Breaking walls and mending organs

In a recent Comment in BMC Biology, Gregory Petsko appeals to some particularly surprising patterns of comorbidity in support of the argument for breaking the traditional boundaries between disciplines in translational research. This ever-topical issue featured at a recent panel session combining two parallel Keystone conferences on Regenerative Tissue Engineering and Transplantation and Mechanisms of Whole Organ Regeneration (co-organized by Rocky S. Tuan and Alejandro Sánchez Alvarado conference), with discussion on how to overcome the main obstacles to translation of basic research into the clinic.

What enables successful translation to the clinic? Michele de Luca was highlighted as a scientist who has made this happen, with success in transplanting human cornea grown from patient’s limbal stem cells in the laboratory. Kenneth R. Chien called for a generation of “scienteers” – researchers with multi-disciplinary training in both basic research and tissue engineering. Practical needs include the establishment of appropriate manufacturing standards (GMP); use of FDA approved materials; methods to deliver technologies, for example, how to implant cells; and develop better animal models applicable to cells or drugs for therapeutic use in humans (with a move away from a focus on mice).

As a final conclusion to the panel discussions, it was agreed that funding bodies (especially the NIH) could do more to promote such interdisciplinary interactions but also that scientists need to write grants in such a way to make this happen. Leading on from this, the panel promoted publication of work in open access general journals to reach “beyond your immediate community”. With this in mind, we welcome such submissions!

J Ann Le Good, Deputy Editor, BMC Biology

Posted by Alice Plane at 17:07    Comments (0)

 

The future of evolutionary epidemiology

The impending age of big data has been inescapable in recent discourse, both scientific and otherwise. The prevailing metaphors cast big data as a tsunami or an avalanche, suggesting natural disaster poised to dash hapless researchers against the rocks. They are, of course, no such thing, and offer many opportunities provided that one is prepared. Some of these opportunities were on show at the Royal Society discussion meeting on “Next-generation molecular and evolutionary epidemiology of infectious disease”.

One focus, inevitably, was next-generation sequencing, with Paul Kellam speaking about its importance in tracking the spread of the three waves of the 2009 H1N1 pandemic at a population level; but also for following the rapid spread of polymorphisms though the virus population within a single patient. Bill Hanage discussed the use of whole-genome data to investigate phylogenetic relationships within highly recombinogenic bacteria like Streptococcus pneumoniae, for which traditional genetic methods simply can’t cut it.

Some notes of restraint were sounded too. Dan Haydon told a cautionary tale about the current inability of deep sequencing to separate foot-and-mouth virus variation within an individual from technical noise, and suggested that in evolutionary studies of this virus, variation between individuals is the highest resolution at which we can currently make reliable inferences (the resulting graphs using "1 cow" as a basic unit of time amused, although we don’t imagine it shall become an SI unit any time soon). Contrary to the “sequence everything” school of thought, Sharon Peacock of the Health Protection Agency made the case for sparing use of whole-genome sequencing in clinical microbiology, where phenotypic tests still offer good effectiveness for their cost and in the majority of cases sequencing is an unnecessary expense.

Epidemiologists are perhaps uniquely interested in co-mapping phylogenetic and spatial data, given the power of explicitly tracking the recent history of disease spread, and there were a number of talks on the potential for spatial phylodynamics in modelling the spread of diseases including rabies and influenza. Perhaps the most striking example of the efficacy of this approach was given by Sharon Peacock, who showed how whole genome sequencing of MRSA allowed spatial mapping of its spread at the resolution of wards within a single hospital.

However, collecting spatial data is no straightforward task, and the future of surveillance was a popular subject. Simon Hay discussed a project to update global risk maps for disease, which are “often diabolical”, through careful curation via survey of the existing data and literature – but this is very costly in time and resources, and the future of this kind of curation might be driven by automated data-mining of resources such as PubMed and GenBank. Larry Brilliant spoke about Google.org’s Flu Trends, which tracks outbreaks through users’ flu-related search terms with surprising success – often reporting peaks in flu activity a week or two ahead of the CDC’s GP-reported data – and went on to give an overview and endorsement of  the current trend for web-based crowd-sourcing of reports through sites like HealthMap and ProMED.

