the Node » Research

How obsession can fuel science blogging: The story of Retraction Watch

Ivan Oransky — Wed, 23 May 2012 12:46:17 +0000

It was a summer afternoon in 2010 when Adam Marcus and I had the phone conversation that led to the birth of Retraction Watch.

We had each been covering medicine and science for more than a decade, and we had come to realize that we shared an unusual obsession: Scientific retractions. We had both experienced what happens when, as a reporter, you peel back the curtains on a mysterious retraction notice. Sometimes, there’s a story so big, major newspapers have to pick up on your coverage, as The New York Times and others did when Adam broke the story of Scott Reuben, the anesthesiology researcher who was forced to retract 22 papers – and go to jail – thanks to fraud.

We also both felt strongly that most journals did a pretty terrible job of publicizing their mistakes. Those realities, taken together with the fun I had been having with my blog Embargo Watch, which I’d founded about six months earlier, prompted me to suggest that we start a blog to monitor retractions as a window into the scientific process.

Adam was enthusiastic, so we launched on August 3, 2010. We figured we’d post a few times per week, whenever we saw an interesting retraction notice and could dig into it. There were fewer than 100 retractions per year, after all.

We – and others who thought this would be an interesting but limited project — were wrong.

That’s because the first weeks we started, two stories broke that thrust retractions into the public eye. One was that of Harvard psychologist Marc Hauser. The other was a seemingly unimportant retraction – of a paper claiming that Jesus cured a woman with the flu – that nonetheless landed us on Colin McEnroe’s show on WNPR in Connecticut.

Unbeknownst to us, we had struck a journalistic gold mine. Our traffic grew quickly. Within a few months, we couldn’t even keep up with all of the retractions we were seeing, thanks to searches and eager tipsters. It turned out that we had launched just in time to report on what would be a record year in retractions in 2011, with some 400.

Retractions are clearly on the increase. And as the Wall Street Journal and Nature have reported, using Thomson Reuters data, they’re outpacing the rate of growth in publications. There are 44% more papers published every year than a decade ago, but at least 10 times the number of retractions per year.

Why the rise? It’s always dangerous to generalize from what are still very small numbers among the more than one million papers published every year – especially when nearly a quarter of the retractions in 2011 belong to one person, the German anesthesiologist Joachim Boldt. But a few trends have manifest themselves. Some of the increase is due to more visibility for papers thanks to online publishing, and to the advent of plagiarism detection software. But journal editors Ferric Fang and Arturo Casadevall have made convincing arguments that the harsh competitive environment in which scientists work today has tempted more researchers to cut corners and commit fraud. As much as that makes some scientists uncomfortable, Fang and Casadevall have received substantial support for their theory.

Retractions may make some scientists worry that their careers have hit a speed bump, but the effects on a body of work are sometimes more indelible than we’d like to think. A recent paper showed that retracted papers are usually only cited a third as often after they’re withdrawn – but there’s other evidence that scientists still tend to cite retracted work in support of their ideas.

Fortunately, some scientists, including Fang and Casadevall, are growing concerned about these trends. They come at a time when drug companies and others are finding that many results aren’t reproducible.

The fact that many notices are opaque – one journal publishes only “This paper has been withdrawn by the authors” or “This paper has been withdrawn by the publisher – contributes to the problem by hiding fraud or giving readers the impression that fraud happened when in fact there was honest error. All of that makes it extremely difficult to determine the real rate of misconduct.

In short, the much-vaunted self-correcting nature of science has some issues.

There are, however, some solutions, based on what others have proposed, and what we’ve seen in our work on Retraction Watch. Editors can:

— Use systems to detect image manipulation and plagiarism
— Require authors to disclose prior retractions and investigations
— Trust anonymous whistleblowers more
— Demand more of institutions, by forcing them to disclose the results of misconduct investigations
— Move more quickly to correct and retract
— Make retraction notices clearer
— Make such notices freely available

We’re grateful that so many readers are paying attention to what we’re doing – and helping us do it better. Some institutions are concerned enough about what’s going on in scientific publishing that they ask us to speak as part of research ethics curricula. We’re always happy to do that, and we’re thrilled to be able to continue our work at Retraction Watch, with the support of an army of scientists around the world.

In Development this week (Vol. 139, Issue 12)

Seema Grewal — Tue, 22 May 2012 11:56:20 +0000

Here are the highlights from the current issue of Development:

Mechanical changes in cochlea development

Correct patterning of the mammalian inner ear sensory epithelium, which contains mechanosensory outer hair cells (OHCs) that detect and amplify sound vibrations and non-sensory supporting cells such as pillar cells (PCs), is essential for hearing. The cell surface mechanical properties of both OHCs and PCs are important for their function but how are these properties regulated during development? On p. 2187, Katherine Szarama and colleagues use atomic force microscopy to show that OHCs and PCs have different cell surface mechanical properties that develop over different time courses. By pharmacologically modulating cytoskeletal elements, they show that the increase in OHC stiffness observed during development depends primarily on actin whereas the development of the cell surface mechanical properties of PCs depends on microtubules. In addition, they report that fibroblast growth factor signalling regulates the developing cell surface mechanical properties of OHCs and PCs, in part by altering cytoskeletal dynamics. These new insights into inner ear development may eventually lead to better treatments for hearing loss.

