BioMed Central Blog
From the Rhine to the Rift Valley: Human population genetics in Genome Biology
Has hypoxia adaptation in the Ethiopian highlands mirrored that seen in Tibet and the Andes? Is there a genetic definition for an Ashkenazi Jew? These are two questions on human diversity that can now be answered, thanks to new research articles published in this month's Genome Biology.
In the first article, the University of Pennsylvania's Tishkoff lab, in collaboration with Addis Ababa University, sought to identify genetic adaptations to high altitude present in the Amhara people of the Ethiopian Highlands. Two other high altitude populations – in Tibet and the Andes – have previously been studied in this way; obtaining Ethiopian samples, however, proved to be a challenging feat.
A set of strong candidate genes for high altitude selection were identified in the Amhara, whose samples were used both for genotyping and for physiological measurements. As with Tibetan and Andean populations, adaptations targeted the HIF-1 pathway, demonstrating the selective pressure brought about by the risk of hypoxia in high altitude environments. While the three populations share an adaptive pathway in common, the individual genetic changes underlying the hypoxia-resistant phenotype were different in the Ethiopian cohort to those seen in Tibetans or Andeans. This example of convergent evolution suggests that the HIF-1 pathway is an inevitable adaptation for any population under selection pressure for hypoxia.
The definition of what constitutes a Jew is an age-old question without a simple answer. The Ashkenazim are a subpopulation of the Jewish people descended from a small founder population based in Western Europe approximately 1,000 years ago; using the largest Ashkenazi genotyping cohort to date, Todd Lencz (The Feinstein Institute for Medical Research) and colleagues were able to determine a distinct genetic signature that can identify Ashkenazi Jews.
Consistent with previous reports, the article concludes that the founding Ashkenazi population likely included both Levantine Jewish and European Caucasian individuals. However, the results presented by Lencz and colleagues powerfully show that, since the founding event, the level of admixture with "host" European populations (and with other Jewish populations) has been extremely low.
The genetic signature also harbors an enrichment of genes associated with disease pathways known to be overrepresented in the Ashkenazi population, and so will therefore help to unravel the genetic basis by which these conditions (including cystic fibrosis and Usher syndrome) have become prevalent among Ashkenazim.
Posted by Naomi Attar at 13:35 Comments (0)
European Journal of Medical Research has now fully launched
Yesterday, European Journal of Medical Research published
its first open access articles with BioMed Central having transferred from I.
Holzapfel Verlag, where it began as a subscription journal in 1995. Edited
by Professor Deiter Häussinger of Düsseldorf University, European Journal of Medical Research publishes articles of international interest from all areas
of medical research, with a strong focus on clinical research. The journal has an Impact Factor
of 1.09
Amongst the first open access articles to be published in the journal is a study from Fircke et al. investigating differences in periodontal damage in HIV patients receiving antiretroviral treatment compared to untreated patients. For further information about the journal, please see Professor Häussinger’s editorial or visit the “About” page.
In conjunction with the transfer of European Journal of Medical Research to BioMed Central, the past three years of archival content will be available online as open access articles soon after launch.
Posted by Georgina Giddens at 13:32 Comments (0)
Invitation to submit to Cancer Bioinformatics thematic series
“Cancer Bioinformatics: Bioinformatic Methods, Network Biomarkers and Precision Medicine” is a special thematic series to be published across BMC Bioinformatics, BMC Cancer, Genome Medicine and Journal of Clinical Bioinformatics (JCBi).
Cancer remains one of the leading causes of death across the globe. Most cancer treatments work for only a subset of patients and there is still a great need for disease-specific biomarkers and individualized medicine, since a large proportion of patients receive ineffective treatments. It is essential that we develop accurate tools for delivering the right treatment to the right patient in the right time, based on biological characterization of each patient’s tumor. There is still a lack of tools for aiding early diagnosis, prognosis prediction, or predicting response to treatment. Increasing evidence that genomic, proteomic, and metabolomic analyses can be utilized to understand molecular mechanisms of cancer has led to increasing work within this area.
