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In 2010, Nature Medicine will celebrate 15 years as the leading translational-research journal. To mark this anniversary, the journal has launched the Nature Medicine Classics Collection. This collection brings together some landmark articles published in Nature Medicine over the past 15 years, making them freely available to all readers together with a series of recent articles on different fields of biomedicine to illustrate the breadth of the journal.
The Nature Medicine editors write: Since 1995, our journal has been at the forefront of publishing translational medicine, way before the term was even coined. Our focus on publishing basic and preclinical work that has direct relevance to human disease has been a key characteristic of Nature Medicine that has helped establish the reputation of the journal in the translational research landscape.
To put together this sampler, we have chosen a series of recent articles from our pages, organized them by therapeutic area, and made them freely available in order to give you a glimpse of the breadth of Nature Medicine's coverage, as well as the quality of the science we publish.
In addition, we have chosen a few landmark articles that we had the privilege to publish over the past 15 years in an effort to illustrate why Nature Medicine is the home of translational research.
Nature Medicine Classics Collection by subject:
Classic articles
Cancer
Cardiovascular disease
Immunology
Infectious diseases
Metabolism
Neuroscience

See also:
Nature Medicine's free podcast.
Journal press releases.
Spoonful of Medicine, the journal's blog.

Posted by Maxine Clarke on November 18, 2009
Categories: Disciplines, NPG special content, Publications | Permalink | Comments (0)

Each year since 1951, young researchers and Nobel laureates have gathered on the shores of Lake Constance for a unique scientific conference. In 2009 the meeting was dedicated to chemistry, and laureates and students all came away enriched by their experiences. Martin Chalfie, one of the three recipients of the 2008 Nobel prize in Chemistry, reports what they learned from each other in the November issue of Nature Chemistry (1, 586-587; 2009) He writes:
"From their reading or from simply listening to my talk, the students generated a large number of fascinating questions. They wanted to know details of the experiments and they wanted to discuss potential future experiments. Conclusions about my research that had taken me years to realize (and which I have not written about or described in my talk) were instantly suggested by several of the students at the session. Seeing their excitement and quickness was humbling, but also invigorating.
The meeting allowed the students (as well as the laureates) to broaden their horizons, to have a chance to meet, exchange ideas, and learn about new areas of research from investigators from all over the world (the conference participants came from 67 different countries). The word 'exchange' is important here, because I don't believe that the real benefits were associated with hearing advice from a bunch of older scientists who had been fortunate enough to get some recognition for their work." The meeting's significance is "the acknowledgement it gives to young scientists, especially at a time when they do not get much recognition, that they are on their way to succeeding in science, and that we think that they are important. Although they really do not need any seal of approval, everyone likes to get the occasional pat on the back."
In a companion article in the same issue of Nature Chemistry (1, 587-590; 2009), Jeffrey R. Lancaster, a fourth-year graduate student in the Department of Chemistry, Columbia University, looks back at what he got out of the Lindau meeting: "two subtle points have ultimately distinguished the Lindau meeting for me as a unique event of which I was honoured to have been a part.
First, conversation and the sharing of ideas were fostered not solely between scientists with comparable levels of experience, but also across scientific generations and geographies. I had worthwhile discussions with my peers from Australia, China, India, the Netherlands, Poland and Spain (to name but a few), and was able to speak to scientists at various stages of their careers, from undergraduate to graduate students, postdocs, professors, governmental scientists and, of course, Nobel laureates. Second, the activities pursued by scientists outside of publishable, academic research also featured prominently at the meeting. That scientists might have a life apart from, and in addition to, their research is most often a topic best reserved for conference happy hours, not keynote addresses."

Posted by Maxine Clarke on October 27, 2009
Categories: Careers, Conferences, Disciplines, Education | Permalink | Comments (0)

We are sad to announce that this month brings the last update of Nature Reports Stem Cells.
When we launched in June 2007, we wanted to support the stem cell field and the interested public by providing freely available content. Stem cell research was then - and is still - exciting and expanding. It requires highly varied experts to think and work together, and it requires the support and understanding of non-scientists. We believe we have been successful in creating a venue that highlights and explores the many facets and implications of stem cell science. It is now time for us to move on to fresh publishing challenges.
We have been helped by many contributors and experts who have generously given their time and insight. We give a heartfelt thanks to everyone who wrote articles or gave interviews, advice, and words of encouragement.
NRSC and its blog, the Niche, will continue to remain online as an archive. Nature and its sister titles remain committed, as ever, to publishing new research and news about stem cells.
Monya Baker, Editor
Natalie DeWitt, Editor at Large

Posted by Maxine Clarke on October 26, 2009
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The road to Copenhagen. With the UN Climate Change Conference just six weeks away, Nature this week (22 October issue) assesses how much - or little - progress is being made on tackling climate change in a set of Opinion articles and News Features, all free to read online for one month from the date of issue, as well as an Editorial (free to read online). The latest round of negotations shows that the gulf between rich and poor nations is as great as ever, and hopes of a strong agreement are rapidly fading. Raúl Estrada-Oyuela, a diplomat who guided the Kyoto negotiations, argues that success in Copenhagen will depend on the skills of the lead negotiator (Nature 461, 1056-1057; 2009) Meanwhile, Rajendra Pachauri, chairman of the Intergovernmental Panel on Climate Change, comments on the Indian negotiation stance (p. 1054), while Jiahua Pan, of the Chinese Academy of Social Sciences, examines the Chinese perspective on reducing global emissions (p. 1055) . A pair of news features take us around the world to look at efforts to adapt to climate change in Bhutan (pp 1042- 1046), and a project in Peru to monitor forest carbon (pp 1048-1052).
Successful international negotiations share some important characteristics with scientific research, argues an Editorial this week (Nature 461, 1027-1028; 2009). Both are iterative processes, in which results from one step help to determine the path forward. They require time and perseverance. And they rarely travel in a straight line. Countries should endeavour to build on the positive actions of the past year, both before and after the Copenhagen summit.
See also: more articles, the free Nature podcast and more online extras.

Posted by Maxine Clarke on October 23, 2009
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In their Perspective 'The Allen Brain Atlas: 5 years and beyond' (Nat. Rev. Neurosci. 10, 821-828; 2009), Allan R. Jones, Caroline C. Overly and Susan M. Sunkin of the Allen Institute describe an experiment on a massive scale: a web-based, genome-wide atlas of gene expression in the adult mouse brain The development of this atlas faced a combination of great technical challenges and a non-traditional open research model, they write, and it encountered many hurdles on the path to completion and community adoption. Having overcome these challenges, it is now a fundamental tool for neuroscientists worldwide and has set the stage for the creation of other similar open resources. Nevertheless, there are many untapped opportunities for exploration.
The Perspective, in the November issue of Nature Reviews Neuroscience, looks back on the 5 years from the inception of the Allen Brain Atlas to the present, highlighting challenges and the contributions that it has made to neuroscience. The authors discuss the advantages and caveats of using this unique resource, how it is currently being used and point to opportunities for further exploration. They conclude by describing the ever-expanding suite of related resources that have become available since the atlas was launched, and comment on those that will be coming in the next few years.

Allen Brain Atlas portal.
Allen developing mouse brain map.
Allen Institute human cortex study.
NeuroCommons project.
Mutant mouse regional resource centers.
Nature Reviews Neuroscience.
About Nature Reviews Neuroscience.

Posted by Maxine Clarke on October 22, 2009
Categories: Disciplines | Permalink | Comments (0)

Are you watching the Nobel laureates on Nature Video? Each year, hundreds of young researchers from around the world meet with Nobel prizewinning scientists on Lindau Island in Germany. In 2009 it was the turn of the chemists, and Nature Publishing Group was there to capture moments of this unique meeting of minds on film.
Nature Video presents five short films on chemistry plus a special film feature on climate change. Join laureates and young researchers as they discuss the future of medicine, consider the ethics of nanotechnologies, plan new collaborations, and seek ways to avoid dangerous climate change. The videos are archived as they are published and can be accessed at this Nature Video Lindau page:
24 August: an introduction to the LIndau meetings and the films
27 August: breaking down Alzheimer’s with Aaron Ciechanover
3 September: nanotechnology, use and misuse with Harry Kroto
10 September: smart drugs and sneaky microbes with Peter Agre
17 September: seeing green with Roger Tsien and Richard Ernst
24 September: catalysts and collaborations with Richard Schrock
1 October: climate change: The two-degree target

Nature Chemistry report of the 2009 meeting.
Films of the 208 Lindau Nobel laurate meeting, on physics.
Nature Physics report on the 2008 meeting.
Multimedia at Nature.

Posted by Maxine Clarke on September 15, 2009
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Translating a basic finding into a new therapy requires us to speak many languages—scientific, clinical, legal and financial. Yet most of us are hopelessly 'monolingual', a limitation that substantially slows translational research. Steps have been taken to address this problem, but a lot remains to be done, as described in September's Editorial in Nature Medicine 'In the land of the monolingual' (15, 975; 2009). The Editorial begins optimistically:
"Congratulations! You've just published a paper in Nature Medicine identifying a new target to treat your favorite disease and are eager to take this finding to the clinic. Excellent, but where do you start? Are you familiar with all the steps you need to take from your discovery to a clinical trial?" It contiunes with much valuable advice and references for those wishing to navigate the translational pathway from bench to clinic, focusing on new initiatives in the main areas of resources and training. Even though there are some positive approaches, the Editorial concludes that "the best ways to facilitate translational research have yet to be discovered. However, their sheer existence offers hope that translational research will become smoother, speeding up the rate at which drugs and medical devices make it to the clinic. At the same time, it is clear that we need to do a lot more on a global scale to empower scientists with the education necessary to make a real translational impact. If each of us tries to become at least 'bilingual', we might feel a little less overwhelmed by the Tower of Babel that translational research has become."

Related article in the same issue of Nature Medicine (15, 1006-1009; 2009):
The advancement of translational medicine—from regional challenges to global solutions
Salvatore Albani & Berent Prakken
The Arizona Arthritis Center, University of Arizona, and the Center for Molecular and Cellular Intervention, University Medical Center Utrecht. Both authors are at Eureka Institute for Translational Medicine, Siracusa, Italy.

Posted by Maxine Clarke on September 14, 2009
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This month's (July) Nature Chemical Biology includes two articles describing how access to the highest quality chemical probes will ensure their prominent position in the biological and drug discovery toolboxes.
Aled M Edwards, Chas Bountra, David J Kerr and Timothy M Willson, in their Commentary (Nature Chemical Biology 5, 436 - 440; 2009) Open access chemical and clinical probes to support drug discovery, say that drug discovery resources in academia and industry are not used efficiently, to the detriment of industry and society. Duplication could be reduced and productivity increased, they write, by performing basic biology and clinical proofs of concept within open access industry-academia partnerships. Chemical biologists could play a central role in this effort.
The authors' main argument is that the development of new medicines is being hindered by the way in which academia and industry advance innovative targets. By generating freely available chemical and clinical probes and performing open-access science, the overall system will produce a wider range of clinically validated targets for the same total resource, arguably the most effective way to spur the development of treatments for unmet needs.
In a related article in the same issue of the journal, 'A crowdsourcing evaluation of the NIH chemical probes', Tudor I. Opera et al. (Nature Chemical Biology 5, 441-447; 2009) write that between 2004 and 2008, the US National Institutes of Health Molecular Libraries and Imaging initiative pilot phase funded 10 high-throughput screening centres, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. The authors 'crowdsourced' the Molecular Libraries and Imaging initiative output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes. Crowdsourcing is a cross-disciplinary alternative way to assess confidence for both chemical probes and drug leads: it pools multiple levels of expertise from translational disciplines, providing a rigorous chemical-probe evaluation process.

Nature Chemical Biology website.
Nature Chemical Biology guide to authors.
Nature Chemical Biology focuses and supplements.
Nature Chemical Biology symposium 2009: Chemical biology in drug discovery.