Resetting after quiescence

During development, networks of regulatory genes control precisely timed sequences of developmental events. In C. elegans, heterochronic genes, which encode several transcription factors and microRNAs (miRNAs) that regulate the expression of these transcription factors, control stage-specific cell-fate decisions. Under adverse conditions, however, second larval stage (L2) worms enter a quiescent state called dauer. Intriguingly, when conditions improve, dauer larvae complete development normally. Here (p. 2177), Xantha Karp and Victor Ambros investigate how cell-fate progression is reset after dauer. Progression from L2 to L3 requires downregulation of the transcription factor Hunchback-like-1 (HBL-1), and, during continuous development, HBL-1 downregulation relies mainly on three let-7 family miRNAs. However, after dauer, the researchers report, lin-4 miRNA and an altered set of let-7 family miRNAs downregulate HBL-1. This shift in the programming of HBL-1 downregulation, they propose, involves the enhancement of lin-4 and let-7 miRNA activity by miRNA-induced silencing complex (miRISC) modulators. The employment of alternative genetic regulatory pathways can, therefore, ensure the robust progression of cell-fate specification after temporary developmental quiescence.

ExE progenitors make an eXit

In female mammalian embryos, inactivation of one of the two X chromosomes in each cell regulates X-linked gene expression. X chromosome inactivation (XCI) is dependent on the non-coding RNA Xist, which is expressed from and coats the inactivated X chromosome. Inheritance of a paternally derived Xist mutation causes embryonic lethality because the inactivation of the paternally inherited X chromosome that occurs in the extra-embryonic lineages of female mouse embryos during imprinted XCI fails. Now, Terry Magnuson and colleagues (p. 2130) describe the exact consequences of failed XCI within the extra-embryonic ectoderm (ExE). The ExE of X/X^Xist– embryos consists mainly of differentiated giant cells and their progenitors, they report, and less differentiated spongiotrophoblast precursors are not maintained. At E6.5, the ExE lacks CDX2, which is required to maintain the ExE’s multipotent state. Moreover, trophoblast stem cell lines derived from X/X^Xist– blastocysts completely reverse normal imprinted XCI patterns. These results suggest that dosage compensation is indispensable for the maintenance of trophoblast progenitors and that imprinted XCI is probably erased in ExE cells.

Gibberellin regulation of flowering

Several environmental cues, including day length, and endogenous developmental signals regulate the transition from leaf production to flower formation in plants. In Arabidopsis, the growth regulator gibberellin promotes this transition most strongly under short day (SD) conditions. Here (p. 2198), George Coupland and colleagues show how gibberellins also promote flowering in response to long days (LDs). The researchers deplete gibberellins in the vascular tissue or the shoot apical meristem by tissue-specific overexpression of GA2ox7, which catabolises gibberellins. Under LD conditions, gibberellins are needed in the vascular tissue to increase production of a systemic signal that is transported from the leaves to the meristem during floral induction. However, in the meristem, instead of activating the expression of the transcription factor SOC1 (which is needed to induce flowering under SD conditions), in response to LDs, gibberellins regulate the expression of SPL transcription factors, which are needed later during floral induction. Thus, the researchers conclude, gibberellins play spatially distinct roles in promoting flowering under long photoperiods.

Migrating primordial germ cells exploit endoderm remodelling

Cell migration through epithelial tissues occurs during development, infection, inflammation, wound healing and cancer metastasis. But how do cells overcome the impermeable junctions between epithelial cells? Leukocytes move out of blood vessels by loosening endothelial cell-cell junctions but do all cells actively remodel tissue barriers during migration? According to Jessica Seifert and Ruth Lehmann, who are studying Drosophila primordial germ cell (PGC) migration through the endodermal epithelium to the gonadal mesoderm, the answer to this question is no (see p. 2101). Although PGC migration requires activation of the G protein-coupled receptor Trapped in endoderm 1 (Tre1) within PGCs, the timing of PGC migration is dictated by the developmental stage of the endoderm. Now, using live imaging and genetic manipulation, the researchers show that PGCs take advantage of developmentally regulated epithelial remodelling, which causes discontinuities in the endoderm, to gain access to the gonadal mesoderm. Thus, Seifert and Lehmann conclude that, rather than actively remodelling tissue barriers, some migrating cells exploit existing tissue permeability.

