BioMed Central Blog

Splicing together collaborations

The recent explosion of publicly available high-throughput data is at least partially responsible for uniting the chromatin, non-coding RNA and alternative splicing fields. This became apparent in the Alternative Splicing – SIG satellite meeting at the recent Annual International Conference on Intelligent Systems in Molecular Biology (ISMB) in Boston, which Genome Biology attended

Public datasets analysed included ChIP-seq data from the lab of Keji Zhao. A mechanistic link between such histone modifications and splicing was explained by Reini Luco of Tom Misteli’s lab. Furthermore, it is not only the chromatin and splicing fields that were united at this meeting. Alternative splicing regulated by noncoding RNAs was also discussed by Eneritz Agirre and Mariano Allo. Again, progression was furthered by the analysis of a public RNA-seq dataset from the lab of Chris Burge. In addition, more ChIP-seq and RNA-seq datasets were presented at the meeting – mining such a wealth of data will only further our understanding of transcript regulation.

Posted by Hannah Stower at 17:59    Comments (0)

 

"Food Pyramid" may require change

In the US, the “Food Pyramid” guidelines, which outline nutritional recommendations to the public, are reviewed on a five year basis. However, this model, adopted by the Dietary Guidelines Advisory Committee, is believed by some scientists to be contributing to the widespread obesity of the nation.

Dr Richard Feinman, founder of Nutrition& Metabolism, appeared on Fox News recently to offer his comments on the shortcomings of the pyramid and the difficulty in trying to overcome them. He describes an outdated and “one size fits all” model that doesn’t cater for individual requirements and fails to incorporate scientific findings. Using the metabolism of saturated fat as an example, he explains that the role of diet is traditionally misrepresented and highlights the importance of mechanisms such as these being properly understood by the public.

When asked his opinion on why information seems to be withheld, Dr Feinman surmises that “it’s very difficult to get such a big structure to move”, even for members of the committee who have genuine concerns, because of the substantial backing the pyramid receives from respected health bodies such as the NIH, American Diabetes Association and private health organizations.

To hear more about Dr Feinman’s perspective on the “Food Pyramid” and the issues surrounding these guidelines, please listen to the Fox News interview.

Posted by Sally Robertson at 16:57    Comments (0)

 

BioPsychoSocial Medicine announce Ikemi Award winner

Every year, BioPsychoSocial Medicine and the Japanese Society of Psychosomatic Medicine present the Ikemi Award in recognition of outstanding research in the field of psychosomatic medicine.

This year, at the 51^st Annual meeting of the Japanese Society of Psychosomatic Medicine, the Ikemi Award was presented to Takehiro Nozaki, M.D., Ph.D. (Kyushu University) for his work on the relation between psychosocial variables and type 2 diabetes. 

The Ikemi award was first introduced in 2002 and is named after the late Dr. Yujiro Ikemi, the first professor of the Department of Psychosomatic Medicine of Kyushu University and leading scientist in the field.

Posted by Srimathy Sriskantharajah at 08:39    Comments (0)

 

Non-productive transcription in yeast

Studies measuring mRNA abundance, such as those using microarrays, have often been used as a proxy for transcriptional control of gene expression. However, the quantity of a given mRNA at any time is a balance between its production and degradation. In an article recently published in Genome Biology, Oliver Rando and colleagues at the University of Massachusetts have shown that mRNA abundance does not always correlate with the quantity of RNA polymerase on a gene, and thus mRNA abundance is not always a good indicator of transcriptional activity.

Rando and colleagues exposed yeast cells to two different stresses. They then measured mRNA abundance using microarrays and PolII localization using chromatin immunoprecipitation. In general, PolII abundance did explain mRNA abundance, but there were genes which showed an excess or dearth of mRNA per PolII molecule. Interestingly, in many cases those genes were also those showing non-productive transcription - transcription of non-coding genes overlapping the coding genes. Rando concludes that genes not involved in normal growth show non-productive transcription, but that when the cells are stressed the polymerase shifts to the 5' end of the genes to transcribe as they are needed.

Thus, not only has this study shed light on how mRNA levels correlate with PolII activity, it has also revealed a potential new way to regulated gene expression via non-productive transcription.

Posted by Andrew Cosgrove at 10:12    Comments (0)

 

Does steroid use lead to aggressive tendencies?

The recent shootings carried out by fugitive Raoul Moat in Northumbria, UK highlight the growing belief that steroid use may be linked to aggressive outbursts. With some 250,000 people using steroids in the UK alone, how likely is it that they pose a threat to society?