Readers will, of course, be wondering about the privacy issues related to these new kinds of data-collection methods, and this was on attendees’ minds too. Nowhere is the discord between the need for patient privacy and the public health benefits of data release more apparent than epidemiology, where the geographic location of a patient – a key piece of information – goes a considerable way to revealing their identity. One unsavoury possibility is the future prospect of using a combination of genetic and epidemiological data to personally identify a key patient; say, “patient zero” for a particular pandemic, or an infection-multiplying “superspreader” for HIV – although it is important to emphasise that neither of these is likely at present. The discussion of these issues was only one aspect of a lively panel discussion to close the meeting, which also took in issues of data quality and accessibility, and how encouraging data citability might be one way to solve them. (Those interested in data citation might like to read the recent blog post and associated BMC Research Notes article on the current gold standard).

For those whose interest in evolutionary epidemiology has been piqued, suggested further reading in BMC Biology comes from Trevor Bedford and colleagues’ recent research modelling the evolutionary reasons for strikingly low standing diversity in the H3N2 flu virus; and Nobel laureate Peter Doherty and colleague Paul Thomas's comment on why knowing which mutations to look for in natural H5N1 flu reservoirs is more important than the perceived dangers which lead to the redaction – now reversed – of the description of particularly virulent laboratory strains.

Posted by Kester Jarvis at 14:19    Comments (0)

 

World Information Society Day

World Information Society Day aims to help raise awareness of the many possibilities that the internet, and other information and communication technologies (ICT), can offer to societies and economies as well as a way to help bridge the digital divide.  

What was once known as the World Telecommunication Day, which celebrated and acknowledged the development in the advances of communication technology, the 17^th May continues to mark the anniversary of the founding of the International Telecommunication Union (ITU) and the signing of the first International Telegraph Convention in 1865. In November 2005 the World Summit on the Information Society called upon the UN General Assembly to declare the 17^th May as World Information Society Day.

As a follow up from the recent launch of ITU’s new global campaign ‘Tech Needs Girls’ this year’s theme is ‘Women and Girls in ICT’ which hopes to highlight the gender inequality that remains deeply entrenched in underprivileged populations and communities. With women and girls being denied access to basic health care, education and to equal opportunities at work, the 2012 theme aims to enforce gender equality as a basic human right and provides the chance for the vulnerable half of the population to march forward as equals.

ITU, UNESCO, UNCTAD and UNDP are actively taking part in the day by co-organising the WSIS Forum 2012 event (14-18 May) which will represent the world's largest annual gathering of the 'ICT for Development' community. There are 18 WSIS Project Prizes that will be awarded to organisations and individuals who have achieved exceptional results in extending ICT access to disadvantaged populations and communities. In addition to the awards there is a special focus on women and technology which will feature experts from around the world and prominent public figures including Academy-Award winning actress Geena Davis.

Posted by Hilary Glover at 11:39    Comments (0)

 

Could biophysics help Novak Djokovic?

Last year, ATP World Tennis Number 1 Novak Djokovic cut out all wheat products from his diet. According to his nutritionist—who “discovered” an intolerance to gluten—It was this drastic change in eating habits that led directly to his current dominance of the game.

Unfortunately, this approach is currently the only effective treatment available for sufferers of the condition, and can feel far from a grand-slam solution to the problem. The widespread use of cereals in the global food industry, especially in the routine use of “hidden” wheat-derived ingredients in processed food, can often make adherence to such restrictive regimes a dispiriting experience.

What if there was an alternative?

In a Correspondence article published today in BMC Biophysics, Stephen Harding and colleagues propose an exciting new way of looking at this issue, through the use of techniques developed in the field of molecular biophysics—and issue a challenge to researchers working in the field to test their idea.

Protein prevention

Gluten intolerance is an autoimmune condition affecting individuals with genetic susceptibility, and occurs as a result of inflammation of the gut in response to exposure to cereal proteins known as gliadins. Although some previous research has looked into the possibility of genetically modifying these proteins in order to prevent this response, this new approach instead focuses on asking whether it would be possible to add a naturally occurring ingredient into the mix that might block this exposure in the first instance.

The candidate ingredients for this are dietary fibre polysaccharides—complex, indigestible carbohydrates that are nevertheless essential for digestion. When consumed, these fibre molecules compete directly with the cereal proteins for exposure to the bowel tissue, forming larger complexes that might be much less able to illicit the harmful inflammatory response. 

Biophysical techniques

One major issue with making this approach a success is identifying suitable polysaccharides that would interact strongly enough with these cereal proteins to prevent inflammation. This is where biophysics can help.

