This post about the Research Works Act and the effect on society journals was written for, and first published on, Reciprocal Space. Reposted with permission, and edited to add a correction.

Much has been said about the RWA, and the involvement of big name publishers. Less discussed, but very important for many scientists, is the role that scientific societies and their journals have, and the impact of current or future publishing practices. Some societies, such as the American Association of Immunologists (AAI), the American Society of Nephrology (ASN), the American Heart Association (AHA), and the American Society for Clinical Investigation (ASCI), publish their own journals. Of these, very few (in this list only the ASCI), have an open access policy. Other societies, such as the Society for Developmental Biology (SDB), publish in journals operated by big publishers, such as Elsevier (in the case of SDB’s journal, Developmental Biology). So where do these societies and their journals stand on RWA?

Well in some cases it’s crystal clear. In letters that responded to a “Request for Information” (RFI) by the Office of Science and Technology Policy, Executive Office of the President, regarding “Public Access to Peer- Reviewed Scholarly Publications Resulting from Federally Funded Research””, the AAI wrote:

“…working in partnership with professional societies and other scholarly publishers offers the federal government the most cost-effective and efficient way of ensuring that private sector, scholarly journals survive, preserving their crucially important service of providing independent, expert peer review (accomplished at publishers’ expense) of government-funded scientific research.”

This refers to their perceived duplication of efforts in having PubMedCentral duplicating published manuscripts. The statement might make sense, if the journals were to offer free access after 12 months. But they continue with:

“…want to express our clear opposition to government mandates which require private sector publishers to make their legally-owned property (i.e., journal manuscripts, published articles and associated data) available online on sites other than our own, or to comply with a government-determined embargo period. These mandates allow the government to take private property without owner authorization or compensation, and threaten the sustainability of our nation’s premier peer-review publishing system.”

So, not so happy about providing free access. They also claim that PMC is an inferior means of disseminating and archiving published material. This is highly debatable, especially the permanence of published work. Finally, they answer many questions posed by the RFI, and include this delightful gem, which we’ve heard from Congresswoman Maloney:

“…increased “free” access is likely to benefit scientists in other nations, whether allies or enemies. In some instances, this will enhance international cooperation in the sciences, but it is not necessarily beneficial to the U.S. economy as even our friendly competitors will gladly take our research findings for free….. Neither publishers, nor the U.S. scientific enterprise, nor the U.S. taxpayer benefits from the “giving away” of our peer-reviewed publications.”

Oh dear. The point really is, these societies make most of their money from their publications, and of course feel threatened.

But then how does ASCI do it, publishing all papers in JCI for free? I don’t have the answer, but perhaps these societies should talk to each other…

In the case of the SDB, it’s a bit more complicated. They too make most of their revenue from their journal. But in this case, they fall under Elsevier’s control, and only receive a fraction of the journal’s revenues (around 10%). What can they do, stuck between a rock and a hard place? Currently they are debating what to do, so the jury is out. The SDB does provide an OA option stemming from agreements with HHMI and Wellcome Trust, that allows researchers to make their paper available as OA for a fee of $3,000. (The Company of Biologists, who publish Development, have a similar hybrid model and offer OA for a fee.)

Then the final question is for those of us who are members of these societies. Do we boycott our own society journals? Do we engage the leadership to try to convey our views? There is no clear answer, but it should be something. The editors of the journals are scientists, just like us. They understand, and they will listen. The societies have existed for a long time, and are an important part of science, in assembling scientists with shared interests in the form of conferences and journals, promoting scientific education, amongst other laudable goals. But many have their survival inextricably linked with their closed access journals.

As scientists we must ask ourselves how to help our scientific societies, while promoting open access.

(4 votes)

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This round-up also includes a few posts from the end of December that didn’t make it into December’s post due to holiday scheduling.

Developmental Biology Bingo Game
We made a bingo game! You all left many suggestions for words to include in a developmental biology bingo game, and BenchFly turned that into a playable game. Visit their site to download bingo cards for everyone in your lab.

SDB CoRe
The SDB has set up a collaborative resource for teaching materials to use in developmental biology courses, and they are looking for submissions. Do you have great visuals that can be used in undergraduate teaching? Let Marsha Lucas know. She left more information in her post earlier this week.

Research

Just before Christmas, Hillel Kugler, of Microsoft Research, wrote about a project he worked on with Jane Albert Hubbard’s lab at the Skirball Institute.