The media have reported that Moat was addicted to the effects of steroids, particularly for body building purposes. But how large a part did they play in provoking his angry and jealous outbursts (a state dubbed as “roid rage”) and to what extent could they have catalyzed an altered emotional state tailored towards such extreme "vengeance"?

Several articles explore this purported link and may shed light on Moat’s own claims of the damage done by broken homes and disturbing thoughts:

In 2007, Substance Abuse Treatment, Prevention and Policy (SATPP), reported a study of 34 anabolic steroid (AS) abusers which explored the link between steroid addiction and social background/current situation with the conclusion that AS users are often from disadvantaged family backgrounds and that they also live their adult lives in difficult social situations.

In a later article, SATPP reported on six cases of individuals who believed they were experiencing steroid related problems. Mood swings, psychological problems, extreme jealousy and even inflicton of animal cruelty are reported as negative side effects across these six interviews.

For general information on the different physical mechanisms and effects of performance enhancing drugs in amateur and professional adolescents, please read Alan Rogol's review article published in Italian Journal of Pediatrics.

The ergogenic effects of steroids are not only highly desirable to competitive body builders, but also appeal to non-athletes interested in potential cosmetic enhancement. Yet, the disturbing evidence is that significant psychiatric symptoms may well manifest in long term users, justifying current apprehension levels.

Posted by Sally Robertson at 13:35    Comments (0)

 

Foetal testosterone linked to autistic traits in toddlers

Recent reports have confirmed a genetic basis for autism, with new evidence suggesting that autistic traits may be caused by genetic errors first introduced during the formation of the egg and sperm. But autism is a complex disorder. In an article recently published in Molecular Autism, Simon Baron-Cohen and colleagues remind us that many other factors can influence the development of autism, even before birth.

Foetal testosterone and autistic traits in 18 to 24-month-old children
Bonnie Auyeung, Kevin Taylor, Gerald Hackett, Simon Baron-Cohen
Molecular Autism 2010, 1:11

Pre-natal testosterone has been linked to cognitive sex differences, and recent studies have revealed a positive correlation between foetal testosterone and autistic traits in 6 to 10 year old children. In their research, Baron-Cohen and colleagues demonstrate that foetal testosterone levels are also a significant predictor of autistic traits in 18 to 24 month old children.

A consistently positive correlation between levels of foetal testosterone and autistic traits in different age ranges suggests a robust association, and highlights the need for further studies into the genetic factors involved. Further work aimed at identifying the underlying sources of variation in autistic traits will, ultimately, contribute to a greater understanding of the complexities of autism recently highlighted by Martin Raff in BMC Biology.

Jenny Withers
Assistant Journal Development Editor

Posted by Victoria Thompson at 17:49    Comments (0)

 

Guidelines needed for clinical trial management - not just reporting

As demonstrated by the response to the publication of the updated CONSORT statement earlier this year, the need for standardized approaches to the conduct and reporting of randomized controlled trials is widely accepted by the clinical research community.This week in Trials, Barbara Farrell and colleagues argue the case for adopting a similar approach to clinical trial management.

Managing clinical trials
Barbara Farrell, Sara Kenyon, Haleema Shakur
Trials 2010, 11:78 (13 July 2010)

Recent research has identified effective management as an essential element in the successful completion of clinical trials, not least in terms of meeting recruitment targets. In spite of evidence to suggest that poor trial management can result in failure - wasting valuable time and resources - there is an apparent lack of published reference material for trial managers.

Farrell and colleagues are keen to see this rectified through a collaborative effort from investigators, trial managers and funders to produce standardized, enforceable guidelines for the management of clinical trials. Moreover, it may be time for greater recognition of trial managers for their role in generating the evidence on which clinicians and policy makers rely.

Posted by Victoria Thompson at 16:26    Comments (0)

 

The fight against crop pathogens

Oomycetes are single celled pathogens of plants; the most widely-known representative of this class is the potato blight pathogen, Phytophthora infestans, which was responsible for the Irish potato famine in the 18th century.

In this issue of Genome Biology, C. Robin Buell and colleagues present the genome and transcriptome of the related plant pathogenic oomycete, Pythium ultimum - a blight pathogen of many ornamental and crop species that is less host-specific than some of its oomycete cousins.

Buell and colleagues compared the genome and transcriptome sequence of P. ultimum with that of P. infestans, the genome sequence of which was recently published in Nature and highlighted in Genome Biology here. Buell and colleagues found that the P. ultimum genome has a very different repertoire of genes involved in pathogenicity compared with P. infestans, including very few Crinkler (cytoplasmic effector proteins) protein-encoding genes, which are abundant in related oomycetes and previously thought to be essential for pathogenicity.