The authors reason that such candidate molecules can be found using a technique known as analytical ultracentrifugation. Senior author Stephen Harding from the University of Nottingham UK explains: “The analytical ultracentrifuge is a high speed centrifuge with an optical system which allows the detection of macromolecules as they sediment under high g-force. It has an inherent separation ability and is highly resolving. It is a free solution technique not requiring immobilisation of macromolecules onto a surface, giving it a major advantage over (other) techniques”

He continued “We use primarily the sedimentation velocity method and use the principle of co-sedimentation: gliadins, particularly digested gliadins have a very small sedimentation coefficient, whereas fibre polysaccharides are generally higher.  From appropriate comparison of mixtures with controls, we can see if the gliadin is picked up by the polysaccharide”

Although the technique itself is not a new one—the Swedish chemist Theodor Svedberg won the Nobel prize for its invention in 1926—modern developments now mean that these interactions can be analysed in exquisite detail.

What next?

Although only a fledgling idea at present, Harding is excited about how future research might tackle this challenge “A complete range of fibre needs to be investigated in a systematic way to see if there are any fibre polysaccharides providing interactions that are strong and robust enough. If this is the case then the particular gliadins and peptide sequences binding to the different polysaccharides would then need to be determined.”

After identification of these molecules, clinical trials could then be considered in patients with the condition. However, despite the potential this might offer for sufferers, the researchers are urging caution at this early stage “We must stress we do not want to give false hope to people who have gluten intolerance problems. This is very much a first stage process and it is possible that no fibre can be found affording an interaction suitable enough… If we can do so this it might provide a useful first step in identifying which fibre merits further investigation”

For researchers in the field, it seems the ball is now in their court.

This Correspondence piece will appear as a guest article as part of the “Advances in Food Allergy 2012” series, further details of which can be found here.

 

Posted by Simon Harold at 10:32    Comments (0)

 

BMC series journals win at the 6th Annual BioMed Central Research Awards

Since 2006, BioMed Central has been running its annual Research Awards, celebrating the excellence in scientific research that is published in our portfolio of over 200 open access journals. 2012 marks an exciting change to the Research Awards, as it is the first year that the awards have been divided into 15 separate categories, giving a larger number of high quality articles the chance to win in their specific subject discipline. The judging panels consist of experts in the respective fields, including but not limited to members of our Editorial boards. These awards also recognise outstanding individual or institutional efforts made to support open access to research.

The winners have recently been announced and we are delighted to say that authors in the subject-specific BMC-series journals have made a strong showing!

For the General Medicine award we are thrilled that Jian Zou and colleagues have won with their article in BMC Cancer on the effect of coffee consumption on cancer incidence. Their research showed that overall an increase in consumption of 1 cup of coffee per day was associated with a 3% reduced risk of 11 different measured types of cancers. The article was published in March this year and has been accessed over 4000 times already, indicating its key importance to the field and its recognition amongst the community and the wider audience.

Coffee consumption and risk of cancers: a meta-analysis of cohort studies
BMC Cancer 2011, 11:96 (15 March 2011)
Xiaofeng Yu, Zhijun Bao, Jian Zou and Jie Dong

BMC Ecology, with authors Volker Witte, Christoph von Beeren and colleagues, also achieved gold by winning the Plant, Animal Sciences and Veterinary Research award with their article on the chemical mimicry employed by the parasitic silverfish when trying to integrate into and exploit ant communities. The silverfish acquire cuticular hydrocarbon signatures directly from the ants cuticles, making them invisible as parasites and accepted (most of the time) as members of the colony. BMC Ecology is a rapidly growing journal, currently being tracked for an Impact Factor, and we look forward to receiving many more high quality articles such as this.

Acquisition of chemical recognition cues facilitates integration into ant societies
BMC Ecology 2011, 11:30 (1 December 2011)
Christoph von Beeren, Stefan Schulz, Rosli Hashim and Volker Witte

Last but by no means least, Eric B Loucks and his colleagues were the winners in the Public Health category with their fascinating article published in BMC Public Health on the inverse relationship between education and high blood pressure, highlighting that this relationship was more marked in females.

Associations of education with 30 year life course blood pressure trajectories: Framingham Offspring Study
BMC Public Health 2011, 11:139 (28 February 2011)
Eric B Loucks, Michal Abrahamowicz, Yongling Xiao and John W Lynch
 
Big congratulations to all of our winners! The awards will be presented tonight at a prestigious ceremony at the Emirates Stadium in London, and we look forward to congratulating the winners in person on both their achievements, and also their support of BioMed Central and open access publishing.  