Tcf21 seals cardiac fibroblast fate

The primary source of cardiac fibroblasts, which are essential for normal heart physiology, is a subpopulation of epicardial cells that has undergone epithelial-to-mesenchymal transition (EMT) and entered the myocardium. But does cardiac fibroblast specification occur early in the formation of the epicardium (which is a multipotent mesothelial layer of cells that spreads over the developing myocardium) or after the epicardial-derived cells have entered the myocardium? Here (p. 2139), Michelle Tallquist and colleagues resolve this puzzle by investigating the role of the transcription factor Tcf21 in cardiac fibroblast specification in mice. The researchers use lineage tracing to show that Tcf21-expressing epicardial cells are committed to the cardiac fibroblast lineage before the initiation of epicardial EMT. Moreover, Tcf21-null embryos fail to develop cardiac fibroblasts and Tcf21-null fibroblast progenitors do not undergo EMT. These results indicate that cardiac fibroblast specification occurs in the epicardium before EMT occurs and, importantly, these findings identify Tcf21 as an essential transcription factor for cardiac fibroblast cell-fate determination.

Plus…

X chromosome inactivation in the cycle of life

Bakarat and Gribnau review new insights into the molecular events occurring during the life cycle of X chromosome inactivation and, in the accompanying poster, provide an overview of the mechanisms regulating X inactivation and reactivation.

See the Development at a Glance poster article on p. 2085

Evolutionary crossroads in developmental biology: cyclostomes

Shimeld and Donoghue summarise the development of cyclostomes (lamprey and hagfish) and discuss how studies of cyclostomes have provided important insight into the evolution of fins, jaws, skeleton and neural crest.

See the Primer article on p. 2091

(note that this article is part of a series of Primer articles on organisms that represent an evolutionary crossroads in the study of evolutionary developmental biology - see the online Featured Topic to view other articles in this series)

Publishing ‘dirty’ data

Katherine Brown — Tue, 22 May 2012 08:30:54 +0000

How much does it matter that the images we publish are neat and tidy? It’s a question I’ve been dealing with over the past couple of weeks, and I wanted to share some thoughts. Here at Development, as at many journals, we check all figures before publication to try and identify potentially inappropriate image manipulation. Whenever we do come across a figure that doesn’t comply with our guidelines on image processing, we contact the authors to ask for clarification, request that the author provides us with the original data – so we can check that nothing fraudulent is going on – and often also ask that the final figure be changed to properly represent the original data. I’m happy to say that problems are few and far between, and that those issues I have come across in the short time I’ve been here have been more a case of beautification than of fraud. But is it okay for authors to ‘clean up’ their images with Photoshop paintbrush tools or the like: not touching the data itself, but rather getting rid of specks of dust or extraneous bits of tissue that are there on the slide?

The images shown here don’t come from any paper, but have been kindly provided by a researcher to illustrate what I’m talking about.

This is a Drosophila wing disc, where clones of cells are marked with GFP, and the entire disc stained with phalloidin in red. Very often in preps like this, you get bits of irrelevant tissue associated with the disc on the slide. But this one looks very clean, right? Wrong. Here’s the original version – you can see that there’s a piece of trachea, stained red, off the left side of the wing disc.

So, thinking that this bit of extraneous tissue is problematic, the researchers have taken the simple solution of photoshopping it out: something that’s very clearly revealed by the standard checks we run on our figures: as shown here.

I’ve seen a seen a few of these cases recently, and in each, the aim of the authors was to ensure that the images were easily interpreted, and that readers weren’t diverted from the data by the extraneous bits of stuff. This may seem innocent, but it could be the first step on a dangerous slope, at the bottom of which lie the clearly fraudulent activities of deleting the bits of data that don’t fit our hypothesis, or making up data that do. Journal guidelines are (or at least should be) pretty unambiguous, and the case above falls foul of this statement taken from our Guide to Authors: “Unacceptable manipulations include the addition, alteration or removal of a particular feature of an image, and splicing of multiple images to suggest they represent a single field in a micrograph or gel.” So while it may seem innocuous, it’s not permitted. Nor is it, at least to my mind, in any way necessary: are we really that easily distracted? Does that little bit of trachea really stop us from seeing the clones in the wing disc? It’s been pointed out to me that the image above could have simply been re-cropped to remove the offending tissue, and if it’s okay to do that, why isn’t it okay to selectively black out those parts of the panel? That’s a reasonable point, and selective cropping is an issue to which I’m not convinced there is a straightforward answer. But I’m guided by the basic principle that the presented data should accurately reflect what you saw down the microscope or on the blot or whatever, and that what may seem irrelevant to you (a higher molecular weight ‘background’ band on your Western) might actually be important to someone else (“Oooh look – this might be a post-translational modification of my protein”).

I well remember from my time in the lab the agony of discovering that the perfect picture was ‘ruined’ by a bit of fluff to the side of the embryo, or because the vibrotome knife had left streaks across the section. And then spending hours re-mounting or re-sectioning to avoid these imperfections. But we all know that science can be an inherently messy endeavour: cells don’t grow in neat rows, and Western blots often give us background bands. So why do we need to hide this when it comes to publication? Of course, it’s vital that the data are clearly presented and understood, but what’s most important is that they accurately represent the experiment, and there’s a danger of losing sight of this in the desire for a beautiful image.

Initiatives like publishing all the uncropped blots that have gone into making the figures in a paper (as pioneered by Nature Cell Biology) are aimed at addressing this issue: by all means show only the relevant bit of the blot in the main figure, but for those interested in the (literally) bigger picture, the whole thing – warts and all – is available. But it can be a pain to find and assemble these files, and we don’t want to make publishing harder than it already is – although there’s a school of thought that says if you can’t lay your hands on the original data, you need to be better at archiving it in the first place!

