BioMed Central Blog
New method for DNA breakpoint detection
Many diseases, including some cancers, are associated with specific chromosomal trans-locations, and a technique reported in Genome Medicine provides a new way to detect these anomalies. The presence or absence of a translocation may have implications for diagnosis, prognosis, and therapy.
The BCR-ABL1 fusion gene is a marker of chronic myeloid leukaemia. Anindya Dutta and colleagues used BCR-ABL1 as a model to test their novel high-throughput technique for interrogation of a specific chromosomal region, which uses DNA capture and enrichment of the region of interest, followed by multiplexed paired-end sequencing. They were able to detect the BCR-ABL1 breakpoint to base-pair resolution in cell lines and clinical samples, and also showed that for formaldehyde-fixed cells and nucleic acids released from dying cells, the sensitivity was higher than that of an RNA biomarker. This technique, called Anchored ChromPET, has the potential to facilitate patient
management by identifying a specific translocation even
when the currently-used clinical methods cannot detect the chimeric RNA transcript.
Posted by Rebecca Furlong at 17:44 Comments (0)
Even low alcohol levels slow reactions in seniors
Recently reported research published in BMC Research Notes has quantified the effect of alcohol consumption on obstacle avoidance. The study demonstrates that even blood alcohol concentrations below accepted drink-driving limits – 0.08% in the UK but subject to some recent debate – significantly impact on the ability of senior individuals to avoid obstacles while walking.
Even low alcohol concentrations affect obstacle avoidance reactions in healthy senior individuals
Judith Hegeman, Vivian Weerdesteyn, Bart JF van den Bemt, Bart Nienhuis, Jacques van Limbeek, Jacques Duysens
BMC Research Notes 2010, 3:243 (23 September 2010)
Thirteen participants with an average age of 61.5 years completed an obstacle-avoidance task on a treadmill after consuming alcohol. Researchers measured the response time of the biceps femoris (the main muscle involved in obstacle avoidance) and found that blood alcohol concentrations of 0.035% upwards resulted in significantly slower response times.
Perhaps unsurprisingly, slower reactions were reflected in a reduced ability to avoid obstacles, leading the researchers to suggest that many alcohol-related falls are due to alcohol's disruptive effect on corrections to the ongoing gait pattern under challenging walking conditions. The conclusion? Even limited alcohol consumption considered safe for driving puts seniors at increased risk of falling.
Posted by Victoria Thompson at 16:32 Comments (0)
Blood pressure and self-monitoring: Is it necessary?
Over the counter medicine, publicly available diagnostic kits, readily available (mis)information on the internet about every sort of medical ailment and how to "cure it"; never has it been so easy for the lay person to try to take control of their own health. Whether this helps or hinders the trained physician is not always clear, however, one readily available health device that could make a difference is the home monitor for blood pressure.
Hypertension (high blood pressure) is the most important risk factor for cardiovascular disease, and lowering blood pressure has been 
shown to reduce this risk. Doctors use blood pressure measurements to help inform management of hypertension, and the methods used to measure blood pressure have changed very little in the last 100 years. In BMC Medicine this month, Paul Padfield discusses "The case for home monitoring in hypertension". As well as outlining some of the history surrounding blood pressure measurements, he describes the merits of the readily available self-monitoring devices, although he clearly cautions that they are not necessarily appropriate for use in all patients. In addition, there are currently few quality control measures in place to ensure that commercial products actually function at an acceptable level. However, taking into account these caveats, Padfield calls for doctors to become more familiar with this common technology and suggests how it can improve the management of this serious condition.
Visit the BMC Medicine website and check out the full commentary to read the insights Padfield has to offer with regard to this topic.
Posted by Robin Cassady-Cain at 13:53 Comments (1)
Article cover pages available in more BioMed Central journals
BioMed Central is extending the option of personal cover pages for the PDF of published articles to more of our journals. The covers, which will be offered at no extra cost to authors published in all BMC-series journals and many of our independent journals, will improve the presentation of printed articles.