The genome sequence of P. ultimum will increase our understanding of the mechanisms of pathogeniticty in this agriculturally important family of crop pathogens.

You can read the article by  Buell and colleagues here.

Posted by Elisabeth Gaskell at 16:06    Comments (0)

 

Conference bursaries enhance malaria mission

BioMed Central is offering a fund to help researchers in developing countries attend the conference, Parasite to Prevention. The conference, held in conjunction with Malaria Journal, takes place in Edinburgh, 20-22 October.

Researchers and graduate students from low-income and lower-middle income countries can apply for a conference bursary to cover the cost of their travel, accommodation and conference registration. Places are strictly limited. The scientific committee will award the conference bursaries based solely on the quality of the abstracts submitted.

The deadline to submit an abstract and apply for a bursary place is 6 August 2010.

This international conference brings together leading researchers and industry representatives who will review important recent findings in parasite and vector biology, disease pathophysiology and immunology, disease treatment, prevention and control. Attendees will learn about the latest developments in key areas and initiatives that are at the forefront of malaria research.

More speakers have now been confirmed for the conference, including Carol Sibley (University of Washington), Andrew Waters (Leiden University) and Tim Wells (Medicines for Malaria Venture).

David Brandling-Bennett, Senior Program Manager at the Bill and Melinda Gates Foundation will give a keynote address at the conference gala dinner on Thursday, 21 October.

Anyone not from low-income and lower-middle income countries, can still submit an abstract for consideration if you register before 6 August 2010.

Posted by Charlotte Webber at 10:37    Comments (0)

 

First articles published in EvoDevo!

 

 

 

BioMed Central launches a new open access journal today - EvoDevo. The journal will publish articles providing novel insights into the translation of genotype to phenotype in a phylogenetic context, and promote understanding of the pattern and process of morphological evolution. EvoDevo boasts an impressive international Editorial Board composed of experts in the field of evolutionary developmental biology (evo-devo). 

In their inaugural editorial, Editors-in-Chief Mark Martindale and Max Telford discuss the importance of the publishing niche that the journal will fill.

“It is an exciting time to be an evolutionary developmental biologist and I am thrilled to be involved in promoting a transdisciplinary approach to understanding the two greatest mysteries of life: how functional organisms arise through their own developmental process, and how this process changes over evolutionary time to give rise to novel forms,” says Mark Martindale. Max Telford adds, “Exciting new opportunities for understanding the patterns and processes of organismal evolution are coming thick and fast from the diverse fields that characterise evo-devo”.

Also published today, Michael Boyle and Elaine Seaver demonstrate how FoxA and GATA456 transcription factors are part of an ancient patterning mechanism that was deployed during early evolution of the metazoan through-gut. In addition, John Finnerty and colleagues report the first evidence for a PRD-class homeobox cluster that appears to have been conserved since the time of the cnidarian-bilaterian ancestor, and Ralf Janssen and Graham Budd present findings suggesting conserved mechanisms of Hox gene regulation across arthropods.

If you are attending the European Society for Evolutionary Developmental Biology meeting in Paris starting tomorrow, please look out for our postcards and copies of the inaugural editorial on the BioMed Central stand. 

For more details on the journal and its articles please visit the journal website, or to find out how to submit a manuscript to the journal please see our instructions for authors.

Posted by Emma Pettengale at 16:08    Comments (2)

 

Population Health Metrics publishes new thematic series highlighting improvements in mortality statistics

   

Accurate mortality statistics are fundamental to help guide priorities in public health policy, planning, and resource allocation. Reliable information on levels of mortality and leading causes of death enables decision-makers to strategically design, fund, and implement programs to ensure the greatest possible impact on longevity and quality of life.

The thematic series, “Measuring mortality in Thailand”, published by Population Health Metrics, describes methods and results from what may be the largest-ever national investigation into the validity and quality of cause-of-death statistics in a developing country, using extensive field studies in Thailand to develop reliable estimates of mortality by age, sex, and cause. A commentary by Peter Byass discusses the four research papers by Rao and colleagues and considers methodological assessments and public health implications. The research papers relate to a detailed investigation of cause-specific mortality in Thailand during 2005, integrating a number of different data sources, including empirical investigations, death certification, and the use of verbal autopsy methods.

The research published in this thematic series could serve as a model for additional investigations into the quality of mortality statistics in other developing countries. The series Editor, Dr. Emmanuela Gakidou, is an Associate Editor for Population Health Metrics.

