Hello! I am Maggie Pruitt, a postdoctoral researcher in the Department of Genetics, Development, and Cell Biology at Iowa State University (Ames, Iowa, USA – think middle America or fields upon fields). I work in Dr. Stephan Schneider’s evo-devo laboratory, and my work mostly focuses on studying components of the Wnt/β-catenin signaling pathway during early Platynereis dumerilii development.

The Schneider lab is part of the small, but growing, Platynereis community. Many of the Platynereis labs seem to study developmental biology or evolutionary developmental biology. While the Schneider lab is focusing on early development and the early gene regulatory networks present in Platynereis, other labs work on eye and brain development, gametogenesis, the molecular mechanisms of how the moon affects the life cycle of Platynereis and how neuropeptides control swimming depth of Platynereis larvae within the water column, to name a few.

Platynereis dumerilii as a model organism

Platynereis is a polychaete annelid and belongs to the clade Lophotrochozoa, which is the third but understudied branch of bilaterally symmetric animals (understudied compared to ecdysozoans like the nematode C. elegans, and deuterostomes like the vertebrate mouse). These worms can be collected in the wild from the coasts of the Mediterranean or coasts of Western Europe; however, they can also be easily cultured in a lab.

Our culture room. Notable features include boxes of adult or young worms, our artificial moonlight, and an injection microscope (yes, we can inject Platynereis embryos!).

As Platynereis is a marine worm, the worms need seawater. Filtered natural seawater (NSW) is by far the best for the worms. But, if your lab is not located close to a seawater source (like us in the middle of the USA) or you want to avoid steep costs for shipping NSW to your lab, you need to get a little creative. Artificial seawater (ASW) can be made using a salt called Instant Ocean. While this can be technically called seawater, the worms (or more specifically the embryos) do not really survive well in it. So…. since the Schneider lab is far from the sea and the worms do not like ASW, what do we use? This is where creativity comes in. Actually, it is where Dr. Dennis Lavrov’s sponge lab (also at Iowa State University) comes in. We provide the salt to make ASW to the Lavrov lab and their sponges. Then, once this seawater has been “conditioned” by the sponges (i.e. when the Lavrov lab needs to change the water in their tanks), we take their wastewater, filter it, sterilize it, and voila! Seawater that our embryos like, cleverly named DSW (Dennis seawater). We use 100% DSW for all of the fertilizations. Once the worms are juveniles or adults, we keep them in a 50/50 mixture of DSW and ASW.

The Schneider lab Platynereis culture is not huge, so optimal breeding success is key. One way to maximize this is to keep the culture on a fairly tight routine. The culture should be maintained at 18^oC or 64.4^oF, a standard for Platynereis labs around the globe, as the speed of early development is very temperature sensitive. In addition to constant temperature, it is good to have the worms on a regular feeding and water change schedule. Our young and adult worms receive minced organic spinach (only the best, pesticide-free spinach is good enough) on Mondays and ground fish food flakes on Fridays. The last incredibly important thing is to have tight control of the daily light and dark periods.

Sexual maturity and spawning in Platynereis dumerilii are synchronized by a lunar cycle. In the lab, the culture is on an artificial light cycle. The worms experience summer all year round, and so have 16 hours of light and 8 hours of total darkness each day. In addition, they are exposed to a 28-day night cycle in which three weeks of pitch-dark nights are followed by 7-days of full moon. Our high-tech recreation of this lunar cycle comes in the form of a $1.99 night light from Walmart, and a very reliable undergraduate researcher as a timer to turn the light on and off on the correct days. Sexually mature worms can be collected 3-6 days after our “moon” phase. Any disruption in this light cycle (exposing the worms to light during the dark phase), like leaving a digital clock on that has a bright backlight, has detrimental effects on the breeding success.