So what do the Node readers think? Have you been tempted to ‘prettify’ your data for publication, or have you actually done it? Are our guidelines clear enough on what you can and can’t do? Do you support initiatives to make the raw data available to the reader, or is it all too much of a hassle? We’d really love your input on what kind of requests or demands a journal should make in terms of data presentation, so please answer the poll below (it’s completely anonymous!) and give us your feedback in the comments section.

Katherine Brown is the Executive Editor of Development

Smart signaling in the developing brain

Erin M Campbell — Thu, 10 May 2012 20:02:36 +0000

The WNT pathway functions in so many processes during development that it is easy to be jealous of its multi-tasking abilities. A recent paper in Development describes the role of WNT signaling in neural stem cell proliferation.

WNT signaling plays an important role in neural development, axon guidance, cell polarity, and stem cell biology. WNT pathway mutations are linked to several different cancers, including medulloblastomas. Medulloblastomas are malignant tumors found in the cerebellum of the brain and are more commonly found in children. Recently, Pei and colleagues asked which cells in the developing cerebellum were responsive to canonical WNT signaling and found that WNT signaling promotes proliferation of neural stem cells (NSCs), the major source of neurons on the cerebellum. WNT signaling, however, did not induce proliferation in granule neuron precursors, the other major class of progenitors in the cerebellum. In addition, Pei and colleagues used transgenic mice with an inducible allele of β-catenin to find that constitutive activation of WNT signaling induced NSC proliferation in vivo. This increase in proliferation, however, caused NSCs to lose the ability to undergo self-renewal or differentiation. The images above show cerebellum tissue from a control mouse (left) and a transgenic mouse with activated β-catenin (right). Constitutively active WNT signaling caused an increase in the population of NSCs (G-FAP, Sox1), which were also actively proliferating (BrdU, bottom).

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

Pei, Y., Brun, S., Markant, S., Lento, W., Gibson, P., Taketo, M., Giovannini, M., Gilbertson, R., & Wechsler-Reya, R. (2012). WNT signaling increases proliferation and impairs differentiation of stem cells in the developing cerebellum Development, 139 (10), 1724-1733 DOI: 10.1242/dev.050104

In Development this week (Vol. 139, Issue 11)

Seema Grewal — Tue, 08 May 2012 11:04:42 +0000

Here are the research highlights from the current issue of Development:

Laminin cue for epithelial polarity

During the development of many animal organs, mesenchymal cells co-ordinately polarize to form epithelial sheets or tubes. In vitro studies have suggested that the extracellular matrix component laminin functions as a polarity cue during this mesenchymal to epithelial transition. Here (p. 2050), Jeffrey Rasmussen and colleagues provide in vivo evidence for laminin’s involvement in polarization by studying the development of the C. elegans pharynx, an epithelial tube that forms from pharyngeal precursor cells (PPCs). The researchers show that cell fate regulators, including the transcription factor PHA-4, cause the PPCs to form a bilaterally symmetric, rectangular array of cells called the ‘double plate’. PPC polarization and apical PAR localisation begin in the double plate cells, which then undergo apical constriction to form a cylindrical cyst. Notably, laminin provides an essential cue that orients the apical localisation of the PAR-3 complex in the double plate but not in the developing C. elegans intestine. Thus, the researchers conclude, laminin is an early polarizing cue for some but not all epithelia.

Why oocytes are predisposed to aneuploidy

During mitosis, the spindle assembly checkpoint (SAC) coordinates proper bipolar chromosome attachment with the anaphase-promoting complex/cyclosome (APC/C)-mediated destruction of cyclin B1 that is required for anaphase onset, thereby avoiding chromosome mis-segregation and aneuploidy. The generation of a Mad2-based signal at kinetochores is central to current models of SAC-based APC/C inhibition: during mitosis, the kinetochores of polar chromosomes (non-aligned bivalents), which are at the greatest risk of mis-segregating, preferentially recruit Mad2, which couples SAC activation to aneuploidy risk. Paradoxically, although an SAC operates in mammalian oocytes, meiosis I is notoriously error prone. Two papers in this issue investigate this long-standing puzzle.

On p. 1947, Keith Jones and colleagues examine the timing of Mad2 loss from mouse oocyte kinetochores. The formation of stable kinetochore-microtubule attachments in mid-prometaphase (3-4 hours before anaphase), they report, coincides with the loss of Mad2 from the kinetochores and the start of APC/C-mediated cyclin B1 destruction. Thus, SAC inhibition of the APC/C ends in mid-prometaphase. However, in a third of oocytes examined, this timing did not coincide with bivalent congression. Notably, the presence of non-aligned bivalents (which were weakly positive for Mad2, under less tension than congressed bivalents, and in the process of establishing correct bi-orientation) did not affect the time between APC/C activation and anaphase onset, and non-aligned bivalents sometimes persisted until anaphase, resulting in homologue non-disjunction. Thus, in oocytes, a few erroneous microtubule-kinetochore attachments may go uncorrected because they do not generate a sufficient SAC ‘wait anaphase’ signal to inhibit the APC/C.

