BioMed Central Blog

First articles published in Genome Integrity

Genome Integrity, a new open access journal launched with BioMed Central, published its first articles today. The journal publishes research on all aspects of genome integrity, the cellular processes underlying maintenance of genome stability, and the effects of instability.

In their introductory editorial ‘Genome Integrity – a new open access journal’ Editors-in-Chief Predrag Slijepcevic, Prakash Hande, John Petrini, and Razqallah Hakem discuss the important publishing niche that the journal will fill in the field of DNA damage response and the associated cellular processes behind genome stability maintenance.

“We strongly believe that this new journal will significantly contribute to the understanding of DNA damage response processes” say the Editors-in-Chief.  

One of the articles published today with Genome Integrity by Professor Keiji Suzuki et al researches the role of ATM activity in DNA damage checkpoints, and another article by Dr Alireza Senejani and Professor Joann Sweasy discusses the incidence of a novel DNA sequence found within a mouse genomic fragment inserted into a plasmid vector.

For more details on the journal and its articles please visit the journal website. For information on submitting to the journal please see our instructions for authors.

Posted by Genevieve Horne at 12:51    Comments (0)

New thematic series to celebrate 2010 International Year of Biodiversity

To celebrate 2010 as the United Nations’ International Year of Biodiversity and the importance of sharing our knowledge of the diversity of the natural world, we present a cross-journal thematic series on Open Access Biodiversity Research.

The rich diversity of life is essential to our presence on the earth and yet it is at risk of decreasing at an accelerated rate due to human activities. The action of the United Nations, in highlighting biodiversity during 2010, is an important chance to increase our understanding of the vital function of biodiversity and a prompt to act now to reduce its loss. To celebrate this initiative, we feature leading research from different disciplines that share common goals in conserving biodiversity.

A recent article published in BMC Ecology by Dr Axel Strauss and colleagues discusses the incidence of functional redundancy in tadpole communities in the species-rich streams in Madagascar, and how this is connected to the accumulation of new traits. Using a very different approach, Dr Clementine Pradal et al, also writing in BMC Ecology, employ a mathematical model to describe the temporal dynamics of an Arctic plant-pollinator network and how climate change could affect these delicate systems. The series also features articles from BMC Biology, BMC Evolutionary Biology, BMC Microbiology and Frontiers in Zoology.

For more information and to read further articles in this series please visit the series webpage.

Posted by Genevieve Horne at 10:46    Comments (0)

Molecular classification for biliary atresia

A molecular signature for biliary atresia classifies samples into inflammation or fibrosis stages at diagnosis and will be valuable for personalized clinical management of this disease, according to research recently published in Genome Medicine.

Biliary atresia is a blockage or absence of the bile duct usually diagnosed soon after birth.  The cause of this condition is not well understood, but the management of the resulting liver fibrosis is well-studied due to its importance for prognosis.  In their study 'Staging of biliary atresia at diagnosis by molecular profiling of the liver', Jorge Bezerra and colleagues asked whether liver gene expression levels at diagnosis could be used to predict disease severity, the response to surgical reconstruction of the bile duct (portoenterostomy), and survival at 2 years of age.  

Differential profiling of liver biopsies showed that a unique molecular signature was associated with each of the histological features of inflammation and fibrosis, and that this signature could be used to classify otherwise ambiguous biopsies into one of the two groups. This signature may relate to the stage of disease at the time of diagnosis, and infants classified with the fibrosis signature (possibly indicating a more advanced stage of disease) had decreased transplant-free survival.  This information may be valuable for clinical management and personalised therapy for this rare congenital condition.

Posted by Rebecca Furlong at 09:59    Comments (0)

BioMed Central launches Japan Gateway

BioMed Central has recently launched a Japan Gateway, bringing together resources and information from researchers across Japan as well as highlighting high-impact research from the region.