Posted by Maxine Clarke on July 02, 2009
Categories: Access, Data availability, Disciplines | Permalink | Comments (0)

Inhibition of the replicative cycle of hepatitis C virus
Richard Bethell, George Kukolj and Peter W. White
Nature Reviews Microbiology, June 2009.
It is estimated that 170 million people globally are infected with the hepatitis C virus (HCV). Chronic HCV infection can result in the development of liver cirrhosis and hepatocellular carcinoma, and therefore represents a substantial public health problem. Current drugs against HCV have poor safety profiles and limited effectiveness, especially against HCV genotype 1. As a result, there is considerable interest in identifying specific inhibitors of HCV replication that could be used either as an adjunct to current therapy or in place of it. A free poster from Nature Reviews Microbiology summarizes the replicative cycle of HCV and the principal targets for specific antiviral agents that are currently being developed.

Download a high-resolution PDF of the poster here.
Further reading (PDF).
Nature Reviews Microbiology website.
A guide to Nature Reviews Microbiology.
About the journal.

Posted by Maxine Clarke on June 29, 2009
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Various codes of conduct have been proposed for nanotechnology —and in the June issue of Nature Nanotechnology (4, 336; 2009), Richard Jones examines what they mean for individual researchers, particularly in the light of the European Commission's code, aimed at academic research rather than at businesses and other commerce.
"How is responsibility divided between the individuals who do science, and the organizations, institutions and social structures in which science is done? There's a danger that codes of ethics focus too much on the individual scientist, at a time when many scientists often feel rather powerless, with research priorities increasingly being set from outside and with the development and application of their research out of their hands. In this environment, too much emphasis on individual accountability could prove alienating, and could divert us from efforts to make the institutions in which science and technology are developed more responsible.
Scientists, however, should not completely underestimate their importance and influence collectively, even if individually they feel impotent. Part of the responsibility of a scientist should be to reflect on how to justify one's work, and how people with different points of view might react to it, and such scientists will be in a good position to have a positive influence on the various institutions they interact with, such as funding agencies. But we still need to think more generally about how to make responsible institutions for developing science and technology, as well as responsible nanoscientists."

About Nature Nanotechnology.

Posted by Maxine Clarke on June 23, 2009
Categories: Communication, Disciplines, Education, Ethics, Public and media | Permalink | Comments (0)

The art of paper folding is a useful way to illustrate some concepts about protein folding in the cell, according to June's issue of Nature Structural and Molecular Biology. "When all goes well, you end up with a beautiful and functional structure. When things go wrong (misfolding), you may get a crumpled mess that needs to be smoothed out (unfolding) to try to start the process over again (refolding), or you may just give up and feed it to the shredder for recycling (degradation). Some unfolded or misfolded conformations can aggregate and generate forms that are difficult to degrade, akin to a pile of sheets glued together, and cause cellular toxicity or death. In fact, defects in protein folding have been linked to a number of pathologies where such aggregates (amyloids) are observed, including neurodegenerative conditions such as Parkinson's, Alzheimer's and Huntington's diseases, although what the toxic species are remains to be determined."
Many of these concepts are covered in the Reviews and Progress articles that comprise a Nature Structural and Molecular Biology Focus on protein folding (free to read online), with an emphasis on recent developments in the field. Online features of the Focus include an annotated collection of 'Classics' —landmark papers that shaped and guided research. This compilation provides a historical perspective on how the field has progressed. The journal editors have also asked researchers about their views on where the field is going—the 'big questions' that still await answers and the technical developments that will make answering those questions possible; you can read these in 'Looking ahead'. And you can browse a library of recent papers on protein folding published in the Nature journals.

About Nature Structural and Molecular Biology.

Posted by Maxine Clarke on June 22, 2009
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New rules for the presentation of statistics in the Nature journals are described in the June Editorial of Nature Cell Biology (11, 667; 2009). From the Editorial:

Thanks to advanced imaging technologies and better integration with molecular and systems approaches, cell biology is undergoing something of a renaissance as a quantitative science. Robust conclusions from quantitative data require a measure of their variability. Cell biology experiments are often intricate and measure complex processes. Consequently the number of independent repeats of a measurement can be limited for practical reasons, yet the variability of the measurements can be rather high. Cell biologists have developed good intuition to guide their analysis of such constrained datasets. Biological complexity and the reliance on intuition can cause culture shock to physical scientists crossing over into cell biology (a kind of extension of the celebrated 'two cultures' concept of C. P. Snow).
With the arrival of quantitative information and '-omic' datasets, statistical analysis becomes a necessity to complement instinct. The problem is that statistical tools are built on basic assumptions such as the independence of replicate measurements and the normality of data distribution. Usually, sizeable datasets are prerequisite for statistical analysis. Alas, these can be as hard come by as a biostatistician (n is typically well below 5). The result is that all too often statistics (frequently undefined 'error bars') are applied to data where they are simply not warranted.
There are no easy solutions to rectify the prevalence of poor statistics in cell biology studies. However, an obvious recommendation is to consult a statistician when planning quantitative experiments. Consider whether n represents independent experiments (you may actually be publishing a measure of the quality of your pipette!) and whether it is large enough for the test applied. Avoid showing statistics when they are not justified; instead, show 'typical' data or, better still, all the measurements. Importantly, displaying unwarranted statistics attributes a misleading level of significance to the data. Always describe and justify any statistical analysis applied. We have updated our guidelines to reflect these recommendations. One key rule: if the number of independent repeats is less than the fingers of one hand, show the actual measurements rather than error bars. If you wish to present error bars, include the actual measurements alongside them.
Finally, please remember that you are interrogating a complex system — be careful not to discard 'outlier' data points on a whim, as they may well be as relevant as clustered measurements. One is naturally inclined to ignore data that does not match the hypothesis tested, but biology is rarely as black and white as we would like. Do not make 'hypothesis driven' research become 'hypothesis forced'!

Posted by Maxine Clarke on June 18, 2009
Categories: Authorship, Data availability, Disciplines, Format | Permalink | Comments (2)

The rise of 'omics' methods and data-driven research presents new possibilities for discovery but also stimulates disagreement over how science should be conducted and even how it should be defined. Is the ability of these methods to amass extraordinary amounts of data altering the nature of scientific inquiry? These are the issues dicussed in the April Editorial of Nature Methods (6, 237; 2009).
"Methodological developments are now making it possible to obtain massive amounts of 'omics' data on a variety of biological constituents. These immense datasets allow biologists to generate useful predictions (for example, gene-finding and function or protein structure and function) using machine learning and statistics that do not take into account the underlying mechanisms that dictate design and function—considerations that would form the basis of a traditional hypothesis.
Now that the bias against data-driven investigation has weakened, the desire to simplify 'omics' data reuse has led to the establishment of minimal information requirements for different types of primary data. The hope is that this will allow new analyses and predictions using aggregated data from disparate experiments."
The Editorial goes on to ask whether the generation of parts lists and correlations in the absence of functional models is, in fact, science? "Based on the often accepted definition of the scientific method, the answer would be a qualified no. But the rise of methodologies that generate massive amounts of data does not dictate that biology should be data-driven. In a return to hypothesis-driven research, systems biologists are attempting to use the same 'omics' methods to generate data for use in quantitative biological models. Hypotheses are needed before data collection because model-driven quantitative analyses require rich dynamic data collected under defined conditions and stimuli.
Correlations in large datasets may be able to provide some useful answers, but not all of them: 'omics' data can provide information on the size and composition of biological entities and thus determine the boundaries of the problem at hand. Biologists can then proceed to investigate function using classical hypothesis-driven experiments. It is still unclear whether even this marriage of the two methods will deliver a complete understanding of biology, but it arguably has a better chance than either method on its own."

Comment on this Editorial at Nature Methods' Methagora blog.

Posted by Maxine Clarke on April 13, 2009
Categories: Communication, Data availability, Disciplines, Format | Permalink | Comments (0)

Timothy M. Vogel and coauthors, in an Edtiorial in this month's (April) Nature Reviews Microbiology (7, 252; 2009) invite the microbiology community to participate in an ambitious and extraordinary sequencing project to decipher the soil metagenome, a goal that is now within reach thanks to developments in high-throughput sequencing.
Metagenomic sequencing efforts are necessary to resolve the intricacies of the soil microbiome and to provide sufficient data to understand the diversity and function of the soil microbial communit. Vogel et al. propose a coordinated international effort, starting with agreement and cooperation from the scientific community in reaching a primary objective: the complete sequencing of a 'reference' soil metagenome. They write: "The soil system chosen for investigation, Park Grass, is an internationally recognized agroecology field experiment that has been running for more than 150 years at the UK agricultural sciences institute, Rothamsted Research. This ambitious reference sequencing effort cannot be undertaken by a single laboratory or even by a single country. We therefore invite the international community to participate in this project, and hope to eventually expand the project to other soil sites. The information gleaned from this project will serve as a starting block or platform for other soil metagenomic sequencing efforts and will generate new hypotheses to test." The TerraGenome international sequencing consortium, which is dedicated to soil metagenomics, has just been launched to coordinate these efforts.

Posted by Maxine Clarke on March 16, 2009
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There is an interesting Editorial in the March issue of Nature Reviews Microbiology (7, 174; 2009; subscription or site licence required) about the development of the field in the past 300-or so years since the time of van Leeuwenhoek. From the Editorial:

Advances in microbiology are largely driven by improvements in technology. The awe-inspiring size of the experiments performed today — such as studies of entire microbial communities — is the result of a centuries-long path of discovery, one advance built on the next. Current technologies have provided us with new insight into entire communities and biomes, and promise to unravel many secrets of the microbial world.....In 300 years, we have gone from observing mixed species in a drop of pond water to isolating and studying individual bacteria to sequencing all species in a sample of seawater. In the process, we have still only discovered perhaps 1% of all bacteria, and possibly an even lower percentage of phages and viruses. Microbiology has come a long way, and has a longer way to go. It will be fun.

Posted by Maxine Clarke on February 17, 2009
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Nature Reviews Molecular and Cell Biology presents a free poster on the productions and actions of small RNAs (ribonucleic acids), by V. Narry Kim and Mikiko C. Siomi. Recent progress in cloning, deep sequencing and bioinformatics have revealed an astounding landscape of small RNAs in eukaryotic cells. Small (20–30-nucleotide) RNAs, in association with Argonaute-family proteins, target messenger (m)RNAs and chromatin, and thereby keep both the genome and the transcriptome under extensive surveillance. The poster depicts our current understanding of the processing pathways of eukaryotic small RNAs and their possible mechanisms of action, and accompanies the Review article 'Biogenesis of small RNAs in animals' by V. Narry Kim, Jinju Han and Mikiko C. Siomi in the February issue of Nature Reviews Molecular and Cell Biology (10, 126-139; 2009).

High-resolution PDF of the poster.
Futher reading about productions and actions of small RNAs.
Nature Reviews Molecular and Cell Biology article series on post-transcriptional control.
See also Nature's Insight on RNA silencing, in the 22 January issue (Nature 457, 395-433; 2009). This collection of five Review articles is free to access online.
Nature Publishing Group RNAi (RNA interference) gateway.

Posted by Maxine Clarke on January 28, 2009
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Every week, the Editors of Nature China survey the scientific literature to identify the best recently published papers from mainland China and Hong Kong and provide a summary of the results. If you are interested in, say, nanotechnology, here are some recent highlights posted on Nature China:
Carbon nanotubes: Domino drive
The potential energy stored in a carbon nanotube can be harnessed to power tiny devices.
Nanofibres: Bright belts
Rare-earth-based nanofibres and microbelts can produce an entire rainbow of colours for electronic displays.
Fullerenes: Symmetry breakers
Researchers in Xiamen are close to making symmetry-breaking buckminsterfullerenes.
Carbon nanotubes: From stress to strength
Prestressed multiwalled carbon nanotubes have enhanced mechanical properties that are ideal for building space elevators.