This series will specifically focus on new developments in cancer bioinformatics and computational systems biology and will present biologically interesting discoveries on cancer using computational methods, in addition to exploring the potential of clinical applications to improve the outcomes of patients with cancer.
Potential topics include, but are not limited to:
- Algorithms for clinical biomarker selection
- Integrative approaches
- Systems biology and network-based approaches
- Novel approaches to clinical trials
- Deep sequencing and proteomic profiling
- Epigenetic mechanisms and RNAs
- Drug discovery and development
- Individualized medicine
Submission of original research, methodology, software, and database articles are encouraged until 1st November 2012 but will be processed as soon as they come in.
Please direct any questions to Xiangdong Wang (Series Editor) at editorial@jclinbioinformatics.com. Please submit your manuscript here: BMC Bioinformatics, BMC Cancer, Genome Medicine and Journal of Clinical Bioinformatics, and state clearly in the covering letter that it is intended for this thematic series.
Posted by Helen Whitaker at 17:12 Comments (0)
Genome Biology’s two-mile high epigenomic epiphanies
"A Lamarckian contribution to natural selection doesn't make much sense to me," says father-of-(modern) epigenetics Andy Feinberg as he opens his talk at the Keystone Symposium on Epigenomics.
Admittedly, expressing skepticism toward Lamarck’s theory on the heritability of acquired traits is hardly controversial in the 21st century, but a number of better accepted theories were also challenged during the meeting, which was held concurrently with the Keystone Symposium on Chromatin Dynamics January 17-22 in Keystone, CO.
Tim Bestor (Columbia) came fully armed and ready for a fight as he took on the prevailing truth in the literature that promoter CpG hypermethylation is a pathogenic feature of many tumors. But, strikingly, the audience response was one of agreement with Bestor's line of argument. An overreliance on tissue culture cell lines was blamed for the unrepresentative reporting of tumor cell methylation patterns.
The importance of avoiding generalizations from results observed in a given cellular context was a strong message from the meeting, and multiple presentations reported remarkably high cell-type specificity for a range of epigenomic features.
Another theory to find itself in the crosshairs was that of an independent functional significance for histone modifications; instead, it was argued that the distribution of these marks is merely reflective of polymerase activity and of chromatin openness.
The conference organizers believe that the turnout (~650 participants) is a world record for an epigenomics meeting, a clear sign that the field is in its ascendancy. Methodological innovations – such as the Dekker lab's HiC approach to mapping the genome in 3D, Paul Soloway's high-throughput fluorescent chromatin sorting, and high resolution DNA-protein interaction mapping methods developed by the Henikoff and Pugh* labs – show that there is plenty of potential for epigenomics to continue its upward momentum. Perfect timing, then, for this year's Genome Biology special issue focusing on epigenomics, for which we are now accepting submissions. BioMed Central is also the publisher of Epigenetics & Chromatin, an open access journal dedicated to this topic, which boasts Steve Henikoff and Frank Grosveld as hands-on Editors-in-Chief.
A final thought: maybe it was just the thin mountain air befuddling the mind, but some of the work presented on heritable epialleles and mobile sRNAs in plants did seem, after all, to offer renewed hope for a quasi-Lamarckian inheritance (propagation of an acquired trait for a few generations, if not in permanency).
*see our Research Highlight by Eric Mendenhall and Brad Bernstein on the Pugh lab's ChIP-exo method
See also: Genome Biology's Twitter stream for a more detailed account of the Symposia
Posted by Naomi Attar at 16:59 Comments (0)
Israel Journal of Health Policy Research – Promoting international interactions
Israel Journal of Health Policy Research, the official journal of The Israel National Institute for Health Policy and Health Services Research, launches today with BioMed Central, under the expert leadership of Editors-in-Chief Avi Israeli and Bruce Rosen.