Sexual maturity can occur in worms as young as three months old, but sometimes we have “geriatric” 18-month-old worms finally maturing. In Platynereis, completed sexual maturity lasts one day/night, so an artificial cycle with artificial light allows for collective sexual maturity in the culture. Maturing worms are easily distinguished from non-mature worms by their change in appearance. Maturing worms have an empty gut and become more opaque. As the worms continue to mature, the females become yellow (lots of eggs) and the males have a cream anterior and a red posterior (lots of sperm and blood vessels).

Anterior halves of a female worm (left) and a male worm (right). The distinctive colors, yellow versus cream/red, are noticeable.

The awesome power of the Platynereis mating system

In the wild, Platynereis will swarm at dusk. However, in the lab we keep the sexually maturing male and female worms in separate bowls so the worms can last until the morning. Matings are easy to set-up; all you need is a glass bowl, some DSW, and a sexually mature male and female. After two worms are placed together in a bowl, they will exchange pheromones, which triggers their nuptial dancing and mating ritual:
 

The female is swimming in small circles, and the male is swimming in large circles.  Pheromones are exchanged, the male first releases his cloud of sperm, and then the female releases her eggs (courtesy of Albrecht Fischer, University of Mainz, Germany).

Go ahead; watch the movie again. It is awesome and is partially responsible for getting me hooked on Platynereis. And at the end of this nuptial dance you are left with thousands of synchronously developing embryos and two dead worms. What a way to end your life, right? Perhaps before we pass judgment on how and when these worms die, I should give a bit more information on their life before the fatal spawning event.

Crash course to the life cycle of Platynereis

One of the many reasons why Platynereis is a good model system for developmental biology is that Platynereis develops rapidly. Platynereis begins as a 160μm egg and after instant fertilization of many eggs at once Platynereis embryos develop synchronously. In fact, the thousands of embryos from a single mating develop synchronously through the embryonic and larval stages. During early development, Platynereis embryos exhibit spiral cleavage. Spiral-cleaving embryos develop by a series of stereotyped asymmetric cell divisions that allows for the identification of individual cells by their positions and size. By 24h, the embryos have developed into a free-swimming larval form, a trochophore that swims freely within the water column, and after just 96h, Platynereis is a three-segmented juvenile worm that stays on the bottom of the dish. Segments are added throughout the lifetime of Platynereis at the tail end from a posterior growth zone, and Platynereis maintains a lifelong capability to grow and regenerate posterior segments after loss. The size of an adult worm varies tremendously, but on average they are about 35mm. During segment proliferation, the sexually immature worms live in self-spun silk tubes. The tubes are open at both ends and allow the worm to “check out” their environment, attack passing worms and prey, and eat their food. In their own world they are mostly holistic vegetarians that turn into fierce cannibalistic predators if the opportunity arises.
 

Here is one of approximately 90 boxes where we house our young and adult worms. In this box, you can see the many worms, each with their own silk tubes. If you look closely, you can even see one worm peeking out of its tube (right of center).

To sexually mature, Platynereis goes through a process called epitoky. Essentially, the whole body of the worm is irreversibly modified for reproduction, and the worm is transitioning from a sexually immature “atoke” form, to a sexually mature “epitoke” form. Some of the radical body modifications during this process include upgrades of motor and sensory organs, tune-ups of the muscular system for speedy swimming, resorbing of some muscles and all of the gut tissues, and the growing of thousands of gametes within their central body cavity. Indeed, the female and male worms are mostly reduced to growth chambers for gametes, bags of eggs and sperm, respectively. Once epitoky is complete, and the worm has reached its climax — one-day of sexual maturity, the worm will leave its silk tube home and swim into the pelagic zone (open water column). Here they will find like-minded partners (the good) or end up as a healthy protein shake for some higher ups in the food chain (the bad). After reproduction, the worms die. Maybe this death is still shocking to you, but the entire body of the worm changed for this one event…. the worm dies after completing a final task. From an evolutionary standpoint, the only task that matters.

A typical day in our laboratory

An ideal day in the lab is one in which everything is working correctly. Since this seems to be a mythical creature, I’ll stick to a typical day in our lab. Our typical days come in two flavors, depending on whether or not we have mature worms for fertilizations.

