The March of Dimes Prize in Developmental Biology was jointly awarded this April to David Page, Director of the Whitehead Institute, and Patricia Ann Jacobs, professor of human genetics at Southampton University Medical School and co-director of research at the Wessex Regional Genetics Laboratory. Both Page and Jacobs specialize in research on human sex chromosomes and the development of sex disorders.
David Page
Page has been studying the human Y chromosome for nearly three decades. He and his colleagues have changed the scientific community’s perception of the Y, revealing the mechanism by which it maintains its genetic diversity through recombination at palindromic regions on the chromosome. He has also investigated the developmental effects that arise when this process doesn’t occur properly, which can lead to a loss of sperm production, sex reversal, and Turner’s syndrome.
Jacobs’ research has also played a fundamental role in establishing current understanding of human sex chromosomes. She is best known for a 1959 paper that first described Klinefelter syndrome, in which males carry an extra X chromosome.
The March of Dimes Prize has been awarded annually since 1996 to scientists whose research has advanced the understanding and treatment of birth defects. Jacobs and Page jointly received the award, worth $250,000, on May 2nd, at the annual meeting of the Pediatric Academic Societies in Denver, Colorado.
(Image from Whitehead Institute for Biomedical Research)
Congratulations to Hozana Andrade Castillo of the University of Sao Paulo in Brazil, whose image of a mouse pharyngeal arch jumped from third place to first place in the last few days of voting. Her image will appear on a cover of Development in the next few months.
Developing pharyngeal arch region of mouse embryo showing immunofluorescence detection of neurofilaments (green), DiI labeling of trigeminal ganglion (red), and nuclei detected with DAPI (blue).
Second place in this round went to the cilia-stained squid image taken by Davalyn Powell of the University of Colorado Denver, followed by the flower-like image of cell division in the slipper limpet (by Anna Franz – University of Oxford) and an ascidian muscle (by Christine Carag Krieger – University of Pennsylvania).
We had over a thousand people vote in this round as many people forwarded the link to their friends. Thanks to everyone for participating and voting!
The next round of images will be up on June 6th. Around that same time, the winning image from the first round will appear on the cover of Development, and that week also marks the start of the 2011 Woods Hole Embryology Course. We’re looking forward to the images from this year!
More and more, the central dogma is becoming well, dogged, for being a dogma at all. As humans, we have 3 billion nucleotides. Only 1% of it makes up our protein coding genes, which led to the development of the central dogma: DNA is transcribed to RNA and translated into proteins. During undergrad, we’re taught that transcription factor proteins bind to sequences in the DNA to either enhance or shut off transcription, thereby discontinuing protein production. Gene regulation seems to follow certain pathways and rules itself.
Then, 20 years ago RNAi was discovered, a whole new field where RNA can also regulate protein production. Generally, small RNAs repress protein coding genes by either causing their mRNAs to decay or inhibiting their translation into protein. They can be naturally produced for the sake of controlling the native genes, following a similar central dogmatic pathway: DNA is transcribed to a precursor RNA, which is converted into teeny RNA strands. These strands are selected by Argonaute proteins (AGOs) and used to target specific protein coding genes to halt their expression.
The progression from DNA to RNA to “something”, is like the foundation of genetics. And gene regulation is about how to control that progression. Evolution develops these elegant pathways to produce “something”, and then it evolved ways to control the pathway.
Well, not always.
Sometimes you can get “unintelligent design.”
Which is what a student joked, at a journal club meeting I’d attended today. The meeting started off as a presentation of a recently published article that assigned a role to an AGO protein in Arabidopsis. It ended up as a digression on evolution and how we perceive it, among other things.
The protein of interest was AGO10, which is somehow involved in miRNA/small RNA directed repression of target genes. But how it exactly it does this, was hazy to us, the observers. By inference, previous studies on its loss of function mutant, ago10/zwille/pinhead had deformed shoot apical meristems. After embryogenesis, the meristems at the junctions of leaves are where new ones form. In the mutants, the meristem is the size of pinhead, smaller than normal (Pictured in F, on the left, versus wild type in C, by Tucker et al., 2008). The protein expression of some transcription factors & signalling peptides changed in the ago10 mutants as well. But what does AGO10 specifically do?
(Picture: A, B = AGO10 expression in the yellow YFP areas of the embryo, at heart stage & torpedo stage. CLV, a stem-cell specific signalling peptide. its expression is weak is in the embryo ago10, as pictured in D, E. (it’s not strong in WT either though) CLV needs AGO10 to be maintained past embryogenesis, in the meristem Tucker et al. 2008).
