Biology Open is a new journal, launching in September 2011, from The Company of Biologists, publishers of Development, Disease Models & Mechanisms, Journal of Cell Science and The Journal of Experimental Biology.

The journal is online-only and Open Access and will publish peer-reviewed research across all aspects of the biological sciences. Biology Open will aim to ensure the timely publication of valid research, avoid the pain of repetitive submission and the excessive demand for additional experiments and decrease the burden of peer review.

The journal is now open for submissions and as well as accepting direct submissions, it will also offer a transfer option from papers originally submitted to the other Company of Biologists’ journals, such as Development.

By focusing on the timely publication of good-quality, sound research rather than its perceived impact, Biology Open is designed to facilitate dialogue and build a valuable body of work supporting the efforts of the research community. The journal will also consider useful reports of negative results.

For more information about Biology Open, please see the journal homepage.

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Here’s a short “behind the scenes” on our paper about visualizing gene expression data, published in Nucleic Acids Research.

When I joined James Briscoe‘s lab as a postdoc, my project’s ultimate goal was (and still is) to decipher and model the gene regulatory network underlying neural tube patterning. For this, I need to know where, when and which genes are expressed in the neural tube. Having spent the first few months optimising a protocol to isolate manipulated neural tube cells, I started generating transcriptome data using Affymetrix microarrays. I quickly realised that the amount of the data these assays produce accumulates very rapidly – we were analysing dozens of samples at the same time and measuring tens of thousands of genes. The complexity of these data made their analysis very difficult. Fortunately around about this time I met Chris Watkins, a computer scientist at Royal Holloway, University of London.

Chris happens to be an expert in the field of “machine learning”, the branch of computer science that aims to develop algorithms that identify patterns in complex data and make decisions based on these patterns. Over the years, he has worked in various fields including epidemiology and artificial intelligence and for a while he was employed by hedge funds analysing financial data. The connection between these fields is the desire to find patterns in large sets of data. So although Chris had never seen or worked with transcriptome data before he was instantly familiar with the problem I faced.

One of the goals with transcriptome data is to define sets of co-regulated genes and identify patterns of gene expression. For this clustering algorithms (e.g. hierarchical clustering, k-means clustering) are often used. These are powerful techniques, however, while using them I realised they have limitations. I was struck by two major drawbacks. First, the algorithms tend to be “black boxes”. They are designed to produce sharp delineations between the clusters of genes and it was noticeable that different methods often produced quite different classifications. It was never clear which method produced the most valid clusters and why one algorithm partitioned the data in one way while another algorithm put the same genes in different clusters. The second drawback of these techniques is that they do not reveal global patterns in the data. You are left with a series of seemingly unconnected lists of genes – clusters – and you are not sure how these clusters relate to one another.

I explained my angst to Chris and he suggested developing a visualization of the data that would allow us to explore it in a more intuitive manner. After some false starts he came up with a method that proved useful. He was aware of a recently developed “dimensionality reduction” algorithm called t-distributed Stochastic Neighbor Embedding (t-SNE) and although it had never been used on transcriptome data before, Chris thought it might be suitable for our needs. What is “dimensionality reduction”? Perhaps the most familiar example is maps of the world – these are 2D representations of the 3D globe. The aim of these maps is to accurately represent the distances between locations on the surface of the earth. Of course it’s impossible to draw the perfect 2D map of the 3D world and depending on the compromises that are made by the map maker you end up with different types of maps – the most familiar are the Mercator and the Gall-Peters projections. Dimensionality reduction algorithms aim to generate 2D projections from data that has more than three dimensions. A set of transcriptome data typically has several different conditions and each of these conditions can be thought of as a dimension (e.g. 6 conditions = 6 dimensions). The expression level of a gene is measured in each condition and these measurements can be thought of as the position of that gene in each condition/dimension. The image you can think about to help understand the idea is a cloud of points in high dimensional space with each point representing a gene. The goal of dimensionality reduction algorithms is to project this cloud of points into two dimensions in a way that preserves the spatial relationships between the points as much as possible.