“In our study, published in Development, we have built a computational model of germline development in C. elegans. In this model, germ cells move, divide, respond to signals, progress through mitosis and meiosis, and differentiate according to a developmental program specified for a “cell”. This developmental program incorporates cellular decision-making that influences germ cell behavior, as defined by a subset of cell components and their dynamic interactions.”

Other research recently covered on the Node included a paper that showed that a small change in bioelectric signals is enough to induce eye development in Xenopus, and an image highlighting the importance of Notch signaling in stem cell self-renewal and intestinal homeostasis.

Write for the Node
If you’re interested in writing for the Node, all you have to do is create an account and wait for approval. But sometimes inspiration is the limiting factor. If you’d love to write, and just want some suggestions and ideas, you can fill out this form, and we’ll occasionally send you some ideas. The first email has gone out this week, but if you sign up now, you’ll get that sent as soon as possible.

Books
Finally, we saw a few more book reviews this month. The last of the Development book reviews went up, in which Wendy Bickmore reviews “The Nucleus” (Edited by Tom Misteli and David L. Spector). We started 2012 with the first Node-exclusive book review: Sasha Terashiva reviewed “The Cell: A Very Short Introduction” (by Terence Allen and Graham Cowling).

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The Society for Developmental Biology (SDB) has launched SDB Collaborative Resources (CoRe), an online collection of images, movies, and diagrams for learning and teaching developmental biology.  SDB CoRe is a free and open website developed to help increase understanding of developmental biology at all levels.

SDB CoRe is easily-searchable and can be browsed by topic, organism, or featured objects.  All objects have short descriptions aimed at helping users learn something about development with glossary words highlighted in green.  Object pages contain references as well as  links to related CoRe objects, links to reviews in the soon-to-be-launched WIREs Developmental Biology, and when relevant, to original research papers in SDB’s official journal Developmental Biology.  All users can create a My CoRe account in order to comment on an object or save it in their favorites.

SDB needs your help in building this community resource!  We are looking for visuals that help explain basic concepts in developmental biology across numerous plant and animal species.  Here are the guidelines for submitting to CoRe.  If you are an SDB member you can login to CoRe with your email address to submit.  Non-members that would like to submit to CoRe please contact me at info@sdbcore.org.  If you have any questions or suggestions for the site please email me as well.  Enjoy SDB CoRe!

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Nature featured a news article about digital lab notebooks, which launched a discussion in various places (including the comments of the article itself) about whether or not they’re useful.

What do you think? Would you use a digital lab notebook in your lab, or would you rather keep your old paper notebook? Or maybe you already keep all your notes in a digital format only. You’re all web-savvy Node readers, of course, but let’s see how digital you are when it comes to benchwork. Here’s a poll:

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EU Initial Training Network searches for 1 PhD Student

CardioNeT – Our Initial Training Network in Cardiovascular Research offers 1 PhD student position at the British Heart Foundation Regenerative Medicine Laboratory, Department of Physiology, Anatomy and Genetics, University of Oxford, UK.

Funded by EU’s FP7, CardioNeT comprises twelve partners from both the academic and industrial sectors and aims to implement a highly multidisciplinary, intersectoral and competitive training programme in cardiovascular research through cutting-edge projects and extensive training in complementary areas.

We are looking for:

• Enthusiastic researchers with a Masters Degree in biomedical sciences and interest in cardiovascular research
• Previous lab experience will be valued
• Good spoken and written command of English
• The PhD may incorporate, although will not be restricted to, one of the following research projects:
• Epicardial signalling during myocardial regeneration in zebrafish
• Identifying the source of new vasculature during zebrafish coronary vessel repair
• The role of inflammation and fibrosis in the regenerating zebrafish heart
• Small molecule induction of human adult epicardium-derived progenitor cells in cardiac repair

We offer:

• 3-year contract to undertake a PhD in cardiovascular biology
• A highly multidisciplinary, intersectoral and competitive training programme in cardiovascular research
• Integration in a European network of scientific excellence, with short stays in partner labs
• Access to state-of-the-art infrastructures
• Very competitive salary (€45,714 per annum)
• Extensive complementary training

Eligibility:
Researchers must be in the first four years (full-time equivalent) of their research careers and have not yet been awarded a doctoral degree at the time of recruitment. In addition, researchers must not have resided or carried out their main activity (work, studies, etc) in the UK for more than 12 months in the 3 years immediately prior to 14 February 2012. There is no restriction on the nationality of the researcher to be hired.