At submission, authors will have the choice of uploading an image either from their article, or another relevant image, to be featured on the personal cover page. The cover page will also include the journal name and logo, article title and the authors’ names. An eye catching electron micrograph, or molecular model, will improve the presentation of printed articles, promote the journal and highlight the authors’ work. The personal covers also provide a great opportunity to get the journal name off the computer screen and on show, with authors able to use their cover page as a poster or flyer. Neural Development, a journal in the BioMed Central portfolio, already produces covers for its articles. A great example from Neural Development is pictured.
We hope that as authors embrace this improvement to article presentation, we’ll be seeing an array of intriguing images from across the scientific spectrum drawing attention to the equally intriguing content of our journals. Personal covers will be available for all BMC-series journals, and many independent journals, from the 1st of October.
Posted by Angela Wipperman at 11:07 Comments (1)
MIQE precis: with reference to reference genes
Genes
that maintain constant expression under
a variety of circumstances are known as ‘reference genes’. They are vital for
researchers who need to quantify gene expression changes in other genes
and need a ‘reference point’ against which to do so. BMC
Molecular Biology, has to date published around 200 reference gene-related
papers from researchers working in such diverse models as peaches,
sharks,
barnacles and glioblastoma to name but a few.
However, to be a true reference gene you
need to fulfil a certain list of criteria and the research field is now united
in requesting that all work be performed to the same accuracy and in accordance
with recommended guidelines. The Minimum Information for Publication of
Quantitative Real-Time PCR
Experiments (MIQE) guidelines were launched over a year ago by an international team of researchers. The aim
of these guidelines was to enable the benchmark technology for measuring gene
expression (quantitative PCR
[qPCR]) to become standardised when reported in research papers.
The MIQE guidelines advise on good assay design and appropriate data analyses
for nucleic acid detection and quantification. BioMed Central supports and
promotes initiatives aimed at improving the reporting of biomedical research,
and refers authors to the MIBBI Portal
(of which MIQE is part of) for reporting biological
and biomedical research. Whilst some authors have included MIQE checklists as
supplemental files with their work (for example here),
there has been some debate as to the utility and ease in doing this in all
cases.
After working with several Editorial Board Members from
BMC
Molecular Biology, we propose that all researchers wishing to publish qPCR
work do so by adhering to our simpler and more abridged 'light' guidelines – MIQE
précis. We also propose that the majority of
reference gene papers are no longer suitable for publication as ‘pure reference
gene papers’, but this information will need to be incorporated as part of a
larger study. Alternatively, authors may publish these more incremental (but
still potentially useful) pure reference gene articles in BMC Research Notes to
contribute to our topical series: “Quantitative Real Time PCR normalization and optimization”.
Incorrectly measuring qPCR does not just have consequences in basic science, as
its misuse in molecular diagnostics can have very serious consequences.
In 2002 Andrew Wakefield caused controversy when claiming that a form of
irritable bowel disease was triggered by the
measles virus.
The findings were subsequently shown to be incorrect,
owing to poor qPCR analysis. This emphasises the need for correct application
of a very common technique. The BMC series of journals requests that all
authors actively use the MIQE précis guidelines before submitting their manuscripts. We have also produced an easy-to-use
checklist that authors are encouraged to include as a supplementary file.
Improving the reproducibility of
biomedical research and making data available in readily interpretable formats is
vital to realising its value in driving new knowledge discovery, and this
scheme joins BioMed Central's many initiatives aimed at promoting best practice in sharing and publishing data.
Ann Le Good
Scott Edmunds
Senior Scientific Editors, BMC-Series journals
Posted by Scott Edmunds at 14:43 Comments (0)
EQUATOR: reporting your randomized trial
The EQUATOR Network seminar, ‘Reporting your randomized trial: CONSORT 2010 and other reporting guidelines’ provided an opportunity for those involved in randomized controlled trials – from planning to publishing – to learn more about the importance of transparent and accurate reporting. In addition, delegates were informed of the essential role of the EQUATOR Network, which aims to increase the value and reliability of the medical literature by promoting high-quality reporting.