"Israel Journal of Health Policy Research (IJHPR) seeks to promote intensive intellectual interactions among scholars and practitioners from Israel and other countries regarding all aspects of health policy, with particular attention to Israel", say the co-Editors-in-Chief in their inaugural editorial. The journal welcomes submissions from any country that are relevant to health-services and public-health policy, and have implications for health and healthcare policy in Israel. The journal aims to "foster wider communication between health scientists and policy analysts in Israel and their colleagues around the world".
Each article that focuses on Israeli healthcare is accompanied by a brief commentary by a leading non-Israeli scholar who explores the international implications of the reported research. For example, Mark Chassin provides an international perspective in his commentary 'Quality of Care: How Good is Good Enough?', which accompanies Dena Jaffe and colleagues research on the quality of community healthcare in Israel.
For further information about the journal’s scope, please visit the journal website, and to receive regular updates of the journal content sign up for article alerts.
Posted by Liz Hoffman at 14:24 Comments (0)
Aquatic Biosystems: Riding the wave
Aquatic Biosystems, previously Saline Systems, was relaunched today with a broader scope to incorporate all aspects of basic and 
applied research on aquatic organisms and environments.
The first articles published today in Aquatic Biosystems include research by Patricia Assuncao et al. on the molecular taxonomy of new strains of Dunaliella, and research by Steve Ferguson and colleagues on predation behaviour and feeding ecology of killer whales in the Canadian Arctic based on traditional Inuit ecological knowledge and scientific observations.
The new journal also has an expanded Editorial Board, who cover new subject areas including fisheries, microbial ecology, population genetics, and aquatic invertebrate ecology. The journal is ideally placed to benefit from the increasing focus on aquatic biological systems within the scientific community and will be key in disseminating the important research results and information published within this field.
Also published in the journal today is an introductory editorial from Editors-in-Chief Shiladitya DasSarma and Edward Phlips, who discuss the changes in aquatic biological systems through time and the timeliness of Aquatic Biosystems’ relaunch.
“The increasing and widening threats posed by the actions of human biosystems to the integrity and sustainability of aquatic biosystems highlight the importance of understanding how these systems function, and their resilience to environmental change. Understanding the aquatic microbial community and its effects on plants and animals is key to choosing a sustainable future. The complexity of this task will require the use of all available resources, including the wide range of technological capabilities driving basic and applied research in the 21st century.”
We look forward to highlighting other leading articles on aquatic biosystems in the future and to you helping us grow and cement the journals’ reputation in the field as the home for all research on aquatic organisms and environments.
Posted by Genevieve Horne at 14:18 Comments (0)
Globalization and Health set to move onwards and upwards in 2012
With the publication of three Thematic Series and with submissions to the journal up by more than a third compared to 2010, 2011 proved to be a great year for Globalization and Health. The journal is set to continue to move with momentum in 2012, with the recent news that it will receive its first official Impact Factor in the summer. The journal currently has an unofficial impact factor of 2.07.
Globalization and Health, which is affiliated with the London School of Economics, publishes high quality research on globalization and its effects on health, on such diverse topics as the politics of the tobacco industry and access to essential medicines. This year, co-Editors-in-Chief Emma Pitchforth and Greg Martin are looking forward to publication of a new Thematic Series entitled: ‘Climate Change and Global Health: Implications for Human Health and Health Systems’. This highly topical series aims to explore the resilience and flexibility of our health systems in the face of possible large-scale disasters linked to climate change.
Globalization and Health welcomes a range of publications, including original research, commentaries, evidence reviews, debate articles and book reviews. To submit your manuscript to Globalization and Health, please click here.
Posted by Ian Ward at 10:53 Comments (0)
A new tool in the fight against healthcare-associated infection
Antimicrobial Resistance and Infection Control (ARIC) has launched with BioMed Central today.
Led by Andreas Voss, ARIC is a global forum for the scientific community working on the prevention, diagnosis and treatment of healthcare-associated infections.
Healthcare-associated infections are on the rise because of changes in healthcare systems and the spread of antimicrobial-resistant strains of both new and well-known pathogens. With increasing numbers of people travelling nationally and internationally, borders to transmission of infections no longer exist and fighting healthcare-associated infections has truly become a global challenge.