Register for Nature China e-alerts, and stay abreast of the latest research in your field from mainland China and Hong Kong.
Nature China main index page.
Nature China subject archive.
About Nature China.

Posted by Maxine Clarke on November 20, 2008
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Development of an effective HIV/AIDS vaccine and new drugs to treat established disease remain an urgent and pressing need. To conquer the enormous challenge demands a far better understanding of the biology of the virus, its interaction with infected cells, and the response of the immune system, than is currently at our disposal. A Nature web focus presents a selection of recent research papers in Nature that advance our knowledge in this regard. Click here to access selected content free online.

Posted by Maxine Clarke on October 14, 2008
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The hype that greeted the development of systems biology was followed by inevitable disappointment. But in reality, much groundwork has been done and tangible progress is expected. In a Nature Commentary (Nature 455, 730-731; 9 October 2008), Adriano Henney and Giulio Superti-Furga broaden a debate that began at a recent workshop in Portofino, Italy, on the application of systems biology to drug discovery by inviting readers to contribute their ideas. Delegates at Portofino drew up ‘roadmaps’ for three areas: metabolic disorders; cancer; and inflammation and infectious diseases — and are developing them as live documents to monitor progress. To comment on the article and related documents, visit the Nature Network forum 'Applying systems biology to benefit human health'.
At the Nature Network forum, Superti-Furga writes about the group's frustration about the scepticism within institutions, biopharmaceutical companies and funding agencies regarding the usefulness of systems approaches to medicine and in particular in drug discovery. Mindful of the danger of encouraging a climate of unrealistic expectations and delusions, "with genomics-like anticlimactic conservatism as consequence", Superti-Furga and colleagues have initiated a community-wide research roadmap proposal. "The purpose is to define the areas worth focusing on to obtain the facts that are needed as proof of concept for the entire community. In a careful process, we have engaged some of you first in interviews, then with on-line questionnaires and finally with a meeting restricted to 25 people that occurred in May (in Portofino, Italy). The outcome of the meeting is summarized in a Commentary that just appeared in Nature (enclosed). So far it has not been practical to engage all of you directly but we now need your help as we are preparing a white paper that covers much more ground of the Portofino discussions and following that measures for implementation."
"We got this rolling and would like to know if the community is willing to participate in the autodiscipline needed to achieve the goals of the recommendations. Moreover, we are looking for further focus and detail on the proposed ideas and on what could be additional ideas that the group may have overseen." The group will post on the following topics:
-Setting data standards
-Optimizing the application of existing tools
-Predictive toxicology
-Therapeutic area focus
-Communication and outreach
Please join the discussion at Nature Network by providing your feedback and proposals.
Applying systems biology to benefit human health forum at Nature Network.

Posted by Maxine Clarke on October 14, 2008
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This month (October 2008) Nature Reviews Microbiology publishes a Focus on Symbiosis . Microbial symbioses include beneficial, harmful and neutral relationships and are important in animal and plant health, immunity and disease, as well as in ecology and the environment. The special Focus issue of Nature Reviews Microbiology highlights exciting advances in understanding of partnerships between organisms and their environments.
Topics covered include manipulation of insects by endosymbiotic bacteria, marine chemosynthetic symbioses, the ancient arbuscular mycorrhiza, model symbiosis systems, the highly distinctive features of gut microbiotas and how they have evolved, and a glimpse of how experimental approaches will shape the future of this fascinating field. These Reviews and Perspectives highlight this emerging and important field. The accompanying library collates the most recent relevant original Research articles, News & Views and Reviews from across Nature Publishing Group.

Posted by Maxine Clarke on October 09, 2008
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The first in a series of Nature debates, Enhancing the Brain, takes place at King's Place in London on Monday 13 October. Experts in science, science policy and science ethics selected by Nature, the leading weekly international journal of science, will discuss the risks, benefits and extent of how far research can extend our mental and physical abilities. The first of two panel events focuses on research underway that is extending the human brain: from intelligence and emotional tolerance, to sleep needs, memory power and more. What are the risks and benefits to the individual and to society of these developments? Would you boost your brain power? Why, when and why not? Should doctors, scientists, students, teachers or soldiers use such aids? Come along and take part in this mind-stretching evening. Tickets are £11.50.
Chair: Ehsan Masood, acting Chief Commissioning Editor of Nature.
Panel:
• Prof Barbara Sahakian, Professor of Clinical Neuropsychology at Addenbrooke’s Hospital, Cambridge.
• Prof John Harris, Lord Alliance Professor of Bioethics at the University of Manchester.
• Prof Nick Bostrom, Director of the Oxford University Future of Humanity Institute.
Booking enquiries can be made by email. To check ticket availability please use the King's Place online booking service.

Posted by Maxine Clarke on October 07, 2008
Categories: Communication, Disciplines, Partners, Public and media | Permalink | Comments (0)

In a Commentary exclusive to Nature (Nature 455, 592; 2 October 2008), Professor Bill Wakeham, Vice Chancellor of the University of Southampton, discusses the findings of his long-awaited review on the state of physics in the United Kingdom. The field is healthy, he says, but scientists need to reclaim the intellectual ownership of research at the margins of the discipline such as medical or atmospheric physics. Read the article free online for two weeks from today, and check out next week’s issue on 9 October for more news and audio. (Nature's website is here.)
There is a Nature Network forum for discussion of Wakeham's key messages that physicists will need to take ownership over their field and capture new funding streams. All are cordially invited to participate.
See also a related Nature news story by Geoff Brumfiel. (Nature 1 October 2008. doi:10.1038/news.2008.1145)

Posted by Maxine Clarke on October 02, 2008
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From an article by Tracy S. P. Heng of Harvard Medical School, in Nature Immunology 9, 1091 - 1094 (2008) :
"The genome-sequencing and variation-mapping projects have established essential genetic 'road maps'. In the same vein, if on a more focused scale, by generating robust expression data and metadata into a centralized and accessible location, the Immunological Genome project should provide an essential 'workbench' for delineating the intricate workings of the immunological genome.
Thanks to the broad and robust approaches allowed by gene-expression microarrays and related techniques, the transcriptome is probably the only '-ome' that can be reliably tackled in its entirety. Generating a complete perspective of gene expression in the immune system offers the potential for deciphering patterns that mirror responses at several levels. At the level of the gene, such data can give insight into how individual genes act along differentiation profiles and cellular responses. It is then possible to define modules or groups of genes whose expression is interdependent and is coordinated by shared regulatory controls. Computational methods for reverse engineering can then be applied to infer a model of the cells' underlying control system. Finally, genome-wide expression data at the highest level of integration provides an objective definition of the relations and distinctions between cells. For example, analyses of relative 'distances' in genomic space have shown that natural killer T cells are actually a subset of conventional CD4+ T cells and not an 'intermediate' between CD4+ T cells and natural killer cells, as is often believed. Thus, insights from genomic profiling may 'fine tune' or revise the classifications and mental representations of immune cells."
The Immgen (Immunologcial Genome Project) website.

Posted by Maxine Clarke on September 29, 2008
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Stay informed about plans for Nature Chemistry, the newest journal from Nature Publishing Group, whcih will be launched in early 2009, by signing up to the journal's email alert. Register to receive both the chemistry@nature e-alert, and when the journal is published, the monthly Nature Chemistry table of contents e-alert.
Nature Chemistry is now accepting submissions through the journal's online submission and tracking system. The first print issue will be published in mid-March 2009, though some papers will probably be published online in advance of print early in 2009.
Nature Chemistry is dedicated to publishing high-quality papers that describe the most significant and cutting-edge research in all areas of chemistry, as well as covering the impact of chemistry beyond the laboratory. See here for more details of the aims and scope of the journal.
See here for the Nature Chemistry guide to authors.
Content types.
How to submit.
The editorial process.
About the editors.

Posted by Maxine Clarke on September 11, 2008
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Chris Condayan, manager of the Public Education Outreach Initiative at the American Society for Microbiology, writes an Editoral in the September issue of Nature Reviews Microbiology (6, 646; 2008) about how self-created audio and video content enable more microbiologists to share knowledge and news online. From his article:

As the science audiences for newspapers, radio and television decline, the future for audio and video podcasts, blogs and social networking looks bright. On the horizon we are starting to see the emergence of science-related social networks and a movement towards 'open science' that allows scientists and researchers to collaborate on projects, communicate results, share data and publish papers with the same recognition that is afforded to colleagues who publish in print journals. Specific details of how open science will work are still murky, and concerns over citation, peer review, accuracy, scooping and accountability resound even among its strongest supporters. But this has not stopped microbiologists from engaging with one another on wikis, such as EcoliWiki, TOPSAN or Proteopedia, or prevented thousands of scientists from sharing their poster presentations, lectures or laboratory methods through iTunes or video destination sites, such as YouTube, SciVee and JoVE. Podcasting for audio or video is generally defined as episodic content that listeners or viewers can subscribe to for free and which they can consume at any time and on any device, whether it be a computer, iPod, mobile telephone or television set. Audio podcasts are easy and affordable to create, and can be used to make a radio-style show or to make lectures available to a wider audience. Uploading and sharing videos on websites such as YouTube, or creating a video podcast show, is more time consuming and requires more equipment and a video-editing software program.

Chris Condayan goes on to provide some examples of microbiologists who produce online resources to educate and promote microbiological research, and the MicrobeWorld sevice of the American Society for Microbiology, which includes the popular resources MicrobeWorld Radio and MicrobeWorld Video.

Posted by Maxine Clarke on September 01, 2008
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Pluripotent cells offer great promise for the future of regenerative medicine. However, cells with pluripotent potential are difficult or impossible to isolate from patients, which makes methods for experimentally induced pluripotency in readily available somatic cells invaluable. Accompanying the September issue of Nature Reviews Molecular and Cell Biology, and free to access online, is a poster by Christopher Lengner and Rudolf Jaenisch, which compares and contrasts the properties of pluripotent embryonic stem cells with those of laboratory-generated pluripotent cells.
In the same issue of the journal is a related Essay, The promise of human induced pluripotent stem cells for research and therapy, by Shin-ichi Nishikawa, Robert A. Goldstein and Concepcion R. Nierras (Nature Reviews Molec. Cell Bio. 9, 725-729; 2008) The abstract:

Induced pluripotent stem (iPS) cells are human somatic cells that have been reprogrammed to a pluripotent state. There are several hurdles to be overcome before iPS cells can be considered as a potential patient-specific cell therapy, and it will be crucial to characterize the developmental potential of human iPS cell lines. As a research tool, iPS-cell technology provides opportunities to study normal development and to understand reprogramming. iPS cells can have an immediate impact as models for human diseases, including cancer.

See also the Nature Reviews collection of articles on stem cells, which is free to access online for six months.

Posted by Maxine Clarke on August 28, 2008
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This month, microbiologists gather at ISME12, the12th meeting of the International Society for Microbial Ecology, in Carins, Australia to deliberate advances in microbial ecology that could benefit the planet. What are the key challenges for this blossoming field? Nature Reviews Microbiology asks this question in its August Editorial (6, 566; 2008).
The Editorial describes the deliberations last year of a group of microbiologists, which crystallized the main questions that face microbial ecologists and how to ensure that the microbiology field continues to meet the important demands that have been placed on it by the need to understand the ecology of two pressing global problems: climate change and disease. The group published a report, Uncharted Microbial World, in February which highlights important gaps in knowledge, including a lack of knowledge of the phages, the most populous group of microorganisms. In the words of the Nature Reviews Microbiology Editorial, "Microbial ecologists have an important part to play in investigations into both public and planetary health. This eloquently written report should provide food for thought for all those with an interest in this important field, and for those lucky enough to be attending ISME12, enjoy the meeting!"