On p. 1941, Liming Gui and Hayden Homer investigate how the SAC responds to polar chromosomes during meiosis I in oocytes. They show that Mad2 is not preferentially recruited to the kinetochores of the rare polar chromosomes that occur in wild-type mouse oocytes or to the kinetochores of the more abundant polar chromosomes that are found in oocytes depleted of the kinesin-7 motor CENP-E. Moreover, in CENP-E-depleted oocytes all the kinetochores eventually become devoid of Mad2, even though the capacity of the chromosomes to form stable attachments to the spindle is severely compromised. These and other findings suggest that SAC signalling is uncoupled from chromosomal position during meiosis I in mouse oocytes, thereby predisposing oocytes to aneuploidy.

Digging out the flowery function of APETALA2

The regulation of gene expression by transcription factors drives cell fate specification during development. In Arabidopsis, transcription factors encoded by four classes of homeotic genes control floral organ identity. The A-class gene APETALA2 (AP2) promotes sepal and petal identity and restricts expression of the C-class gene AGAMOUS (AG), which specifies stamen and carpel identity, but how does AP2 perform these functions? On p. 1978, Xuemei Chen and co-workers report that AP2 recognises and acts through an AT-rich sequence element. The researchers show that AP2R2 (one of two DNA-binding domains in AP2) binds a non-canonical AT-rich target sequence in vitro and that the presence of this sequence in the second intron of AG is important for the restriction of AG expression in vivo. Other experiments indicate that AP2 directly regulates AG expression in young flowers through this sequence element, which is highly conserved in Brassicaceae. Together, these findings shed light on the molecular mechanism underlying AP2 action and provide a missing link in the mechanisms controlling flower development.

Membrane trafficking and epithelial polarity

Biological tubes composed of polarized epithelial cells perform many functions in multicellular organisms. The establishment and maintenance of epithelial polarity depend on polarized trafficking of membrane components to the apical or basolateral domains of epithelial cells, but exactly how trafficking regulates epithelial polarity is unclear. In this issue, two papers describe a new and unexpected role for the post-Golgi vesicle coat clathrin and its adaptor AP-1 in apical sorting and lumen formation in the C. elegans intestine.

On p. 2061, Grégoire Michaux and colleagues report that the clathrin adaptor AP-1 is required for epithelial polarity in the C. elegans intestine. Depletion of AP-1 subunits does not affect the establishment of epithelial polarity or the formation of the intestinal lumen, the researchers report. However, they show that AP-1 is essential for the apical localisation of the oligopeptide transporter PEPT-1 and the polarity proteins PAR-6 and CDC-42, and for the basolateral distribution of the monocarboxylate transporter SLCF-1. They also show that AP-1 depletion triggers the formation of ectopic apical lumens between intestinal cells along the lateral membranes later during embryogenesis.

On p. 2071, Verena Gobel and colleagues perform an unbiased RNAi screen for apicobasal polarity and tubulogenesis defects in the C. elegans intestine and identify clathrin and AP-1 as being required for apical polarity and lumen formation. The researchers show that clathrin/AP-1-mediated polarized transport co-operates with a sphingolipid-dependent apical sorting process. Furthermore, they report, the depletion of clathrin, AP-1 or glycosphingolipid biosynthetic enzymes causes a set of apical membrane proteins (including PAR-6) to mislocalise basolaterally and generate ectopic lateral lumens. Finally, they show that clathrin-coated and sphingolipid-rich vesicles assemble at polarized plasma membrane domains in a co-dependent and AP-1-dependent manner.

Together, these findings suggest that clathrin/AP-1 controls both basolateral and apical sorting, an unexpected finding given that, until now, clathrin and its AP-1 adaptor had been thought to regulate only basolateral sorting in mammalian epithelia. Importantly, these findings indicate that this newly discovered clathrin/AP-1 function in apical sorting is required to regulate epithelial polarity in vivo in a tubular epithelium and that the clathrin/AP-1 apical sorting pathway converges with a sphingolipid-dependent apical trafficking path.

Plus…

Tet family proteins and 5-hydroxymethylcytosine in development and disease

Over the past few decades, DNA methylation at the 5-position of cytosine (5-methylcytosine, 5mC) has emerged as an important epigenetic modification that plays essential roles in development, aging and disease. In this Issue, Tan and Shi provide an overview of the role of Tet family proteins and 5hmC in development and cancer. See the Primer article on p. 1895

25 years of Development!

The Journal of Embryology and Experimental Morphology (JEEM) was founded in 1953, but it wasn’t until 1987, in a bold move by The Company of Biologists and the journal’s editors, that the journal was rebranded, restyled and relaunched as the journal we now know as Development.

We’ll be celebrating celebrating our quarter-century throughout the year, but to kick-start the celebrations we’ve invited past and present Editors in Chief of Development to share their memories and thoughts on their time in charge.