Therefore, it is important to share knowledge in this field on a global scale. This was highlighted at the 1st International Conference on Prevention and Infection Control and consequently ARIC was born.
With the support of an internationally recognized Editorial Board, ARIC aims to become the leading resource for the dissemination of scientific knowledge on all aspects of healthcare-associated infections. Please visit the journal website to learn more about the ARIC and to submit your research.
Posted by Srimathy Sriskantharajah at 17:15 Comments (2)
An event to celebrate the launch of Flavour – a new journal from BioMed Central
BioMed Central is collaborating with the London Gastronomy Seminars and the Centre for the Study of the Senses, University of London, to host an evening exploring how flavour shapes our world.
Flavour and the
New Nordic Cuisine is a seminar to celebrate the launch of Flavour,
a new interdisciplinary journal from BioMed Central covering the
psychophysical, psychological and chemical aspects of eating food, as mediated
through all the senses. Flavour publishes peer-reviewed research on all aspects of eating food including
contributions from neuroscience, genetics, psychology and sensory science.
Flavour encourages contributions not only from the academic community but also from the growing number of chefs and other food professionals who are introducing science into their kitchens, often in collaboration with academic research groups.
Speakers Per Møller, Ole Mouritsen and Lars Williams will discuss how we perceive taste and flavour, whilst describing new food and flavourings developed by Noma and the Nordic Food Lab for the New Nordic Cuisine.
Flavour and the
New Nordic Cuisine is at 6.30 pm on Wednesday 28th March 2012
at Senate House, University of London, U.K. For further information and to
purchase tickets, visit the London Gastronomy Seminars website.
Posted by Laura Winton at 14:00 Comments (1)
BMC-series journals on track for Impact Factor
BMC Biophysics, BMC Ecology and BMC Endocrine Disorders have all recently been accepted for
indexing by Thomson Reuters and are on course to receive their first Impact
Factors. We are delighted that these
journals have been selected for indexing, joining the many other journals in the
BMC series to have an Impact Factor.
BMC Endocrine Disorders has been tracked from publications in 2009 and is due to receive its first Impact Factor in 2012. A recent blog post discusses one of the special thematic collections in BMC Ecology, which has likely contributed to the increased visibility and recognition of the journal.
This is great news too for BMC Biophysics, considering it is less than a year since the journal re-launched on the BioMed Central platform. Since re-launch the journal has recruited a new Editorial Board consisting of world-renowned experts in the field.
In 2011 we
published many interesting articles, including one from our
Section Editor, Gerhard Gompper, which is an important theoretical contribution
to the field. In it, the authors
introduce and analyze a
discrete filament-motor protein model of subcellular microtubule self-assembly
in fission yeast, which demonstrates spontaneous generation of a number of
steady states, including spindles, nematics, and asters. We think this study
highlights the power and flexibility of online open access publishing in
biophysics, as the authors were able to directly link the article’s text to
their video figures. View their hypnotic animations of microtubule vortices here. 
The journal has already had a strong start to 2012 by publishing an exciting article by Qin et al. describing the structural determination of the EphA4 ligand binding domain, providing the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity. An accompanying commentary by Ruth Nussinov and Buyong Ma in our flagship biology journal BMC Biology says: “These snapshots of multiple conformations of the free EphA4 LDB provide a unique insight into the conformational dynamics of EphA4 and the Eph-ephrin signaling pathways.”
After such a great start we are looking forward to what 2012 has in store for these journals and would invite you to submit your next research article to BMC Biophysics, BMC Ecology and BMC Endocrine Disorders.
