Posts tagged: Biology

Beyond ENCODE – let’s continue the conversation


As the human genome sequence was completed, so the deep analysis of it began in earnest with the ENCyclopedia Of DNA Elements (ENCODE) project – intended to identify all functional elements in the human genome.

The project involved a worldwide consortium of research groups and the data emerging can be accessed through public databases. BioMed Central has published a selection of the early findings.

ENCODE initiatives lead to modENCODE a project aspiring to identify the functional elements in the genomes of the model organisms Caenorhabditis elegans (nematode) and Drosophila melanogaster (fruit fly). The extension of the ‘ENCODE approach’ to other model organisms allows further biological validation of the findings coming from the human genome project.

And building on ENCODE doesn’t …

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Cancer and diet – how to ask the right questions

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In the panel discussion at the end of the first BioMed Central conference on Metabolism, diet and disease, the panellists confronted the overwhelming evidence for a link between obesity and cancer. The panel discussion at the second picked up where the first left off – Can cancer be prevented by diet?

The only categorical answer came from Stephen O’Keefe, starting from the epidemiology that shows a 100-fold difference in colon cancer risk between African Americans (high) and rural Africans (low). If you switch their diets – and he has done the experiment – the gut microbiota, he reports, switches within two weeks, with known carcinogens going up in the guts of the rural Africans and conversely down in African …

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June blogs digest: Alcohol and football, eating disorders in men, irreproducible research, and more

Alcohol advertising Warsaw

Missed out on some of our posts in June? No need to trawl the archives – we’ve pulled together the highlights for you right here.

Do we need a red card for alcohol advertising in football?

With the World Cup kicking off on 12th June, we braced ourselves for the highs and lows of a month of football. But getting bitten by Luis Suarez might not be the only danger of the tournament. In a guest post, Dr Jean Adams, a Senior Lecturer in Public Health at Newcastle University, UK, told us about her latest research into alcohol advertising in football, published in BMC Public Health.

The perfect body? How eating disorders and body image are a threat to …

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Word of caution: a new method to study RNA-seq biases

Shaury Nash CC BY-SA

As next generation sequencing methods quickly become ubiquitous tools of genomics, more and more effort is directed to understand what are the limitations of these approaches. These limitations present themselves quite often in the form of coverage biases.

Last year Genome Biology published a study from David Jaffe and colleagues that looked at coverage biases in DNA sequencing. The authors used a suite of computational tools for bias assessment and applied them to a number of commonly used technologies. It turned out that, for instance, PacBio coverage is the least biased; and that high- and low-CG regions and long runs of homopolymers are very prone to coverage biases. They emphasized that the presence of such biases may lead to …

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Can you show us that again please?


For almost thirty years, David Stern has been obsessed with the fact that male fruit flies ‘sing’ to females. His work on this problem, published today in BMC Biology, has got him thinking about reproducibility in science. In this guest post, he sets out his prescription to help scientists check whether research results are reliable

As an undergraduate at Cornell in 1985, I looked for a research problem that combined my interests in genetics, evolution, and behavior. Kyriacou and Hall had recently reported that the period gene, which regulates circadian rhythms, also controlled a rhythm of fruit fly courtship song and that evolution of period explained a species difference in this courtship song rhythm. This seemed …

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How to disarm a superbug – a story told by forensic genomics

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bmc biol

Inexplicably absent from the current fad for Scandi-dramas is a mystery thriller set among the geysers, glaciers and Guðmundsdóttirs of Iceland.

One compelling candidate for filling this void is Prof Karl Gústaf Kristinsson, a medical microbiologist at Reykjavík's Landspitali University Hospital, and his quest to tell the story of the superbug PMEN2.

The pneumococcal detective

Prof Kristinsson has been on the case of Icelandic varieties of the multidrug resistant pneumococcus PMEN2 since the early 1990s, just a few years after it first invaded the island.

Rather than a red jumper, his tools of investigation have been a variety of molecular biology techniques, such as Sanger sequencing and restriction enzyme digests, which he has used to characterize the …

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Make your mealtimes more tasteful

Wassily Kandinsky's 'Painting Number 201', recreated by Michel et al.

Research published today in our journal Flavour shows that food arranged to resemble famous artworks tastes better than food in a traditional or neat presentation. So we thought we’d get everyone to improve their meals with an art-inspired presentation.

Tweet your examples of art-inspired food presentation using the hashtag #ArtisticTaste, and let us know whether it’s made your mealtime more fun. We’ll be sharing our favourites on Twitter from @BioMedCentral, and collecting up more on our Facebook page.

Here at BioMed Central, we never shy away from a challenge, our crack team had a go at making some themselves. Once they’d had a little think about what they wanted to recreate and chosen their ingredients,  we …

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Weaving a web of knowledge about silk and venom

Photo credit: Marshal Hedin

To create new materials that mimic the strength and flexibility of black widow spider silk and drugs based on its potent venom, we need a full list of the proteins involved and what they do. Two BMC Genomics papers published today make a start on this task. In this guest post, Jessica Garb, an author on both papers, talks about how she and the team took an inventory of the proteins in black widow spider silk and venom glands, and what this means for biomaterials and medicine.

Spiders are widely admired for two of their most fascinating adaptations: silk and venom production. The silks and venom of black widows (Latrodectus hesperus)  are highly prized because of their impressive properties, …

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The gut-brain axis: what’s the relationship between our bowels and our brains?

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What is the nature of the relationship between the brain and the gut? This is a question that has fascinated scientists and clinicians for decades, and there appears to be no simple answer to it. It seems the more research that is done on this topic, the more complex and extensive the interactions are found to be.

This communication between the endocrine and nervous systems has been termed the gut-brain axis (or brain-gut axis), and is thought to be involved in many regular functions and systems within the healthy body as well as in many diseases.

Today is World Digestive Health Day, and we’re marking the date with the launch of an article collection, bringing together research from a …

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Erase/Rewind: editing the epigenome


Recent developments in genome-editing technologies have turned the biotech industry's dream of mastering nature into a fast approaching reality. Want to change the color of an ear of corn? All you need to do is edit the relevant gene using the CRISPR/Cas system.

But some traits cannot be edited at the genomic level. The three ears of corn above may have strikingly different appearances, but they are genetically identical – varying only in their epigenomes.

Biotech strategies using genome engineering are impotent when it comes to epigenetically regulated phenotypes. Instead, epigenome-engineering tools are called for. And, as participants heard at May's meeting of the London Epigenomics Club, these prophesized epigenome-engineering tools are now a reality.

How to edit

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