Allison Hirst, Research Fellow for the EQUATOR Network, started proceedings at Oriel College, Oxford, with an introduction to EQUATOR and a virtual tour of the resources available at www.equator-network.org. In addition to an easy-to-use library of reporting guidelines for different study types, the EQUATOR website provides resources aimed at helping journal editors and peer reviewers to use and implement reporting guidelines, as well as information for those looking to develop new guidelines.
Doug Altman, Chair of the EQUATOR steering group and co-Editor-in-Chief of Trials, talked us through the need for good-quality reporting and the development of the CONSORT guidelines for reporting clinical trials. Using a series of examples, Professor Altman illustrated the difference between poor reporting and flawed methodology, and how the latter can often be hidden by the former. CONSORT for abstracts was introduced by Sally Hopewell, Senior Research Fellow for the CONSORT group. Highlighting the fact that some researchers’ access to peer-reviewed articles is limited to the abstract, Dr Hopewell also demonstrated that word limits need not be a hindrance to good abstract writing by preparing a real-life example in under 300 words.
To finish the afternoon, Emma Veitch, Senior Editor at PLoS Medicine, shared the journal’s experience of implementing the CONSORT guidelines. As well as reminding authors of the importance of adhering to relevant guidelines to facilitate review of their work, this presentation in particular was a timely reminder for editors of their role in helping to ensure complete and accurate reporting of clinical trials – a responsibility that journals like Trials are keen to meet through their support of EQUATOR and its aims.
Posted by Victoria Thompson at 12:04 Comments (0)
Open Access Week 2010 - spread the word!
Open Access Week 2010 is just around the corner. Taking place between 18th-24th Oct, this global event aims to open the public’s eyes to the benefits of open access in scholarly publishing and its impact on scientific progress across disciplines and society as a whole.
BioMed Central will join in the Open Access Week celebrations due to take place across the 69 countries now registered on the Ning network.
Scheduled events include: Maximize the impact of your research - a lecture meeting, celebrating the 3rd anniversary of Otaru University of Commerce Repository (Japan) and Putting the Wisconsin Idea Online at the University of Wisconsin (USA) a seminar on the boundary-spanning implications of the internet
Open Access Week organizers, SPARC, have also set a global challenge in the run up to the week, asking the research community to report on the power of open access. Upload your stories, videos, blog posts or more to the Open Access Week website and show the world how OA has helped you to advance your research.
If you want to participate, the Open Access Directory (OAD) will provide a comprehensive database of all events running throughout the week. Event organizers can enter their details directly and share them with others, in true open access spirit.
It is encouraging to see so many developing countries participating in Open Access Week this year. To help increase awareness of open access in low-income nations, BioMed Central is hosting a two-day conference in Kenya to coincide with a sponsored shipment of refurbished PCs to Kenyatta University.
As always we will be attending the Berlin 8 Conference next month to discuss progress strategies, best practices, and future challenges for open access.
Our mascot, Gulliver, the open access turtle will be kept busy as he travels with us to conferences and visits universities, libraries and labs all over the world in a bid to bring research out of its shell.
Posted by Charlotte Webber at 10:07 Comments (0)
BioMed Central vs Nature - the aftermath
On a slightly wet and windy Wednesday afternoon in London, 40+ BioMed Central and Nature Publishing Group employees converged on Regent's Canal to battle it out in a 10km run. Both teams did exceedingly well, with the majority of BioMed Central's 18 runners coming in in under an hour. Congratulations to our HR Manager, Tom Townsend, who won the race with a time of 44 minutes - impressive considering the many obstacles presented by the meandering course. Tom was quickly followed by our Managing Director, Matt Cockerill and OA mascot, Gulliver Turtle. Hannah Stower from the Genome Biology editorial team was the fastest of the female finishers in 47 minutes. Well done to all who participated, especially those who had done very little training!
