesis, i.e. that to get a cancer you needed a hit in both copies of a tumour suppressor gene. This hypothesis was based on retinoblastoma. Whereas the RB1 gene is expressed everywhere, WT1, by contrast, is very confined in its expression during development, being restricted to the urogenital system. So, while mutations in this gene give rise to kidney cancer, they can also give rise to urogenital developmental anomalies. When I returned to Australia I continued to work on WT1. However, I was now based in a research institute with strong developmental biology, such as the work of Peter Koopman and Toshiya Yamada, so I changed direction to study WT1 and other genes in kidney development.

 

How important were the years that you spent as a postdoc in Edinburgh?

They had an enormous impact. I was a Royal Society Fellow, a relatively new scheme at that time. I had offers in the USA, but I had visited Nicholas in Edinburgh and really wanted to go to the MRC. The unfortunate rule of that fellowship was that after two years I had to return to Australia. But those years in the MRC were incredibly important to me. They shaped how I work as a scientist, how I interact with other scientists and how I approach answering questions in science. Nicholas was an extremely positive mentor and it was great to interact with people such as Wendy Bickmore, Ian Jackson and Veronica Van Heyningen. It was a very formative period of my career.

 

What are the challenges of establishing your lab in a relatively isolated country like Australia?

One of the surprising things about being in the UK was that amazing scientists wandered through the building on a regular basis. That didn’t happen in Australia. At that time there was no internet. The latest copy of Nature arrived by sea. By the time it appeared in the library it was already three months out of date. The isolation was immense. It was very difficult to keep pace with what was happening in science and to be at the forefront of anything because we were so far behind in our capacity to know what else was happening. I found that acutely oppressive when I came back to Australia in 1992.

The internet completely changed that. It made international collaboration feasible. We have real-time access to journals, we can search for articles (and there is far more published now than anyone could ever consume), we can electronically communicate in real time, and so on. Science has become much more feasible at an international level. Indeed, I have collaborations all around the globe. However, Australia is still a very long way to anywhere. To actually meet someone and talk face to face, which is quite important, you must travel. And I travel extensively. I don’t think people in the USA, for example, understand how taxing that is. I remember doing a talk in Italy where I was on the ground for less time than I was in the air. That is not that unusual, but it is pretty physically brutal. So, Australians travel a lot because they have to.

 

You initially established your lab in Brisbane but recently moved to Melbourne. What were the reasons for this change?

I was at the University of Queensland for 23 years, and that is a very long time to be in one place. I was in a really excellent institute, but my research evolved to have a regeneration and stem cell aspect to it, and I was relatively alone there in that respect. We were on a large academic campus but quite remote from any hospital. I did my PhD at the Queensland Medical Research Institute, which was located at a hospital, and my thesis supervisor was the head of oncology and haematology, so I had been in an environment quite closely associated with patients. I wanted to move back to an environment that had, first of all, more stem cell biology, and second, access to nephrologists. At the Murdoch Childrens Research Institute I am physically located in a children’s hospital. I now have very close associations with clinical geneticists and nephrologists, and we are setting up a clinic where we derive patient stem cell lines. That has been a really good part of the move.

 

What scientific questions is your lab working on at the moment?

We are the kidney development, disease, repair and regeneration lab, because we cover quite a wide range of kidney medicine. However, everything we do is underpinned by our understanding of kidney development. That is paramount. My most important message is that stem cell biology on any organ requires you to understand that organ intimately, so understanding development is key. We then use that information to direct stem cells towards a kidney fate in order to understand the relationship between development and disease. We also look at what the postnatal kidney can or can’t do to repair itself. We increasingly do human pluripotent stem cell work, but we still investigate really fundamental developmental biology questions – for example, how cells move, how they communicate with each other, how they self-organise during development, and what genes they express at what time.

 

Last year your lab published a high-profile paper in Nature, reporting the generation of kidney organoids from human iPSCs. Had this always been a goal of your lab?

It was a very specific and deliberate objective. Around 15 years ago, when stem cell biology was really starting out (around the time that Jamie Thomson derived the first human pluripotent stem cell lines and Perry Bartlett showed evidence that there were postnatal stem cells in the brain) I decided to change our research focus towards regenerative medicine. We started with every option on the table. We didn’t know what the postnatal kidney could do (we now know that it can repair quite well but can’t regenerate), whether there were postnatal stem cells or whether pluripotent stem cells could be differentiated to a kidney fate. In fact, cellular reprogramming was not even discussed at that time. There were a lot of things we wanted to try for kidney regenerative medicine and the differentiation of pluripotent stem cells was one of those. We were very systematic and it took quite a long time to get there.