One group discovered that AGO10 doesn’t really help in repression. It actually indirectly causes the activation of target genes. AGO10 is a decoy for the main AGO1, that performs 90% of miRNA directed repression in Arabidopsis plants. However, it’s a decoy for one miRNA alone (so it seems). It binds and sequesters miR166/165, a well studied miRNA that is deeply conserved in mosses and higher plants. By sequestering it, miR166/65 is prevented from binding to AGO1 and regulating its targets (HD ZIP proteins). Effectively it’s as if miR166/65, the silencer, has been silenced itself. By a massive protein no less.
Oddly, AGO10 is most abundant in one tissue type, the developing embryo. So it only catches up all the miR166/65 population in that one tissue. If it doesn’t, as suggested by ago10, then the embryo develops into mutant plant.
But why would plants bother developing this? Couldn’t nature have just evolved so that miR166/65 isn’t transcribed in the embryo? So that some transcription factor or miRNA shuts it off. Like, why produce something and then evolve a whole protein to muffle its activity? It’s like..evolution forgot to turn off the tap or shut the door, and created a massive sink or club bouncer instead. Energy wise, it seems a waste though. Evidently there probably is an unknown purpose.
The authors of the paper suggest that miR166 is required in specific cells, but not all cells of the developing embryo. So miR166 is allowed to be expressed but AGO10 prevents it from being spread elsewhere..assuming that miRNAs can travel…
(A-C: WT, CLV expression is maintained throughout embryogenesis and meristem development. Without AGO10 in D-F, its expression disappears).
It’s funny. We have these commonly accepted notions about gene regulation engrained in us from years of training. With the result that when we’re faced with something altogether new, we’re not sure what to make of it. We’re not even sure if we can accept it, but there it is. It’s like realizing black swans with ghoulish red eyes exist in Australia.
Sources/References:
Lab discussion with students at the Research School of Biology at ANU, led by PIs Tony Millar and Iain Searle.
Zhu H, Hu F, Wang R, Zhou X, Sze SH, Liou LW, Barefoot A, Dickman M, & Zhang X (2011). Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development. Cell, 145 (2), 242-56 PMID: 21496644
Pictures: Tucker MR, Hinze A, Tucker EJ, Takada S, Jürgens G, & Laux T (2008). Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo. Development (Cambridge, England), 135 (17), 2839-43 PMID: 18653559
This is a retelling of the student and post-doc workshop from the second day of the BSDB/BSCB joint spring meeting that took place in Canterbury at the University of Kent. The session emphasised the need for accurate science and scientific involvement in public communication. It ended up a bit longer than I’d intended, but this is something I’m really enthusiastic about and felt it needed to be shared in detail. I hope you find it helpful.
Panellists:
Dr Peter Wilmshurst – A consultant cardiologist, known for his refusal to falsify or withhold data in pharmaceutical studies. He was being sued for libel and slander by NMT medical until the company entered liquidation in April.
Rose Wu – A representative for the charity Sense about Science which works tirelessly despite limited funding to improve the public image of science, aids accurate reporting of scientific issues in the media and campaigns for further government support for research.
Dr Jenny Rohn – A UCL post-doc by day. Also known for her punditry, she runs the popular science communication website lablit.com has been interviewed numerous times for tv and radio. She has published numerous stories and editorials and two fictional novels Experimental Heartand The Honest Look, communicating science through the engaging and emotional personal lives of scientists. She was also central to the campaign to save UK science funding.
I’ve been asked to present the back-story behind our recently published manuscript in Development “Transcription precedes loss of Xist coating and depletion of H3K27me3 during X-chromosome reprogramming in the mouse inner cell mass.”
Mammalian dosage compensation occurs by silencing one X-chromosome in female cells, termed X-chromosome Inactivation (XCI). Balancing X-linked gene transcription is critical for female development, and in most cells, the absence of XCI is lethal. Interestingly, female mouse germ cells and inner cell masses (ICMs) appear to be an exception, capable of handling imbalances in X-linked gene dosage and exhibiting activation of both X-chromosomes. These uncommitted cells have the unique ability to reset the epigenetic profile of inactive X-chromosomes. As a graduate student, I was drawn to investigate the mechanism of X-chromosome reactivation because I wanted to understand how epigenetic reprogramming occurs naturally in the embryo.