See the Editorials from Chris Wylie, Jim Smith and Olivier Pourquie.

Inflammation and Atherosclerosis – September 20-21, 2012 in Munich, Germany

Abcam Events — Wed, 02 May 2012 08:59:11 +0000

Upcoming deadlines: oral abstracts – June 11, 2012

Topics:
• Genes, lipids and systemic inflammatione
• Early inflammatory and immune-driven atherogenesis
• Atheroprogression, ER-stress and unstable plaques
• Novel therapeutic options involving miRNAs

Speaker list:
Full speaker list available on meeting website.

Meeting website:
http://www.abcam.com/Munich

Interview with Beddington Medal winner Boyan Bonev

Eva Amsen — Fri, 27 Apr 2012 08:09:35 +0000

Each year, the British Society for Developmental Biology awards the Beddington Medal for the best PhD thesis in developmental biology. At the 2012 BSDB meeting, this award went to Boyan Bonev, who completed his PhD in Nancy Papalopulu’s lab at the University of Manchester. At the conference, Boyan gave a talk about his PhD work, describing how microRNA-9 promotes neural progenitor heterogeneity in a context-dependent manner. Find out more about Boyan’s work, and what he’s up to next, in this interview.

What was your thesis about?

My graduate work was about the role of the microRNA miR-9 in neural development. MicroRNAs are a really exciting part of the genome, because they’re small, non-coding RNAs. They were discovered about ten years ago, and since then there’s been a tremendous amount of research carried out to find out what exactly their role is. There are many occasions where microRNAs have an essential role, particularly during development. What I wanted to find out is how miR-9 regulates neural development, in particular in vertebrates. MiR-9 has a really interesting expression pattern: the microRNA is present in the brain, but expressed differently in different parts of the brain. So, the really cool thing about miR-9 is that it turned out to have a context-dependent function, and this is really the key highlight of my thesis. It means that in some parts of the brain miR-9 does one thing, and in other parts it does something else. During development it also changes its function. For example, in my talk I talked about progenitor heterogeneity, and how miR-9 can regulate this, but we also looked at its function in mature neurons, where it does something else entirely, which is to modulate axon branching and axon extension. It’s really cool how nature seems to be using one molecular mechanism in a different way, depending on where you look along the anterior-posterior axis, or at which developmental stage the organism is, to get feedback about what decisions the cells need to make.

You showed work in both frog and mouse. Which one do you prefer to work with?

To be honest I find working with both of them really exciting. Working with frogs is a little bit easier, because they develop externally, so it’s easier to get sufficient numbers and it’s easier to manipulate them from the very beginning. They’re a really good model organism for studying early developmental events in particular. However, to work on something that is more closely related to the human brain, which is ideally what we want to understand, mouse is the better system. That’s why I started to work more and more on mouse, especially in the last part of my PhD. Other than that they’re both really nice organisms to work with.

In your talk you described how a microRNA target in turn regulates the microRNA. Is that a common mechanism?

There are not that many instances where such negative feedback regulation is known, but I think it’s becoming more and more prevalent that this is indeed a very interesting type of regulation. Not just for microRNAs, but also in the case of transcription factors with negative feedback loops. I think what is really important to consider is that these transcription factors and microRNAs do not work in isolation – they all work together with all their partners. And these kind of feedback loops, whether they are coherent or incoherent feedback loops, are the ones that buffer against developmental noise or reinforce a decision. In our case this was a negative feedback loop that was doing both, because it was promoting oscillations, but it was also reinforcing developmental decisions.

What are you doing now?

I was supposed to have a bit of a long break between my PhD and before I started my postdoc, but it boiled down to about ten days in the end. Right now I’m going back to my home country, Bulgaria, to have the rest of the ten days off. At the end of the month I’m leaving for the States to start working on my postdoc.

What will you be doing in your postdoc?

That’s going to be another cool and exciting project. It’s also related to non-coding RNAs and neural development, but it’s completely different from what I’ve been doing so far. It focuses on a different, newer, type of non-coding RNAs: long non-coding RNAs. I told you that microRNAs are about ten years old - well, these long ncRNAs are about 3-4 years old.

I’m going to Harvard, where I will be working in the lab of John Rinn, who is one of the guys who discovered long ncRNAs, and in Paula Arlotta’s lab, who is an expert in mouse neural development, in particular mouse cortical development. I’m going to be working with both of them to try to figure out the function of long ncRNAs in mouse neural development.

Do you have any advice for new PhD students?

Be persistent. At some point, things will probably stop working, and you’re going to be struggling to figure out why they’re not working. What I always say is that the result is the result. Your inability to figure out why it is like that is the problem. But usually things like technical difficulties or problems with the model organism have a meaning, and you have to be persistent and really go down to the details to figure out what’s going on.