In the absence of sexually mature worms, a typical day in the lab consists of cloning, cloning, cloning, and maybe some more cloning. The goal of most of the cloning work is to make an in situ probe, and determine the expression pattern of the gene over the first 24h of development. The lab has an ever-growing list of interesting genes to clone, so this is a lab effort. I seem to spend most of my time working with all of the hard-earned embryos I collected in previous weeks (it can be hard to share embryos from late night fixations or embryos treated with pharmacological inhibitors). My favorite, and most frequent, activity is performing in situs. Cloning a new gene can be quite satisfying, but not nearly as much as uncovering a beautiful expression pattern that perfectly fits your hypothesis.

In the presence of sexually mature worms, I can typically be found running between our molecular lab (located on the 5^th floor) and our culture room (located on the 7^th floor). Maybe I’m being silly, but I feel extremely lazy taking the elevator up two flights of stairs. Since we only have sexually mature worms for less than two weeks each month, I try to take advantage of these days. Some of the fertilizations need to be saved to propagate the culture, but I try to use the rest. So, these days begin with a short run up to the culture room to set-up fertilizations. I’ll try to have a plan-of-action for the day, like how I plan to use the embryos, but sometimes, the worms just do not cooperate. Females weren’t feeling the males, all males and no females, etc. Pending total failure with the fertilizations, the embryos will be 1) used for microinjection or a pharmacological inhibitor experiment, 2) fixed for in situ hybridization or immunohistochemistry, or 3) used for RNA isolation. These days can get pretty hectic, but being busy means you and the lab will be set, sample-wise, for the weeks without the matures. It is only when slippery fingers make an appearance and multiple tubes of embryos or entire plates of treated embryos are dropped that these days are the worst. When this happens (yes, it happens), I usually get a coffee, then finish the day pretending the lab is in the absence of matures…. until the next morning.

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

(8 votes)

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StemCellTalks is a Canadian high school stem cell outreach initiative that has been running in 7 cities in Canada since 2010. The program has featured over 50 stem cell “experts” during this time, involved the participation of over 500 gradute student volunteers and reached over 5000 grade 11/12 students. This year, sponsored by Stem Cell Network and Let’s Talk Science, the Vancouver chapter was able to partner with the International Society for Stem Cell Research and send five talented student bloggers – Lauren Dobishok, Tanner Jones, Mindy Lin, Vivian Tsang and Michelle Tse –  to its Annual Meeting, which was hosted in Vancouver last week from June 18-21th. Three of these blog posts (here, here and here!) have been featured on another excellent stem cell blog – Signals – and we are happy to be able to share the final two posts here on The Node!

By Michelle Tse (Little Flower Academy, Vancouver, British Columbia, Canada)

At the ISSCR, I noticed the passion and dedication for stem cell research present and the pure desire to better the lives of humanity. The delegates determination to improve research studies pushes me to potentially carry on such a career in the near future.

My morning session consisted of the Tools for Basic and Applied Stem Cell Biology seminar, in which researchers from all over the world gave presentations on topics that went from reprogramming stem cells to the steps required for a research study to be translated for clinical use. Amidst many barriers, these scientists continue to show the world that hard work eventually will pay off. Our afternoon consisted of all five of us attending the Presidential Symposium, where we had the privilege to hear several different speakers present their latest unpublished research. Once again, although challenging to understand, it was extremely fascinating to be given the chance to hear about the latest news in this field of science and, in this case, it actually is the latest unpublished news! Our day ended with us attending the amazing exhibition hall where we all had the chance to personally talk to researchers from various parts of world and what they do for a living. The advantage to going to their booths? Lots and lots of freebies!

While all presentations were equally fascinating and eye opening , Dr. Debbie French’s (Children’s Hospital of Philadelphia) presentation on hematopoietic disease modelling using iPSCs (induced pluripotent stem cells) definitely stuck with me the most. The talk sparked my interest, and it was undoubtedly because her examples used, Down syndrome, Glanzmann thrombasthenia and Juvenile myelomonocytic leukemia (JMML) were diseases I knew of to a certain extent. Dr. French’s presentation widened my knowledge on iPSC’s and hematopoietic disease modeling for all three of these conditions. This was a completely new area of research to me and I was able to get so interested from that 15-20 min talk.