 

Your ‘mini-kidneys’ paper was extensively covered in the mainstream media. How was your experience interacting with the media?

It would be lovely to control the media but no one can. Sometimes I cringe when I read what journalists write. They make broad generalisations that might lead a patient to think that a cure is around the corner, which is not true. This is the nature of the media. Some of the interviews I did were, I think, poorly represented, whereas some of them were great. You just roll with it. I don’t worry too much about those events that are less than perfect, because I can’t control them.

 

The organoid field is a new and exciting area. How much potential do you see in these techniques? Do you think it will be possible to build a full organ in a dish, as the media claims?

I think the media overestimates how far we have come. Organoids are fascinating and a really exciting area, but we are a very long way away from the clinic. ‘Organs in a dish’ is a funny expression, but I actually believe that although we have a long way to go, we will genuinely get there. I think there are some very short-term outcomes from this type of research that fall into the remit of both fundamental and translational biology. This is the first time that we can really start to pull apart human development. The developing human itself is not something we have had any access to, so we do have a circular problem: how can you know that what you are growing from a human cell is actually like a human? From what we can see so far, however, it is a pretty remarkable model. Hence, it really is a door into human development and that is very exciting. From a more practical point of view, I am very interested in what can be achieved with disease modelling and drug screening, even personalised drug screening. However, we need to be vigilant about how we develop these tools. I am already seeing publications claiming that organoids in a dish are accurately modelling disease but there are such challenges with interclonal and experimental variation that I think this still has to be definitively proven.

In the long term what we have is an approach where cells organise themselves based on embryological principles, and this is amazing from a fundamental science point of view. It will actually give us a handle on how cells self-organise. We make a lot of assumptions about how self-organisation works: cells differentially stick to each other or make growth factors that make other cells wander towards them. Now we have models where we can really pull that apart. From a translational point of view, this sort of information will then become an engineering challenge. How do we build these structures with a vasculature? How do we ensure a degree of anatomical correctness that will be helpful for patients? For example, the kidney organoids are currently of no value to a patient that requires a transplant as they have no exiting ureter to remove the urine. The kidney is, I would argue, the hardest thing you could ever try to generate in vitro. It is architecturally completely constrained and its function is totally dependent upon its anatomy. What we have at the moment is too small and indeed dysplastic, so there is a lot that we have to do better. But I think it is achievable with time.

 

You recently started your guest editorship with Development. What do you hope to achieve in this year with us?

I am really keen to encourage more of the development field to embrace what stem cells can give us, despite some reticence so far. There are enormous opportunities here to look at development in a different way. I want to open the door on investigating human development using directed differentiation, especially using these types of organogenic models (Little, 2016).

 

How do you see the relationship between the developmental biology and stem cell fields evolving?

I think the nexus between developmental biology, cell biology and stem cell biology is very exciting. There have been amazing advances in imaging in the developmental biology field, particularly by those working on what we would call ‘simple’ organisms, such as the worm or the fly. They have phenomenal expertise in temporal-spatial imaging, right down to the cellular level. Meanwhile, the cell biologists are building tools to look at mechano-biology and real-time reporting of pathway activity. To layer these advances on organoid creation from a pluripotent cell in a dish, which is where stem cell biology is going, is an enormously powerful approach.

 

What kind of papers would you like to see more of in Development?

I would like to see more papers looking at the fundamental processes governing how cells organise themselves, whether that’s during normal organogenesis in vivo or in a model in vitro. In the past, molecular biology superseded fundamental, anatomical developmental biology. Looking at aspects such as self-organisation was put to one side because it was considered too descriptive. I think it would be valuable to bring these fields back together and ask ‘what is the molecular basis of self-organisation during embryogenesis?’.

 

You were a member of the Australian Government’s Strategic Review of Health and Medical Research in 2013. Do you think it is important for scientists to play a role in policy?

Yes. I have had the opportunity to play a role in national scientific policy throughout my career. I was not only involved in this review but also in a seminal review of health and medical research in Australia in 1998, when I was still a young scientist. I have played roles within the Research Committee of the National Health Medical Research Council, have advised the federal government on science policy and around the debate on embryonic stem cells, and the state government on biotechnology policy. I simply see this as part of my professional obligations as a scientist. Too many young scientists forget that science is a less tangible product, not like making bricks or building boats. We are still primarily funded by tax payers, in Australia almost exclusively. The tax payers expect health outcomes, particularly in health and medical research. If we do not engage, not just in policy discussions but also in public communication, we only have ourselves to blame if the public loses interest in funding science, or worse, loses faith in scientists. One thing that I learnt very early is that there is a tendency for scientists to think that we just need to educate everyone and then they’ll understand why science is important. It is not about education. People can make decisions without facts and often do. They don’t need to be educated, they need to be engaged with. That is a very different process. It means you need to be in the room, to be having the conversation and discussing what you are doing and why.