The Japan Gateway also hosts a new brochure (available in both Japanese and English), which demonstrates the benefits of publishing in open access journals. Profiles of highly respected scientists who have chosen to publish with us, including Masahiro Fujii and Yoshihide Hayashizaki, are also featured. The gateway also provides details of our journals with affiliations to Japanese societies:

• BioPsychoSocial Medicine, the official journal of the Japanese Society of Psychosomatic Medicine
• Sports Medicine, Arthroscopy, Rehabilitation, Therapy & Technology, the official journal of the Japanese Orthopaedic Society for of Knee, Arthroscopy and Sports Medicine

Using Springer’s innovative AuthorMapper, the Japan Gateway is also able to visually map the locations of BioMed Central authors from Japan and those-co-authoring with Japanese authors.

Pay a visit to the new Japan Gateway now to see the wide variety of resources available for scientists and clinicians in Japan.

Posted by Charlotte Hubbard at 03:34    Comments (0)

The real difference between me and you: a map of structural variation in the human genome

As we have been told many times since the publication of the human genome, the age of personal genomics is upon us. However, the vast difference between one human genome and the next, in the form of single nucleotide polymorphisms (SNPs) or other structural variations, is only just becoming apparent with the sequencing of more personal genomes.

In this month’s issue of Genome Biology, Steven Scherer and colleagues present a new map of the structural variation in the human genome.

This map presents more detail on structural variations, such as copy number variations (CNVs), insertions and deletions (indels), inversions and SNPs than ever before. The authors detected over 12,000 structural variants, impacting nearly 5,000 genes, that were not detected in the first published genome sequence of a personal human genome, that of J. Craig Venter. The authors highlight that up to 2% of our genome may differ from that of our neighbours and that SNPs alone only account for 0.1% of this variation.

This resource will provide an essential template for analysis of structural variation in future personal genomes.

Read about this exciting advance here.

Posted by Elisabeth Gaskell at 16:50    Comments (0)

Sequence periodicity discovered in human genome

In an article just published in Genome Biology, Charles Hebert and Hugues Roest Crollius of the Ecole Normale Supérieure in Paris have shown the existence of a novel periodicity of nucleotide frequencies in the human genome that may have implications for the positioning of nucleosomes and gene regulation.

In their study, Hebert and Roest Crollius have aligned human genes relative to their transcription start sites and observe a pattern of YY dinucleotides (where Y is either C or T) spaced 10 base pairs apart in phase with the transcription start site. Importantly, analysis of nucleosome-positioning data shows that the nucleosomes are associated with the dinucleotides. The pattern is enriched in genes with binding sites for the EP300 nucleosome-modelling protein. The authors speculate that the repeating pattern may help to position the nucleosomes in such a way that they are easily modified by EP300, thus facilitating their displacement by RNA polymerase, although this model is currently speculative and will require confirmation in future work.

Nevertheless, this work presents an exciting new pattern in the human genome, and has implications for how positioned nucleosomes affect the transcription of genes.

Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes

Charles Hebert and Hugues Roest Crollius, Genome Biology 2010, 11:R51

http://genomebiology.com/2010/11/5/R51 

Posted by Andrew Cosgrove at 12:27    Comments (2)

Diagnosing Alzheimer's disease - how good is neuropathology?

Advances in clinical diagnostics, such as neuroimaging, as well as the development of new biomarkers, have raised questions as to whether neuropathological assessment is both accurate and specific enough to diagnose Alzheimer's disease (AD).  Two articles published last week in Alzheimer's Research & Therapy address this issue and make up a pro/con debate discussing whether neuropathology can confirm the exact diagnosis of AD.

Arguing the case for, Margaret Esiri stresses that neuropathology is still the gold standard by which to reach a reliable diagnosis of AD and suggests that because diseases change and evolve over time, only this tool is in a position to provide a concrete distinction between pathological processes.  Esiri acknowledges that novel clinical diagnostics will have a part to play in the future, but that until our understanding of AD improves neuropathology still has a future in elucidating the molecular and cellular mechanisms involved.