Posted by Genevieve Horne at 10:21    Comments (0)

 

Out of cite: a new standard in data citation

 

The availability of data, its rapid and comprehensive dissemination, is central to efficient scientific research. Transparency and reproducibility all suffer when the provision of scientific data is restricted, a problem which is particularly vexing as we enter the era of ‘big data’ studies. One factor hindering data dissemination is the fact that researchers are rarely given proper credit for making their data available in the same way they are when publishing an article. This is furthermore not helped by the  lack of a universally recognised tagging system for publishers to link individual authors to their deposited data. Data sets are therefore prevented from being cited in the same way as a published article, disincentivizing researchers from committing the time and effort needed to make their data publicly available. 

A new correspondence article by GigaScience Editor Scott Edmunds published in BMC Research Notes discusses how the employment of ‘Digital Object Identifiers’ can help overcome this problem. A ‘Digital Object Identifier’ or DOI is a line of code used to make an electronic object such as a paper or a dataset permanently identifiable, allowing for a much more lasting form of linking than simply referring to its URL. This form of continual linking from a single access point allows data sets to be cited and referenced in journal articles in the same way as an ordinary research article.

Published as part of the ‘Data Standardization, sharing and publication’ series, Edmunds et al.’s correspondence highlights an article recently published in Genome Biology as an example of good citation practice. Illustrating genetic variation in sweet and grain sorghum, the article was submitted to the journal in the ordinary manner. The data set associated with the paper was then cited in the manuscript’s references section using a single citable DOI hosted on GigaScience’s integrated cloud computing-based GigaDB database. In its final form the authors’ work is accessible to the reader as a traditional academic article permanently linked to the data which support their analysis. Both the manuscript and the data set are available as singularly citable objects giving everyone involved in the production of the data appropriate recognition.                                                                                                                                

This format, described by Edmunds as “a new gold standard” , is the model that he and the team behind GigaScience are seeking to encourage.  Set up in conjunction with BioMed Central and BGI, formally known as the Beijing Genomics Institute, GigaScience integrates manuscript publication and data hosting, utilizing BGI’s powerful data storage and cloud computing infrastructure. Working with DataCite, GigaScience and GigaDB ensure that all submitted data sets receive a DOI making them independently citable.

Encouraging the creation of open and accessible scientific data whilst ensuring that its producers are given the proper recognition for their work is a challenge facing publishers in the ‘big data’ era. The successful adoption of the GigaScience model, as exemplified by the sweet and grain sorghum article, will be an important step forward in removing the constraints on extensive data dissemination.

 

Posted by Jack Cochrane at 15:17    Comments (0)

 

An interactive introduction to metabolomics

What is metabolomics and how is it being used to predict and manage disease? That’s the subject of Genome Medicine's and BioMed Central’s first interactive graphic.

This graphic is part of a series in Genome Medicine dedicated to the advances and state-of-the-art approaches in the use of metabolomics to understand, prevent and treat disease.

Metabolomics is the measurement of all the metabolites (small molecules produced by physiological processes, such as respiration and digestion) within a cell, tissue, organ or body. The metabolome alters in response to the environment, disease, nutrition and other factors, providing a dynamic picture of living organisms.

The omic approaches of genomics, proteomics and transcriptomics are widely used in academia and industry but until recently one piece of the puzzle was missing (or at least wasn’t widely used). As Tim Veenstra, a researcher at the National Cancer Institute in the United States and Special Issue Editor for Genome Medicine, writes in a forward-looking and optimistic Editorial, metabolomics is now ready to take its place as the final omics technology, completing the puzzle.

This is an exciting time for metabolomics research because not only is the technology ready - mass spectrometry and nuclear magnetic resonance  together provide a highly sensitive, quantitative and relatively cheap approach – but the need for such information is apparent too. Whether metabolomic information is used to improve genome wide association studies or improve screening and diagnosis of breast cancer, researchers and clinicians from all fields are now rushing to combine metabolomics with their existing studies. 

A combination of genomics, proteomics, transcriptomics and metabolomics will truly usher in the era of genomic medicine.