The initial tests of the t-SNE method seemed to indicate it worked nicely for transcriptome data. We then managed to persuade a computer science undergraduate, James Smith, to spend the summer in our lab turning the t-SNE computer code into a little package that made it much easier to use. This allowed me to try it out on many different data sets, some of my own and some published by other labs. As you can see in the paper (and in the image below of Fang et al.‘s data from developing human embryos) the method nicely projects complex gene expression datasets into a two-dimensional map in a way that makes the relationships between genes easy to visualize and understand.

Each gene is represented by a point on the map and is surrounded by genes that have similar expression patterns in the data set. The software tools that James wrote over the summer allowed easy interactions with the maps and provided ways to visually cluster genes. One of these support tools – Chris called it “neighbour plots” – produced some really beautiful images.

My experience with the t-SNE algorithm, so far, is that it makes identification of co-regulated genes much easier and more intuitive than other methods. One thing that I’ve found is that it is particularly useful when used in conjunction with established clustering methods. Overlaying onto a t-SNE map the cluster assignments, from a regular clustering algorithm, using different colours provides a way to assess and explore the partitioning decisions in the clustering. And it’s finally allowing me to start to make sense of some of the data I’ve been generating.

All the code for using the t-SNE algorithm for gene expression data is available from our website – here. It’s in the form of a MATLAB-implemented graphical user interface. If you try it out and have ideas of how to improve or change it, do let me know!

Bushati N, Smith J, Briscoe J, & Watkins C (2011). An intuitive graphical visualization technique for the interrogation of transcriptome data. Nucleic acids research PMID: 21690098

Fang H, Yang Y, Li C, Fu S, Yang Z, Jin G, Wang K, Zhang J, & Jin Y (2010). Transcriptome analysis of early organogenesis in human embryos. Developmental cell, 19 (1), 174-84 PMID: 20643359

(7 votes)

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The Cambridge Stem Cell Initiative encompasses 200 researchers spanning fundamental science through to clinical applications. Our goal is to advance disease modelling, drug discovery and regenerative medicine through understanding the genetic and biochemical mechanisms that control stem cell fate.

The Coordinator will enhance the performance and profile of Cambridge as a world-leading centre of excellence in stem cell biology and regenerative medicine. You will be responsible for developing resources to facilitate the coordination, networking and information exchange. You will have outstanding organisational and administrative experience and be comfortable working to tight deadlines with minimal supervision.

The post will be based in the Wellcome Trust Centre for Stem Cell Research and report directly to the Centre Director. You will have a degree (or equivalent) and have worked within the HE or research sector in a senior administrative role. You should have demonstrable experience in data management, report writing, in WEB-based communication and event organisation. You will have well-developed interpersonal skills with excellent verbal and written communications ability.

You will be IT literate with experience. You will be self motivated and able to work both on own your initiative and as part of a team.

Offers of employment will be conditional upon occupational health clearance and satisfactory proof of the right to work in the UK.

To apply, please visit our vacancies webpage: http://www.cscr.cam.ac.uk/vacancies.html
Informal enquiries are also welcome via email: cscrjobs@cscr.cam.ac.uk

Applications must be submitted by 17:00 on the closing date of 19th August 2011.

Interviews will be held on the morning of 26th August. If you have not been invited for interview by this date, you have not been successful on this occasion.

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Last week, the butterfly keepers at the Natural History Museum in London came across an incredibly rare phenomenon: a lateral gynandromorph. This butterfly is both male and female, and the division is bilateral, with the left half being male and the right female. This occurrence is almost certainly the result of chance improper separation of the sex chromosomes during the first division following fertilisation, hence its rarity. As well as being a great find for the lepidopterists at the NHM (and I would heartily encourage anyone even remotely interested in the diversity of animal form to visit the 9 million or so butterflies and moths at the museum), it illustrates wonderfully well that there is more than one developmental route to sexual identity.

The question of what makes males and females different from one another has an extremely long history (but I know better than to speculate on such differences and so will here refer only to their developmental basis), and has naturally been the subject of intense investigation by biologists. There are essentially two models of how this is achieved during somatic development: either through the concerted action of hormones emanating from a sex-specific gonad, or else through an inherently genetic mechanism where each cell knows what sex it is; as with so much else in development, the crucial distinction is between a non-cell autonomous and a cell autonomous process.