 

What is your advice for young scientists?

Follow your heart. You have to be fundamentally passionate about finding an answer to a question. Have lateral vision and take every opportunity that comes your way. Don’t assume that what you read is right and question everything.

 

What would people be surprised to find out about you?

First and foremost, I’m a mum with two kids. In high school I was the top student in my year at art and English, not science. Perhaps this is why developmental biology is attractive to me. It is so beautiful. I actually won a prize in creative writing as a teenager. Someone recently asked me whether I still do any creative writing. I write grants and manuscripts. That is a creative process, even if it is describing data. I still paint for leisure, although not often enough.

 

Reference:

Little, M. H. (2016). Closing the circle: from organoids back to development. Development 143, 905-906

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In Development this week (Vol. 143, Issue 6)

Posted by , on 15 March 2016

Here are the highlights from the current issue of Development:

 

Knocking the SOX off obesity

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Growth restriction in utero is associated with increased risk of obesity in later life. Recently, epigenetic inheritance was identified as an important component of this phenomenon, but the precise molecular mechanisms that underpin the association between growth restriction and obesity remain unknown. Now, on p. 950, Walter Stünkel and colleagues report a role for SOX6 in adipocyte differentiation, and suggest that SOX6 may be a key player in the association between growth restriction and obesity. By comparing adipocytes differentiated from mesenchymal stem cells from normal and growth-restricted newborn umbilical cords, the authors show that SOX6 is upregulated in growth-restricted adipocytes and that it activates key adipogenic players including PPARγ, C/EBPα and MEST. The authors also show that SOX6 interacts with β-catenin, possibly inhibiting WNT/β-catenin signalling to promote adipogenesis. Importantly, the role of SOX6 in regulating adipogenesis was also demonstrated in vivo, using Sox6 antisense oligonucleotides to target white adipose tissue in mice. Taken together, these data demonstrate a clear role for SOX6 in regulating adipocyte differentiation and adipogenesis in vivo, and provide a possible mechanistic link between growth restriction in utero and obesity in later life.

 

New player in neonatal heart repair

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The mammalian heart has a transient regenerative ability during the neonatal stage. This ability depends on the replicative potential of endogenous cardiomyocytes; however, the underlying transcriptional network that controls cardiomyocyte replication during neonatal heart regeneration remains poorly understood. In this issue (see p. 936), Bin Zhou and colleagues investigate the role of GATA4 – a transcription factor that is crucial for cardiac specification and development – in cardiomyocyte turnover and neonatal heart repair. The authors utilised cryoinjury and apex resection models in a neonatal transgenic mouse in which they could control expression of GATA4 specifically in the cardiomyocytes. Following injury, the authors observed severely compromised ventricular function in Gata4-ablated mice, which was accompanied by reduced cardiomyocyte replication and hypertrophy. Importantly, the authors identified FGF16 as a downstream effector of the Gata4-ablated phenotype, and showed that cardiac-specific overexpression of FGF16 promoted cardiomyocyte replication and improved heart function after injury. These data identify GATA4 and FGF16 as important mediators of neonatal heart repair and bring hope for the possibility of paracrine-mediated repair in the adult heart.

 

A better MAP(K) for tubule elongation

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Branching morphogenesis is fundamental to the development of multiple organs, including the lungs, kidneys, vasculature and mammary glands. Tubule elongation is a crucial part of branching morphogenesis and relies on the balance between cellular proliferation and migration to achieve appropriate growth. In the developing mammary gland, receptor tyrosine kinases (RTKs) regulate tubule elongation, but the relative contribution of proliferation and migration is largely unknown. Now, on p. 983, Andrew Ewald and colleagues use fluorescent reporters and real-time imaging to investigate the role of RTK signalling in tubule elongation in a 3D mouse mammary tissue culture system. The authors show that ERK signalling is required for cell migration and elongation of budding branches, but that cell proliferation is not acutely required for branch elongation. Importantly, the authors show that mosaic expression of MEK, which activates MAPK, is sufficient to induce initiation and elongation of mammary branches. This study provides a fundamental advance in our understanding of the cellular mechanism and molecular control of tube elongation in the developing mammary gland.