 

Posted by Maria Hodges at 11:20    Comments (0)

 

Join us at the Royal College of Ophthalmologists Annual Congress

BMC Ophthalmology will be attending this year’s The Royal College of Ophthalmologists Annual Congress in Liverpool. The three day conference is the UK’s largest ophthalmology conference and will feature various poster sessions and workshops, plus a wide array of talks from world renowned experts in their fields highlighting the newest and most exciting developments in clinical research based ophthalmology.

From retinal imaging to inflammatory eye disease, strabismus to glaucoma and beyond, all areas of ophthalmology will be covered.

We’re looking forward to the congress. Please do get in touch if you’re also attending on emilie.aime@biomedcentral.com – it would be great to see you there.

Emilie Aimé
Executive Editor
BMC Ophthalmology

 

Posted by Genevieve Horne at 14:29    Comments (0)

 

Celebrating the launch of Agriculture & Food Security

The Bibliotheca Alexandrina emulates the Ancient Library of Alexandria as a major centre for scholarship and dissemination of knowledge.  It is in this spirit that the Library organises the biennial BioVisionAlexandria meeting, bringing together distinguished speakers, including Nobel Laureates, from around the globe.

 

The ideology of BioVisionAlexandria 2012 is reflected in our vision for Agriculture & Food Security.  Thus, the meeting seemed the perfect setting to celebrate the journal’s recent launch, which was marked by a session at the meeting chaired by one of the Editors-in-Chief, Malcolm Elliott, on ‘Towards Global Food Security: The 21st Century Challenge’.

Editorial board member Nina Fedoroff – current President of the American Association for the Advancement of Science – spoke first, discussing hydroponics and aquaponics as technologies for sustainable food production.  She was followed by Editor-in-Chief Magdy Madkour, who spoke about the impact of climate change on arid lands agriculture.  The session concluded with a presentation from board member Clive James reviewing the contribution of biotech crops to food, feed and fibre security and sustainability.

Over 100 delegates and invited speakers attended an evening reception hosted by BioMed Central.  Ismail Serageldin, “Librarian of Alexandria” and Director of the Bibliotheca Alexandrina, joined the Editors-in-Chief in addressing those convened regarding the importance of new research and policies to ensure food and nutritional security through sustainable agricultural practices.  He welcomed Agriculture & Food Security as a timely addition to the academic literature, providing a peer reviewed outlet for work addressing and debating these issues.

Stay up to date with articles Agriculture & Food Security is publishing by registering for alerts.  All articles published in the journal are open access - read the launch editorial and published articles online now.  Submit your own research to Agriculture & Food Security to disseminate your findings to a wide international audience.

Editorial Board Lunch

Clockwise from bottom left: Sir Peter Lachmann, Adel El-Beltagy, Fiona Pring (BMC), Klaus Ammann, Salah Soliman, Bilijana Papazova Ammann, Magdy Madkour, Clive James, Malcolm Elliott, Nina Fedoroff, Nandita Quaderi (BMC).

Posted by Fiona Pring at 15:26    Comments (0)

 

World Lupus Day

Every day, more than 5 million people worldwide struggle with the often debilitating health consequences of systemic lupus erythematosus (SLE), a chronic autoimmune disease capable of damaging virtually any part of the body, including the joints, skin, lungs and brain.

SLE makes the immune system unable to differentiate between antigens and healthy tissue, which causes the body to direct antibodies against the healthy tissue leading to swelling, pain, and tissue damage.

There is currently no cure for SLE, but there are a number of new drugs being researched or in clinical trials. Eight years ago, an international steering committee representing SLE organisations from 13 different nations created a Proclamation - a call to action for governments around the world to increase their financial support for SLE research, awareness and patient services.  World Lupus Day has been observed on 10th May every year since 2004.

This year, World Lupus Day coincides with the publication of the first-ever guidelines for the diagnosis and management of lupus nephritis, a potentially fatal kidney disorder that occurs in approximately 50% of lupus patients. Unlike previous guidelines, the new guidelines are specific to lupus nephritis and include newer treatments, techniques for detecting renal disease, as well as treatment of pregnant SLE patients with kidney involvement.

The pathogenesis of this very complicated disease is a particular focus of current research. In a previous issue of Arthritis Research & Therapy, Zickert and colleagues provide important new evidence implicating high-mobility group box 1 protein (HMGB1), a prototypic alarmin that is released from activated and dying cells, as a mediator of lupus nephritis. Defining more precisely the role of HMGB1 in lupus will require treatment studies to block the activity of this alarmin in animal models and ultimately patients. Nowling and Gilkeson provide an overview of the current research and knowledge concerning mechanisms of renal injury in both lupus-prone mouse models and human lupus patients.