Clearly, it was an amazing opportunity to attend such a world-renowned science research conference and meet so many new people. I hope to hear more about the world of stem cell and the research behind it in the near future as I start my journey into university.

(2 votes)

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‘Increasing knowledge leads to triumphant loss of clarity’

‘The study of segmentation: that way leads only to madness’

Alfred Romer (1894 – 1973), Director of the Museum of Comparative Zoology and Professor of Biology, Harvard University

Some problems in biology excite such interest as to become symptomatic of a field. This is true, I think (I hope), of all biology, but it is definitely truer of some fields than others. Evolutionary biology is one such field. And segmentation is one such problem. Since the great pre-Haeckelian 19^th century comparative embryology tradition, the developmental biology of organisms has been correctly viewed as the prism through which the evolutionary history of animals must be viewed and understood (not ever since though – developmental and evolutionary biology fell out with each other for most of the middle of the twentieth century). For most of that time, it was also viewed as the primary source of evidence for the actual phylogeny of the animals – our shared family tree over the last 580 million years (I use this date perhaps ill-advisedly – the date of the origin of animals is another of those problems about which people are prepared to loose their temper).

The history of animal history

There are fundamentally two ways to start developing as an animal (assuming you are one of the 99+% that are bilaterally symmetrical). Once you have gone from a ball of cells to a hollow ball of cells with a hole through which cells will pass to make your gut, you have two options: you can make the hole (the blastopore) into your anus, or into your mouth. Once achieved, you then have an anterior-posterior axis, which can be organised in two ways: it can be segmented, or not. (Actually, this is not true; lots of animals are ‘pseudosegmented’, but more of that perhaps in future).

As such, zoologists for most of the last 150 years have assumed that having a segmented body axis was a shared derived feature of particular animal groups: (annelid) worms and insects must be closely related because they are both segmented. At least, they must be more closely related to one another than they are to odd-looking, unsegmented things like clams or penis worms. If everyone agrees on something for over a century, it tends to be very difficult to convince people otherwise. Unless you are on the cusp of a revolution…

Revolutions

In 1997, an ingenius pioneering application of DNA data to reconstructing the animal family tree suggested that in fact insects and worms are very distantly related, and that their shared segmental architecture was in fact nothing to do with their position in the phylogenetic tree. This paper¹ not only set the stage for the explosion in genomic approaches to addressing phylogeny that have dominated the big journals ever since, but it reignited one of the oldest controversies in biology: how old is segmentation? Is it a (relatively) recent invention in the lineages in which it is found (vertebrates, arthropods and annelid worms), or does it in fact date back to that pioneering worm crawling around in the mud with it’s newly invented bilateral symmetry about 550 million years ago?

Well, thanks to developmental biology (essentially Christine Nusselhein-Vollhard et al. with flies in the 70s and 80s and Olivier Pourquie et al. with vertebrates in the 90s, 00s, and 10s), we know (or perhaps knew) that flies segment using engrailed, wingless and hedgehog, a transcription factor and a couple of secreted signals respectively, but that vertebrates use a curious ‘clock’ of oscillating Notch signalling as they grow that interacts with an FGF- and Wnt- secreting posterior ‘growth zone’; vertebrates, unlike flies, grow from the back. So, pretty different. In 2003, building on this pioneering work in traditional models, Guillaume Balavoine’s group showed that the upto-that-point-largely-ignored annelid worm perhaps forms segments using the fly system: engrailed and Wingless². So, the ancestor of worms and flies (which incidentally was the ancestor of all animals who turn the hole into the mouth, rather than the anus – the Protostomes) by extension was segmented using engrailed and wingless. Vertebrates, though, are different: segmentation in them is not homologous to the protostome (‘first mouth’) condition of annelids and flies. Case closed. Interesting stuff: nobody was right, segmentation was very old, but that first bilaterally symmetrical worm in the mud (550 million years ago) perhaps wasn’t split into segments.

