Posts tagged: BMC Biology

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

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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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The agony of choice: conservation biology and choosing what to save

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Image credit: Wikimedia

You’re a conservationist with a list of threatened species and a limited budget. What are you going to save? Pandas or polar bears? Corals or condors? Leopards or leatherbacks? You have little time to deliberate, and you need a rational basis for your decision.
 

Performing phylogenetic triage

How to advise those in the unenviable position of making these decisions was the focus of a meeting on ‘Phylogeny, extinction risks and conservation’ last week at the Royal Society, where the central issue was how to exercise this kind of “phylogenetic triage” in the face of inevitable biodiversity loss.

We need some way to choose which species will …

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Cancer and diet – what you eat, or how much?

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The epidemiological evidence now seems overwhelming: obesity is a major cause of cancer, which will rise with the rising tide of obesity in the well fed Western world. Elio Riboli will speak on what epidemiology can tell us about how our physiology and habits contribute to the probability of developing cancer at the second BMC conference on Metabolism, diet and disease, and in an interview for BMC Biology he explained how perceptions have changed in the past ten years.

Red and processed meat have notoriously been incriminated in increased risk of cancer, an association recently confirmed by a paper in our sister journal BMC Medicine, with fruit and vegetables, long advocated for health and long …

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Cancer, metabolism and the wisdom of Lewis Cantley on fructose

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When we published Luc Tappy’s Q&A on fructose toxicity two years ago at the time of our first conference on Metabolism diet and disease, he took the line that fructose is harmless to people not at special risk of developing metabolic disease, but could reasonably and on the whole should be avoided by people who are at risk, since it is dispensible and may, for reasons connected with our metabolism and homeostatic circuitry, exacerbate any tendency to overeating and obesity.

He didn’t say it was addictive and best avoided altogether, along with any other sweeteners – which is the conclusion that Lew Cantley now arrives at, in a short interview for BMC Biology to introduce some …

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Sigma factor networking and bacterial versatility

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False colour E. coli

In the bacterial RNA polymerase transcription complex, the sigma factors play the role of guide, specifying where in the genome the complex binds – and thereby which genes are turned on at any one time.

Lab favourite E. coli has seven such sigma factors, one of which has a ‘housekeeping’ role in standard conditions, with the other six swapping into the complex under particular individual stresses – perhaps the most important (at least from a human perspective) role of these alternative sigma factors being the regulation of virulence genes.

A new study from Bernhard Palsson and …

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Celebrating ten years of BMC Biology in pictures

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The BMC Biology iconic image (left) [1] was devised as a representation of the breadth of content of the journal, but its phylogenetic tree enclosed in a lipid bilayer cannot do full justice to the real variety of research papers that we publish. So to celebrate the anniversary of the launch of BMC Biology – in November 2003 – we have built on our iconic image with a pictorial representation of the content over the years (below), and here is a guided tour clockwise from the top.

At the top of the image, Jim Brandle and colleagues [2] look in plant leaves at the localization of elastin-like polypeptide (here, expressed with a green fluorescent …

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Questioning cell geometry: an interview with Wallace Marshall

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Wallace Marshall has been intrigued by the question of what regulated cell size since his childhood, when a book showing electron microscope images of cells showed their remarkably regular shape and structure, and led him to wonder how this could be. He returns to the question in his introduction to BMC Biology‘s Forum article on the topic, which forms part of BMC Biology’s series on Cell geometry – and now in an audio interview.

Will there be a universal mechanism across organisms that determines how the size of a cell is regulated? Whilst Wallace thinks that the authors of our Forum article start to answer this important question in several different organisms, there is still …

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Evolvability and the inexplicable

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The theory of evolution by natural selection is unarguably the most influential in the  history of biology, but it has been dogged with controversy since its inception, and not just because of ideological resistance to its implications for our ancestry. One of the more compelling obstacles to its acceptance has been the existence of extremely complex adaptive structures such as (famously) the eye, which seem to defy explanation by the gradual accrual of random changes. Darwin worried about it, and accepted the contribution of inheritance of acquired characters in part to explain the otherwise apparently inexplicable. This Lamarckist position became untenable however when Weismann established the separation of germline and soma in the late 19th century; and …

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Electricity generation and fish populations: how a power station provided a rich biological dataset

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Many nuclear power stations in the UK are built on the coast, where the easy availability of sea water offers a natural solution to cooling the carbon dioxide used to moderate the reactor temperature. Hinkley Point B station is situated on the Bristol Channel for just this reason, and as one adventitious consequence, its water intakes have been a rich source of biological data for the last 30 years.

Tidal currents in the Bristol Channel can be strong (witnessed in the Severn Bore, which forms further upstream), and fish feeding on the coastal mudflats may be pulled into the station’s water intakes. They aren’t allowed, of course, to reach the station …

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The remarkable and still mysterious cancer resistance of blind mole rats

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Blind mole rats (Spalax spp) are extraordinary rodents that spend most of their lives underground, digging in poorly ventilated tunnels.  Their ability to conduct intensive aerobic work under low oxygen pressures is remarkable, as is their lifespan of 20 years or more, which despite its length is not associated with spontaneously arising tumors.  A paper published in BMC Biology now shows that their resistance to cancer extends to chemically-induced tumors, and that normal fibroblasts from these animals have the ability to suppress cancer cell viability and growth.

The BMC Biology paper by Manov et al reports that while laboratory mice and rats develop multiple skin cancers in response to applied carcinogens, the skin lesions produced by this …

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