Posted by Maxine Clarke on August 05, 2008
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Despite a cooling of interest by the media, Tadataka Yamada, Alice Dautry and Mark Walport emphasize in a Nature Commentary (454, 162; 2008), that a vaccine stockpile may be invaluable for preventing an avian-influenza (H5N1) outbreak in humans from quickly becoming a pandemic, and urge the vaccine research and development community not to become complacent about this important issue. Although their respective institutions — the Bill & Melinda Gates Foundation, the Pasteur Institute and the Wellcome Trust — are working with other parties to develop new resources and collaborative opportunities to provide vaccines where they may be needed most (the developing world), the authors say a wider community response is also needed.
In a related Commentary in the same issue (Nature 454, 160; 2008), Steven Salzberg calls for greater transparency in the viral-strain selection process for the human influenza vaccine. The vaccine for the 2007–2008 season failed for predictable and, says Salzberg, avoidable reasons. If the process remains closed, and researchers are denied access to sequencing data used in the selection process, future vaccine failures could be more dramatic and deadly.
There is a related (free access) Editorial in the same issue of the journal, The long war against 'flu (Nature 454, 137; 2008).
What do you think? Can a pre-pandemic vaccine curb a major catastrophe? And are the cooperative attitudes that Yamada, Dautry and Walport advocate exactly the kinds of things that are lacking from efforts to develop seasonal flu vaccines? These questions and others are being discussed online at the Nature Network Opinion forum, in which Steven Salzberg, author of one of the Nature Commentaries, writes: "What our governments can and should do is launch a crash program to create vaccines using non-egg based methods. This could allow us to get a new vaccine – if a pandemic strain appears – into production in a matter of weeks. In the meanwhile, we just have to hope that a pandemic doesn’t happen." Join the conversation at Nature Network.

Posted by Maxine Clarke on July 28, 2008
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Danae Rebecca Dodge of the Graduate School of Archaeology, University of Sheffield, UK, writes in Nature's Correspondence pages (Nature 454, 27; 2008):

As a PhD student in archaeology and genetics, I am all too aware of the difficulties in crossing a gaping discipline divide, as well as of their effect on academic career prospects, as discussed in the Naturejobs article 'Assembly work' (Nature 453, 422–423; 2008).
For my master's degree in biomolecular archaeology, I needed a foot in two UK universities: one in the University of Manchester's biology department and the other in the University of Sheffield's archaeology department. My former lecturers later became part of the Manchester Interdisciplinary Biocentre (MIB) and the MSc course shifted to Sheffield, where eventually the programme ceased.
This closure was a disappointment for the nascent field of bioarchaeology, set to thrive only on a foundation of solid postgraduate training. Although the MIB and other new centres for interdisciplinary research are enthusiastically welcomed, they are few and far between and so able to offer only limited postdoctoral prospects.
Opening such centres and creating training programmes is not enough — it is also necessary to make interdisciplinary fields attractive to graduates and for senior academics to appreciate their significance. This would improve project turnover, bringing more funding to collaborative projects that would sustain interdisciplinary centres and allow academics from each discipline to gauge publications on an equal footing.
Perhaps then my search for a postdoctoral position in bioarchaeology would be easier. Although interdisciplinary projects are viewed as hot topics, in reality they lag behind as they await official establishment and recognition.

Posted by Maxine Clarke on July 17, 2008
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Every field of research has influential papers that have shaped and guided future work. In the July issue of Nature Structural and Molecular Biology (15, 655-657; 2008), Reinhard Jahn gives his picks for membrane fusion and a little bit of history about how the field has developed. He writes:

Over the past 30 years, three main lines of research have made important contributions to our present understanding of the molecular mechanisms involved in membrane fusion: (i) the development and quantitative treatment of physical models describing the fusion of planar and curved bilayers at various levels of complexity and detail; (ii) the structural and mechanistic insights obtained from the investigation of fusion proteins of enveloped viruses, with research on the fusion protein of the influenza virus having made seminal contributions; and (iii) the study of fusion proteins involved in fusion events of eukaryotic cells, with the most important work being carried out on the SNARE proteins and associated regulatory proteins. In what follows, I will briefly discuss the studies that have helped form the basis for all subsequent work in the field of membrane fusion. The papers describing these studies make up my personal list of 'classics'.

Please see Nature Structural and Molecular Biology for the rest of this article, and the list of selected papers.
This issue of the journal also features a focus of articles on membrane fusion, an in-depth look at a process essential for communication within and between cells via reviews, an essay, classic papers and a library of resources.

Posted by Maxine Clarke on July 16, 2008
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In the July issue of Molecular Systems Biology (4 , Article number: 201 doi:10.1038/msb.2008.39; 2008), Jonathan A Sagotsky et al. in their article "Life Sciences and the web: a new era for collaboration, write:

The World Wide Web has revolutionized how researchers from various disciplines collaborate over long distances. This is nowhere more important than in the Life Sciences, where interdisciplinary approaches are becoming increasingly powerful as a driver of both integration and discovery. Data access, data quality, identity, and provenance are all critical ingredients to facilitate and accelerate these collaborative enterprises and it is here where Semantic Web technologies promise to have a profound impact. This paper reviews the need for, and explores advantages of as well as challenges with these novel Internet information tools as illustrated with examples from the biomedical community.

Posted by Maxine Clarke on July 14, 2008
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Nature Geoscience publishes a regular feature called BackStory, at the back of the journal or on the journal's website, in which the authors of a paper in the current issue of the journal answer questions about their field work -- providing an unusual perspective on the region of the world that contributed to the paper. The Backstory in the July issue (Nature Geoscience 1, 482; 2008), Sailing for a stretched lithosphere, describes how Jenny Collier and colleagues, having managed to get themselves and all their instruments on board a ship not too far away from an imminent war zone, enjoyed the serenity of life at sea as they investigated the rifted continental margin of India.

How long did it take to plan the fieldwork?

Two years elapsed between getting the project approved and setting sail. We wanted to use a particular vessel, the RRS Charles Darwin, which was already in the Indian Ocean and had the scientific capability that we needed. Unfortunately, we had to join a rather long waiting list. Coordination was a nightmare — our scientific instruments were all in different parts of the world, taking part in experiments that were also subject to scheduling changes. When we finally had our chance, the build-up to the Iraq invasion resulted in several changes to our port of embarkation. It was a huge relief when we finally set sail with all the equipment onboard!

See Nature Geoscience's website for the rest of the Backstory.
The paper featured is: The relationship between rifting and magmatism in the northeastern Arabian Sea, by Timothy A. Minshull, Christine I. Lane, Jenny S. Collier & Robert B. Whitmarsh (Nature Geoscience 1, 463-467; 2008).

Posted by Maxine Clarke on July 03, 2008
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In its June 2008 issue, Nature Methods presents a free-access focus on single-molecule techniques. Biologists are becoming increasingly interested in methodologies that can examine the mechanism of action of fundamental biological processes at the molecular level. The Nature Methods focus consists of four review articles that provide practical guidance for some of the techniques that are most integral to in vitro single-molecule experiments. These cover single-molecule fluorescence methods; microfluidic flow cells to manipulate experimental conditions during experiments; and force-spectroscopy techniques such as atomic force microscopy (AFM) and optical traps to manipulate individual molecules themselves.
From the focus's Editorial: The ability to analyse biological systems at the single-molecule level opens avenues of investigation that are not possible using techniques that measure aggregate properties of molecular populations. This new vantage point can yield important insights. A textbook example is that of molecular motors. Although classical biological assays for motor function show that these molecules support constant-velocity movement, studies of individual molecules revealed that they take discrete individual steps. The technique that allowed these crucial biological observations came from the physics field in 1986—a momentous year that saw the first demonstration not only of the optical tweezers technique used in the subsequent molecular motor study but also of the atomic force microscope. Created by physicists, these force-spectroscopy methods form much of the backbone of the field of research now devoted to studying biological systems at the single-molecule level."

Please read on at the Nature Methods focus website. Comments from readers are welcome at Methagora, the Nature Methods blog.

Posted by Maxine Clarke on June 10, 2008
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Nature Publishing Group presents a Collection on Neurotechniques, which includes original Research, Progress and Review articles as well as Research Highlights from Nature Methods and Nature Reviews Neuroscience. This collection aims to inspire and provoke thought by drawing attention to groundbreaking advances in technology that hold great promise for the pursuit of answers to long-standing questions, such as how brain regions are connected, what contributions single neurons and populations of neurons make to behaviour and cognition, and what role cell dysfunction has in neurological disorders. This collection is freely available until November 2008. It also contains a library of links to articles published by Nature Publishing Group journals on the topic.

Posted by Maxine Clarke on June 04, 2008
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Cigarette smoking is the leading preventable cause of death and disease in the United States. Understanding the genetic and pharmacological factors surrounding nicotine and other substances of abuse will lead to insight into ways to prevent psychological dependence and addiction A special web focus, presented by Clinical Pharmacology & Therapeutics, is a compilation of some key articles from Clinical Pharmacology & Therapeutics, Nature Medicine, Nature Reviews Drug Discovery, Neuropsychopharmacology and The Pharmacogenomics Journal on smoking, nicotine and addiction; many of them free to access online. Examples of featured articles include:
Development of Procedures for Early Human Screening of Smoking Cessation Medications
KA Perkins, C Lerman, ML Stitzer, CA Fonte, JL Briski, JA Scott & KNR Chengappa.
Contingency Management: Utility in the Treatment of Drug Abuse Disorders
ML Stitzer & R Vandrey.
Smoked Marijuana as Medicine: Not Much Future
H Kalant.
Clinical Pharmacology of Nicotine: Implications for Understanding, Preventing, and Treating Tobacco Addiction
NL Benowitz.
By Now, “Harm Reduction” Harms Both Science and the Public Health
AI Leshner.

Posted by Maxine Clarke on May 27, 2008
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From Nature 453, 145 (8 May 2008):
Two research centres will open their doors in Cape Town, South Africa, this month in a bid to bolster theoretical physics and mathematical sciences across the continent.
A pan-African centre of the existing African Institute for Mathematical Sciences will be launched on 12 May, followed the next day by the National Institute for Theoretical Physics, to be headquartered at the Stellenbosch Institute for Advanced Study.
The two institutes are funded mainly by the South African Department of Science and Technology. The pair will work closely with each other, using mainly local scientific talent to contribute to regional cosmology and astrophysics programmes such as SALT (the Southern Africa Large Telescope) in Sutherland and MeerKAT, a radio-telescope facility under construction in the Karoo desert.

Posted by Maxine Clarke on May 15, 2008
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The USCD-Nature Signaling Gateway would like to apply for continued funding from the US National Institutes of Health. If you are a researcher in this field, or if you are interested in this area and have been reading the articles and other content on the Gateway, please show your support by writing a letter to the team via this web form, before 30 May. Your response will help keep the content on the site freely available for all users.
The UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. The gateway represents a unique collaboration between the University of California San Diego (UCSD) and Nature Publishing Group, and is designed to facilitate navigation of the complex world of research into cellular signalling. Information and data presented here are freely available to all. It is powered by the San Diego Supercomputer Center (SDSC). It has won the Association of Learned and Professional Society Publishers (ALPSP) Award for Publishing Innovation for ‘a significantly innovative approach to any aspect of publication’.
The Signaling Gateway site has three main components: a data centre (repository and toolkits); Molecule Pages (structured data on key proteins); and Signaling Update (news and comment). The Signaling Gateway is an example of a pioneering business model that allows the scientific community free access to the wealth of cell signaling information through sponsorship, described in an article by Electronic Publishing Services as ‘the door to the future’

Posted by Maxine Clarke on May 07, 2008
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A key priority in translational cancer research is the discovery of molecular biomarkers that improve the early diagnosis of cancer and guide cancer prognosis, including the design and assessment of new therapeutic avenues. A Nature Insight in the current issue (Nature 452, 547-589; 3 April 2008) highlights key approaches for the discovery and validation of cancer biomarkers, at the level of DNA, RNA and protein analysis. It also focuses on non-invasive imaging tools and serum analyses that will be important in detecting tumours and monitoring the course of cancer therapy. Translating these advances into personalized cancer care will entail challenges far beyond the scientific discovery and validation strategies. We hope that the articles in this Insight not only bring together key aspects of the translational research into cancer biomarkers but also draw attention to associated issues such as trial design, tissue collection and regulatory requirements. This Nature Insight is freely available online for six months.