Interviews will take place in Oxford between Wednesday 22nd and Friday 24th February 2012. The studentship will start on Monday 1st October 2012.

Those interested please send CV, a cover letter justifying the interest of the applicant in the project, and the names of two referees to sally.harte@dpag.ox.ac.uk

General enquiries should be addressed to paul.riley@dpag.ox.ac.uk

Application deadline: 12 noon on Tuesday 14th February 2012

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Conference page: http://www.cnrs.fr/insb/cjm/2012/Vincent_e.html

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Here are the highlights from the current issue of Development:

Neuronal cell fate: windows of opportunity

It is becoming increasingly evident that both vertebrate and invertebrate neural progenitor cells exhibit programmed temporal changes in their competence to generate specific neuronal cell types, but how is this competency controlled? Two articles in this issue address this question by studying Drosophila neuroblast lineage progression.

On p. 657, Michael Cleary and co-workers investigate the role of Polycomb repressor complexes (PRCs) in regulating neuroblast competence. In the Drosophila neuroblast 7-1 (NB7-1) lineage, the transcription factor Kruppel (Kr) specifies the third-born U3 motoneuron, but competence to generate U3 cells is limited to early divisions and is gradually lost when the neuroblasts transition to making interneurons. The researchers show that PRC loss of function extends the ability of Kr to induce U3 fate, whereas PRC gain of function causes precocious loss of competence to make motoneurons. The analysis of other neuroblast lineages that undergo a motoneuron-to-interneuron production transition demonstrates that PRCs also act to restrict motoneuron competence in these lineages. The researchers thus propose a model in which PRCs act to set up motoneuron-specific windows of competence in various neuroblasts that transition from motoneuron-to-interneuron production.

On p. 678, Stefan Thor and colleagues focus on the Drosophila embryonic neuroblast NB5-6T lineage to investigate how cell proliferation and cell fate specification are integrated during development. NB5-6T neuroblasts give rise to a lineage of 20 cells, including a differentiated set of neurons that are born at the very end of the lineage and that express Apterous: the Ap neurons. The authors identify two independent factors, Prospero and Notch, that act in concert to control the proliferation of NB5-6T daughter cells as the lineage progresses temporally; Prospero controls daughter cell proliferation in the early lineage and Notch activity then limits daughter cell proliferation in the late lineage, when Ap neurons are generated directly from neuroblasts, resulting in a programmed differentiation switch. Thus, the authors conclude, the control of neuronal daughter cell proliferation is integrated with temporal progression to ensure that the correct numbers of each unique cell type are generated.

Bypassing auxin signalling

Plant development is regulated by a number of mobile factors. The Arabidopsis BYPASS1 (BPS1) gene was previously shown to control shoot and root development by preventing formation of a mobile compound, but how this compound functions and whether it modulates other signalling pathways is unclear. Now, Leslie Sieburth and colleagues show that Arabidopsis BPS1, as well as two related genes, BPS2 and BPS3, control the production of a mobile factor, the bps signal, which regulates patterning and growth in parallel with auxin signalling (p. 805). By analysing single, double and triple mutants, the researchers show that all three BPS genes control bps signal synthesis. Importantly, bps triple mutants display severe embryogenesis defects, including disruptions to vascular, root and shoot stem cell populations. Finally, bps triple mutants exhibit normal auxin-induced gene expression and localisation of the PIN1 auxin transporter, suggesting that the bps signal functions in an auxin-independent manner. Although the nature of the bps signal remains unknown, these studies identify a novel pathway that regulates multiple stages of plant patterning and growth.

ABC of germline development

Plasma membrane ABC transporters serve dual functions in the cell: they export toxins to protect against damage and morphogens to mediate communication. It is thought that the activity of ABC transporters in embryos and stem cells should be high, so that mutagens are efficiently removed. Here, Joseph Campanale and Amro Hamdoun (p. 783) report the surprising finding that ABC transporter activity is reduced in germline precursors, the small micromeres, of the sea urchin embryo. This reduction in efflux pump activity can likely be ascribed to an increase in the rate of endocytosis specifically in the micromeres. What are the functional consequences of manipulating ABC transporter activity? The authors take a first step towards understanding this, showing that ABC transporter inhibition disrupts migration of the small micromeres at later stages of embryogenesis. While there is still much to be understood about the regulation and role of these plasma membrane pumps, this study provides evidence for the developmental importance of controlling their surface expression and activity.