In his counter viewpoint, Kurt Jellinger argues that although neuropathology has provided us with a large amount of data on the pathogenesis and pathophysiology of AD, there are a number of drawbacks associated with it (such as a quantitative nature and the existence of co-existing confounding processes in aged brains) and we should increasingly be focusing on using harmonised techniques to improve the accuracy and reproducibility of AD diagnosis.  Only this, he stresses, will allow us to devise successful neuroprotective and treatment strategies for the future.

Alex Kroll - Senior Assistant Editor, Alzheimer's Research & Therapy

Posted by Frances Mulvany at 09:38    Comments (0)

Trials publishes first extended protocol

Yesterday, Trials published a substantially extended version of Zinkstok and colleagues' protocol for a randomized controlled trial of a new combination therapy for ischemic stoke, which was originally published in Cerebrovascular Diseases. In this extended protocol, the authors expand upon key methodological elements of their study, giving full details of enrollment procedures, outcome measures and planned statistical analyses as well as providing example data collection forms as additional files.

A randomised controlled trial of antiplatelet therapy in combination with Rt-PA thrombolysis in ischemic stroke: rationale and design of the ARTIS-Trial
S M Zinkstok, M Vermeulen, J Stam, R J de Haan, Y B Roos, Artis Study group
Trials 2010, 11:51 (12 May 2010)

Transparency and completeness in published protocols helps to maintain an accurate record of clinical trials that have been undertaken and allows for the critical evaluation of published results papers. Similarly, complete disclosure of trial results in line with reporting guidelines is essential if we are to prevent bias in the scientific literature. As part of our commitment to improving the performance and reporting of clinical trials - and given that the space available for publication in the journal is almost limitless - Trials actively encourages the submission of extended protocols and expanded reports of completed trials, provided that they make a significant additional contribution to the scientific record.

Posted by Victoria Thompson at 08:48    Comments (0)

On its 10th anniversary Ensembl publishes a thematic series with the BMC-series

The last 15 years has seen an explosion in genomic research and sequenced genomes. With the build up to sequencing larger chordate genomes it became very clear that manually annotating the billion base pairs of sequence produced was not practical and automated annotation systems were required. Several large organisations have helped address this issue, but the Ensembl project, a joint venture between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, has in particular provided high-quality integrated annotation on vertebrate genomes within a consistent and open source infrastructure. This year marks the 10^th anniversary of the Ensembl project’s launch, and BioMed Central is today publishing a thematic series of articles describing the construction, content and current use of Ensembl's resources.

The first six articles published today in BMC Bioinformatics and BMC Genomics, co-ordinated by Paul Flicek at Ensembl and the European Bioinformatics Institute, reveal in detail how many of the comparative genomics, variation and regulatory data resources have been constructed. The first article describes the comprehensive web-based functions available for tabulating and visualizing genome variants. A second related article discusses the database and software library supporting the integration of variation data into the existing Ensembl resources.

To be able to keep up with the ever increasing number of genomes reported (51 in the last release), Ensembl has had to use automated workflow systems. Jessica Severin and colleagues present an artificial intelligence pipeline ‘eHIVE’, based on a self-organizing workflow system akin to the behavior of honey bees, to provide updates to its comparative genomics resources. Benoît Ballester and colleagues also demonstrate how the Ensembl microarray annotation protocol handles the release of the latest commercial arrays. To keep a pace with both the increasing demands of users and the terabytes of data now available from the website, Anne Parker and colleagues show how they use caching and optimization techniques alongside Web 2.0 technologies to improve the performance of the Ensembl website.

A final article by Giulietta Spudich and Xosé Fernández-Suárez uses several examples to offer a practical guide for using Ensembl to learn about genomic annotations in regions of interest.

While most of this detailed “behind the scenes” information will not significantly alter the way users access genomic data, it guides molecular biologists to the full range of tools available to them. It will also be of great value to researchers building other bioinformatics applications, and demonstrates how Ensembl is constantly adapting and updating their tools to be able to prepare for its next decade.