Shane Canning
Journal Development Editor
Simon Harold
Executive Editor
Posted by Shane Canning at 12:36 Comments (0)
Norwegian attacks July 2011: The emergency medical service response report
The two horrific attacks on 22nd July 2011 of the car bombing at the Government district in Oslo, and the shooting of participants at a national Labour Party youth camp on nearby Utøya island, saw one of the worst massacres Norway has faced. The devastating actions of a single perpetrator left a total of 77 people dead, and a nation questioning the motives of such actions. The scale of these two attacks was unprecedented in Norway, and understandably required an enormous amount of effort and resources from the police and emergency medical service (EMS). Six months on, a study describing the immediate prehospital EMS response to these incidents and a corresponding commentary by Prof David Lockey have been published in Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine.
The Norwegian study objectively describes the two events separately, giving details of emergency medical service response times to the scene, triage procedures and scene descriptions. Co-author Dr Stephen Sollid, Consultant Anaesthesiologist at Oslo University Hospital, and Medical Advisor at the Norwegian Air Ambulance Foundation explained,
“It was quite impressive to experience the way personnel from different systems were able to establish a working casualty clearing system. This was probably in the spirit of everyone pulling their weight under the given circumstances, but it is an experience that will certainly stay with those of us that took part in the rescue work that day and should inspire - at least - other EMS systems in Norway”.
In the initial analysis following the attacks, the police were criticized for their response time to Utøya island, and the transport issues faced with lack of helicopters and boats. The Norwegian air ambulance service were able to provide sufficient support for the pre-hospital medical services, and with approximately 60 flights logged, it is clear that availability of these resources is paramount for emergency incidences.
The report will allow other EMS services to analyse and provide improved emergency responses to future incidents. Unfortunately it is near impossible to predict when such attacks will next occur, and a state of preparedness is all that is possible.
Posted by Shivani Patel at 15:27 Comments (0)
Ovarian cancer is the fifth most common cancer affecting women in the UK, and 6,500 women are diagnosed every year. Cisplatin is commonly used to treat ovarian cancer, but it is associated with side effects in some people, and some types of this cancer are resistant to cisplatin treatment. There is thus a pressing need for the development of new drugs that are effective against ovarian cancer in people who are less responsive to cisplatin.
The novel anti-cancer drug Diindolylmethane (DIM) has previously been shown to prevent the growth of ovarian cancer cells, without affecting normal cells. In a new study published by BMC Medicine, Kandala and Srivastava shed light on the mechanism by which DIM affects ovarian cancer cells. The authors show that DIM works by blocking production of the transcription factor STAT3, whose normal role is in cell growth and division. STAT3 is present at abnormally high levels in many types of cancer, and has been implicated in cisplatin resistance. They found that DIM blocks STAT3 activation by the immune system messenger interleukin 6 (IL-6), and also reduces the amount of IL-6 in ovarian cancer cells.
Importantly, Kandala and Srivastava also showed that DIM enhanced the anti-cancer effects of cisplatin in both human ovarian cancer cells and in mice, where a combination of both drugs reduced tumour growth by an extra 50% compared with cisplatin alone. DIM is an exciting potential future therapy for ovarian cancer, which could overcome the problems with cisplatin resistance in some women.
Posted by Claire Tree-Booker at 10:10 Comments (0)
Gut Pathogens making a positive impact in 2012
The year has started positively for Gut Pathogens with the news that the journal will receive its first Impact Factor in June 2012. Gut Pathogens is aiming to be ranked in the first quartile of Gastroenterology and Hepatology journals.
Gut Pathogens, an internationally recognized journal, boasts an Editorial Board consisting of leading researchers from around the world. A key factor in the journal’s success has been its commitment to publishing articles that are topical and relevant to researchers in this field. In particular, Gut Pathogens has consistently published highly popular articles on probiotics, and is becoming a key journal for researchers in the field to submit their research. The journal will continue to publish high quality articles on probiotics in the future. (Image credit: Probiotic Lactobacillus salivarius. Sleator, Gut Pathogens 2010 2:5)
There has been an increasing interest in pathogens such as Clostridium difficile, E. coli and Salmonella because of the significant emerging health problems they are causing in western countries. Gut Pathogens would like to invite scientists to submit their research on these and similar themes to the journal for publication in 2012.