Mammals fall into the former category, with male phenotype specified by a genetic cascade beginning with the expression in the gonad primordium of the Sry gene, which sits on the Y chromosome. Remarkably, experimental introduction of the Sry gene can cause a female mouse embryo to develop as a male. This mode (if not the exact same genetic components) had been widely assumed to operate in most vertebrates. However, work published last year using elegant grafting experiments with transgenic GFP chickens, showed that in contrast, bird somatic cells know their sex. The motivation for this work was the presence of three lateral gynandromorphs amongst the flocks of the Roslin Institute in Edinburgh. Like the butterfly at the NHM, these curious creatures are male on one side and female on the other, and studying them showed that, contrary to expectations, this was not the result of aneuploidy, but rather was the result of them being genuine male/female chimaeras: one side composed largely of genetically normal male cells, and the other of genetically normal female cells. Their different responses to the hormones circulating during development were therefore cell-autonomous – like butterflies, the chick soma knows what sex it is. Thus, despite its rarity in nature (of the 9 million butterflies and moths at the NHM, only 200 are gynandromorphs, though only the new one is split down the middle), gynandromorphy can tell us fundamental things about the way animals determine their sexual identity. It also makes amateur lepidoptery an even more rewarding passtime.

References:

http://www.nhm.ac.uk/about-us/news/2011/july/dual-sex-butterfly-hatches-at-natural-history-museum99300.html

Zhao et al. (2010) Somatic sex identity is cell autonomous in the chicken. Nature 464: 237-242.

Kashimada & Koopman (2010) Sry: the master switch in mammalian sex determination. Development 137: 3921-3930.

(7 votes)

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Welcome to my report from the 9th Annual ISSCR Meeting in Toronto, 2011. This is  the final part, covering the events of day four of the conference (Saturday); Follow these links to read my account of day one, day two, and day three.

Day 4 – Saturday 18th June

There is a great amount of interest in therapies involving the use of stem cells, but unfortunately it would seem that the case has been overstated, as was suggested by Irving Weissman on the first day of the conference. Nevertheless, it was very great to see some fantastic talks during the ‘Therapeutic Approaches to Stem Cells’ plenary, where the research behind already promising therapies was revealed.

To start off, Leonard Zon (Children’s Hospital and Dana-Farber Cancer Institute at Harvard) presented work studying haematopoiesis in zebrafish, which are used for screening drugs to increase HSC numbers (for exmaple pGE2). Ken Chien (Massachusetts General Hospital) showed his work directing in vivo heart cell fate using modified RNAs, a treatment shown in mice to repair infarcted heart muscle and increase coronary vasculature.

Chris Breuer from Yale School of Medicine described his work with engineering vascular grafts for use in reconstructive surgery. The main problem with using non-living vasculature for repairing congenital heart defects is that once implanted shortly after birth, they don’t grow, and so need to be replaced. Chris and his colleagues have managed to engineer large blood vessel grafts that contain living endothelium (generated from bone marrow derived mononuclear cells) that integrate seamlessly into the recipient’s existing blood vessels. The most interesting part of this reconstruction is that the cells that make up the new vessel, once the biodegradable polymer scaffold has disappeared, are not those bone-marrow derived cells that were originally implanted, but cells that have migrated from the neighbouring blood vessels, akin to how skin wounds heal.  One problem that they have encounted when using this in human patients has been the narrowing of the vessel. Whilst macrophage infiltration is essential for the forming of new vessel tissue (in addition to removing the scaffold), it appears that excessive infiltration is the cause of this narrowing. As such, current work which aims to design a ‘cell-free’ graft will have to take this balance into account.

Next, Michele De Luca (University of Modena and Reggio Emelia, Italy) presented amazing work repairing corneal injuries by using stem cells derived from the limbus, a region of the between the sclera and the cornea – video demonstrations of the delicate sugery already being performed on patients was not for the squeamish! Sheng Ding (Gladstone Institute of Cardiovascular Disease) gave a talk outling his work identifying small molecules that replace reprogramming factors and increase reprogramming efficiency, with a view to generating functional cardiomyocytes. Finally, renowned journalist Charles Sabine, addressing the ISSCR as a patient’s advocate of Huntington’s Disease, talked frankly about his life dealing with the consequences of his family’s history and his subsequent diagnosis of this condition – an incredibly moving speech which aimed to inspire stem cell researchers to strive for future cures.