 

PLUS…

 

Closing the circle: from organoids back to development

Organoid imageThis Editorial, from our Guest Editor Melissa Little,  looks at the emerging field of in vitro organogenesis and discusses how organoid technology can be applied to better understand developmental processes. Read the Spotlight on p. 905

 

An interview with Melissa Little

MelissaMelissa Little chats about her research and career, the potential of the organoid and stem cell fields, and what she hopes to achieve during her guest editorship with Development. Read the Spotlight on p. 907

 

 

***  find out more about our upcoming Special Issue on Organoids ***

 

From single genes to entire genomes: the search for a function of nuclear organization

DEV910Here, Ringo Pueschel, Francesca Coraggio and Peter Meister highlight the genome-wide techniques that have been used to shed light on the mechanisms of genome folding and unravel the regulatory functions of nuclear organization. Read the Review on p. 910

 

Development of the lymphatic system: new questions and paradigms

DEV924Jonathan Semo, Julian Nicenboim and Karina Yaniv discuss the molecular mechanisms controlling lymphatic system development and highlight recent findings that shed light on previously uncharacterised sources of lymphatic endothelial cells. Read the Review on p. 924

 

 

 

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Editorial- Closing the circle: from organoids back to development

Posted by , on 15 March 2016

This editorial was written by Melissa Little and first appeared in Development.

 

Organogenesis is an inherently fascinating developmental process. It requires the creation of complex form and function from a collection of distinct cell types, all of which come together without a template. To achieve this, cells within the developing organ undergo differentiation, migration, proliferation and appropriate growth and scaling in a spatially and temporally controlled manner. Moreover, many organs retain throughout life a capacity to regenerate or repair in response to injury in order to maintain function. Studies on both embryonic organogenesis and postnatal tissue homeostasis and repair have been essential foundations to the field of stem cell biology, as it is the stem/progenitor populations involved in these processes that are key. To date, our understanding of organogenesis, and to a lesser degree stem cell biology, has largely been based on animal models. The conservation of genes across organisms perhaps emboldened the view that we can infer knowledge of human development from animal models, but the lack of parallels shows that this is not the case. Instead, it is our capacity to examine stem cells from humans that is filling this gap. It is now possible to recreate miniature approximations of many human organs, referred to as organoids, entirely in vitro. Generated from either human pluripotent stem cells (PSCs) or human adult epithelial stem cells, organoids offer unprecedented insights into human developmental processes and can also be used to model postnatal repair and disease. As a result, organoid biology is at the forefront of our developmental studies in the human. For this reason, I am honoured to have been appointed Guest Editor at Development, with a particular focus on the emerging field of in vitro organogenesis, and with the aim of publishing a Special Issue on the topic (for more details, see below).

Two of the most seminal breakthroughs in recent decades have been the derivation of the first human embryonic stem cells (Thomson et al., 1998) and the reprogramming of human somatic cells to pluripotency (Takahashi et al., 2007). The development of protocols to direct the differentiation of human PSCs towards specific endpoints has resulted in the generation of derivatives of all three germ layers, including nerves, cardiac muscle, pancreatic beta-cells, hepatocytes and blood. Most of these studies have drawn heavily on our underlying knowledge of the morphogens involved in patterning the same cell types during embryogenesis. While initial focus was placed on generating specific target cell types, the cultures themselves began to reveal order amongst the complexity, with the formation of highly patterned multicellular structures in vitro. This occurred most notably when cultures were provided with some degree of three-dimensional space within which to interact; for example, as part of an embryoid body or with the support of an extracellular matrix such as Matrigel. The first study to recognise the emergence of a self-organising but recognisable tissue from human PSCs was less than five years ago, with the generation of a patterned optic cup from the group of Yoshiki Sasai (Eiraku et al., 2011). What followed this seminal study was a growing number of reports describing organotypic morphogenesis as a result of the directed differentiation of human PSCs. Human PSC-derived organoids of the cerebral cortex, adenohypophysis, small intestine, stomach, lung, liver and kidney have now been reported (reviewed by Huch and Koo, 2015). In all cases, these organoids contain distinct cellular components patterned in a morphologically appropriate fashion – a level of cellular complexity previously thought unattainable in vitro.

These advances are exciting not only because they represent the long-term possibility of organ regeneration, but also because they provide a new approach to studying human morphogenesis and development. But the challenges here are immense. Are we sure that a cerebral organoid that appears to show evidence of an appropriate multicellular composition and gene expression profile is a sufficiently accurate model of human brain development? Can we reliably sustain such tissue long enough under appropriate conditions to allow it to mature as it would in vivo? If these questions are not appropriately addressed, there is a danger that the field will become absorbed by the characterisation of what are no more than in vitro dysmorphologies or models of abnormal patterning. This will require disciplined and thorough analyses that take into account what the stem cell field, particularly the induced PSC field, already appreciates is substantial experimental variability. Access to human fetal tissue signatures has been, and will continue to be, essential to ensure that we are on the right track. Indeed, single-cell profiling data comparing human cerebral organoids with developing human fetal brain show remarkable congruence, which is very encouraging (Camp et al., 2015). Based on the assumption that PSC-derived organoids do indeed represent a model of human development, we can be sure that their application will extend beyond developmental biology to personalised drug development, disease modelling, functional genomics and even bioengineering.