Spiderman

However, at about the same time Wim Damen et al. published an astonishing study³ showing that the spider uses Notch oscillations to make its abdominal segments, and in a 2008 paper⁴ showed that it uses Wnt signalling in a posterior growth zone. What? So, worms are like flies, but fish are like spiders. What the hell is going on? Around this time I was actually trying to become a zoologist, and was totally confused about the state of the art. I was in good company. The majority of zoologists threw up their arms and resigned themselves to agreeing with Romer (see above). Those that didn’t, who generally where those actually working on the problem, started to pick holes in the annelid data, which was admittedly the weakest amongst the three segmented taxa. It is important to underline here that this is absolutely through no fault of the annelid investigators. It is bloody hard to work on non-traditional model organisms (my phd was on one), and anyone who does so has my undying respect and admiration, both for scientific reasons and because of how impressed I am by their workrate and endeavour. In any case, I suspect (I don’t know) that most in the field were happy to accept that the ancestral worm-in-the-mud (called ‘Urbilateria’) was segmented, using the vertebrate/spider system of a Notch clock.

Spiderwoman

I have never met Wim Damen, though one has to admire the intellectual courage it takes to start working on a spider – a lot of people will have thought that it was a daft idea. However, the credit now passes to Evelyn Schwager, who worked with him on the next batch of surprises, and who pleasingly is now working in Romer’s old department at Harvard. ‘Underlings’ (we know who we are) never get the attention or praise that they (we) deserve and so while I don’t know this to be true, at this point I want to emphasise the reaction when Evelyn presented her beautiful data⁵ at the European Evolutionary Developmental Biology Conference in 2008 in Ghent in Belgium. She showed that in fact, spiders use the gene Hunchback, which is called a ‘gap’ gene in Drosophila because it acts high up in the segmentation hierarchy (above engrailed, wingless and hedgehog), to accomplish segmentation, but only in the thorax. So, remarkably, the thorax is ‘fly/annelid-like’ and the abdomen is ‘vertebrate-like’. All great scientific findings or breakthroughs that I have seen possess that ability to make an audience of peers gasp. Schwager and Damen in their experiments managed to halve the number of thoracic segments in a spider and film it. A room of arthropod experts see, on the screen, a 4-legged spider running around. A 4-legged spider. Cue gasps.

Intrepid worms

Fast forward a couple of years to 2010, and the worm guys (I know they hate being called that) produced some delightful further data, filling in the gaps in their engrailed–wingless story to include hedgehog signalling⁶. Coupled with the spider story, it seems that we have solved segmentation, and it went like this:

1. Urbilateria evolves segments using the Notch clock.
2. This is a BRILLIANT invention and it takes over the world (its descedants comprise, remember, over 99% of all animals).
3. Those that turn that the blastopore into a mouth also evolve the hedgehog–engrailed-wingless system for making segmented structures as well (but why? And how? Lots of work to be done…)
4. Some of these lineages (possibly most) loose one or both of these ways of segmenting a structure, because there are many ways to make a living as an animal and lineages are just as likely get simpler as to get more complex (Aristotle was wrong about this).

Intrepid chicken (bits)

Except that vertebrates don’t have to do it using the clock, it now seems. In some beautifully old-fashioned (not in the sense that they are out-dated, but that they possess a lot of explanatory power – this is a compliment) ex vivo culture experiments Claudio Stern and colleagues have just upset the apple cart⁷ (though by this point it is perhaps more accurate to say that after the apple cart was knocked over, and all the apples were stolen, replaced with oranges, that were again stolen after the cart was knocked over again, Stern and colleagues have made us question whether we actually need apple carts in this day and age). They have shown that it is possible to make somites, the segmented, epithelialized blocks of mesodermal tissue that are the basis of vertebrate segmentation without an oscillating clock of Notch signalling.