All articles in Arthritis Research & Therapy’s recent SLE review series, edited by Dr David Pisetsky (Duke University School of Medicine), are free to access and are available online here.

Posted by Abigail Jones at 10:33    Comments (0)

 

Interventions given during pregnancy improve outcome for obese women

The incidence of maternal obesity is on the rise, with one in five pregnant women estimated to be obese. This poses great risk for both mother and baby; obese women are more likely to develop gestational diabetes and gestational hypertension than mothers of normal weight, and pregnant women with extreme obesity are at 1.6 times greater risk of suffering a premature birth. Maternal obesity is also associated with  increased risk of miscarriage, congenital abnormalities and long-term health risks for the baby, including autism and obesity in future generations.

The National Institute for Health and Clinical Excellence (NICE) has issued guidance recommending that healthcare professionals educate women on the health risks of obesity during pregnancy. Guidance is mainly focused on weight loss when planning a pregnancy, and it is recommended that women have a balanced diet combined with an active lifestyle. However, around 50% of pregnancies are unplanned, highlighting the importance of weight-loss interventions during pregnancy.

In a systematic review and meta-analysis published in BMC Medicine, Oteng-Ntim and colleagues show that lifestyle interventions during pregnancy are associated with improved pregnancy outcome. The study analysed published randomised controlled trials (RCTs) and non-RCTs including individual and group-based dietary and exercise interventions. The authors found that interventions are associated with a reduction in maternal weight gain and prevalence of gestational diabetes, suggesting that interventions during pregnancy are beneficial. However, there were no significant effects on other outcomes, including caesarean delivery and birth weight. 

The study by Oteng-Ntim and colleagues shows that lifestyle interventions during pregnancy can be used to reduce adverse maternal outcomes, and highlights that more high-quality trials are needed to assess the effect on infant outcomes.  Following this insightful study, future research should address whether following diet and exercise recommendations during pregnancy reduces birth weight and caesarean delivery; Oteng-Ntim and colleagues showed that studies investigating these outcomes were of low quality. If future research yields positive results, interventions targeting obesity in pregnant women could be offered routinely to improve both maternal and infant pregnancy outcomes.

Posted by Claire Tree-Booker at 10:00    Comments (1)

 

Data mining, flamenco dancing and Darwinian evolution

Evo* is the umbrella conference of a number of sub-conferences featuring the latest theoretical and applied research in the field of evolutionary computation. Evolutionary computation is a fascinating subfield of artificial intelligence which takes inspiration from nature and the theory of Darwinian evolution to produce highly optimized processes and networks. It is often applied in computer science, but at Evo* it is applied to areas as diverse as music and art to risk management. This made for an eye-opening few days.

The conference began with an exciting plenary talk by Prof Dario Floreano (pictured below), in which he wowed everyone with his development of flying robots which can autonomously regulate altitude, steering, and landing using only perceptual cues. His vision to allow robots to ‘live in the 3rd dimension’ also featured robots which are programmed to behave altruistically. One wonders how far we may be from robots as sophisticated as ‘the Terminator’ (I refer here to the friendly one).

The EvoBIO track, which was sponsored by the BioMed Central journal BioData Mining features research which applies methods of evolutionary computation to machine learning and data mining. This year’s research ranged from the utilization of an artificial bee colony algorithm to improve the inference of phylogenetic trees, to Genetic Programming applied to Lévy flights (a class of random walks inspired by observing animal foraging habits). Another paper presented by Bill Langdon examined what appears to be unintentional infection of the human genome in laboratories, the contaminated samples of which have been unwittingly deposited in GenBank.

As part of an ongoing arrangement with EvoBIO, BioData Mining offers free publication each year to the winner of the best paper award and a discounted Article Processing Charge to all runners up. This year’s winner was Lars Rosenbaum, whose research examines particle swarm optimization applied to ligand-based virtual screening experiments. Particle swarm optimization (PSO) is a computational method that optimizes a problem by iteratively attempting to enhance a candidate solution relating to a given measure of quality.

But it wasn’t just all about data mining and Darwinian evolution; a lot of thought was put into the evening events, where we were treated to Spanish tapas and flamenco dancing at a medieval castle. The panoramic views from the castle allowed delegates to contemplate the meaning of life and perhaps the nature itself that provides such meaningful inspiration to this area of research. I found the research presented at this conference not only valuable to science, but quite remarkable.