Glutamate keeps hair follicles in touch

The hairs of our skin are mechanoreceptive: displacement of the hair is detected via sensory afferents in the hair follicle piloneural collar. In this complex structure, neurons, Schwann cells and keratinocytes are closely apposed, and interactions between these three cell types may influence differentiation and function of the piloneural collar. Here, David Owens and colleagues demonstrate that glutamate, which is known to mediate communication between neurons and Schwann cells in the central nervous system, has analogous activities in the periphery (p. 740). Signalling between VGLUT2-expressing neurons and NMDA receptor-expressing Schwann cells directs both formation and maintenance of the piloneural collar in mice. In conditional VGLUT2 mutants, the Schwann cells are disorganised and overall collar structure is severely disrupted. Moreover, treating the skin of adult mice with an NMDA receptor antagonist impairs touch-evoked responses, demonstrating defects in piloneural collar activity. Thus, continuous glutamate signalling between neurons and Schwann cells in the piloneural collar of the skin is essential for the integrity and function of this elaborate mechanosensory structure.

FGF signalling: keeping migrating cells on track

In Drosophila embryos, the longitudinal muscle cells surrounding the gut – the caudal visceral mesoderm (CVM) – arise in the posterior mesoderm and migrate anteriorly to reach their destination where they differentiate. Although this represents the longest cell migration event of Drosophila embryogenesis, the signals directing it are poorly understood. On p. 699, Angelike Stathopoulos and colleagues identify the FGF ligands Pyramus and Thisbe as crucial guidance cues for the CVM, signalling via the Heartless receptor to promote proper migration. The researchers use detailed live imaging and cell tracking analyses to describe wild-type migration, and analyse the consequences of disrupting FGF signalling, revealing defects in migration speed, directionality and cell survival. Intriguingly, by manipulating both the levels and location of ligand expression, they provide evidence for synergistic effects of Pyramus and Thisbe, although the mechanistic basis of such synergism remains to be investigated. Together, these data establish a new system for studying collective cell migration, and suggest additional complexities in FGF ligand-receptor interactions and signalling.

Plus…

Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock

The segmentation clock is an oscillating genetic network thought to govern the rhythmic and sequential subdivision of the elongating body axis of the vertebrate embryo into somites. Recent work, reviewed here by Oates et al, has provided evidence for how the period of the segmentation clock is regulated and how this affects the anatomy of the embryo. See the Review article on p. 625

Myoblast fusion: lessons from flies and mice

The fusion of myoblasts into multinucleate syncytia plays a fundamental role in muscle development and function. Here, Abmayr and Pavlath review the molecular events that drive myoblast fusion in the Drosophila embryo, in developing and regenerating mouse muscle, and in cultured muscle cells. See the Review article on p. 641

(1 votes)

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Postdoctoral Position in Chordate Comparative Embryology

A recent PhD or junior-level Postdoctoral Fellow is sought to join the Rui Diogo laboratory, at the Howard University College of Medicine, Department of Anatomy (Washington DC).

We are interested in a candidate that will contribute to uncover evolutionary and developmental mechanisms underlying both hard tissue (cartilages and bones) and soft tissue (mainly muscles) formation and patterning during ontogeny of a wide range of vertebrate taxa, as well as soft tissue in non-vertebrate taxa such as sea squirts. Some of the issues and broader questions in which we are particularly interested include: the parallelism between ontogeny and phylogeny, the remarkable similarity between the hard and particularly the soft tissues of the upper and lower limbs of tetrapods, the importance of evolutionary reversions/neotenic events, the study of birth defects and their implications for medicine and for the understanding of evolutionary biology, and the regeneration of hard and soft tissues in key vertebrate taxa. For more information about these subjects and about other issues being studied in the lab, please see www.ruidiogolab.com.

The successful candidate will have a PhD degree with a broad experience in molecular biology and developmental biology (e.g., doing/using developmental techniques such as antibody staining, in situs, and cell tracing, among others), backed by publications in peer-reviewed 
journals, and also some experience in comparative anatomy. He/She will have the skills and motivation to pursue a career in research, be interested in studying and comparing a wide range of taxa and various model organisms and in discussing various evolutionary and developmental issues.