Posted by Maxine Clarke on April 03, 2008
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Nature Publishing Group has launched an Asia Materials website, featuring highlights of some of the best research from all fields of materials research published in the Asia-Pacific region. A substantial share of the world’s materials research output comes from Asian countries, and the Asia-Pacific region is making rapidly increasing contributions to global scientific research. In response to these developments, scientists from Tokyo Institute of Technology (members of the Global-Center of Excellence programme on materials science), together with NPG Nature Asia-Pacific, the Asia-Pacific wing of Nature Publishing Group, have launched NPG Asia Materials in preparation for establishing a new research journal devoted to materials research. Each month, NPG Asia Materials will be updated with short, easy-to-understand highlights of research articles recently published by scientists of the region in leading journals covering all fields of materials science. An Editorial Committee manages the site and selects research highlights from the papers recommended by the site's Advisory Board. You can register for regular e-mail alerts for NPG Asia Materials.

Posted by Maxine Clarke on April 02, 2008
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Nature Neuroscience presents a special focus on decision-making in the April 2008 issue and available online, highlighting recent achievements in this field. The ability to make appropriate choices is critical for survival. Successful decision making requires the integration of sensory information, motivational states and potential outcomes to select the best action. Recently, there has been great progress in our understanding of the neural mechanisms supporting decision-making in a wide range of contexts, including risky choices and social interactions. This special focus on decision-making contains four reviews that highlight recent achievements in this important field.
An introductory article, by Nature Neuroscience associate editor Hannah Bayer, describes how the research described in the focus has made substantial progress and, in future, should lead to a more developed understanding of this behaviour that makes us unique individuals.

Posted by Maxine Clarke on April 01, 2008
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The Nature Reviews journals are presenting a collection of articles on stem cells, free to access online for six months. Stem-cell research has a history of more than 20 years, and has made some outstanding contributions to our understanding of haematopoiesis (the formation of blood cells) and embryology. The field has been transformed by successes achieved in culturing embryonic stem cells and in manipulating their differentiation in vitro. We are gaining a better understanding of both embryonic and adult stem cells at the molecular level and of how they behave in their biological context — progress that is of great significance in cell and developmental biology. An introductory editorial and summary of some of the articles in the collection can be read here.
Read more on the topic at Nature Reports Stem Cells, with its associated blog The Niche.

Posted by Maxine Clarke on March 27, 2008
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Hearing about past and present issues in the world community of immunology can enrich all of us, according to the Editorial in this month's (April) issue of Nature Immunology (9, 331; 2008). The journal is publishing a series of commentaries on immunology in various places in the world, to demonstrate how, as a community, immunologists work and live together to advance the discipline.
Beginning with a piece by Agustin Lage on immunology, public health and biotechnology in Cuba in February (Nat. Immun. 9, 109-112; 2008), this series provides information on funding and infrastructure for immunology, special projects, and people, places and events. It also provides an opportunity for readers to compare and contrast the familiar scene in their own regions with that of other places. Commentaries now scheduled or under consideration survey the scene in India, the Middle East, Argentina, Russia and South Africa, and, in the current issue, Xuetao Cao discusses immunology in China (Nat. Immun. 9, 339-342; 2008).
The commentaries will not cover immunology comprehensively, but will present a few well chosen places—and well-chosen authors—to provide insight into new projects, ideas and concerns. In the words of the Editorial: "We hope that these commentaries, which will appear periodically over the next year or so, will enrich understanding of the familiar and the not-so-familiar in the world of immunology."

Posted by Maxine Clarke on March 24, 2008
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'Heritability in the genomics era — concepts and misconceptions' is the latest title in the Nature Reviews Genetics series on fundamental concepts in genetics. The article is published in the April issue of the journal, by Peter M. Visscher, William G. Hill and Naomi R. Wray (Nat. Rev. Genet. 9, 255; 2008 | doi:10.1038/nrg2322).
An at-a-glance summary of the key points in the article is available. Heritability is one of the oldest parameters in genetics, but also one of the most misunderstood. The authors explore exactly what heritability means, the pitfalls to avoid when using it, and its continued relevance in the genomics era.

Posted by Maxine Clarke on March 20, 2008
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In an editorial in Molecular Systems Biology (3, 158; 2008), Synthetic biology: promises and challenges,
Luis Serrano of the Centro de Regulación Genomica in Barcelona addresses wide-ranging and fascinating aspects of this nasent field. He asks why Europe is "lagging behind the US? Perhaps it is due to a general problem in Biology research and the way Europe has structured its research. In particular, Europe will need to take more and bolder initiatives in funding and building new institutes to create the necessary critical mass, and should raise its ambition for starting novel research areas. Competitive European groups in areas related to Synthetic Biology definitely exist, mainly amongst the very top EU institutes, where the system is more flexible and excellence is actively pursued. But these few world-class laboratories are usually small, scattered and in many cases have just entered into the field of Systems Biology and, therefore, do not have the capacity to fully embark into Synthetic Biology. As in many other fields, if Europe wants to stay competitive, we will need a major overhauling of the system, promoting excellence, flexibility and young investigators with new crazy projects. In this sense the European Research Council (ERC) initiative may represent a decisive step forward."

Posted by Maxine Clarke on March 11, 2008
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Starting this month (March 2008), Nature Methods strongly recommends deposition of proteomics data to public repositories before manuscript submission. From the Editorial in the March issue of the journal (Nat. Meth. 5, 209; 2008):
"Several proteomics data repositories are now available that differ in terms of their goals, structure and the formats they accept. They include PRIDE, PeptideAtlas, Global Proteome Machine Database (gpmDB) and the file distribution system Tranche. The newest addition, Human Proteinpedia, is a community-based annotation tool that hosts experimental data (Nat. Biotechnol. 26, 164; 2008).
Importantly, the major database administrators have shown their willingness to work with users and with each other to facilitate data deposition. At this stage, the process can still be labor-intensive, but a repository like PRIDE provides extensive technical assistance. Under the umbrella of the ProteomExchange consortium, the major repositories are also devising ways to share their data in a collaborative fashion, capitalizing on their complementarities to minimize submission hassle while maximizing benefits.
We support these efforts and consider it premature to recommend a particular repository. Rather we will rely on community experience to determine which database or combination of databases emerges as the most useful. However, there are specific features that editors favor. In particular, we like the possibility currently offered by PRIDE and Human Proteinpedia to provide peer reviewers with access to datasets associated with a manuscript before public release, in an anonymous fashion, and to coordinate public release of the data with publication. "

Nature Methods welcomes comments on this Editorial, and the recommendations it makes, at the journal's blog Methagora.
The Nature journals' policies on data and materials availability, including links to editorials on these policies, can be found at the author and reviewers' website.

Posted by Maxine Clarke on March 10, 2008
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The latest in Nature's Insights series is Cardiovascular disease (Nature 451; 21 February 2008), the most common cause of death worldwide and becoming even more prevalent as the population ages. New therapeutic targets are being identified as a result of emerging insights into disease mechanisms, and new strategies are also being tested, possibly leading to new treatment options. Improving diagnosis is also crucial, because by detecting disease early, the focus could be shifted from treatment to prevention. This Insight collection of an Editorial and eight Review and Progress articles is freely accessible online.
Editorial: Cardiovascular disease
Michael Basson
Reviews and Progress articles:
Translating molecular discoveries into new therapies for atherosclerosis
Daniel J. Rader & Alan Daugherty
Triggers, targets and treatments for thrombosis
Nigel Mackman
Tackling heart failure in the twenty-first century
James O. Mudd & David A. Kass
A genetic framework for improving arrhythmia therapy
Björn C. Knollmann & Dan M. Roden
Stem-cell therapy for cardiac disease
Vincent F. M. Segers & Richard T. Lee
The developmental genetics of congenital heart disease
Benoit G. Bruneau
The search for new cardiovascular biomarkers
Robert E. Gerszten & Thomas J. Wang
Imaging of atherosclerotic cardiovascular disease
Javier Sanz & Zahi A. Fayad
An index of all Nature's Insightscollections is available here.

Posted by Maxine Clarke on March 04, 2008
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Respiratory diseases, including allergies, asthma and chronic obstructive pulmonary disease, are a major public health burden worldwide.The latest WHO statistics (2007) estimate that 300 million people worldwide have asthma, 210 million people have this type of pulmonary disease, and millions of people are affected by allergies. Each year, 250,000 people die of asthma. The prevalence of these diseases is increasing, and there is a continued need for new and improved therapies. A March 2008 Focus issue of Nature Reviews Immunology highlights the latest advances in our understanding of the immune bases of these respiratory diseases and how this knowledge can be translated into effective treatment strategies, in five review articles and four research highlights. All Focus articles are freely available online for the month of March.
See here for a listing of all previous focuses at the journals Nature Immunology and Nature Reviews Immunology.

Posted by Maxine Clarke on March 04, 2008
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Aled Edwards of the Structural Genomics Consortium, University of Toronto writes in a Correspondence in this month's issue of Nature Structural & Molecular Biology (15, 116 ;2008):
The Structural Genomics Consortium (SGC) is a public-private partnership that places the three-dimensional structures of proteins of relevance to human health into the public domain without restriction on use. Over the past 3 years, the SGC has deposited the structures of more than 550 proteins from its Target List into the Protein DataBank (PDB); this accounts for about one-quarter of the new structures of human proteins in the PDB over this period ('new' is defined as <95% sequence identity to proteins whose structures were already available in the PDB) and the majority of the new structures from the human parasites that cause malaria, cryptosporidiosis and toxoplasmosis. Over the next 4 years, the SGC is committing to determining the structures of another 600 proteins from its Target List, including eight human integral membrane proteins.
The SGC has been releasing the coordinates for all the SGC structures into the PDB immediately after they meet the SGC quality criteria, even if the ultimate intention is to describe the work in the peer-reviewed literature. This data release policy, which has often meant that coordinates were available for several months before the manuscript was even written, has not limited the ability of our scientists to publish.
In keeping with our policy to make our data available as soon as possible, the SGC is now also providing 'pre-released' coordinates on its website when a new SGC structure is submitted to the PDB, allowing scientists to access the structural information while the deposition files are being processed. Scientists should ensure that the revised coordinate file is downloaded once it is released by the PDB.

Posted by Maxine Clarke on February 12, 2008
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Nature Clinical Practice Cardiovascular Medicine is pleased to announce the launch of a new Clinical Research section. It plans to publish its first original research articles in mid-2008.
Valentin Fuster, Editor-in-Chief of the journal, writes: “Our goal is to serve the community of clinical cardiologists, and demand for this expansion has come from its members. By adding outstanding original clinical research to the latest review content, we can provide everything a busy cardiologist needs to keep up to date with advances in the field. Feedback from our contributors and readers has told us that they want a journal that not only provides timely and succinct analysis of recent advances to ease reading workload, but that they also want original research of the highest quality. We agree and aim to satisfy that demand.”
The field of cardiology is very fast-moving and there is an immense amount of research published each week. Nature Clinical Practice Cardiovascular Medicine will present only well-chosen, robust research and it will review the rest. Filtering is key – we filter all the research published each week by scanning the literature and reviewing salient issues, and will filter our original research submissions to provide only strong, clinically relevant papers. Instructions for authors are available here; the online submission page for the journal is here; find out more about the journal here; or you can contact the research editor by email for further information about submissions of original clinical research papers on the development of new technologies or methodologies that improve understanding of cardiovascular disease or impact on diagnosis or management; new information on clinical outcomes and economics from clinical trials; and new approaches to promote cardiovascular health. A free sample issue is available here.