For the final concurrent sessions, I attended the ‘Epigenetic Programming of Stem Cells’ track, which Yi Zhang (University of North Carolina) opened by talking about Tet proteins and the control of DNA methylation in ESCs. Next, Andrew Xiao (Yale) discussed the role of the histone variant protein H2A.X in ESCs, and Kevin Huang (UCLA) discussed his bioinformatics-based research into the regulation of the mESC transcriptome by DNA methylation.

Alessandra Giorgetti from Centre of Regenerative Medicine in Barcelona described her work involving the transdifferentiation of cord-blood derived CD133+ cells towards the neural lineage. This transdifferentiation process, which did not go through a pluripotent stem cell state, required only one transcription factor, Sox2, could be enhanced by using cMyc. The resultant neural progenitor cells gave rise to functional mature motor neurones in vitro and in vivo. Finally, Suneet Agarwal (Boston’s Children’s Hospital) returned to Tet proteins, this time focussing on the role of Tet2 in mESCs and myeloid tumourigenesis.

The final session of the meeting began with the presenation of the first McEwan Centre Award for Innovation to Shinya Yamanaka and Kazutoshi Takahashi, for their pioneering work to generate iPS cells from somatic cells using various combinations of pluripotency related transcription factors. Upon acceptance of the award (which names both senior and junior researchers of discoveries), Shinya described himself as a less than enthuastic physician before resorting to work as a scientist, and also recounted the early days of Kazutoshi’s PhD in his lab, where he consistently made mistakes that I’m sure most members of the audience are very familiar with! Kazutoshi, for his part, self-depricatingly played down his own contribution towards the innovation –  “all I did was transfection”. Shinya closed their acceptance speech by expressing gratitude for international support during the aftermath of the earthquake that hit Japan earlier in the year, and extending a warm invitation to next year’s ISSCR meeting in Yokohama.

In the closing plenary, ‘Regulatory Networks of Stem Cells’, Rick Young (Whitehead Institute, MIT) presented his lab’s work on the role of Oct4, Sox2, and Nanog in the transcriptional control circuitry of ESCs. Stuart Orkin (Harvard) presented work identifying the components of the Polycomb Repressive Complex-2 (PRC2)  and its role in controlling pluripotency in ESCs and cancer. Judi Lieberman (CBR Institute for Biomedical Research) described a genome-wide siRNA screen to identify selective inhibitors of triple negative breast cancer, which unexpected came up with proteosome components. Finally, in the Anne McLaren Memorial Lecture, Nicole Le Douarin (Academie Des Science, France) described her extensive research in the field of neural crest development, identifying the neural crest as a pluripotent organ which contributes cells to every tissue in the body.

And so ends four days of brilliant science. This year’s ISSCR meeting was my first, and it was a great experience, not least for the sense of community that the ISSCR has strived to create. I’d highly recommend anyone involved in stem cell research to head to Yokohama next year (or Boston the year after) for it.

~Richard Berks

PS. As a small cheeky plug, I’d like to point you towards a blog I write (on a regrettably infrequent basis), Coffee & Cake, Pizza & Beer, which has so far concerned itself with life as a PhD student in biological sciences. I hope to have an article about my experience from the ISSCR meeting up soon.

(3 votes)

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Welcome to my report from the 9th Annual ISSCR Meeting in Toronto, 2011. This is  part three, covering the events of day three of the conference (Friday); you can read the coverage from day one here and day two here.

Day 3 – Friday 17th June

Starting off the day and the ‘Reprogramming and Fate Conversion’ plenary session, Shinya Yamanaka (Center for IPS Cell Research & Application, Japan), somewhat of a celebrity at the conference for his work to generate the first human iPSCs, talked about his lab’s ongoing work in this field, on the comparison between iPSCs and ESCs, and the use of Glis1 as a reprogramming factor. John Gurdon (from the eponymous Gurdon Institute in Cambridge) presented his work studying the reprogramming of a somatic cell nuclei by nuclear transfer into Xenopus oocytes, a reprogramming event that occurs, unlike iPSC reprogramming, at a 100% efficiency. Eric Kallin stepped in for Thomas Graf (both from Center for Genomic Research, Spain) to talk about the role of Tet2 in the transdifferentiation of B cells to macrophages. From Mount Sinai Hospital in our host city, Andras Nagy described his lab’s work using transposons to reprogram somatic cells towards induced pluripotency, and also unveiled a multi-centre project to comprehensibly map the time course for changes in protein, RNA, and DNA during reprogramming, appropriately named “Project Grandiose” – the results of which are due at next year’s conference. Finally, Rudolf Jaenisch (Whitehead Institute for Biomedical Research) discussed his work investigating the efficiency of reprogramming.