There are funds available for two years, the first contract being for one year, the second contract depending on the productivity, interest and dedication of the candidate. There are possibilities to continue being part of the lab after the two-year period of the post-doc position. The post-doc will also have the opportunity to take classes, and then to be instructor, of human gross anatomy; this will further allow him/her to also postulate for faculty positions in medical schools in the DC area (including Howard University) as well as in other regions.

Interested candidates should send a CV including research interests, a list of publications and the names and contact information for three references to Rui Diogo, at rui.diogo@howard.edu. Please write “post-doc in Diogo’s lab” followed by your last name in the email subject.

Howard University is a historical University situated in the center of Washington DC, which is a beautiful, green and enjoyable city with numerous cultural and outdoor activities. The Department of Anatomy provides a prosperous, resourceful and multidisciplinary environment for biomedical research, includes faculty with a broad experience in developmental biology, paleontology, neurobiology, comparative anatomy and medicine. We have strong ties with surrounding institutions, particularly with George Washington University, and the candidate will probably have the opportunity to do part of his/her research at those institutions and thus to expand his/her knowledge and academic connections.

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If you’re interested in the role of the internet in science and science communication, you should keep an eye on Twitter from today until Saturday. Specifically, the tag #scio12, which is being used by the annual Science Online conference in North Carolina.  (Here’s the link to see the newest tweets tagged #scio12, but I’ve also collected a few interesting ones in the Storify shown at the end of this post.)

I’m not attending this year, but I’ve been a few times before. The meeting is very broad, covering scientific publishing, data sharing, blogging, science journalism, science art and everything in between. The thing that sets it apart most from many scientific conferences is that many of the participants know each other very well, personally, but have never met. The meeting originated as “science blogging” conference, and brought together people who had been talking to each other online for months or years. As a result, in between serious discussions titled “Self-censorship in physician writers” or “Using altmetrics to track the online impact of your research” the schedule leaves room for social events, and participants have been planning podcasts and chocolate swaps for months. For many people, this conference is the event of the year, where they get to see old friends again. For others, it’s a place to promote their latest science book, to introduce their new software for scientists, to recruit science communicators, or simply to take a step back from their research and look at science from a new angle.

The several hundred tickets for the conference sold out within minutes, so there’s a good chance that, like me, you’re not there. I’ll do my best to follow the meeting over Twitter the next few days, and collect the most interesting things in the Storify below. Join me in following along with Science Online online!

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BASIC SCIENTIST

ASSISTANT, ASSOCIATE, or PROFESSOR

DEPARTMENT OF OTOLARYNGOLOGY / HEAD AND NECK SURGERY

STANFORD UNIVERSITY SCHOOL OF MEDICINE

Faculty Position in the University Tenure Line- Basic Sciences

Stanford SOM

The Department of OHNS (http://med.stanford.edu/ohns/) is recruiting for a basic science tenure-track faculty position.  The successful candidate will be appointed at the level of assistant, associate, or full professor.

Scientists from a wide variety of disciplines are welcome to apply as long as their research relates to issues relevant to otolaryngology.  A few illustrative fields include developmental biology, genetics, molecular and cellular biology, biophysics, cancer, auditory physiology, voice physiology, auditory and vestibular prosthesis development, bioengineering, stem cell and gene therapy.  Collaborations with academic clinicians is encouraged.  The successful researcher will be part of an interdisciplinary and collaborative team in a lab close to Stanford campus with ample opportunity for interaction with a broad spectrum of scientists including world-class programs in neuroscience, genetics, biomedical engineering, and bioinformatics, to name a few.

Resources available include substantial funds for equipment acquisition and program initiation, as well as appropriate laboratory facilities.

The predominant criterion for appointment in the University Tenure Line is a major commitment to research and teaching.

Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty.  It welcomes nominations of and applications from women and members of minority groups, as well as others who would bring additional dimensions to the university’s research, teaching and clinical missions.

Letters of inquiry and curriculum vitae as well as the names and addresses of five references should be sent to:

Stefan Heller, PhD – Chair of Basic Science Search Committee

Department of Otolaryngology – Head & Neck Surgery

801 Welch Road, Stanford, CA 94305-5739

sheller@ohns.stanford.edu

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