Organoids can also be generated from adult stem cells, such as those first reported by the group of Hans Clevers from the intestinal epithelium (Sato et al., 2009). This capitalises on the presence of an epithelial stem cell population in many postnatal organs. Organoids have now been derived from the epithelial stem cell populations of a wide variety of postnatal tissues, including lung, colon, prostate and liver (reviewed by Huch and Koo, 2015). In all instances, these organoids are composed exclusively of epithelial cell types supported by the provision of an extracellular matrix surrogate for surrounding mesenchymal tissues. Adult stem cell organoids have taught us much about the regenerative populations present in many postnatal tissues and the mechanisms by which these populations maintain homeostasis. Their applications in the understanding of disease and in personalised drug screening are now coming to the fore.

Organoids will not only advance our understanding of human development and tissue turnover, but also of morphogenetic principles. A major paradigm in morphogenesis has been the concept of positional information, initially described by Wolpert (1969). That concept proposed that morphogenesis during embryonic development results from the relative position of cells with respect to each other and the secreted morphogen gradients they experience. Revised views of this concept have taken into account a capacity for heterogeneous populations to create form without a predefined pattern – a phenomenon known as self-organisation. This has never been more evident than in what is now being observed in organoid studies, where complicated, multicellular form is created from a single starting cell type, and without the complete set of spatial cues normally present in an embryo. The robustness with which a complex structure can arise in vitro is surprising. More importantly, it provides the field with a capacity to re-evaluate the underlying principles governing morphogenesis and tissue homeostasis. Coupled with continuous advances in our capacity to image developing tissues at the resolution of individual cells across time and space, investigations into how organoids arise could well lead to rapid advances in our understanding of fundamental developmental principles.

The excitement of what organoid biology can add to our understanding of development has grown exponentially over the last few years, with several scientific meetings dedicated to discussing progress in this area. Development recognises that this is an exciting and rapidly expanding area, which is why we are announcing a Special Issue on organoids, to be published in early 2017. This will include Review articles from the pioneers and leaders of the field, as well as primary papers on topics ranging from methods and techniques for organoid formation to modelling developmental processes and diseases using organoids, in both human and non-human systems. As Development’s Guest Editor, I will be taking a lead on coordinating this Special Issue, and invite interested readers to find out more about it – including further details on the issue’s scope and how to submit your work for consideration – on our website (http://dev.biologists.org/content/special-issue-organoids). We look forward to receiving your submissions.

In summary, the past decades have seen developmental biology guide us into stem cell biology, with developmental principles continuing to underpin this field. This is perhaps nowhere as compelling as in the generation of organoids. In turn, the generation of organoids is beginning to teach us not only about human development, but also about general developmental principles, helping to build an information flow in the reverse direction in a way that was previously impossible. The challenge now is to close the circle completely using organoid systems to reinforce the link between stem cells and developmental biology, which will bring these two fields closer together than ever before.

 

References

Camp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Bräuninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M. et al. (2015). Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl. Acad. Sci. USA 112, 15672-15677.
Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K.,  Adachi, T. and Sasai, Y. (2011). Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51-56.
Huch, M. and Koo, B.-K. (2015). Modeling mouse and human development using organoid cultures. Development 142, 3113-3125.
Sato, T., Vries, R. G., Snippert, H. J., van de Wetering, M., Barker, N., Stange, D. E., van Es, J. H., Abo, A., Kujala, P., Peters,  P. J. et al. (2009). Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262-265.
Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K. and Yamanaka, S. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872.
Thomson, J. A., Itskovitz-Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S. and Jones, J. M. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282, 1145-1147.
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What would you ask Nobel Prize Laureate Shinya Yamanaka?

Posted by , on 14 March 2016

It’s been 10 years since induced pluripotent stem cells (iPSCs) were first reported from the lab of Prof. Shinya Yamanaka. Since then, the field of direct reprogramming has grown immensely, and iPSCs have proved themselves to be an extremely useful and versatile tool, enabling research into basic developmental biology, the mechanism of reprogramming itself, as well as translational avenues of drug discovery and cell therapies.