We look forward to the next Evo* conference, which takes place in Vienna. Hasta la vista until next year!

Posted by Gabriella Anderson at 18:39    Comments (0)

 

Introducing the BioMed Central author academy

Publishing research in international English-language journals, to reach the widest possible audience, is a critical goal for scientists.  A search of the expanded Science Citation index shows that 93% of the content is published in English.

Clearly, authors who are less practised in reading and writing in English need to work much harder than their peers, in order to communicate their findings. With this discrepancy in mind, BioMed Central has formed a partnership with a language editing company Edanz,  to serve authors who wish to have their work edited by a scientific expert who is a native speaker of English. The Editors at Edanz have now pooled their expertise to create the BioMed Central author academy,  a free online learning resource for authors on writing and publishing in scientific journals.

As well as advice on how to structure and write a good research article, the author academy includes help on choosing a target journal and publication ethics. Edanz have strong history of mentorship through running author workshops across Asia and the middle East, and more recently with BioMed Central in Brazil.  BioMed Central and Edanz are committed to engaging with scientists globally, to help increase the chance of successful publication. Let us know what you think about the new author academy.  

Posted by Helen Whitaker at 16:52    Comments (0)

 

Greater Depths to the Deepwater Horizon oil disaster

Two years after the Deepwater Horizon drilling disaster in the Gulf of Mexico, the extent of its ecological impact is still to be fully assessed. In field studies from coastal marsh areas four months after the spill, exposure to the oil has been linked to divergence in genomic expression and aberrant protein expression in killifish (Fundulus grandis) gills, indicative of exposure to hydrocarbon-like chemicals. Deep water coral communities are also affected: in a study by Fisher and colleagues four months following capping of the well at a site 11 km from the Macondo well, widespread signs of stress in corals (tissue loss, bleaching and covering by brown flocculent material – floc) were visible. Analyses of the floc adherent to corals show petroleum biomarkers associated with the spill.
 
In a recent paper published in BMC Biology, Michael Barresi and colleagues report the results of an investigation of the possible lasting damage to marine life using the well characterized laboratory zebrafish as a powerful model for assessing the effects of toxicants from oil samples on embryonic development. They found that water-soluble components of crude oil samples from the Deepwater Horizon disaster containing polycyclic aromatic hydrocarbons cause defects in embryonic zebrafish development, leading to circulatory, locomotor and brain defects.They were also able to identify some of the molecular pathways activated by the oil.
 
Following the second anniversary of the Deepwater Horizon oil spill (on April 20), a panel of experts funded by the National Center for Ecological Analysis and Synthesis have recommended that strategies to deal with such deep water spills may need to change in future to meet the special ecological challenge of oil retained at depth in the ocean. In light of the research by Barresi and colleagues on zebrafish, it seems that profound effects of the oil spill may continue to surface and the committee’s concerns on the ecological risk are well founded. 

J. Ann Le Good, Deputy Editor, BMC Biology

Posted by Kester Jarvis at 16:16    Comments (0)

 

Painless publishing and the roots of the re-review revolt

Over the past few weeks, eLife has posted a manifesto, and EMBOencounters and Journal of Cell Biology  have published editorials, all promising strategies to avoid the iniquities of iterative reviewing, recently also the focus of invective from Hidde Ploegh and Gregory Petsko. We have addressed the problem with a policy we call  re-review opt-out.

Clearly the movement to refocus journals on promoting the publication of papers, rather than assiduously filtering them, is gaining ground.

Lest it be overlooked in the more recent coverage, I should like to take the opportunity to assign credit to a rather earlier attempt to draw attention to the plight of postdocs and untenured academics whose careers are imperilled by publication delays due to obstructive referees and unduly compliant editors.

Some years before Ploegh inveighed in Nature against the tyranny (sic) of ‘reviewer experiments’, or the manifesto of eLife inspired an enthusiastic endorsement from Petsko in Genome Biology, Raff, Johnson and Walter made precisely the same points in a succinct and eloquent letter to Science entitled ‘Painful Publishing’.

They were a large part of the inspiration for our own re-review opt-out policy, now in its fourth year of operation, and this is a good time to acknowledge the debt.

Miranda Robertson
Editor, BMC Biology

Posted by Alice Plane at 18:17    Comments (2)