In the ‘Haematopoietic Stem Cells’ concurrent session, host Tannishtha Reya (UCSD) presented work concerning Numb & Mushashi in control of asymmetrical division in CML, and Momoko Yoshimoto (Indiana University School of Medicine) gave a talk entitled ”Multipotent haematopoietic progenitors arise at the extra-embryonic yolk sac prior to hematopoietic stem cell emergence in the mouse embryo’. Next, Trista North (Harvard) talked about the control of HSCs in Zebrafish by reactive oxygen species and HIFα, and Rong Lu (Stanford) described her work using genetic ‘barcodes’ to track single murine HSC differentiation in vivo – multiple short DNA sequences are integrated using lentiviruses into HSCs, and after transplantation, the differentiated progeny are harvested and sequenced for the presence of these ‘barcodes’.

To finish, the other host of the session, Andreas Trumpp from DKFZ in Germany, battled through technical difficulties to give a talk that roughly divided into two parts. Firstly, he discussed the discovery of a particular subset of HSCs which divided extremely slowly (estimated at 5 divisions in a lifetime). This dormant HSC population sheds light onto how leukaemic stem cells evade damage by chemotherapy. Application of IFNα or LPS could ‘wake-up’ dormant HSCs and LSCs, indicating a potential mechanism with which to improve chemotherapy. To finish off his talk, Andreas switched to looking at breast cancer, and whether Metastatis Initiating Cells (MICs) could be identified in tumour cells circulating in the blood (called Circulating Tumour Cells, or CTCs). The key was to find CTCs of a breast cancer stem cell phenotype that had hallmarks of Mesenchymal-to-Endothelial Transition.

Back in the main lecture hall for the ‘Stem Cell Metabolism and Ageing’ plenary, Sean Morrison (University of Michigan Centre for Stem Cell Biology) derscribed his work attempting to characterise the haematopoietic stem cell niche. Irina Conboy (UCBerkley) presented work on the regulation of the Muscle Stem Cells and niche during ageing. Amy Wagers (Harvard) later on in the session gave a talk on a similar topic, including the identification of small molecules involved in muscle repair and the role of calorie intake in muscle damage.

Margaret Goodell from Baylow College of Medicine talked about her lab’s work investigating the role of DNA methylation by Dmnt3a in the regulation of haematopoietic stem cells. A conditional mutant mouse that deletes Dmnt3a in haemtopoietic cells (Mx1-Cre) showed an unexpected phenotype upon serial reconstitution of irradiated recipients; the recovery of the numbers of stem cells increased dramatically with each subsequent graft, with their differentiation capacity decreasing. This indicated that Dmnt3a is involved in the control of self-renewal and differentiation of HSCs. When global DNA methylation was analysed, both hypomethylated and hypermethylation was observed; these differentially methylated regions corresponded to genes upregulated and downregulated in leukemias, respectively. However, gene expression data did not strongly correlated with the DNA methylation patterns, and it was still unclear why, despite a variety of haematological disorders commonly showing mutations in Dmnt3a, these mice didn’t succumb to such diseases.

Read on for my report from final day of the ISSCR meeting here.

(3 votes)

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Welcome to my report from the 9th Annual ISSCR Meeting in Toronto, 2011. This is  part two, covering the events of day two (Thursday) of the conference, you can see part one here.

Day 2 – Thursday 16th June

Arriving late at the first plenary of the day, “Tissue Stem Cell Origins”, I managed to catch Michael Rudnicki (Ottawa Health Research Institute) talk about his work on role of Carm1 in muscle stem cell function. Next, in a talk entitled ‘Endothelial Origins of Haematopoietic Precursors’, Elaine Dzierzak of the Erasmus Stem Cell Institute in the Netherlands present her lab’s work identifying the emergence of haematopoietic progenitors from the aortic endothelium during early mouse development. The visualisation of these ‘haematopoietic clusters’ has been made possible by making the embryo transparent and using multi-colour confocal imaging, giving a 3D map of vasculature and the establishment of early haematopoiesis, starting at E9.5 and peaking a day later. Finishing off the plenary session was Hans Clevers from Hubrecht Institute, and his lab’s fascinating work identifying intestinal stem cells in vivo, involving some ingenius imaging work,  and their role in cancer, involving self-replicating and self-organising ‘miniguts’ (see the recent Nature paper from his lab for work on Wnt signalling in regulating instestinal crypt stem cells).

