Open Reading Frame brings together a selection of recent publication highlights from elsewhere in the open access ecosystem. This week we take a look at the past few weeks in biology.


How many mutations are acquired during a lifetime?
Analysis of blood cells taken from a 115-year old woman has revealed that the number of somatic mutations acquired in healthy blood is around four mutations per year. Somatic mutations differ from germ-line mutations because they are acquired during normal cellular development, mostly during cell division, with frequently-dividing cells being more susceptible to tumour development. By studying the frequency of these mutations in one of the oldest humans to have ever lived, researchers have been able to gather crucial information on how cellular fitness of progenitor stem cells affects selection of normal blood cells from which they derive. In this particular individual, the majority of cells in the blood compartment appear to have been derived from the offspring of just two stem cells. They find that these mutations are most likely the result of the normal cellular aging process, with most characterised as harmless ‘passenger’ mutations occurring in the non-deleterious regions of the genome.
Holstege et al. Genome Research


The single strain of bacteria with a big role in the carbon cycle
Oceans cycle the greatest quantity of carbon of all the earth’s systems, and represent a huge global store of carbon. The speed of carbon cycling through this system is driven by the microbial communities that live in the ocean, which had previously been assumed to scale with the diversity of different microbial species acting on the system. However, that assumption may now have to be revisited because of new findings from Scripps Institution of Oceanography, USA. Studying the single bacterial strain Alteromonas, researchers created ocean microcosms of this species living in seawater, and measured the flux of carbon within the system. They found that within only five days, this single strain had consumed the entire pool of dissolved organic carbon, although after a year of incubation it entered a period of physiological dormancy. They also find that despite competition from other bacterial species for this resource, and intense grazing pressure from predators, the strain was still able to persist and dominate these experimental communities – demonstrating that it may be possible for a single bacterial strain to dominate the carbon cycle of an whole ecosystem.
Pedler et al. PNAS


Chernobyl birds brave radiation through adaptation
Blood samples taken from birds living in Chernobyl, the site of the 1986 nuclear power plant accident, reveals surprising levels of adaptation in the face of harmful ionizing radiation. Using an approach that controls for the level of relatedness between species, a team of researchers collected data from 16 different bird species, measuring parameters likely to be influenced by the effects of radiation. These parameters included the body condition of birds, levels of DNA damage, and the amount of an antioxidant called glutathione, used to infer levels of oxidative stress. Correlating these with levels of radiation at specific locations in which the birds were caught, they find that contrary to what might be expected, body condition actually increased, whilst oxidative stress and DNA damage decreased, in areas where ionizing radiation was highest. The authors also show that there may be costs for birds that produce more of a melanin-based pigment called pheomelanin, as this was correlated with more harmful radiation-related effects. Production of this pigment also has an added consequence of using up valuable reserves of the antioxidant glutathione, representing an evolutionary constraint to adaptation in this system.
Galván et al. Functional Ecology


Keeping jumping genes under control
Retrotransposons are stretches of DNA that are amplified within an organism after copies are created and transported to other locations in the genome. Despite their presence in all eukaryotic organisms, these so-called ‘jumping genes’ are mostly benign, although in some instances they may disrupt crucial genetic processes if they are inserted into functionally important genes. Until now, the precise mechanism by which the movement of one of these jumping genes, called LINE-1, is controlled within the genome was not known. Now, researchers have found evidence of what had previously been suspected – that an enzyme called APOBEC3A limits the movement of LINE-1 by altering its sequence when in single-stranded form. Under these conditions, the base uracil switches places with that of cytosine in the sequence, limiting the spread of the retrotransposon due to cellular mechanisms that seek out and destroy unwanted copies of uracil.
Richardson et al. eLife


30 years of HIV evolution in North America
Similar to the development of drug resistance, pathogenic escape from the host immune system can favour the evolution of certain strains of virus through selective pressures. To investigate how this has influenced the evolution of HIV during an epidemic, researchers have compared changes in the DNA sequences of immune-related genes in HIV sufferers with the sequences of the HIV strains that have infected them. To track how these interactions have influenced pathogen evolution through time, they compared samples taken from HIV sufferers from four major North American cities that experienced HIV epidemics during the periods 1979–1989 and 2000–2011. The findings suggest that although the diversity of HIV sequences appears to have increased during this time – in part due to immune-related pressures – the frequency of these changes appear to be relatively low at present, and therefore not of immediate concern for the development of immune resistance.
Cotton et al. PLoS Genetics


Metabolism pre-dates the origin of life
The metabolic networks operating within organisms are highly complex, producing precursor molecules for key biological processes involving DNA and RNA. However, establishing the evolutionary origins of these processes presents a chicken-or-egg type problem: did the metabolic networks of extant organisms evolve from primitive versions, or were the foundations of metabolism established early on in our evolutionary history, before life even began? By reconstructing scenarios reminiscent of early earth, researchers find evidence supporting the latter hypothesis. Cooking up a mixture of  chemicals under conditions replicating the composition of the prebiotic Archean ocean, they find that specific metabolic pathways can be recreated in the absence of enzyme-catalysed reactions. Instead, the iron rich environment at this time would have played the crucial catalysing function, which would have most likely formed the key molecules allowing RNA to encode information.
Keller et al. Molecular Systems Biology


Written by Simon Harold, Senior Executive Editor for the BMC Series. 


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