Population Health Metrics is ready to receive manuscripts on all aspects of the measurement of health at the population level.

Posted by Blog Maintenance at 11:58    Comments (0)

 

Marking 30 years of critical care medicine

The International Symposium on Intensive Care and Emergency Medicine (ISICEM) is celebrating its 30th anniversary in 2010, and to acknowledge this milestone Critical Care has published a related viewpoint article by Editor-in-Chief Professor Jean-Louis Vincent, ISICEM chairman.

This article, co-written by several members of Critical Care’s Editorial Board, is an account of the last 30 years in the field of critical and intensive care medicine. As well as discussing the advances made in specific areas such as sepsis, respiratory failure and cardiovascular disease, the authors are very honest in disclosing that, overall, there have been few major developments in new therapies for intensive care patients. Despite this, notable advances in the process of care and thus patient outcomes are also described.

Looking ahead to the next 30 years the authors speculate that improved communication between research scientists and ICU physicians, better models to test the effect of complex interventions, and improvements to critical care in developing nations will be seen. We congratulate the organisers of ISICEM on this anniversary, and look forward to reporting on the next exciting developments in the field.

Viewpoint articles require a subscription to access. If you are not a subscriber you may sign-up for a free 30-day trial.

Posted by Surayya Johar at 09:44    Comments (0)

 

Breast Cancer Research now the leading breast cancer-specific oncology journal

The release of the 2009 Impact Factors has seen Breast Cancer Research become the top-ranked breast cancer-specific oncology journal with an Impact Factor of 5.33, and means that of 165 oncology journals, Breast Cancer Research is ranked 21st overall.

This move represents a significant milestone for the journal, which was launched in 1999, and is a reflection of the hard work of the international Editorial Board, led by Editor-in-Chief Professor Lewis Chodosh, University of Pennsylvania, USA. Breast Cancer Research, launched as a forum for translational research, has constantly evolved in order to reflect the changes in the field. Our scope has also expanded in this time to include articles of exceptional interest in all areas of biology and medicine relevant to breast cancer, including normal mammary gland biology, with a special emphasis on the genetic, biochemical, and cellular basis of breast cancer.

Posted by Surayya Johar at 11:38    Comments (0)

 

Visit BioMed Central at ISMB 2010

 Conference activities include:

Posted by Sara Eve at 16:52    Comments (0)

 

Elucidating genetic susceptibility to lupus – credit where credit’s due

“We have way more data than we can possibly analyse”, said Arthritis Research & Therapy Editorial Board member Prof Edward Wakeland, in concluding his keynote address to the 9th International Congress on Systemic Lupus Erythematosus in Vancouver.

The Wakeland Laboratory are generating data that should help elucidate the genetic basis for human susceptibility to lupus. They aim to sequence the genome of 600 patients with systemic lupus erythematosus (SLE) – a disease thought to affect more than 250,000 US citizens  – in the next 16 months. They have sequenced 107 patients so far and are on track to achieve their goal, facilitated by modern ‘deep sequencing’ technology. Control data for the project are being provided by the 1000 Genomes Project.

But generating terabytes of sequence data is just the beginning.  Prof Wakeland explained that there are 89 genomic segments of potential interest but this is more than one lab is able to analyse, and on the second day of the congress he offered the data out to the community to collaborate with his group.

The web-based interface by which the Wakeland lab will make its data available to collaborators is not yet completed, but the proposal seems to be another example of genomic researchers being ahead of the curve in scientific data sharing.

Indeed, collaboration on – and driving – future research is one of the many benefits of openly sharing research data, and the potential for collaboration with large genomic datasets is vast. And where researchers must publish or perish, offering co-authorship on articles to collaborators might seem logical. However, by contributing data alone researchers will not meet the authorship criteria of the ICMJE, which are endorsed by many journals including BioMed Central’s. Moreover, researchers might not want to endorse the findings of every article resulting from their data.

So is it time for a rethink? Authorship criteria offer protection as well as a means of giving academic credit, so ambitious projects such as the Wakeland group’s instead add to the urgent need for data sharing to be recognised by academic institutions and the broader scientific community, particularly as plans for sharing data are increasingly a requirement of research funding agencies, such as the NIH and Wellcome Trust.

Prof Wakeland explained that his group have had a policy for sharing data from the outset. “All of the sequencing data was generated in my laboratory, using samples predominantly obtained from the OMRF. The size of the data set is mammoth already and we are unable to analyze all of the gene segments that are available,” he said.

Posted by Iain Hrynaszkiewicz at 13:01    Comments (0)