Posts tagged: BMC Biology

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

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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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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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Can you show us that again please?

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Drosophila

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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Erase/Rewind: editing the epigenome

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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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How do geckos climb?

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What do insects and geckos have in common? The answer, from the recent Royal Society conference on cell adhesion, is that their climbing mechanism depends on van der Waals forces (as well as friction and shear stress). However, at a structural and molecular level, the way they attach to surfaces is different. This was the focus of the conference – to understand the forces involved in cell adhesion, how geometry is important, and what we understand about adhesion at a molecular level.

Kevin Kendall (the main conference organiser) introduced the meeting by reminding everyone that it was 100 years since Ross Granville Harrison demonstrated that embryonic cells could be grown in culture outside of an organism – and …

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How to model a cat – and how not

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Writing in 1945 on the role of models in biology, Arturo Rosenblueth and Norbert Wiener (founders of cybernetics, arguably a precursor of today’s systems biology) said, “The best material model for a cat is another, or preferably the same cat”. In a review in BMC Biology, Jeremy Gunawardena revisits the topic and confronts again the thorny issue of how to marry the elegance and precision of mathematical modeling to the messy reality of biology.

 

Gunawardena, who is a mathematician by training, provides a highly readable historical and personal perspective on how to approach models of biological systems for biologists. Currently, forward or reverse modeling are the two strategies described in the literature.

It is forward modeling that is the …

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Weapons of low-mass destruction: small ORFs in the uncharted parasite genome

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bmc biol

In our genomes, there is a whole host of genes hiding in plain sight. These genes are not included in major genome annotation efforts and are widely ignored in the literature, even though in some cases they have been conserved for as long as 550 million years.

So how have these genes remained hidden? There is a short answer to this. Literally so: the genes are short.

Scientists and computer algorithms that hunt for genes expect their prey to take the form of long sequences of hundreds of nucleotides, and quite simply ignore or discard candidates that do not meet this criterion.

But they are perhaps unwise to do so, suggest a number of recent reports, including an article in BMC

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