Most of what is known about the molecular events that initiate XCI has been extrapolated from observations of XCI in mouse cells. In the mouse embryo, the choice of which X-chromosome to be silenced is made stochastically; maternal and paternal X-chromosomes have an equal chance of being silenced and the end result is a random pattern of XCI. In contrast, extraembryonic tissues exhibit an imprinted form of XCI, and the paternal X-chromosome appears to be predetermined for silencing. It has been the prevailing opinion in the field that a master controller, the Xist non-coding RNA, regulates XCI. Xist RNA has been linked to almost every step in the XCI mechanism, including choice, initiation, and maintenance; however, its exact role is still unknown. What is clear is that Xist transcripts coat the X-chromosome in cis, recruiting epigenetic modifying proteins that are responsible for forming inactive-X heterochromatin.
It had previously been shown that in all cells of the female preimplantation mouse embryo, Xist transcripts coat and recruit the repressive histone modification H3K27me3 to the Xp. However, X-linked gene expression at single cell resolution had not been directly analyzed, relative to cell fate in the embryo. In our manuscript, we definitively show that all cells, irrespective of lineage, establish imprinted XCI by the early blastocyst stage. This sets up a situation in the ICM; epiblast cells must undergo a reactivation/inactivation cycle. During ICM maturation, epiblast cells exhibit progressive upregulation of Nanog expression, coincident with their transition to ground-state pluripotency. Curiously, Xist is a target of OCT4, SOX2, and NANOG. Based on the concept that Xist is the master regulator of XCI, it had been predicted that progressive upregulation of NANOG in the ICM leads to Xist repression, resulting in loss of Xist coating and triggering reactivation of Xi genes.
We used a knockout of Grb2 to upregulate Nanog expression in the ICM. As might be predicted, increased NANOG dosage led to Xist repression, indicated by loss of Xist coating. However, X-linked gene silencing is maintained in cells that lack Xist coating, perhaps suggesting that induced epigenetic reprogramming is incomplete in these cells. These provocative results point to other factors, in addition to Xist, that are needed initiate Xi gene silencing. Recent results from Kalantry et al. Nature 2009, Namekawa et al. Mol. Cell Biol. 2010, and Okamoto et al. Nature 2011 support these conclusions and the need for the field to reconsider mechanisms regulating XCI. (more…)
Last month, the advocate-general of the European Court of Justice gave his opinion on a long-running legal debate about a patent filed several years ago in Germany. If the Court follows his recommendation, patenting of applications using embryonic stem cells will be prohibited on moral grounds.
13 leaders of major stem cell projects in Europe responded to the advocate-general’s statement with an open letter published in Nature this week. They express serious concerns about the impact of a patenting ban on European research.
EuroStemCell, Europe’s stem cell hub, has collected comments and information about this case on its Stem cell patents topic page. Visit the site to read the open letter and find out more about the case.
As humans we can see a limited assortment of electromagnetic wavelengths, known as the visible spectrum of light, a.k.a. colours. (Other wavelengths we cannot see include UV rays, X rays or infrared). Why is it that we can differentiate light colours? Its likely to do with adaptation to the environment. Plants and animals have evolved different physiological responses to various wavelengths of light.
As mammals we have biological clocks, or circadian rhythms that respond to light. Dark or blue light set off signalling mechanisms, which ultimately regulate the melatonin levels in our system. Melatonin is a hormone which can induce sleep, if at sufficiently high levels in our system. (Hence your doctor prescribing you melatonin if you have trouble sleeping at night. Suffice to say countless grad students are probably on this stuff right now). (Photo: Festival Colours by jmtimages, Flickr CC)
Plants also have a light-sensing system, which can respond to different times of day and seasonal changes. This can determine fruit maturation and changing colour in the leaves etc. For plants, blue light has a revitalizing (instead of drowsy) effect. If you’ve ever left your plants without light for too long, they go yellow. Irradiate them with a little blue, and the green will return within a couple of days. (Photo: Autumn Colours in Australia’s National Capital, personal collection).
Interestingly, plants and animals have the same type of photoreceptors to blue light, called Cryptochromes (CRYs), even though they elicit a different response. (Photoreceptors = light absorbing molecules or pigments.)
CRYs initiate the light response, analogous to a molecular domino effect. The pigments bind specialized proteins that in turn, regulate transcription factors that can switch on the light response genes involved in development. Termed as photomorphogenesis, light dependent changes in development can include initiation of flowering, or extension of roots in germinating seeds.