Next week, I’ll be heading to Kyoto to interview Prof. Shinya Yamanka who, together with Sir John Gurdon, was jointly awarded the Nobel Prize for Physiology or Medicine in 2012 for the discovery that mature cells can be reprogrammed to become pluripotent.

As part of my interview, I’m going to ask Shinya the best, most interesting question put forward by the community – that’s YOU!

So: what would you ask Shinya? Now’s your chance. Submit your questions in the comments below, via our facebook page or on twitter using #askshinya.

The video forms part of Development’s interview series. Watch my interview with Prof. Austin Smith, where he chats about his role as an Editor at Development, and what it takes to be a good scientist. Plus, keep watching as Austin tries to identify stem cell scientists from photos taken before they were famous. Can you tell who they are? Watch the video and see for yourself.

 

 

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Science consulting: helping out a scriptwriter

Posted by , on 13 March 2016

During my years in New York, I unexpectedly experienced an interesting form of science outreach. I randomly met a film director at a party, Sasha Collington. This director explained to me that she needed the help a biologist to work on her new script. I accepted right away for three reasons. First, curiosity. Second, because just like many other experimental scientists, I get very frustrated with dead-end experiments and I regularly start questioning the meaning of my life. I liked the idea of being directly and immediately helpful to someone. Third I get angry a lot when I hear all the scientific none-sense or the misleading and condescending over-simplification of science in articles or movies. I was therefore tempted by this opportunity to get the science as accurate as possible.

 

Consequently, we exchanged several emails and met a few times. She began by explaining the story she was working on. The film, in production, is called “Love Type D”:

 

 

In her film, the outcome of relationships is governed by biology. We are either dumpers or dumpees. Therefore she was looking for ideas about what kind of biological concept could explain this, how could the characters experimentally test it and whether or not they could overrule it. I understood that she was not looking to double check the science in her script. She was not looking for technical or procedural details either. I rather felt that she was looking for general biological knowledge to nourish her artistic creativity. It was thus a broad discussion, very upstream in the film making process. After her description of her project, I started talking a lot. She had in mind to go for some king of genetic phenomenon, so I explained her the basics of genetics and epigenetics. What is a gene? What is the difference between a gene and an allele? What is chromatin? How is gene expression regulated? How are genes related to phenotypes and why is it much more complicated that we once thought? What are the classic techniques used to identify genes or to assess their level of expression? She was very active in the discussion. I could tell that she was trying to see how she could use those pieces of information to help her story. Indeed, she was asking a lot of questions about practical aspects: what kind of experiments could we use? Could a child perform that experiment? Would the reagents be accessible to a non-scientist? This is where it became really interesting because I perceived a bit better what it means to talk about science with non-researchers.

 

When it comes to discussions within the scientific community, I am personally very opposed to the storytelling approach. I feel that science is turning into a marketing activity and I really dislike that. It shifts the focus away from data and logic toward fancy tales. However, in this context of communication between an artist and a scientist, and between this artist and her public, I realized that storytelling was not hurting and, on the contrary, was necessary to convey the message properly. First, I understood that aesthetic is important. As an artist using a visual medium, her recurring worry was to know how a given experiment would look like. Would the result appear on a screen? On a paper? In a test tube? Does it have colours? Does it move? Does it make a sound? Does it have to be in the dark? Questions I never even thought of. We had to forget “unfilmable” or visually unexciting experiments such as western blots or ELISA. We were rather trying to imagine microscopy-based results that would visually make sense on the screen. I perceived the benefit of taking into account the visual content and not just the conceptual content. That is something I will keep in mind whenever I have to communicate with people from outside the academia.

Second, I understood the importance of analogy. Among the various scientific concepts we explored, she particularly liked the notion of chromatin compaction and decompaction during the epigenetic regulation. She liked it because it spontaneously evoked the idea of a book that someone closes or opens. It is something the public unconsciously knows very well and therefore they would almost emotionally connect with this scientific concept. I realized that making something “understandable by the public” did not mean “absence of complicated words”, or “not too many parameters”, it rather meant using concept people could relate to. Next time I have to interact with non-scientific people I will try to appeal to those “cultural images” they have instead of falling into the (condescending) trap of over-simplification.

Finally, I had expected that the biggest obstacle would be the knowledge gap between us. But it rather turned out that the main difficulty is the divergence of objectives. I wanted to get the script scientifically accurate whereas her prime goal was, understandably, to have a scientific element that would serve the story: something clear, coherent and pretty. Because of this divergence, we spent quite some time trying to come up with ideas that could be both scientifically and artistically satisfying. I felt a bit like a very annoying person, repeating things such as “well, not exactly…”, “no it’s more complicated”, “I guess we could say that only if…” and often “well, we don’t really know.” I guess that this is a common feeling among people who happened to serve as consultants. We may come off as dull, picky mood-killers. But that’s ok. We are here to give a scientific point of view to something. That is, to provide logical, accurate, fact-driven interpretations or ideas. When advising a film scriptwriter or director, it is important to keep acting as scientists, and not trying to anticipate or satisfy the artist expectation or vision. Even if we reinforce the image of nerdy researchers by doing so.