The concurrent sessions of the conference started today (five parallel sessions each day), and so I took the opportunity to dart between seminar rooms to see a variety of talks. First up, in the ‘Stem Cells & Tissue Engineering’ session, was Peter Zandstra (University of Toronto), speaking about his group’s work with the integration of reprogramming, pluripotency maintenance, and differentiation into a suspension-culture bioreactor, in particular for differentiation towards pancreatic and cardiac lineages. I found it fascinating, and timely – if regenerative medicine is ever going to be available to large numbers of people, it will have to be at an industrial scale, and Peter’s talk outlined some of the first steps towards these goals.

I then went to the ‘Human iPSCs and ESCs’ session. Amy Wong (Hospital for Sick Children, Toronto) talked about generating lung airway epithelium from Cystic Fibrosis patient-derived iPSCs in liquid-air interfaces, which would be useful for modelling the disease. Shannon Buckley (NYU School of Medicine) gave a talk on Ubiquitination, an often forgotten mechanism of regulation of ESC self-renewal and differentiation. Natalia Ivanova (Yale) gave an overview of the interactions between Nanog, Sox2, and Oct4 as a regulatory module in hESCs, and Duanqing Pei (GIBH, China) discussed his lab’s methods to increase the efficiency of inducing pluripotency, something that, again, will be critical if ‘personalised medicine’ using patient derived iPSCs is ever to become a realistic prospect for the majority.

The final plenary session of the day was concerned with the biology of Cancer Stem Cells. To start off, Thea Tlsty, from University of California in San Francisco, described the discovery of a new population of cells derived from triple negative breast cancers.  They have the ability to form mammospheres, which have all the normal breast tissue structures and can produce milk under hormonal stimulation, both in vitro and upon xenograft in vivo. However, the real intrigue begins as she described how these cells will also produce cells of all three germ-layer lineages when implanted in various locations, and can also form teratomas, properties normally reserved to desribe human pluripotent stem cells. These cells, though mortal, can even be cultured as hESCs, and bear their normal pluripotency markers of Nanog, Sox2, and Oct4. Thea concedes that more investigation is needed, and has cautiously named these cells ePPSCs – endogenous, provisionally pluripotent, somatic cells (perhaps to avoid any wrath from Irv Weissman!?)

Pier Paolo Di Fiore (University of Milan) talked about the role of Numb regulation of Notch signalling in breast cancer stem cells, using ex vivo self organising organs called ‘mammospheres’, echoing Hans Clever’s talk from earlier in the day. Stanford’s Michael Clarke presented his group’s work in the haematopoietic system, specifically looking at Bmi1 and cancer stem cell self-renewal.

In the Ernest McCulloch Memorial Lecture, John Dick from the University Health Network in Toronto, reflected on the necessity of functional assays to describe the differentiation capacity of haematopoietic stem and progenitor cells, thus underlining the importance of McCulloch’s contributions to the field. He then went on to talk about the concept of ‘clonal evolution’ in human leukaemias, the phenomenon where the major disease causing leukemic population is in fact one of many competing clones. When treatment kills off the major clone sending the patient into remission, previously hidden clones are now free to proliferate and cause a relapse. John stated that consolidating this model with that of the ‘cancer stem cell’ is the current challenge, and finished with describing some recent papers that start to bridge the gap between genetic and functional diversity of cell populations in a variety of leukaemias.

The second day of the ISSCR meeting ended with a reception, whilst half of the poster presenters stood faithfully by their offering of from the 1,500 posters. Later that evening, 1,000 people (allegedly) crammed into a club in downtown Toronto for a “social evening”, which I’m sure resulted in many sore heads the next morning! (mine included…). Read on for the report from day three here.