Currently, characterizing the molecular interactions in the plant blue-light/CRY1 response seems to be a hot topic. Two highly similar articles were just published in Genes & Development, which was drawn to my attn by Eva (cheers). They were produced by two different research crews, using virtually the same methods to similar results. It’s not by total coincidence either. Characterizing molecular interactions in plants involve the same gold standard biochemical and genetic assays (i.e. transgenic plants, yeast hybrid systems, loss-of-function mutants etc.)
In summary: the blue-light/CRY1 pathway doesn’t directly switch genes on. instead, it switches off the default dark condition mechanism. In the dark, SPA1 and COP1 proteins negatively regulate the light signalling pathway. Active COP1 normally marks transcription factor HY5 for degradation. SPA1 binds COP1 to enhance this activity. If HY5 were allowed to accumulate, it promotes the expression of multiple genes involved in photomorphogenesis, such as flowering, or germination.
What the groups found: Blue-light triggers CRY1 to bind SPA1. This in turn inhibits SPA1 binding to COP1. In 2001, another group found that CRY1 can also interact directly with COP1 to inhibit its activity in a 2nd way. Result: no COP1 activity, HY5 accumulates. Photomorphogenesis is observed. (CRY1 could not bind SPA1 in the dark, or under red light).
(photo: blue light, by psychiks, Flickr CC. does this make you feel sleepy?)
Some discordance over the CRY1-SPA1-COP1 interaction: One group claims that CRY1 causes SPA1 to dissociate from COP1. (exact mechanism unclear, allosteric binding = conformational change?) the other group suggests that CRY1 impedes COP1 and SPA1 binding, possibly by sandwiching itself between them. Refer to sandwich model in Liu et al. 2011 Figure 4D, or kit-kat dissociation model in Lian et al. 2011 Figure 5G. Devil’s in the details: both groups developed their models based on two biochem assays ~ yeast two/three hybrid and co-immunoprecipitation. However, they only tell you if things bind or not. Interestingly, blue-light and CRY1 were required to prevent SPA1 and COP1 binding. Under blue light, CRY1 could bind both COP1 and SPA1, just not sure how.
The interaction hasn’t been characterized in animals, although they do contain the CRYs. Mammals even have COP1, which can also mark other transcription factors for degradation. Inexplicably, breast cancers were found to have over-expressed levels of COP1. Not sure if CRY also inactivates mammalian COP1, although, one group did stick the mammalian COP1 into Arabidopsis, and found it reacts to blue-light. Interestingly, photoreceptors and COP1 were initially found in Arabidopsis. (score 1 for the plant model of genetics).
Plants:
Liu B, Zuo Z, Liu H, Liu X, & Lin C (2011). Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light. Genes & development PMID: 21511871
Lian HL, He SB, Zhang YC, Zhu DM, Zhang JY, Jia KP, Sun SX, Li L, & Yang HQ (2011). Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. Genes & development PMID: 21511872
Both research groups hail from China and the US. They’re also based in some of the top universities in the world (Peking Uni, UCLA etc.), which makes for some hefty competition, among neighbours no less.
Human Photoreceptors and COP1: Yi C, & Deng XW (2005). COP1 – from plant photomorphogenesis to mammalian tumorigenesis. Trends in cell biology, 15 (11), 618-25 PMID: 16198569
Yi C, Wang H, Wei N, & Deng XW (2002). An initial biochemical and cell biological characterization of the mammalian homologue of a central plant developmental switch, COP1. BMC cell biology, 3 PMID: 12466024
Cashmore AR (2003). Cryptochromes: enabling plants and animals to determine circadian time. Cell, 114 (5), 537-43 PMID: 13678578
We’ve had to find a new location for Thursday’s (today’s) Node meetup at the BSDB meeting.
Find us Thursday April 28 at 8PM in the Gulbenkian Cinema Cafe/Bar.
This is the cafe with the big windows that you pass when you follow the footpath from Eliot Dining Hall to the Woolf College building. This happens to be *exactly* where you will be walking around that time when you go from dinner to poster viewing, so you might as well pop in!
Addendum: We have just found out that there will be a theatre production at Gulbenkian which has intermission from 8:15 to 8:35. This means that there will also be about 200 theatre-goers in the bar at that time. We have the Node banner with us, so you will be able to spot us. However, if it gets too noisy, we might move to the Woolf building earlier, and use one of their upstairs seminar rooms. But just look for the banner: if it’s not in the cinema bar, we’re in the Woolf building.