Competition aside, our aim was to raise money for our partner charity, Computer Aid International, which distributes reconditioned computer equipment for educational use in developing countries. We’re thrilled to say that the run raised more than £1700 for the charity, giving a significant boost to our ongoing fundraising efforts. It's still not too late to make a contribution - you can show your support for BioMed Central open access team and for Computer Aid by donating online.
A big thank you also to our friends and rivals at Nature, who have blogged their own report on the run. We look forward to taking them on again next year.
We've also posted more photos from the event to our Facebook page.
Posted by Charlotte Webber at 18:17 Comments (0)
In partnership with Computer Aid International, BioMed Central will be hosting a two-day conference on open access publishing at Kenyatta University in Nairobi, Kenya, from 10-11 November 2010. Open access to the results of scientific and medical research has potential to play an important role in international development, and this conference will discuss the benefits of open access publishing in an African context, from the perspective of both readers seeking access to information, and researchers seeking to globally communicate the results of their work.
The conference will bring together researchers, librarians, university administrators and funders to discuss the issues surrounding access to scientific and medical research, and the role that open access journals can play. The program will include speakers from all sectors including academia, NGOs, industry and government bodies. The event will also feature break-out sessions to allow stakeholders to provide input on a variety of topics. A detailed program will be announced shortly.
There is no cost to attend the conference, but space is limited. To reserve your place, or to sign up to receive additional information, please email: events@biomedcentral.com
Posted by Charlotte Webber at 15:19 Comments (1)
Who is healthier? Take part in a survey to help improve global health policy decisions
The Institute for Health Metrics and Evaluation, which houses Population Health Metrics, has launched a new Health Measurement Survey. With unprecedented money and attention pouring into international health, the need for accurate data on global health patterns is a matter of utmost urgency. This research survey will measure the impact of different diseases and injuries and help researchers assign values to different health outcomes.
The survey is part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2010 led by the Institute for Health Metrics and Evaluation at the University of Washington, in collaboration with four other leading institutions: Harvard University, Johns Hopkins University, the University of Queensland, and the World Health Organization.
The survey will ask you to imagine different health outcomes and compare them to each other. For example: "Imagine two people – the first person is completely blind, and the second person suffers from constant intense back pain. Who is healthier overall?"
By participating in the survey, you will contribute to the scientific understanding of global health problems and ultimately enable policymakers and health care leaders to make better decisions based on stronger evidence. Your participation in this study is completely voluntary, and your responses will be anonymous.
The survey can be found here: http://gbdsurvey.org/ and summary survey results will be posted online at www.healthmetricsandevaluation.org upon completion of the study in 2011.
Posted by Kath Nolan at 14:18 Comments (0)
Biology Direct launches new online submission system
Biology Direct – which operates a novel scheme of open peer review – has launched a new online submission system to make submission to the journal considerably more straightforward.
The journal launched in 2006 as an experiment in open and published peer review; an “unapologetically ambitious” attempt to establish a new system of peer review which, by publishing the comments of the reviewer alongside their name, would reduce abuses in the peer-review process and stimulate productive scientific debate at the same time.
Manuscripts published in the journal appear alongside named reviews, with the authors given the option to provide a public rebuttal.
The introduction of a dedicated in-house team has considerably lessened the workload for authors wishing to submit a manuscript; authors were previously responsible for soliciting the reviews by contacting members of the journal’s Editorial Board directly. The new system allows authors to select potentially suitable reviewers from the Editorial Board at the time of submission; the in-house team then contact the suggested reviewers on the authors behalf.
Biology Direct publishes original research articles, hypotheses, opinions, comments, discovery notes and reviews in three subject areas: Genomics, Bioinformatics and Systems Biology; Immunology and Mathematical Biology.
For more information on the journal, and its novel scheme of peer review, please see the journal about page.