(2 votes)

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Attendence from over 3,800 delegates, around 140 speakers, and 1,500 posters on display over four days, in the wonderful city of Toronto:  the 9th Annual Meeting of the International Society For Stem Cell Research (ISSCR) was always going to be a great conference, and we certainly weren’t disappointed.

The quality of the research presented was high, and there were far too many talks to easily summarise in one article, so I’ve decided to split up my report into four parts, one for each day. In each, I’ve summarised the talks I saw from that day, and written a bit more about two or three of my favourite talks, from the big names in the field to some of the lesser-known (but equally engaging) researchers. If you’ve anything you’d like to add, please feel free to comment at the bottom of any of the articles.

Day 1 – Wednesday 15th June

Attracted by the promise of an interesting set of talks at the interface of academia and industry (not to mention a free breakfast!), to start off my conference I headed along to the Lonza-sponsored symposium entitled “Novel Stem Cell Tools – applications in Research, Drug Discovery, and Cell Therapy”.

Linzhao Cheng, from John Hopkins University in Baltimore, discussed his group’s work generating induced pluripotent stem cells (iPSCs) from blood cells. Using a plasmid delivered by electroporation, they have found that mononuclear CD34+ cells from the peripheral blood are more ammenable to reprogramming than the traditional fibroblast (increasing speed and efficiency of iPSC generation), as well as being a more easily accessable source of human cells. He also discussed work involving zinc finger nuclease-mediated gene targetting to correct Chronic Granulomatous Disease, which was used to insert a functional copy of the gene gp91 into a ‘safe harbour locus’ AAVS1.

We also heard talks concerning the derivation of neurones from pluripotent stem cells: from Xianmin Zeng (Buck Institute, California) about promising work in the generation of dopaminergic neurons from hPSCs for cell therapy and drug screening to treat Parkinson’s Disease, and from Alexa Poole of California Stem Cell Inc. about their new products involved motor neuron progenitor cells from in-house derived xeno-free cGMP-grade hESCs.

After the break, I headed over to a packed seminar room to see the Symposium to honor Ernest ‘Bun’ McCulloch, whose work developing Colony Forming Unit (CFU) assays paved the way for further functional assays to test stem cell pluripotency. Talking were Valerie Wallace (Ottawa Hospital Research Institute) about her work concerning the role of Hedgehog signalling in the development of the neural retina, Mickie Bhatia (McMaster Stem Cell and Cancer Research Institute) discussing heterogeneity amongst hESCs and it’s implications, and Bing Lim (Genome Institute of Singapore and Harvard Medical School) giving a fresh perspective on pluripotency factors as factors essential for differentiation.

The conference proper began with the Presidential Symposium, chaired by exiting ISSCR President Elaine Fuchs. After an address Robert McEwan from McEwan Centre for Regenerative Medicine, and a presentation of the ISSCR Public Service Award to  Robert Klein (Chairman of Independent Citizen’s Oversight Committee at CIRM), four speakers were invited to give a talk from a historical perspective of stem cell biology and regenerative medicine. Firstly, Janet Rossant from the Hospital for Sick Children in Toronto gave lecture on the importance and limitations of functional assays for pluripotency. George Daley from Children’s Hospital Boston gave his historical account of the origins of stem cell research, nuclear transfer, reprogramming, and cell therapy.

This year’s Keynote Lecture was delivered by Robert Langer from MIT. Author on over 1,100 papers and holder of over 760 patents, he gave a certainly non-exhaustive (but nonetheless exhausting!) whistlestop tour of his lab’s research, focussed on the development of materials designed to improve cell and gene therapy and solve particular problems in surgery. For example, a thermoresponsive material, changing its properties when going from room temperature to body temperature, had been developed for use in minimally invasive surgery, resulting in a thread which when knotted would tighten itself – amazing to watch on video! In addition, by dropping tiny quantities of polymers onto a microscope slide, a polymer microarray was developed, allowing for high-throughput screening of polymers which would support feeder-free growth of human hESCs. Similar screening methods were used to find chemicals that increase the efficiency of gene delivery into hESCs.