Bonev, B., Pisco, A., & Papalopulu, N. (2011). MicroRNA-9 Reveals Regional Diversity of Neural Progenitors along the Anterior-Posterior Axis Developmental Cell, 20 (1), 19-32 DOI: 10.1016/j.devcel.2010.11.018

Dajas-Bailador, F., Bonev, B., Garcez, P., Stanley, P., Guillemot, F., & Papalopulu, N. (2012). microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons Nature Neuroscience, 15 (5), 697-699 DOI: 10.1038/nn.3082

The IMPC: a new era in mouse genetics

sallan — Thu, 26 Apr 2012 08:00:39 +0000

The sophistication of genetic tools and the relative ease of breeding and housing mean that the mouse is the most widely used mammalian organism for basic and biomedical research. The genotype-phenotype information that will emerge from the efforts of the International Mouse Phenotyping Consortium (IMPC), now well into its first year, will advance all areas of the biological sciences, from behaviour to drug discovery, oncology to developmental biology.

The IMPC is one of the largest model-organism-based initiatives ever funded. Its aim is to generate and comprehensively characterise the phenotypes of viable knockouts for every gene in the mouse genome, and to compile the information in a public database (Brown & Moore, 2012). In practical terms, this means creating ~20,000 viable mouse lines and phenotyping them using dozens of tests, a feat that will be carried out through the coordinated efforts of several institutes in nine different countries. Moreover, the ~30% of knockouts that are expected to show embryonic lethality will be characterised, where possible, using specialised tests performed during embryonic development. The number and sophistication of tests used for phenotyping will likely increase as the protocols are refined and improved, and as notable mouse strains are selected for specialised phenotyping in secondary screens. For example, histopathology – the analysis of disease correlates through microscopic examination of tissues obtained from necropsy or biopsy – provides invaluable information that is complementary to in vivo assays, but it can currently only be performed on selected lines owing to economical and logistical constraints (Schofield et al., 2012).

The resources that will be generated by the IMPC include free access to all knockout mouse lines (or sperm) and a comprehensive database of corresponding phenotype information. These resources generated will be of value to investigators at all levels, and in many disciplines, from undergraduates to group leaders, basic scientists to clinicians.

Further reading

Brown, S. D. M. and Moore, M. Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium. (2012). Dis. Model. Mech. 5, 289-292.

Schofield P. N., Vogel, P., Gkoutos G. V., Sundberg, J. P. (2012). Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. Dis. Model. Mech. 5, 19-25.

Straight talk with… Steve Brown. Interview by Hannah Waters. (2011). Nat. Med. 17, 1332.

January 2012 DMM Podcast: Paul Schofield on histopathology in high-throughput phenotyping of mutant mice.

IMPC website: http://www.mousephenotype.org/

In Development this week (Vol. 139, Issue 10)

Seema Grewal — Mon, 23 Apr 2012 08:45:17 +0000

Here are the highlights from the current issue of Development:

A TOR de force in the haematopoietic niche

During development and homeostasis, it is essential to coordinate growth with the availability of nutrients. The interconnected insulin/IGF (IIS) and target of rapamycin (TOR) pathways integrate tissue growth with dietary conditions in Drosophila, and now Marc Haenlin and co-workers show that these pathways play a crucial role during haematopoiesis in the Drosophila lymph gland (p. 1713). The larval lymph gland contains a group of stem-like progenitor blood cells (prohaemocytes) that are kept in an undifferentiated state by cells of the posterior signalling centre (PSC), which serves as the stem cell niche. The researchers show that the IIS and TOR pathways regulate the size of the haematopoietic niche by regulating cell size and cell proliferation in the PSC. In addition, they show that IIS and TOR signalling are required in prohaemocytes to control their maintenance, and disruption of these pathways, induced genetically or by starvation, results in the precocious differentiation of these progenitors. Importantly, these studies highlight that blood cell development is coupled with nutritional status.

A MAP(K) of germline self-renewal

Spermatogonial stem cells (SSCs) have the remarkable ability to self-renew and support spermatogenesis throughout life. It is known that fibroblast growth factor 2 (FGF2) promotes SSC self-renewal but the factors acting downstream of FGF2 are unknown. Here, Takashi Shinohara and colleagues show that FGF2 regulates SSC self-renewal via MAP2K1 and the Etv5 and Bcl6b genes (p. 1734). Using an in vitro mouse germline stem (GS) cell culture system, the authors show that GS cells require FGF2 for continuous proliferation, and that a specific MAP2K1 inhibitor reduces GS cell proliferation and MAP2K1 phosphorylation. By analysing target genes that are regulated by MAP2K1, the researchers identify Etv5 and Bcl6b, and show that overexpression of these genes in GS cells promotes proliferation in an FGF2-independent manner, confirming that they act downstream of MAP2K1. Furthermore, transplantation of Bcl6b-expressing GS cells into mouse testes induces germ cell tumour formation, suggesting that excessive self-renewal can promote tumourigenesis. The identification of these genes provides key insights into the mechanisms controlling SSC self-renewal.