Posted by Maxine Clarke on January 18, 2008
Categories: Disciplines, Publications | Permalink | Comments (0)

This month's Nature Medicine features a question and answer interview with Marc Hodosh, senior director of the Archon X prize, who explains why genomics was chosen for an X prize and predicts what lies ahead for the field (Nat. Med. 14, 8 ; 2008). These days, if you want to have your entire genome sequenced, you need to spend about a million dollars and wait for months. The Archon X prize for genomics—an international competition for speedy gene mapping—might change this by giving companies a huge incentive to develop better DNA sequencing technologies. The $10 million prize, first announced in late 2006, was donated by Stewart Blusson, a philanthropist and mining multimillionaire. Announcement of a winner, thinks Hodosh, is probably two to four years away. Read the full article, by Genevive Bjorn, at the Nature Medicine website.

Posted by Maxine Clarke on January 14, 2008
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Alex Witze (currently at AAS) passes on some questions for "sci/pop culture buffs":
In what popular movie does Daryl Hannah play an astronomer? (Answer.)
- What Japanese car company is named after a well-known star cluster? (Answer.)
- What science fiction story, written by an astronomer under a pseudonym, features a Hertzsprung-Russell diagram of stellar evolution? (Answer.)
- Can you recite the most famous neutrino poem, and name the poet? (Answer.)
And here's really geeky one I haven't a clue about - if you know, comment below please!
- What rock group had its members' names included in a reference in the Astrophysical Journal, unbeknownst to the editor? (Answer is provided here, with additional story by Oliver Morton).

Posted by Maxine Clarke on January 11, 2008
Categories: Disciplines | Permalink | Comments (0)

The Neuroscience Gateway has moved to a new URL, www.neuroscience-gateway.org. Building on the success of the gateway, developed in collaboration with the Allen Institute for Brain Science, Nature Publishing Group is now expanding the gateway in new directions. Please update your bookmarks to the Allen Brain Atlas.
The site will continue to provide updates about the latest research, news and events, and will soon be including new features reflecting recent trends in neuroscience research. We hope you'll continue to find the Gateway a useful tool to track progress in neuroscience, and we'll provide more news about the site's development in the coming months.
We welcome suggestions and feedback from the neuroscience community, both at the Neuroscience Gateway and at Action Potential, NPG's neuroscience blog. We also encourage neuroscientists and others interested in the field to join the free neuroscience group on Nature Network, in which editors Noah Gray and Kathryn Devaney run an interactive journal club and host other discussions on what’s new in neuroscience research and publishing.

Posted by Maxine Clarke on January 11, 2008
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Nature Publishing Group (NPG) and BioCentury Publications, Inc announce a new electronic publication, SciBX, that will distill and analyse newly published life-science research to help the translation of academic science into commercial products. The preview edition of SciBX (for Science-Business eXchange) is available from the organisation's website: the publication will be distributed to subscribers every Thursday, starting on 31 January 2008.
SciBX will evaluate hundreds of high-impact, peer-reviewed scientific articles every week and select the most commercially relevant findings that merit deeper analysis. This multidisciplinary approach will provide scientific context, identify potential commercial impact and describe the next steps required to translate the newest laboratory developments into innovative healthcare solutions.
According to Medline, more than 600,000 articles were added to its database in 2006 alone. SciBX will filter this flood of scientific data, and analyse key findings within the most current scientific and business context. It will be an indispensable resource for biotechnology and pharmaceutical companies, business development specialists, drug discovery and development teams, venture capitalists and other investment professionals who wish to identify new projects and potential new partners, to find enabling technology, and to be aware of competitive advances.
Please download the free preview edition of SciBX , which contains sample articles, including:
- Analysis – Providing in-depth review of new research findings and an essential understanding of the next steps required to transform these developments into commercial value.
- The Distillery – Filtering and classifying the important current research papers in biotechnology, life science and chemistry, the Distillery goes beyond the abstract to explain the science, its commercial relevance, licensing status and identify companies known to be working in the area.
Further information about the publication, the team producing it and the companies supporting it can be found at the SciBX website.

Posted by Maxine Clarke on January 09, 2008
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Join Nature editor and writer Alexandra Witze at the 211th American Astronomical Society meeting in Austin, Texas from 8-11 January. She'll be sending diary reports to our In The Field blog as astronomers gear up for the International Year of Astronomy in 2009.
The AAS meeting schedule is here, with links to the abstracts of all the presentations.

Posted by Maxine Clarke on January 08, 2008
Categories: Communication, Conferences, Disciplines | Permalink | Comments (0)

Owing to my end-of-year holiday, I am a little late bringing you news of the Nature Methods' Method of the Year 2007, which is next-generation sequencing. The journal is publishing in its January 2008 issue a series of free articles showcasing how these novel sequencing methods came into their own in 2007 and the incredible impact they promise to have in a variety of research applications.
From the Nature Methods editorial announcing the winner:
"If the choice of next-generation sequencing as Method of the Year was uncontroversial among our team, we did have other ideas and enthusiastic discussions. To share that excitement, we included a shortlist of Methods to Watch. It is an incomplete and subjective selection, established by Nature Methods with the input of other editors at Nature, Nature Reviews and Nature research journals. Some of these Methods to Watch are, thanks to recent developments, on the cusp of turning around fields of research. Others, by contrast, do not yet have a technical solution but rather represent areas in which methodological developments are sorely needed.
We welcome your comments on our choices as well as your suggestions of other methods to keep an eye on. (To share your thoughts please visit methagora.) We firmly intend this event to become an end-of-the-year tradition, and we hope for your participation in next year's nominations!"
You can add your comments and, as the year progresses, 2008 nominiations at this methagora post.
The announcement and features about the Method of 2007 are at this Nature Methods web focus, including the Methods to Watch articles.

Posted by Maxine Clarke on January 04, 2008
Categories: Awards, Disciplines | Permalink | Comments (0)

Two scientists writing a Commentary article, "Professor's little helper", in the current (20 December) issue of Nature (450, 1157-1159; 2007) want to stimulate your brains – in more ways than one.
Barbara Sahakian and Sharon Morein-Zamir from the Department of Psychiatry at Cambridge University argue that the increased usage of brain-boosting drugs by ill and healthy individuals raises ethical questions that cannot be ignored. An informal questionnaire Sahakian and Morein-Zamir sent to some of their scientific colleagues in the United States and United Kingdom revealed fairly casual use by academics, and we now want to hear your views on the topic.
The authors' arguments can be read in more detail in their Commentary at Nature (450, 1157-1159; 2007). A Nature editorial in the 15 November issue (Nature 450, 320; 2007) also discussed some of the ethical issues surrounding drug-based enhancement in healthy individuals inspired by a longer discussion paper from the British Medical Association.
To trigger broader discussion of these issues Sahakian and Morein-Zamir propose the following questions:
> Should adults with severe memory and concentration problems be given cognitive enhancing drugs?
> If such drugs have only mild side effects, should they be prescribed more widely for other psychiatric disorders?
> Do the same arguments apply for young children and adolescents with neuropsychiatric disorders, such as those suffering from ADHD?
> Would you boost your own brain power?
> How would you react if you knew your colleagues – or your students – were taking cognitive enhancers?
> How should society react?
Please contribute to this online discussion. We especially want to hear from you if you’re already using these drugs – or if you know people who are. What are your reasons for taking, or not taking, them?
For the next two weeks, the authors of the Nature Commentary will be joining in the conversation at the Nature Network forum: we look forward to meeting you there.
See also the related post, Brain doping, over at Action Potential.

Posted by Maxine Clarke on December 20, 2007
Categories: Disciplines, Education, Ethics, Public and media | Permalink | Comments (0)

Bali has not been the only island that has just hosted a climate-change conference. The BBC World Service's Digital Planet today runs a short feature and podcast about Nature Publishing Group's Second Nature, an archipelago of islands in Second Life, in which climate scientists – or their representational avatars – have been hosting talks and discussions. Timo Hannay, publishing director at Nature Publishing Group, describes how we went about achieving this series of virtual talks in a podcast which is available for one week only (until Tuesday 25 December) via the Digital Planet site.
Full reports of the Second Nature conference are at Joanna Scott's Nature Network blog. A brief description of the virtual conference's aims is here, with full presentations, Q/As and slides of the first two talks, by Tara LaForce of Imperial College London and Euan Nisbet of Royal Holloway College London.
You can follow our coverage of the real UN climate change conference at Climate Feedback blog -- just keep scrolling, there are many excellent posts from Olive Heffernan, Editor of Nature Reports Climate Change, who was in Bali for the duration.

Posted by Maxine Clarke on December 18, 2007
Categories: Author services, Communication, Disciplines, Partners | Permalink | Comments (0)

Nature's latest Insight collection of reviews, Proteins to proteomes (Nature 450, 963-1009; 2007) is freely available online. Proteins are the most diverse and versatile set of biological macromolecules, having crucial roles in all biological processes. Now that whole complements of proteins (proteomes) for many cell types have been identified, we can begin to address the central question of how the innumerable protein functions are integrated so that a living cell interacts coherently with its environment. The Insight collection of five reviews covers vibrant areas of research in the 'protein world', journeying from single-protein dynamics, to functional proteomics and drug discovery, via new technological developments in structural, computational, evolutionary and cellular biology.
The Insight supplement is available here.

Posted by Maxine Clarke on December 17, 2007
Categories: Disciplines, Publications | Permalink | Comments (0)

Nature Geoscience, whose first print/online edition will be published in January 2008, has published its first papers -- as advance online publications. Among these are a Commentary by Martin Visbek, "From climate assessment to climate services", who writes "If we fully embrace past assessment and ongoing future projections of regional climate change as the task of integrated climate services, the IPCC [Intergovernmental Panel for Climate Change] can be relieved of the duty of providing up-to-date assessments of climate change. This would allow the panel to move to the decadal assessments that best suit its primary task: reviewing emerging scientific knowledge and best practices to evaluate global climate change."
Also just-published are Letters by Parsons et al., on quiet zones in the San Andreas fault; and by Beerling et al. on cold intervals in the "greenhouse world" of the Mesozoic.
Nature Geoscience is accepting manuscripts that report new research in the Earth and planetary sciences, aimed at a broad interdisciplinary audience of geoscientists. View the complete Guide to Authors here. Submit your papers via the journal online submission system here.

Posted by Maxine Clarke on December 14, 2007
Categories: Disciplines, Publications | Permalink | Comments (0)

From Nature Reports Stem Cells: November was an eventful month for stem cell research. First came the finding that embryonic stem cells could be made from cloned primate embryos; a week later came announcements that human skin cells could be genetically engineered to be virtually indistinguishable from embryonic stem cells. Meanwhile, advances continued apace. The International Society for Stem Cell Research hosted its first conference in China, attracting hundreds of scientists (see this post on The Niche). Researchers in cardiovascular medicine debated how to apply knowledge toward therapies. And scientists from disparate disciplines pursue culture conditions better able to mimic what cells experience in vivo.
Achieving pluripotency in human cells
In October, we asked for feedback on how to tell when human cells deserve the label of pluripotency. Kyoto University's Shinya Yamanaka discusses experimental design where having a positive control is impossible. The University of Sheffield's Peter Andrews suggests that the term, like 'gene', might be more useful if it can mean a variety of subtly different things. Others offer the notion of a 'pluripotency score'.
The collective wisdom is on The Niche.
Last month’s breakthroughs reprogramming adult human cells and cloning primate embryonic stem cells, make the need to define pluripotency all the more pressing. Nature Reports Stem Cells has put together a collection of relevant articles.
For these and more news, journal club, features and summaries of latest research, please visit Nature Reports Stem Cells, a free interactive forum for stem-cell scientists and others interested in the discipline to communicate about the research, policy, ethics, business and medicine of stem-cell science.