Finally, to round up the Presidential Symposium, former ISSCR president Irving Weissman (Stanford) gave a deliberately confrontational yet entertaining speech concerning who is to blame for the rise of unregulated stem cell treatments – in short, part of the blame was from scientists who over-hyped their work, giving stem cell status to cells that aren’t, and claiming major advances without appropriate function assays. His talk also included an assessment of the ISSCR public information program ‘A Closer Look at Stem Cell Treatments’.

The first plenary session of the conference – “Totipotency and Germline Development “ was the last session of the day, and I managed to catch a talk by Azim Surani (Gurdon Institute, Cambridge) on the role of epigenetic reprogramming in germ cell lineage, and Max Plank Institute’s Hans Schoeler‘s talk comparing the induction of pluripotency in somatic cells with that in germ line cells.

The conference had gotten off to a fine start, but I knew once the concurrent sessions started it’d only get more frantic! Follow this link to see the second part of my report..

(3 votes)

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Last May the Instituto Gulbenkian de Ciência (Oeiras, Portugal) hosted the EMBO Workshop on Biophysical Mechanisms of Development (EMBO BMD 2011). As one of the organizers my main mission was to put together a Science and Art contest and exhibition, related with the workshop theme, which we entitled “The Physics of Life”. We were particularly interested in work reflecting the topic of the workshop but we also accepted images related with the broader area of Biophysics or “The Physics of Life”.

The exhibition was aimed at highlighting not only the beauty and art that can be found in research images, but also the artists translations of a scientific theme. Thus, both scientists and artists were invited to apply.

We received a total of 52 images from scientists and artists from six different countries (Portugal, Spain, UK, Holland, Brazil and USA), including renowned science artists like Rob Kesseler and Andrew Carnie.

The submitted images were available for online voting at the workshop Facebook page, and the 20 images with the highest number of votes (or “likes”) were selected for display at “The Physics of Life” exhibition.

Picture types ranged from digital compositions, paintings, graphic art, macro- and microphotographs, and featured several different organisms, such as fungi, animal cells, embryos, flowers and trees. You can see the submitted images in the Facebook photo album “SciArt images in contest” and the selected ones in “The Physics of Life” exhibition.

The 20 selected images were printed and exhibited during the EMBO BMD 2011 workshop, and they remain on display at Instituto Gulbenkian de Ciência.

The winner of the contest, elected by a jury composed of members of the Organizing and Scientific Committees of the workshop, was Elsa Abranches, a post-doctoral researcher working in neural differentiation at Instituto de Medicina Molecular (Lisbon, Portugal), with the image “The Heart of a Brain“.

At the end of the workshop, we received very positive feedback on the exhibition. If you are planning on organizing such an event, I can tell you that it is very rewarding, specially thanks to all the beautiful images we received. For details on organization layouts, check our SciArt exhibition webpage here.

(8 votes)

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Sperm stem cells have a lot riding on their success.  Not only must they produce the actual sperm, but they must maintain a life-long supply.  So, the self-renewal of spermatogonial stem cells is a finely-tuned talent of these stem cells.  A recent paper in the Journal of Cell Science describes the role of Wnt signaling in spermatogonial stem cell maintenance.

Stem cells possess two key properties that make them so special – the ability to produce different types of specialized cells, and the ability for self-renewal.  As spermatogonial stem cells (SSCs) must provide a life-long supply of sperm, their self-renewal is very important.  Recently, a group looked at SSC maintenance and found a role for Wnt signaling in the process.  Yeh and colleagues used clusters of SSCs in vitro to show that Wnt5a promotes the maintenance of SSCs as a cell-extrinsic factor, and functions independently of B-catenin signaling.  Although Wnt5a does work independently of B-catenin in many diverse examples, this paper is the first to show this non-canonical pathway functioning in stem cell maintenance.  Yeh and colleagues also found that Wnt5a is expressed in vivo in cells of the testes in newborn mice.  Finally, SSC clusters expressed the Wnt5a receptors Fzd5, Fzd7 and Ror2.  In the images above, Wnt5a gene expression (red) is found in Sertoli cells (green), which serve as “nurse” cells in the testes.

For a more general description of this image, see my imaging blog within EuroStemCell, the European stem cell portal.

Yeh JR, Zhang X, & Nagano MC (2011). Wnt5a is a cell-extrinsic factor that supports self-renewal of mouse spermatogonial stem cells. Journal of cell science, 124 (Pt 14), 2357-66 PMID: 21693582

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