Notch tips the balance in the pancreas

In the developing pancreas, the branched epithelium can be separated into tip and trunk regions, with the tip domain generating acinar cells, and the trunk domain differentiating to endocrine and duct fates. Although Notch signalling is known to be important for proper pancreatic development, particularly in maintaining the progenitor state and inhibiting premature endocrine differentiation, its precise roles in regulating cell fate remain unclear. Here (p. 1744), Jan Jensen and co-workers disrupt Notch signalling in the mouse in a mosaic fashion, revealing a function for Notch in regulating trunk versus tip cell fate. Overexpression of a dominant-negative Mastermind protein, which blocks Notch-dependent transcription, leads to loss of endocrine and duct cells, suggesting that Notch signalling promotes trunk cell identity. Mechanistically, Notch promotes the expression of the trunk-specific transcription factor Nkx6.1, via direct binding of RBP-jκ at the Nkx6.1 promoter. These data thus establish a crucial role for the Notch pathway in directing endocrine and duct cell differentiation in the pancreas.

Eve and Grain guide the way for axon pathfinding

Accurate axonal pathfinding relies on the tightly regulated expression of guidance cues and their receptors, but the links between transcriptional regulators and downstream guidance factors are poorly understood. Genetically amenable Drosophila motoneurons provide an ideal system for analysing the control of guidance receptor expression. It is known that two transcription factors, Even-skipped (Eve) and Grain (Grn) are expressed in the aCC and RP2 motoneurons, and that projection of these neurons to the muscle requires the Netrin receptor Unc-5. Now, Juan-Pablo Labrador and colleagues dissect out the relationships between these factors (p. 1798). The researchers find that Eve and Grn independently promote Unc-5 transcription, and that both are required to generate sufficient Unc-5 expression for proper pathfinding – likely via an enhancer element in unc-5 intron 5. Overexpression of both Eve and Grn in another motoneuron population induces ectopic Unc-5 and hence axonal redirection. Thus, the combinatorial effects of these two transcription factors together direct expression of the key guidance receptor, and so define the axon’s path.

Planar cell polarity: fattened up

The atypical cadherin Fat (Ft) is crucial for planar cell polarity (PCP) in Drosophila. Four ft homologs (Fat1 to Fat4) have been identified in mammals, but the functional roles of these homologs and any possible redundancies between them are unclear. Here, Helen McNeill and colleagues study the genetic interactions between mammalian Fat genes and show that Fat proteins act both synergistically and antagonistically to regulate multiple aspects of tissue morphogenesis in mice (p. 1806). For example, the authors show that Fat1 and Fat4 synergise during kidney, cochlea and cranial neural tube morphogenesis. Importantly, the researchers also show that the effects of Fat4 are modulated by atrophins, which are known components of PCP signalling in Drosophila, suggesting that Fat-atrophin interactions play an essential and conserved role in planar polarity. These findings reveal a high degree of complexity in mammalian PCP and highlight the wide-ranging effects of Fat cadherins on animal development.

Complexity in the kidney

The kidney comprises multiple cell types of both epithelial and mesenchymal origin, with highly defined regional subdivisions in the ductal systems. A full understanding of kidney development requires that each cell type can be uniquely identified by specific molecular markers. To this end, Andrew McMahon and colleagues have undertaken a comprehensive analysis of the RNA expression patterns of nearly one-thousand transcription factors in the embryonic mouse kidney (p. 1863). Their results not only identify novel markers, but also reveal an unexpected degree of restriction in expression of many factors, suggesting that anatomically defined compartments may be further subdivided at the molecular level. Moreover, this in situ dataset provides a starting point to understand the transcriptional networks underlying cell type specification. As proof of principle, the authors use published microarray and expression data to bioinformatically identify putative targets of five transcription factors and to uncover potential network topologies. This valuable resource has been made available to the community via the GUDMAP database.

Stem cells at home

Erin M Campbell — Thu, 12 Apr 2012 18:23:11 +0000

We depend on our own comfort zones to keep us grounded, and stem cells are no different. A recent paper in Development describes how the adhesion that keeps a stem cell in its niche is regulated.

A stem cell’s niche is important in maintaining its long-term undifferentiated state. A great model of stem cell niche biology is the Drosophila testes, in which germline stem cells (GSCs) reside next to somatic hub cells within their niche. GSCs maintain proximity to the “hub” through the use of E-cadherin-based adherens junctions. A recent paper identifies a new player in adhesion of GSCs to the hub. Srinivasan and colleagues found that the receptor tyrosine phosphatase Lar (Leukocyte-antigen-related-like) promotes GSC-hub adhesion through E-cadherin. Lar, typically associated with axonal migration and synapse formation, is also required for proper localization of Apc2 and E-cadherin localization, in turn regulating centrosome positioning and asymmetric division. Without Lar, fewer GSCs were found at the hub. Images above show localization of Lar (red in merged, white in right image) at the GSC-hub interface (arrowheads) in Drosophila testes (early germ cells are green). Lar is also seen between sister cells of early spermatogonial cysts (arrows), which have the ability to later replace lost GSCs.

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

Srinivasan, S., Mahowald, A., & Fuller, M. (2012). The receptor tyrosine phosphatase Lar regulates adhesion between Drosophila male germline stem cells and the niche Development, 139 (8), 1381-1390 DOI: 10.1242/dev.070052