Scott Edmunds

Senior Scientific Editor, BMC Series journals

Posted by Scott Edmunds at 16:26    Comments (0)

Canine vector-borne diseases – a new thematic series

Parasites & Vectors has published a thematic series grouping together a number of articles recently presented at a symposium on canine vector-borne diseases (CVBDs) in New York in April 2010.

 The aim of the 5th Symposium on Canine Vector-Borne Diseases, sponsored by Bayer Animal Health GmbH, was to facilitate the advancement of understanding in the diversity and prevalence of canine vector-borne diseases, and their significance for veterinary and public health.

 The articles address a number of such diseases, looking at the biological interactions between ectoparasite, pathogen and host, as well as their distribution across the globe. Contributions to the thematic series, edited by Chris Arme, include original research articles, alongside several reviews and short reports.

 If you are interested in publishing articles or proceedings from a conference in a BioMed Central journal, either as a thematic series or journal supplement, please contact journals@biomedcentral.com for further information.

Posted by Srimathy Sriskantharajah at 09:30    Comments (0)

Transcriptional control in flies

In a paper recently published in Genome Biology, Boris Adryan (Cambridge University) and Sarah Teichmann (LMB) have presented evidence that calls in to question currently-held beliefs about how transcription factors (TFs) coordinate gene expression during development to specify the fates of the different tissues in the body.

It has been assumed that transcription factors are expressed in the manner of a cascade, with one TF turning on the expression of others resulting in groups of TFs acting in a cooperative manner to specify cell fate. In this study, Adryan and Teichmann have analysed gene expression data from Drosophila melanogaster development to investigate when every transcription factor is expressed. 95% of TFs were expressed at some time during embryonic development.

Perhaps the most important finding of the study is the combinatorial complexity of TF expression.  The vast majority of the 69,500 possible combinations of pairs of TFs are expressed in at least one tissue at one time. Thus, the co-expression of TFs is extremely plastic.  Rather than having tissue-specific TFs dictating the cell fate in different organs, what actually appears to happen is that the specific combination of TFs at a given point is what determines the cells' fates, with different combinations of the same set of TFs determining different tissue types.

You can read Uwe Ohler’s commentary on the paper, also in Genome Biology, here

Posted by Andrew Cosgrove at 17:56    Comments (0)

Novel format for gene variant reporting

The Locus Reference Genomic (LRG) sequence format, recently reported in Genome Medicine, allows a single fixed record containing a reference DNA sequence and all relevant transcripts and protein sequences to be associated with an updateable layer of gene variant coordinates, which should reduce errors in reporting and lead to improved communication about genomic variants.

Nature Genetics this month stated that the LRG agreement has provided a platform which allows the editors to adjust journal policy, mandating the use of Human Genome Variation Society (HGVS) allele naming conventions in manuscripts submitted to Nature Genetics.

Dalgleish and colleagues propose that variants associated with human genetic disease can be documented using this format, which was designed for the specific purpose of gene variant reporting and which builds upon the NCBI RefSeqGene project.  LRG records will have long-term stability, being created and maintained by the NCBI and the EBI, as well as flexibility, which will allow their use as an up-to-date reference for clinical genetic tests even as more disease variants are discovered. 

Posted by Rebecca Furlong at 15:27    Comments (0)

Bona fide ancient DNA sequence from Neandertal bone

An article published in Genome Biology assesses the pitfalls of sequencing ancient DNA and presents a new approach for improved identification of ancient DNA sequences.

The DNA sequence of extinct species are of enormous value in determining evolutionary relationships to living species. However, ancient DNA from fossil is notoriously difficult to sequence due to the presence of bacterial contamination and DNA damage. Kay Prüfer and colleagues at the Max-Planck Institute for Evolutionary Anthropology investigated the biases inherent in short read sequencing of ancient DNA samples with an analysis of Neandertal (Homo neanderthalensis) DNA, generated as part of the Neandertal genome project, from 38,000-year-old fossil bone. The full draft Neandertal genome sequence is published today in Science by the Neandertal Genome Analysis Consortium.