Posted by Srimathy Sriskantharajah at 15:54 Comments (0)
Global lipid profiling provides clues to schizophrenia pathogenesis
Recent research published in Genome Medicine presents a comprehensive, global view of lipid abnormalities associated with schizophrenia, providing new pathophysiological insights into the disorder.
Following on from their earlier work published in Genome Medicine, which reported metabolites that differentiate schizophrenia from related disorders, Matej Orešič and colleagues from the VTT Technical Research Centre of Finland used metabolomics (a high-throughput method for detecting small metabolites) to determine the lipid profile of people with schizophrenia. In psychiatric research, several theories have been proposed to explain how brain function may be altered by changes in lipid composition, and this study sought to understand which specific pathways are affected in schizophrenia.
The group analyzed the lipid content of serum samples taken from monozygotic twins that are discordant for schizophrenia i.e. only one twin in each pair is affected. The advantage of this unique study design is that discordant twins are an ideal population for investigating the contribution of genetic factors to disease etiology. Age and gender matched healthy twin pairs were included as controls, and neurocognitive and magnetic resonance image data were available for selected twins.
Compared with healthy controls, individuals with schizophrenia had higher triglyceride levels and showed signs of insulin resistance, in line with earlier reports. However, the patients’ unaffected co-twins were also found to be insulin resistant, providing new evidence that this could be an inherited trait associated with predisposition to schizophrenia. Affected twins also had lower levels of phospholipid derivatives called lysophosphatidylcholines (lysoPCs). This change, which was not observed in healthy co-twins or controls, correlated with decreased cognitive speed. Because lysoPCs are involved in blood-brain barrier transport of polyunsaturated fatty acids, the authors conclude that a drop in their levels may be responsible for changes in neurotransmission and weaker cognitive performance. They also propose that lysoPC deficiency could make schizophrenia patients more susceptible to infections. These findings pave the way for further research into the role of lysoPCs in schizophrenia.
The mechanistic insights reported by Orešič and colleagues may be useful for the discovery of new drug targets for schizophrenia. In addition, the work demonstrates how a discordant twin study design can successfully uncouple genetic and environmental factors, allowing disease-specific inherited traits to be accurately defined.
Posted by Paraminder Dhillon at 13:49 Comments (0)
“Journal of Negative Results in Biomedicine's immediate goal is to provide scientists and physicians with responsible and balanced information in order to improve experimental designs and clinical decisions”, comments Prof Bjorn Olsen, Editor-in-Chief of this journal.
The importance and usefulness of negative results is something that is arguably overlooked in the scientific arena; they are often perceived as less important due to the fact that they fail to confirm various hypotheses. This view however is gradually changing, with a growing awareness of how constructive and useful they can actually be to science.
Journal of Negative Results in Biomedicine promotes the publication of negative results and data, and supports the idea that scientists should be provided with balanced information which can offer a more complete scientific record, thereby reducing the risk of publication bias or later rebuttal of research. Prof Olsen and JNRBM co-founder, Dr Christian Pfeffer, also strongly believe that “such "negative" observations and conclusions, based on rigorous experimentation and thorough documentation, ought to be published in order to be discussed, confirmed or refuted by others”.
Perhaps in reflection of this rising awareness of the importance of publishing negative results, 2011 saw an increase in submissions to JNRBM, leading to the recruitment of a number of Associate Editors to provide their scientific expertise to assist with the peer-review process. The Associate Editor model is a strategy which Biomed Central successfully introduced in 2008 in order to improve speed and quality of peer-review on its BMC series journals. The hope is that adopting a similar model for JNRBM will lead not only to a more efficient peer-review process, but also an improved capacity to publish even more of this incredibly valuable research.
To submit your manuscript documenting negative data or results, please click here. If you are interested in writing a Commentary article about your views on negative results, please email bjorn_olsen@hms.harvard.edu to discuss your proposal.
Posted by Gabriella Anderson at 17:39 Comments (0)