 

Overall, this experience was a lot of fun. I loved this opportunity to see how a script was being made and to experience the different perception of what is biology. I would gladly do it again, especially if it is at a downstream step, such as technical coaching during the shooting. Was my help useful? I like to think it was. At least to get her started on the scientific part of her script, to set some landmarks in her mind that would help her come up with that part of the story. Regarding the scientific accuracy, which was one of my objectives, I think it did not work out as well as I thought. There are other limitations in a film production (time, money, space, material, actors…). Seeing that your advice is not always followed must probably be frustrating for scientific consultants, but that’s the way it is. After all, it remains a piece of fiction.

 

 

Outreach logo new squareThis post is part of a series on science outreach. You can read the introduction to the series here and read other posts in this series here.

 

 

 

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PhD position opened in Switzerland for a developmental / cell biologist

Posted by , on 11 March 2016

Closing Date: 15 March 2021

Evolutionary developmental genetics of reptile skin colour

In the context of evolutionary developmental biology analyses of reptilian skin colours and colour patterns, we offer one PhD position for an outstanding, highly motivated, and creative experimental wet-lab biologist with strong skills in developmental biology and cell biology.

Michel Milinkovitch’s group at the University of Geneva (UNIGE) integrates the expertise of developmental biologists, evolutionary biologists, computer scientists and physicists for an improved understanding of the mechanisms generating a diversity of skin colours and colour patterns in reptiles.

We have recently shown (Saenko et al. 2013) that the extensive variation of skin colours and patterns in Sauropsida reptiles is generated by precise co-localisation of interacting pigmentary and nano-structural elements. In this framework, we have also shown (Teyssier et al. 2015) that chameleons shift colour through active tuning of a lattice of guanine nanocrystals, which photonic effect is filtered by a layer of pigments. In addition, we have built extensive transcriptomic and genomic resources (Ullate-Agote et al. 2014; Tzika et al. 2015) for mapping colour mutations in our new model species of snakes and lizards. For example, we recently mapped and identified the mutation responsible for the amelanistic mutation in corn snakes (Saenko et al. 2015).

The successful candidate will (i) participate to linkage mapping of multiple colour and colour pattern mutations in snakes and lizards and (ii) use molecular/cell/developmental biology methods (microscopy, immuno-histochemistry, in-situ hybridisation, transcriptomics, in-vivo assays, ex-vivo cultures, etc.) to characterise the effects of these mutations on neural-crest cell migration, as well as on the physiology of pigmentary and structural-colour cells. The new PhD student will also interact with a physicist PhD student who is mathematically modelling the reaction-diffusion processes that generate colour patterns in snakes and lizards.

Candidates must have a Master in biology or biochemistry. Skills and experience with developmental biology and/or cell biology are mandatory. Skills in biophysics are useful. The successful candidate will have a genuine interest for organismal biology and will appreciate interactions with physicists and computer scientists.

The University of Geneva (UNIGE) is world-renowned for its research in Biology and Physics.  UNIGE is among the top 1% best universities in the world and the Faculty of Sciences is ranked 32th world best (Shangai Academic Ranking of World Universities).

PhD students are remunerated according to the standards of UNIGE, which are very generous when compared to other international programs.

Geneva is an international city occupying a privileged geographical situation.

Candidates must send their application – in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two persons of reference – to:

Prof. Michel Milinkovitch (Michel.Milinkovitch@unige.ch), Laboratory of Artificial & Natural Evolution (www.lanevol.org), University of Geneva, Switzerland.

Refs: Saenko, Teyssier, van der Marel & Milinkovitch. Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards. BMC Biology 2013, 11: 105; Teyssier Saenko van der Marel & Milinkovitch. Photonic Crystals Cause Active Colour Change in Chameleons. Nature Communications 6: 6368 (2015); Tzika, Ullate-Agote, Grbic & Milinkovitch. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics. Genome Biol. Evol.  7: 1827-1841 (2015); Ullate-Agote, Milinkovitch & Tzika. The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int. J. Dev. Biol. 58: 881-888 (2014); Saenko, Lamichhaney, Martinez Barrio, Rafati, Andersson & Milinkovitch. Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Scientific Reports 5, 17118 (2015) .