Senior Journal Development Editor
Posted by Elizabeth Bal at 18:16 Comments (0)
Novel data integration framework
Anduril is an open-source computational framework for the combined analysis of molecular and clinical information developed by Sampsa Hautaniemi and colleagues to allow integration of clinical information with large-scale molecular datasets such as transcriptomes, miRNA, single nucleotide polymorphisms, copy number variation and methylation data. In a recent article published in Genome Medicine they describe this tool and demonstrate its utility in an analysis of glioblastoma multiforme patient data from The Cancer Genome Atlas.
Their analysis of molecular and clinical data from 338 glioblastoma multiforme patients suggested several novel candidate genes related to disease progression. In particular, increased expression of the Moesin gene appeared to have a strong association with poor patient survival, and functional analyses confirmed that depletion of this gene inhibited cell proliferation, making it a good candidate for further study of this poorly-understood disease.
Anduril's benefits include the ability to analyse heterogenous large-scale disease data to generate testable predictions for future functional studies, and may be used by scientists without bioinformatics training to interpret the increasingly complex datasets generated by current medical genomics research.
Posted by Rebecca Furlong at 15:41 Comments (0)
From biosafety to forensics: Investigative Genetics can provide the answers
"Because of the developments and capabilities afforded to us today to unravel the mysteries of life, this has to be the most exciting time to be a biological scientist. The 21st century is truly the century of biology”. So says Bruce Budowle, who began a distinguished career in forensic genetics at the FBI laboratory at Quantico and is now Executive Director of the Institute of Investigative Genetics at the University of North Texas.
Bruce, together with Antti Sajantila (University of Helsinki) and Manfred Kayser (Erasmus University), is co-Editor-in-Chief of Investigative Genetics, a new journal with a focus on how molecular genetics can answer questions in a wide range of science disciplines with societal relevance such as forensics, biosafety and evolutionary, anthropological and historical studies. In Tales the double helix tells, the first of his regular series of columns, Mark Jobling shares his thoughts on how DNA-based research is rapidly evolving under the influence of technological advances, commercialisation, the internet, politics and wishful thinking.
Other articles published at launch include: the use of next-generation massively parallel (MPS) sequencing to detect strain-specific polymorphisms in Bacillus anthracis (anthrax) spores – the speed and accuracy of this technology makes it a powerful tool for investigating biocrimes or infectious disease outbreaks; an opinion piece on whether the NIH policy on sharing GWAS data may prove to be counterproductive and the development of single base extension assays to resolve Y chromosome haplotypes in sub-Saharan African populations.
For more details please visit the journal website or sign up for article updates.
Posted by Emma Pettengale at 13:00 Comments (1)
BMC Research Notes topical series on qRT-PCR normalization and optimization
By measuring the kinetics of the reaction in the early phases of the polymerase chain reaction (PCR), quantitative real time PCR (qRT-PCR) allows the rapid detection and quantification of nucleic acids. As part of BioMed Central’s ongoing efforts to promote data standards and encourage the normalization and optimization of widely used technologies - as exemplified by the BMC Research Notes series on microarrays - BMC Research Notes is launching a new topical series on quantitative real-time PCR normalization and optimization.
qRT-PCR is a commonly used technology with a wide range of applications such as viral quantitation, pathogen detection, quantification of gene expression and oligonucleotide array validation. But the validity and reproducibility of results of qRT-PCR studies depend on a number of factors including the appropriate selection and validation of reference genes, the sufficient reporting of experimental settings - details of which are listed in the MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) and ultimately the use of validated statistical tools and methods of data analysis.
The series, edited by Dr Joshua Yuan Associate Professor in Bioinformatics at the Texas A&M University Department of Plant Pathology and Microbiology, brings together descriptions of reference genes [1, 2] and potential associated experimental artifacts as well as tools for the improvement of RT-PCR performance [3, 4] and data analysis.
Guillaume Susbielle
In-house Editor - BMC Research Notes
Posted by Victoria Thompson at 17:27 Comments (1)