In the embryo somites are added two at a time (one on either side of the spinal cord) as the presomitic mesoderm, the tissue undergoing the Notch oscillations, undertakes a mesenchymal-to-epithelial transition. This MET happens as a result of the slow removal of the signals (FGFs and Wnts) that derive from the posterior growth zone of the embryo. Since the embryo is growing, this yields a moving wavefront of signalling; the whole thing is termed the ‘clock and wavefront’ model, and was first posited in the 1970s.

However, the new study shows that if you take presumptive mesoderm from the posterior primitive streak (the name of the growth zone in chicks ie the tissue that will become presomitic mesoderm, but hasn’t yet expressed the Notch oscillations), expose it to the BMP inhibitor Noggin for a few hours to generate a dorsal mesoderm (ie. somite) fate, and then implant it back into the yolk of an egg, but away from the embryo, you generate somites. All at once. Upto 15 of them. And crucially, without Notch oscillations, and nowhere near the wavefront. The generated somites even possess the Hox expression appropriate to the time at which they were dissected from the primitive streak, so they carry patterning information too, though they don’t possess the anterior-posterior polarity of normal somites. Still, astonishing stuff.

So, worms are like flies, but fish are like spiders, which are also like flies, but chicks (which are essentially just highly evolved fish) are not even necessarily like chicks. I know what Romer would have said.

¹Aguinaldo, A., Turbeville, J., Linford, L., Rivera, M., Garey, J., Raff, R., & Lake, J. (1997). Evidence for a clade of nematodes, arthropods and other moulting animals Nature, 387 (6632), 489-493 DOI: 10.1038/387489a0

²Prud’homme, B., de Rosa, R., Arendt, D., Julien, J., Pajaziti, R., Dorresteijn, A., Adoutte, A., Wittbrodt, J., & Balavoine, G. (2003). Arthropod-like Expression Patterns of engrailed and wingless in the Annelid Platynereis dumerilii Suggest a Role in Segment Formation Current Biology, 13 (21), 1876-1881 DOI: 10.1016/j.cub.2003.10.006

³Stollewerk, A., Schoppmeier, M., & Damen, W. (2003). Involvement of Notch and Delta genes in spider segmentation Nature, 423 (6942), 863-865 DOI: 10.1038/nature01682

⁴McGregor, A., Pechmann, M., Schwager, E., Feitosa, N., Kruck, S., Aranda, M., & Damen, W. (2008). Wnt8 Is Required for Growth-Zone Establishment and Development of Opisthosomal Segments in a Spider Current Biology, 18 (20), 1619-1623 DOI: 10.1016/j.cub.2008.08.045

⁵Schwager, E., Pechmann, M., Feitosa, N., McGregor, A., & Damen, W. (2009). hunchback Functions as a Segmentation Gene in the Spider Achaearanea tepidariorum Current Biology, 19 (16), 1333-1340 DOI: 10.1016/j.cub.2009.06.061

⁶Dray, N., Tessmar-Raible, K., Le Gouar, M., Vibert, L., Christodoulou, F., Schipany, K., Guillou, A., Zantke, J., Snyman, H., Behague, J., Vervoort, M., Arendt, D., & Balavoine, G. (2010). Hedgehog Signaling Regulates Segment Formation in the Annelid Platynereis Science, 329 (5989), 339-342 DOI: 10.1126/science.1188913

⁷Dias, A., de Almeida, I., Belmonte, J., Glazier, J., & Stern, C. (2014). Somites Without a Clock Science, 343 (6172), 791-795 DOI: 10.1126/science.1247575

(4 votes)

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Here are the highlights from the current issue of Development:

Eye’s got rhythm

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

Keeping dendrites in check

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

Sampling the SAM

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

Characterising developmental ‘super-repressors’

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

Plus…

Amyloid precursor protein and neural development

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

The roles and regulation of multicellular rosette structures during morphogenesis

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

Heterogeneity and plasticity of epidermal stem cells

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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