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Postdoc position to study Mechanisms of neural progenitor specification

Posted by , on 11 March 2016

Closing Date: 15 March 2021

A full 3-year ANR funded postdoctoral position is available at the Centre de Biologie Intégrative Toulouse to study mechanisms by which time is translated into a precise developmental sequence in the context of neocortex development. This position is part of the postdoctoral program of CBI Toulouse (http://cbi-toulouse.fr/eng/). Our research focuses on the role of local cell-to-cell communication via Eph:ephrin signaling in the specification of neural progenitors in the mouse. The specific aim of the proposed project is to identify the cellular and molecular mechanisms linking Eph:ephrin signaling to neural progenitor fate decisions, concentrating on the transcriptional response elicited downstream of Eph activation in neural progenitors.

The project includes genome-wide gene expression analyses (RNA-Seq and ChIP-Seq) to fully characterize the repertoire of genes downstream of Eph:ephrin signaling in cultured progenitors and the assessment of candidate genes in regulating the production of projection neurons in vitro and in vivo. The succesful candidate should have a PhD and a strong background in genome-wide gene expression analyses. Expertise in cell culture and/or mouse genetics would be a plus. The position is available from october 2016.

Highly motivated candidates should send a brief description of their research interests and career goals, their CV, and contact information for three references to Alice Davy (alice.davyatuniv-tlse3.fr)

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Researchers dig up new molecular details on “the other type” of stem cells

Posted by , on 11 March 2016

  • Scientists at IRB Barcelona and CSIC reveal that the combination of two molecular signals determines which cells that have already differentiated can regain their stem cell properties.
  • Their studies on fruit flies allow for advancements in the field of regenerative medicine and a better understanding of processes involved in cancer.

In a study published this week in PLos Genetics, scientists Nareg J. Djabrayan and Jordi Casanova from the Institute for Research in Biomedicine (IRB Barcelona) and CSIC, have identified two molecular signals and the pathway of

Nuclei of Drosophila trachea cells during the transition from larvae to an adult fly. The cells in the Tr2 segment are dividing; they are the facultative stem cells. (N.J. Djabrayan, IRBBarcelona)
Nuclei of Drosophila trachea cells during the transition from larvae to an adult fly. The cells in the Tr2 segment are dividing; they are the facultative stem cells. (N.J. Djabrayan, IRBBarcelona)

events that allows cells in a tissue that are already specialized to regain their behaviour as stem cells. The study offers new information about how cells become differentiated and how “this other type” of stem cells, called facultative, get activated, which is of particular interest in cell reprogramming, regenerative medicine, and in understanding cancer.

Facultative stem cells are being identified more and more often in human tissues and organs, but much less is known about them compared to typical stem cells, which have distinct morphological traits. “The existence of facultative stem cells indicates that many differentiatied cells continue to have great plasticity and are able to respond in situations of stress, such as in wounds or in the regeneration of worn out tissues,” explains Jordi Casanova, head of the Development and Morphogenesis in Drosophila group at IRB Barcelona.

“This plasticity is good if it is well regulated. If any of the mechanisms involved becomes unbalanced, it becomes dangerous,” adds Casanova. “In fact, cellular plasticity in tissues that regenerate often, are associated with organs that have a high incidence of cancer, such as the colon or blood,” he explains.

A combination of signals in space and time

The researchers looked at the moment when a Drosophila larva changes into an adult fly. “This model is a good one to identify and study facultative stem cells because there are some cells in the larva that will give rise to the adult fly and they get activated during the switch from larva to adult, a transition which could be considered a condition of stress,” explains Casanova.

Concretely, the researchers studied cells with facultative stem cell traits in Drosophila trachea. They showed that only some cells in the tissue receive a spatial signal that marks them. Then, when the transition occurs, a second signal is sent, triggered by hormones, that prompts the reactivation of the stem cell programme. This signal reaches all cells in the tissue, but only those that have been marked previously with the spatial signal are reactivated as stem cells.

“Understanding these signal regulation mechanisms is fundamental in order to control, for  example, the reprogramming of cells,” indicates Casanova. Using the same model, the scientists now want to investigate which mechanisms allow differentiated cells to maintain their plasticity and how they go from being a differentiated cell to a stem cell and vice versa.

 

Reference article:

Snoo and Dpp act as spatial and temporal regulators respectively of adult progenitor cells in the Drosophila trachea

Nareg J-V Djabrayan and Jordi Casanova

PLoS Genet. (2016 Mar 4) DOI: 10.1371/journal.pgen.1005909

 

This article was first published on the 11th March 2016 in the news section of the IRB Barcelona website

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