Posted by Maxine Clarke on December 13, 2007
Categories: Disciplines | Permalink | Comments (0)

Nature Biotechnology and Nature Reviews Drug Discovery announce a joint web focus, Antivirals, hosting a collection of Reviews, Research Highlights and Commentaries covering the science and business of antiviral drug research and development, highlighting innovative approaches and lessons learned from decades of antiviral drug development, as well as identifying key issues for future antiviral drug discovery and potential solutions. The web focus also includes an online library of recent research papers and review content from other Nature Publishing Group journals. All articles, and selected content from the library, are freely available from December 2007 until June 2008.

Posted by Maxine Clarke on December 10, 2007
Categories: Author benefits, Disciplines | Permalink | Comments (0)

Plus has teamed up with Nature to bring maths to the Nature Network. Plus's blog calls Nature Network a "stage for science discussion, allowing scientists to meet, interact, comment on the latest news, debate current topics or exchange information. Members can create groups for their own labs or organisations, or for their own subject area. The mathematics forum is now brought to you by Plus. We're aiming to provide a platform for anyone who wants to discuss maths, whether it's actual maths, maths teaching, the portrayal of maths in the media, or good and bad maths content elsewhere on the internet." Plus is also organising a science writing competition, open to new writers who can explain a mathematical topic or application they think the world needs to know about. The winning entries will be published in the June 2008 issue of Plus, and the winners will receive an iPod and signed copies of popular maths books. Closing date 31 March 2008.

About Plus: "Plus is an internet magazine which aims to introduce readers to the beauty and the practical applications of mathematics. Plus provides feature articles, which describe applications of maths to real-world problems, games, and puzzles; reviews of popular maths books and events; a news section, showing how recent news stories were often based on some underlying piece of maths that never made it to the newspapers; a puzzle for you to sharpen your wits against; a lucky dip of mathematical curiosities; and opinions on various maths-related topics and news stories. We have a regular interview with someone in a maths-related career, showing the wide range of uses maths gets put to in the real world. And all past issues remain available online, which besides making for good browsing is, we hope, a useful resource for maths school students and teachers."

Posted by Maxine Clarke on November 08, 2007
Categories: Disciplines, Partners, Writing | Permalink | Comments (0)

There is an interesting historical piece in the current issue of Nature Reviews Genetics (8, 897-902; 2007) by Marsha Richmond of Wayne State University, Detroit, entitled Opportunities for Women in Early Genetics. From the abstract:
"Although women have long been engaged in science, their participation in large numbers was limited until they gained access to higher education in the last decades of the nineteenth century. The rediscovery of Mendel's work in 1900 coincided with the availability of a well trained female scientific workforce, and women entered the new field in significant numbers. Exploring their activities reveals much about the early development of the field that soon revolutionized biology, and about the role of gender in the social organization of science."
See here for the complete article.

Posted by Maxine Clarke on October 22, 2007
Categories: Careers, Disciplines | Permalink | Comments (0)

Nature Neuroscience presents a special focus on emotion and emotion disorders, published in the September 2007 issue and accessible online. Regulation of emotion is becoming better understood, but despite the societal costs of disorders like depression and anxiety, their causes remain unclear. Five review articles in this issue provide perspective on this literature.
New insights into BDNF function in depression and anxiety
Keri Martinowich, Husseini Manji & Bai Lu
Social learning of fear
Andreas Olsson & Elizabeth A Phelps
Long story short: the serotonin transporter in emotion regulation and social cognition
Turhan Canli & Klaus-Peter Lesch
Adult hippocampal neurogenesis in depression
Amar Sahay & Rene Hen
Targeting abnormal neural circuits in mood and anxiety disorders: from the laboratory to the clinic
Kerry J Ressler & Helen S Mayberg

Posted by Maxine Clarke on September 21, 2007
Categories: Disciplines, Publications | Permalink | Comments (0)

Nodalpoint has recently updated its list of high-quality computational biology and related weblogs. If you have a bioinformatics or related blog and want to be included, or if you want to suggest a blog for inclusion, please go to the Nodalpoint link above and submit your suggestion via the weblinks form. And if you don't have a blog and wonder why a scientist should want to blog, I borrow from a 2005 Nodalpoint post a quote from physicist Sean Carroll, who blogs at Cosmic Variance:

"It can serve a useful purpose in providing some expert commentary when something hits the news, like Hawking's ideas about black holes last summer," says Carroll. "And I like to think that it does provide a window into the wider concerns of an academic scientist when I talk about dinosaurs or theater or music. Writing it has made me more disciplined and careful about my ideas and how I express them; you can't get away with things in front of a thousand readers that you might in casual conversation."

Posted by Maxine Clarke on August 30, 2007
Categories: Disciplines | Permalink | Comments (0)

The August editorial in Nature Biotechnology, 'Time for leadership' (Nat. Biotechnol. 25, 821; 2007) describes how the example set by leading proteomics laboratories will be a major factor in determining the successful implementation of new reporting guidelines in the wider community.
The August issue of the journal includes two perspectives that propose reporting guidelines for proteomics and molecular-interaction data sets (p. 887 and p. 894). The "minimum information about a proteomics experiment" (MIAPE) and an associated module on molecular interaction experiments (MIMIx) were developed by the Proteomics Standards Initiative of the Human Proteome Organization with the aim of standardizing the reporting of proteomics research.
The editorial goes on to state: "Whether Nature Biotechnology ultimately elects to require compliance with the MIAPE guidelines will depend on their reception by the scientific community. This March, we began recommending (not requiring) that proteomics and molecular-interaction data sets be deposited in a public repository before the associated manuscript is submitted to this journal (Nat. Biotechnol. 25, 262, 2007). But we would not consider enforcing the MIAPE guidelines until such time as the proteomics community has reached a consensus that the benefits of compliance outweigh the burden.
Before this can happen, at least two critical pieces of infrastructure must be in place. First and foremost, appropriate software tools must be developed and made freely available to all. Second, databases must improve their capabilities for transferring and storing MIAPE-compliant data sets."
We welcome your comments as the Nature journals further develop their policies in this area.

Posted by Maxine Clarke on August 17, 2007
Categories: Data availability, Disciplines | Permalink | Comments (0)

We are delighted to announce the launch of a new journal, Nature Chemistry, in the first part of 2009. Alongside the highest-quality original research, Nature Chemistry will cover news, commentary and analysis from and for the chemistry community, as well as striving to develop a voice that chemists care about.
Over the past five years, Nature Publishing Group (NPG) has expanded its portfolio of Nature journals in the physical sciences, with Nature Materials, Nature Physics, Nature Photonics and Nature Nanotechnology.
Nature Chemical Biology marked NPG's first major foray into chemistry publishing. Launched in June 2005, Nature Chemical Biology has established itself as the home for primary research covering the interface between chemistry and biology. Its first impact factor is 12.409, making it the number one primary research journal in related chemical sciences.
Nature itself has also expanded its coverage of chemistry, with the addition of several chemists as editors to select papers for publication and to report news on chemistry in the News and Views and News sections of the journal.
We have also created additional online services and publications, such as the Sceptical Chymist blog, chemistry podcasts, a chemistry subject area, and our bi-monthly chemistry e-alert about what is new for chemists and chemistry. We also regularly provide hundreds of job opportunities for chemists via naturejobs.

We are looking for a Chief Editor who is able to develop, launch and establish Nature Chemistry as the essential publication for the chemistry community. The role will be based in NPG's Boston office.
Applicants must have a strong track record of research in a chemistry discipline, as well as significant editorial and/or senior research experience. They must demonstrate a good understanding of the challenges faced by researchers in both academic institutions and industry.
This is a demanding and extremely stimulating role, which calls for a keen interest in the practice and communication of science. The successful candidate will therefore be dynamic, motivated and outgoing, and must possess excellent interpersonal skills.
Applicants should include a covering letter stating their suitability for this post, as well as their salary expectations, a current CV and a statement (maximum 1,500 words) that encapsulates their vision for the content, competitive position and longer-term development of Nature Chemistry.
Applications should be sent to Denise Pitter, Personnel Assistant at londonrecruitment@macmillan.co.uk. Applicants should clearly mark on their submissions the reference number. Incomplete applications will not be considered. Closing Date: 24 September 2007

Posted by Maxine Clarke on August 16, 2007
Categories: Careers, Disciplines, Publications | Permalink | Comments (0)

The Nature journals this month (August) feature several editorials on the publishing process. A short round up (with links) follows:

Nature Genetics (39, 931; 2007), in 'Compete, collaborate, compel', calls for procedures for microattribution to be established by journals and databases so that data producers have an overwhelming incentive to deposit their results in public databases and thereby to receive quantitative credit for the use of every published data accession.

In 'Got data?', Nature Neuroscience (10, 931; 2007 ) points out that data sharing is not only good citizenship for researchers, but is also required by funding agencies and many journals. The scientific community needs to develop better incentives to encourage compliance and reward those who share.

And in 'Name that gene!', Nature Structural & Molecular Biology (14, 681; 2007) warns that scientists coin new terms, or neologisms, at a tremendous pace, but name choice can have unforeseen results.

Posted by Maxine Clarke on August 09, 2007
Categories: Access, Data availability, Disciplines, Publishing | Permalink | Comments (0)

There is no greater burden of responsibility for scientists than that placed on those who conduct medical research on human subjects, according to an Editorial in Nature this week (448, 511-512; 2007). On the rare occasions that this duty is inappropriately discharged, the results can be devastating. Even so, once the initial outcry dies down, little tends to change.
The diverse collection of institutional review boards (IRBs) that oversee such research in the United States barely qualifies as a 'system'. Despite repeated attempts by the Institute of Medicine and others to highlight their shortfalls, the quality and effectiveness of the boards remain patchy (see the News Feature on page 530 of the same issue of the journal).
To strengthen the way human clinical trials are overseen, adequate funding for the Office for Human Research Protections and more widespread accreditation of the IRBs (ensuring proper training and support for committee members) would be a start. But this is not enough, states the Editorial -- real improvements in the IRB procedures are required. Some have suggested that the review of multicentre studies needs to be centralized, and certainly clearer ethical guidelines for local review boards could be provided (for example, on the question of payment for volunteers).
The Nature journals' policy for authors concerning research on human subjects is available here. As ever, your comments and suggestions are welcome.

Posted by Maxine Clarke on August 08, 2007
Categories: Disciplines, Ethics | Permalink | Comments (0)

Via The Seven Stones: the Royal Society seeks your views on the emerging area of synthetic biology. According to the society," this is your opportunity to shape the focus of the Royal Society's policy future work in this important area. We welcome views from individuals or organisations by 27 August 2007."
Synthetic biology is an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.
Biologists have traditionally sought to understand how life works. In contrast, synthetic biologists seek to design and build new biological systems. The application of engineering principles to the design and construction of complex biological systems is likely to provide a step change from the tweaking of existing genomes usually described as genetic engineering.
Here is the Royal Society's "Call for views" document.

See the Nature newsblog for Oliver Morton's reports from the second Synthetic Biology conference at the University of California, Berkely, 20-22 May 2007.

Posted by Maxine Clarke on August 02, 2007
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In today's era of start-ups, spin-offs and university–industry collaborations, it pays to be knowledgeable about patents and how they can help. So starts the Editorial in the new issue of Nature Photonics (1, 355; 2007)

"All too often scientists are deterred from patenting by misconceptions about how expensive or time-consuming the process might be. True, the cost of filing and maintaining a patent has to be considered carefully, but the financial or commercial benefits may be worth it."

Read on at the Nature Photonics website.

