Posts tagged: BMC Biology

Keeping it clean: Spotlight on contamination in microbiome studies

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Figure 1 Summary of 16S rRNA gene sequencing taxonomic assignment from ten-fold diluted pure cultures and controls. Salter et al. BMC Biology 2014, 12:87

A study published today in BMC Biology has found that many published microbiome studies may have been contaminated. In this guest post, Susannah Salter and Alan Walker, authors on the paper, tell us more about what they found.

 

The last decade has seen amazing developments in DNA sequencing technology. One area that has benefitted tremendously from these advances is the field of microbiology, as it is now possible to characterise microbial communities (“microbiota”) at previously unimaginable depths.

 

As a result microbiota research is currently booming, led by many recent large-scale, world-wide initiatives such as The Human Microbiome Project, MetaHIT, and the Earth Microbiome Project, which use the power of sequencing to try and understand …

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Questioning regeneration: answers from Alejandro Sánchez-Alvarado

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planarian

Alejandro Sánchez-Alvarado’s dynamic enthusiasm comes through as he talks about his passion: regeneration. In an interview for Biome he reflects on his personal experiences in science that have shaped his current research.

 

Planarian flatworms have remarkable regenerative capacity, being able to regenerate a whole organism from a tiny fragment of its body (for a general introduction see his Q&A  in BMC Biology ) but what led Alejandro to work on this organism?

 

A focus on the past and a chance meeting at a conference were his inspiration. His interest was aroused on finding the book ‘Regeneration’ by TH Morgan, who is as Alejandro comments “the father of modern genetics on Drosophila”, and who undertook “forgotten classic” …

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Biology – The foreseeable future

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BMC Biol iconic image

It’s a year and a half since we last looked at what our Editorial Board thinks we still need to know about biology, and it’s Biology Week in the UK. Good enough reason for another look at the open questions our expert Board thinks are most pressing, interesting or neglected in biological science.

Do we know our planet?

Ecology, not surprisingly is replete with open questions. We don’t know how biodiversity comes about (Anne Magurran), or how to predict what our blundering footprints will do to it (Anne Magurran and Charles Godfray, who roped in Robert May to help frame the questions), or whether biodiversity offsetting is a real possibility for making good the damage done by …

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tRFs and the Argonautes: gene silencing from antiquity

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In Greek mythology, the Argonauts are a band of heroes who accompany Jason on his quest to find the Golden Fleece, a garment whose origins likely lie in the use of sheep fleeces as sieves to collect gold flakes from running water.

In a new paper published in BMC Biology, Anindya Dutta and colleagues mine Argonaute (sic) datasets for biology's very own hidden gold: previously neglected fragments of tRNA molecules, known as tRFs.

Here's seven awesome things you need to know about tRFs:

1) tRNA molecules are routinely degraded by the cell into tRNA halves and smaller fragments (tRFs), which can be created from both the 5' and 3' ends of each tRNA. Some studies have argued that these degradation products …

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Ebolavirus – Possibility and reality

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The horrible crisis that is unfolding in Africa, with ebolavirus infection now threatening to become endemic, has its roots in many causes, of which the current state of understanding of the virus and the means of its control must be the least.

It’s not that we don’t know what to do

Ebolavirus outbreaks can be brought under control within weeks by established containment measures. But in this case, it was three months before the virus was recognized as the cause of the outbreak and another five before WHO declared a public health emergency, with the humanitarian response following only some weeks after that.

Meanwhile densely populated towns, and not just rural areas, are affected; the populations of the affected areas are …

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Keeping up with the Jobses: the role of technology in reproducible research

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Group photo (click for full picture)

AllBio's workshop on 'reproducibility in research' saw a metaphorical bottle smashed against the bow of The Genome Analysis Centre (TGAC)'s shiny new training facility.

Fueled by hackpads, marker pens and a mountain of tea and biscuits, the workshop (a mixture of research scientists, PhD students, coders, funders and publishers) set about asking the question: 'what are the barriers to reproducible research?'


Group photo (click to enlarge)

Running to stand still

AllBio was established to bring the technology of bioinformatics to a diverse set of biological disciplines, but with this workshop it stepped across to research's flipside: publishing.

Whether data or papers, it is clear that advances in technology have much to offer when it comes to improving …

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A new impact factor, a model modeler, and how to make a syllabub

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Proto_Phylo_Variants_final_RGB

This year, the impact factor of BMC Biology has increased for the second year in succession, to reach 7.4. Although like (probably) most of you, we have serious reservations about the value and validity of impact factors as a measure of quality, we know how much they matter in practice to research biologists competing for jobs and funds; so it would be silly to say we don’t care about them. And it is especially important to acknowledge our debt to all the Editorial Board members, off-Board experts, and referees, without whose help we should not have been able to achieve this.

Our saddest news this year is the loss of Julian Lewis, one of the most thoughtful and sagacious of our …

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An update on the Earth Microbiome Project

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When BMC Biology launched its iconic image we acknowledged the extreme artistic licence of portraying selected vertebrate phyla pictorially while whole microbial kingdoms were denoted with a single blob. This was not intended to signify a lack of interest in the microbial world on our part, and to update our readers on a major effort to explore its taxonomic diversity and role in the biosphere, we invited the instigators of the Earth Microbiome Project (EMP), launched in 2010 with the aim of sampling the microbial diversity of the planet, to give us a progress report.

In their short comment article on the achievements and aspirations of the EMP, Jack Gilbert, Janet Jansson and Rob Knight deliver a positive …

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Commonality and what is the hydrogen atom equivalent for cell shape?

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Stentor image 2 for cell geometry

The design principles of cell shape are the main focus of Wallace Marshall’s lab at the Department of Biochemistry & Biophysics, UCSF. As the inaugural contributor to our series on Cell geometry  (see: “Origins of cellular geometry”) he discusses in this guest post the role of mathematical modelling and the lessons of physics in the context of a new review article by Fred Chang and Kerwyn Casey Huang “How and why cells grow as rods”, just published in the series.

 

Predictive models are the difference between alchemy and chemistry. Everyone seems to agree that simple, quantitatively predictive models, of the type seen in physics, are something we should strive for in cell biology.

Just collecting lists of …

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Cancer and diet – how to ask the right questions

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Apple&cells_2014_all green_small

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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