To identify the endogenous Neandertal sequence from the contaminating bacterial sequences Prüfer and colleagues perform pairwise comparisons of the sequence data to the genomes of  closely related living primate and mammalian species. The authors discuss other ancient extinct species to which their approach for ancient DNA shotgun sequencing could be applied, such as mammoth, cave bear, sabre tooth cat and  ground sloth. It could also be used to study living species when no reference genome sequence is available.

Read the Prüfer and colleagues method here in Genome Biology.

Posted by Emma Ralph at 12:20    Comments (0)

Introducing the Open Data Award

In recognition of the fact that science publishing now goes beyond the traditional journal article, we have teamed up with Microsoft Research and Panton Principles to introduce the Open Data Award as part of our 4th Annual Research Awards. Data sharing, its preservation and re-use, is an increasingly important part of the research and publication process. But there are many challenges associated with openly sharing scientific data, particularly when sharing goes against cultural or community norms. 

The Open Data Award celebrates researchers who have published in any of our 207 journals during 2009 and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data.

We are honoured that Peter Murray-Rust, Cameron Neylon, Rufus Pollock and John Wilbanks of Panton Principles, along with Lee Dirks of Microsoft Research, have agreed to judge the awards along with our in-house Editor, Iain Hrynaszkiewicz, Managing Editor of our special medical journals.

The shortlist will be announced in the coming weeks and the winner will be revealed at the awards ceremony on Thursday, 10 June in London.

Posted by Charlotte Webber at 11:50    Comments (0)

Macha online - a guest post from Computer Aid

Computer Aid International's Stephen Campbell visited the community of Macha to see the impact of the Internet and the research it enables, on an African community.

You won't find the community of Macha on many maps. It's 50 miles from the nearest road in the Southern Province of Zambia, itself a land-locked southern African country - it's pretty much the last place you'd expect to find a community logged on to the Internet.
 
Taking advantage of a satellite link installed by John Hopkins University Malaria Research Institute, the LinkNet Cooperative (formed three years ago by the community and staffed by talented self-taught local youngsters, none of whom have graduated beyond grade 12) has established the largest wireless Mesh Network in Sub-Saharan Africa.
 
Wireless routers, similar to those used in homes in the UK, are used to spread a single internet connection across a wide area. This lowers costs enough to make internet connectivity affordable for homes, small businesses, schools and the local hospital and nurse training college.

By researching crop types, local farmers have already diversified  - many have substituted part of their maize crop (a staple subsistence crop) with sunflower oil which generates vital cash in the local market. A small cash income for a family there sends children to school and can cover medical expenses for ill family members.

Doctors and nurses at the local hospital can seek advice on treating patients from specialists in the capital. Screening for malaria has improved thanks to the John Hopkins link and rates of malaria have dropped by 90%. Local people are using the internet for research to establish businesses whilst transaction costs for basic goods have reduced considerably.

The community has moved from net migration to cities, to net immigration from surrounding areas as income, healthcare, employment and small enterprise opportunities have increased beyond all recognition. Perhaps the biggest development, again driven by Internet-based research is the development of a bio-fuel, Jatropha, from scrub land on the edge of town. A fully-grown Jatropha tree can generate 1.5 kilos of fruit per year in this climate and, crucially, the crop times are compatible with the maize growing season - providing 400 farmers with a cash income initially and, longer term, a ready supply of fuel. The community expects to be self-sufficient in fuel inside three years.
 
There are thousands of communities like Macha across sub-Saharan Africa. Macha proves that access to information is the critical first ingredient in helping local communities to help themselves. We're proud to have the support of BioMed Central to help more and more projects like this.
 

Posted by Charlotte Webber at 13:03    Comments (0)