Two postdoctoral positions are available immediately at the University of Pennsylvania: (1) to analyze the gene regulatory network underlying neural crest formation (Hong & Saint-Jeannet, 2007. Mol Biol Cell 18, 2192-2202; Hong et al., 2008. Development 135, 3903-3910); and (2) to characterize the molecular regulators of cardiac neural crest migration (Lee & Saint-Jeannet, 2011. Development 138, 2025-2034). Interested candidates must have a PhD, MD or VMD degree and a strong background in developmental biology and/or molecular biology.
Please submit your CV, and contact information for 2 references to Dr. Jean-Pierre Saint-Jeannet, University of Pennsylvania, School of Veterinary Medicine, Department of Animal Biology, 3800 Spruce Street, Philadelphia, PA 19104, USA. e-mail: saintj@vet.upenn.edu
The Node’s staff asked me to write a short “behind the scenes” on our paper just released in the May 15 issue of Development, “Cardiac neural crest is dispensable for outflow tract septation in Xenopus” http://dev.biologists.org/lookup/doi/10.1242/dev.061614
In the summer of 2008 when Dr. Young-Hoon Lee joined my laboratory from Chonbuk National University for a sabbatical we discussed a number of potential projects, and very quickly decided to analyze the contribution of the neural crest to the cardiovascular system in Xenopus laevis. This was a project that we considered several years earlier when Dr. Lee was a postdoc in my lab, but at the time Young-Hoon opted for a different line of research. To address this question we started using the lipophilic dye DiI to label the putative cardiac neural crest in neurula stage embryos. We found that the label cells were consistently excluded from the outflow tract septum. We were a little skeptical about this result, because of what we know of the cardiac neural crest in other species, but mostly because only a small number of neural crest cells is being labeled by DiI injection, and we could not exclude the possibility that unlabelled neural crest cells were contributing to the outflow tract septum. We then decided to move to a tissue transplantation system, where entire segments of the neural crest from RFP-labeled embryos were grafted onto an unlabeled host embryo. These experiments are not trivial and I have to give credit to Young-Hoon for his persistence and exceptional technical skills. Again in these experiments RFP-labeled neural crest cells were exclusively confined to the aortic sac and arch arteries and never populated the outflow tract cushions, confirming our initial observations using DiI. Consistent with these observations, upon cardiac neural crest ablation the outflow tract and the spiral septum developed normally and expressed the molecular markers specific to these lineages. This was a surprise. In chick and mouse the cardiac neural crest provide the separation for the systemic and pulmonary circulations at the arterial pole, remodeling the outflow tract into two vessels by forming the aorticopulmonary septum. In zebrafish where there is no separation between both circulations cardiac neural crest cells contributes myocardial cells to all regions of the heart. In Xenopus we were expecting to find something that was in between fish and amniotes. This is not the case – in frogs cardiac neural crest cells stop their migration before entering the outflow tract. Our next challenge was to determine the embryonic origin of Xenopus outflow tract septum. We were greatly helped in this quest by a recent study from the group of Michael Kuhl at Ulm University (Germany) that carefully mapped the cardiogenic lineages in Xenopus (Gessert and Kuhl. 2009. Dev Biol 334: 395-408). By transplantation of GFP-labeled regions of the cardiogenic mesoderm we found that the septum was derived from the second heart field, presumably by epithelial-to-mesenchymal transformation of the endocardial cells lining the cardiac cushions.
The picture below shows a lateral view of a host Xenopus laevis embryo after transplantation of both an RFP-labeled neural crest graft (red) and a GFP-labeled second heart field graft (green).
How to explain these differences in the deployment of cardiac neural crest across species? With a single ventricular chamber the separation of the pulmocutaneous and systemic blood is incomplete in frogs. Therefore a possible explanation is that in species that have an evolutionary need for a fully divided circulation the neural crest was recruited into the outflow tract septum to help complete the separation of both circulations at the arterial pole of the heart. (more…)
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It’s funny. We have these commonly accepted notions about gene regulation engrained in us from years of training. With the result that when we’re faced with something altogether new, we’re not sure what to make of it. We’re not even sure if we can accept it, but there it is. It’s like realizing black swans with ghoulish red eyes exist in Australia.
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