Further information about patents in photonics is provided in the Commentary "Patenting photonics research" by Andrew Fearnside later in the issue (Nature Photonics 1, 357-359; 2007).

Posted by Maxine Clarke on July 03, 2007
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Frank Gibson, a Research Associate at Newcastle University, UK currently working on the e-neuroscience project CARMEN, has written an essay Do scientists really believe in open science? , in which he collects current opinions of “Open Science”. He was stimulated to write the essay because of his role in the CARMEN project which, he writes, has exposed him to a domain of the life-sciences to which "data sharing and publicly exposing methodologies has not been readily adopted, largely it is claimed due to the size of the data in question and sensitive privacy issues."

The essay is available here. It addresses definitions of "open science" and summarizes the standards used in disciplines other than neuroscience. You can see the Nature journals' policies on data availability here, which apply to all the original research articles our journals publish. Via this web page, you can provide us with your comments and views on recent journal editorials about emerging policies on data availability in a range of disciplines and circumstances.

Among other aspects of "open science", Dr Gibson discusses the "open notebook" approach pioneered by J-C Bradley. He also notes that Postgenomic produces an "up-to-the minute list of the open science discourse". (Postgenomic is a website that tracks hundreds of science blogs and "does interesting things with that data".) "Although early days", continues Dr Gibson, "maybe even the "open science group" on Scintilla (still undecided on Scintilla) will be the place in future for fostering the open science community".
Scintilla is one of Nature Publishing Group's very latest products. It collects data from hundreds of news outlets, scientific blogs, journals and databases and then makes it easy for you to organize, share and discover exactly the type of information that you're interested in. For example, you can keep track of life science podcasts, or the latest papers on schizophrenia, DNA methylation, physics or immunology. It is free to join, so take a look at what it has to offer and, if you wish, contribute to the open science group, or join one of the many other interest groups there.

Posted by Maxine Clarke on June 27, 2007
Categories: Data availability, Disciplines | Permalink | Comments (0)

The ENCODE (Encyclopedia of DNA Elements) project has set out to identify all the functional elements in the human genome. Detailed in a Nature web focus, a pilot project on 1% of the genome reveals new insights about how the information coded in the DNA blueprint is turned into functioning systems in the living cell. You can download a free poster at the Nature web focus, read the free-access article by the ENCODE project team (Nature 447, 799-816; 2007), and read related news stories, articles and information about the project.

Posted by Maxine Clarke on June 14, 2007
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From this week's Correspondence page (Nature 447, 775; 2007): Ours is a world in crisis. We are despoiling our habitat, outstripping our resources and failing to provide an acceptable living standard for much of the world's population. Although academic institutions are equipped to help remedy these problems by informing the leaders of tomorrow, they often fail to do so. Increasing pressure for specialization has led universities to trade breadth for depth in curricula, thereby depriving students of an understanding of complex, interconnected global issues. For example, solutions to our energy crisis span economics, engineering and politics, yet the typical student is exposed to only a portion of this spectrum.
Here, we propose a first step in addressing such shortcomings. We, the undersigned graduate students, have created a campus-wide 'State of the Planet' course at Cornell University under the mentorship of faculty members Tom Eisner and Mary Lou Zeeman.
Our goal is threefold: to improve understanding of complex issues; to add global context to disciplinary education; and to motivate action and involvement. To this end, we recruited experts, mostly resident faculty members and community leaders, to address the challenges we agreed were paramount.
Administrative support was quick to materialize, as was a pool of enthusiastic participants. We launched the course in January 2007, after campus-wide publicity highlighting its multidisciplinary nature. Our 250 current students come from 45 different majors ranging broadly across the humanities and basic and applied sciences. In lectures, experts familiar with our most pressing global problems emphasize how solutions span disciplines. Students participate in discussion groups led by graduate assistants, where they not only build on ideas presented in lectures, but also set up projects aimed at solving problems.
Mid-semester student evaluations have been overwhelmingly positive, with 93% saying that the course has changed their views on education, career plans and lifestyle, and 95% believing that their peers should also take this course.
Comments include: "This course has influenced my perspectives on almost everything, from the food I eat to how long I leave my computer on" and "The course demonstrates how many different skills and backgrounds can help shape policy that is instrumental for the planet."
We are continuing to expand our course in the hope that it will become a campus-wide requirement. Our vision is that other universities will adopt similar courses as a curriculum component for all students. We extend an open invitation to like-minded people at other institutions to join us, and others launching parallel efforts, in what we believe will be a modest but fundamental change to university education.
We maintain the optimistic belief that, given the right information, people will change their habits and their world. But the burden is on us, as educators, to motivate this change.
Krystal L. Rypien, Jill Anderson, Jason Andras, Rulon W. Clark, Gretchen A. Gerrish, James T. Mandel, Marie L. Nydam & Daniel K. Riskin
Department of Ecology and Evolutionary Biology, Cornell University.

Posted by Maxine Clarke on June 14, 2007
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The authors of a controversial paper on stem cells publish a correction of their work in this week's issue of Nature (447, 880-881; 2007) but state in it that the errors do not affect the conclusions of the article. A News story also in this week's issue (Nature 447, 763; 2007) describes how the paper in question, published in 2002, claimed to find evidence for so-called 'multipotent adult progenitor cells', or MAPCs, in mouse bone marrow (Y. Jiang et al. Nature 418, 41–49; 2002). The work was led by Catherine Verfaillie, now director of the Stem Cell Institute at the Catholic University of Leuven.
From the News story: The paper challenged the prevailing idea that only stem cells derived from embryos were highly flexible. Some of its results have been reproduced by other labs, but no one has been able to replicate the work independently in its entirety. "I believe that despite the hype over the mistake, we and Nature made the conclusion that the final findings of the paper still stand," says Verfaillie.
This February, an investigation convened by the University of Minnesota — Verfaillie's former institution — found that her group had used incorrect procedures in the Nature paper, and that some of the data contained in it might be flawed. The investigation was a response to questions from a reporter from the magazine New Scientist, who pointed out that the figure from the Nature paper that has now been corrected was partly reproduced with different labels in another paper in another journal, Experimental Hematology (Y. Jiang et al. Exp. Hematol. 30, 896–904; 2002).
In response to the investigation, Nature convened a peer-review panel to analyse the data from the 2002 paper. According to Nature, the experts concluded that although the figure data were flawed, the paper's conclusions are still valid. No allegations of fraud or misconduct have been levelled at Verfaillie or anyone from her group. Verfaillie says her group cannot explain how the errors in the Nature paper occurred: "Why this happened, we have not been able to determine," she says.

Posted by Maxine Clarke on June 14, 2007
Categories: Data availability, Disciplines, Ethics, Policies | Permalink | Comments (0)

James A. Smith and Genna E.Carey of the University of Adelaide ask in this week's Nature Correspondence page (Nature 447, 638; 2007) how we can practically encourage and foster interdisciplinary research. They say:
Despite a shift towards an interdisciplinary research culture, we are yet to grapple with how to support a growing number of interdisciplinary researchers. As interdisciplinary postgraduate research students, we face this reality head-on.
We have found it difficult to synthesize the separate perspectives of two or more disciplines into a meaningful middle ground. Unless the scientific community identifies strategies for supporting interdisciplinary researchers to negotiate this middle ground, little progress can be made. Here we suggest two useful approaches.
First, interdisciplinary researchers are expected to develop a different skill set from that of their single-discipline colleagues. In this 'interlocker' role, they engage in a shared conversation between disciplines and work through the tensions this creates. This is more than simply negotiating the different languages and ways of working — it is about appreciating a breadth of knowledge in theory, approach and discourse.
Unfortunately, few systems accommodate this type of researcher — as is sadly demonstrated by emerging frameworks designed to assess research quality in New Zealand, the United Kingdom and Australia. Interdisciplinary committees are needed to assess research proposals, to review grant applications and to examine theses. This would be more effective than the current practice of putting interdisciplinary researchers in assessment 'silos' where they are unrealistically measured against, and by, people in a single discipline.
A second challenge is the disjunct between, on one hand, rhetoric encouraging inter-disciplinary research and, on the other, the lack of institutional structure and support for it. Although we are encouraged to work in interdisciplinary environments and to join interdisciplinary research clusters, we face numerous administrative hurdles. Cross-enrolment of interdisciplinary students is seldom acknowledged, and adequate resources and structures — such as guidance on writing for interdisciplinary audiences, or longer candidatures for postgraduate students — are rarely provided to support the interdisciplinary researcher.
It would be simple for institutional leaders to ask current interdisciplinary researchers about the challenges they face and to document these issues. These leaders could then address the issues by formalizing the interdisciplinary researcher role and reducing demands to satisfy the needs of multiple disciplines. Supportive environments must be created if we are committed to achieving interdisciplinary research goals.

See also this Recruiters article (Nature 445, 950; 2007) by A. Paytan and M.-L. Zoback.

Your views are welcome.

Posted by Maxine Clarke on June 06, 2007
Categories: Careers, Disciplines | Permalink | Comments (2)

In a meeting report in the current issue of Molecular Systems Biology (3, 105; 2007), Trey Idecker, Vineet Bafna and Thomas Lemberger write that "a key challenge of systems biology is that it must integrate several disciplines, each with a very different culture for disseminating results. Within biology, manuscripts describing new work are almost always published in peer-reviewed periodicals. In contrast, within computer science and the engineering fields, new methods and results are typically presented as full-length papers at meetings and workshops. Just as journals have editorial boards that handle review of manuscripts, such conferences assemble large and reputable programme committees, which fulfill the same purpose. Publication in the best conferences, as for the best journals, is highly competitive.

This past December, several hundred scientists convened in La Jolla, California for the Second Annual RECOMB Workshop on Systems Biology (December 1–3, 2006). The meeting, which was held jointly with the RECOMB Workshop on Computational Proteomics, took place at the California Institute for Information Technology and Telecommunications in the University of California San Diego campus. RECOMB, which stands for Research in Computational Biology, has for a decade sponsored conferences that attract high-quality papers in bioinformatics, primarily from computer science.

In an effort to integrate the computational and experimental biology communities, RECOMB and Molecular Systems Biology entered into a partnership by which original, peer-reviewed papers are presented orally at the Workshop on Systems Biology and then appear as full-length manuscripts in the pages of the journal. The precise publication model was formulated after much discussion between the editors of the journal and the organizers of RECOMB. It is original and, we hope, will serve as a case study for future conferences."

See the Molecular Systems Biology website for more news of this project.

Posted by Maxine Clarke on May 14, 2007
Categories: Data availability, Disciplines | Permalink | Comments (0)

This month's molecule is... | nodalpoint.org

If you like to keep up to date with interesting protein molecules, the blog Nodalpoint recommends a couple of good minireview sites that feature a different structure each month, "worth a quick read because they can help bio-literate users to increase and reinforce their knowledge relatively quickly."

Posted by Maxine Clarke on March 29, 2007
Categories: Disciplines | Permalink | Comments (0)

This month's Editorial in Nature Chemical Biology, A mechanistic meeting point, addresses the divergent ideas among different communities of scientists of what constitutes mechanistic insight into a biological system. From the Editorial:

"Obviously, it is ideal for scientists from many disciplines to agree that a scientific result is insightful and exciting, because it means that the conclusion crosses scientific borders. Accordingly, chemical biologists should plan their projects and publications to consider each of these fundamentally distinct approaches from the outset. Interaction with colleagues and collaborators with different backgrounds can facilitate these excursions into foreign intellectual territory. In addition, authors should use referee reports as an important guide for developing improved papers that more effectively balance the requirements of research at the interface of chemistry and biology. The integration of expectations concerning mechanistic insight into a new, cohesive, community mind-set will serve as the foundation for chemical biology moving forward."

Posted by Maxine Clarke on February 22, 2007
Categories: Disciplines, Publications | Permalink | Comments (0)