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.
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Social interactions shape the baboon’s gut microbiome
The importance of the gut microbiome on overall health is well established. However, the factors that affect the composition of gut bacteria are still far from clear. New research on baboons suggests that an individual’s social relationships have a significant impact on their gut microbiome. Sequencing of the microbiomes of a well-studied group of wild baboons has produced clear evidence that their direct social interactions with each other (such as reciprocal grooming) directly affects the bacterial composition of their guts. The researchers were able to exclude any potential effects of kinship or shared diet and environment from their findings, making this the first study to implicate direct physical contact as a factor affecting the gut microbiome. Given that humans engage in similar physical contact with close social partners (such as hugging or kissing) it does seem possible that social interactions also shape our own gut microbiomes.
Tung et al. eLife
The perils of being an older parent
It is a widely proposed theory that reproducing at an older age comes with costs to the resulting offspring. However, testing this theory in wild, non-human animals has been difficult. New research makes use of an isolated population of house sparrows, living on an island off the coast of England, to test this idea. This sparrow population has been studied for decades and the age of individuals is known, allowing the relationship between the age at which birds reproduce and the eventual success of their offspring to be measured. The results show a strong negative relationship between parental age and lifetime fitness of the offspring; that is, birds with older parents went on to produce less offspring themselves than birds with younger parents. As all the birds in this study were cross-fostered (that is, raised by birds other than their genetic parents), this effect is unlikely to be due to an environmental effect, but rather suggests some kind of epigenetic inheritance.
Schroeder et al. PNAS
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Velvet worm, velvet worm, does whatever Spiderman can
The velvet worms are an obscure group of animals, looking superficially similar to caterpillars or centipedes (but not closely related), that have a remarkable hunting strategy: they are able, rather akin to Spiderman, to eject two streams of sticky slime up to around 30 cm, several times longer than their body, to ensnare their prey. When they prey is caught by this sticky barrage it hardens, leaving them immobilised for the velvet worm to casually inject digestive enzymes and eat the remnants. A new study reveals the propulsion mechanism of the worms’ slime jets. The authors find muscle structures around the slime reservoirs contract to eject slime through a narrowed tube, accelerating the stream. However the muscles in the oral papillae—the adapted legs that act as the nozzles—are not fast enough to create the side-to-side spraying action that is vital for covering a wide area in slime. Instead they found that this oscillation results from a dynamic, unstable interaction between the slime flow and the soft, elastic papillae, the same effect as a thrashing garden hose. The article has some wonderful video footage of a velvet worm slime attack from a bug’s perspective. Well worth watching, but don’t let it give you nightmares.
Concha et al. Nature Communications
Shining a light into the dark world of gut microbes
The guts of mammals contain a world of diverse bacteria, and sequencing methods have described much about the communities of these microbes and about their genomes. However, what is harder to ascertain is the function and significance of the genes identified, due to the difficulties in growing the bacteria in culture outside of the gut and the absence of standard genetic manipulation methods as used on other bacterial species. A new approach clones genetic fragments from the gut bacterium Bacteroides thetaiotaomicron into a lab strain of E. coli. Inoculation of these into germ-free mouse guts showed which genes were important for successful colonization of the gut: certain carbohydrate utilization genes were particularly important. The knowledge gleaned from studies using this kind of approach could lead to an understanding of how to engineer functions into microbes with novel health benefits.
Yaung et al. Molecular Systems Biology
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Can light extend lifespan?
One of the biggest contributors to aging in animals is the decline of mitochondrial function, as mutations to mitochondrial DNA result in declining production of the ATP that provides the energy for other cellular functions. It is known that in the retinas of mice, exposure to near infrared light arrests this decline and increases the production on ATP in the retinas of older mice. Could this effect be reproduced across a whole animal? New research on the model fruitfly Drosophila suggests it can. Flies exposed to near infrared light for 20 minutes a day throughout their lives had improved ATP levels and greater mobility after seven weeks of age (when mitochondrial function normally start to decline) and had longer lifespans than control flies. Reproducing these results on larger animals will be difficult; the light would not penetrate to all the cells of, say, a mouse. However the researchers do suggest that exposure to near-infrared light could become a simple way for humans to extend lifespan and improve function in old age.
Begum et al. Biology Letters
Taking the p-value
It is well known that the scientific literature contains many potential sources of bias. Particularly notable is the tendency for more positive results to be published than are identified in studies. The pressure on scientists whose careers are measured by publications in high impact journals and the tendency of such journals to favour striking positive results provides one route to this bias. Another is known as “p-hacking” or “inflation bias”. This is a side-effect of the practice during statistical analysis of considering arbitrary thresholds of statistical p-values: on one side of the cut-off the result is “significant” and the other it’s “non-significant” (a throwback to times when statistical tests were calculated with the help of printed tables of values). Researchers may be tempted to tinker with their data or stats methods, or get just a few more samples, purely in order to stumble over the finishing line of p=0.05 into scientific respectability. A new study examines this effect by text mining the scientific literature to pull out the p-values reported in tens of thousands of articles. The authors found a significant and otherwise inexplicable bump in the number of papers reporting just under p=0.05, providing clear evidence of p-hacking. The authors explain how one negative effect is on meta-analyses that pull together other datasets to come to a better overall picture, which assume the underlying studies unbiased—they recommend that meta-analyses should henceforth take p-hacking into account. From the perspective of Open Reading Frame this study clearly demonstrates one benefit of open-access publishing: the authors were only able to conduct this study because their text-mining software could read the full-text of open access articles.
Head et al. PLoS Biology
Written by Christopher Foote, Executive Editor for the BMC Series and Tim Sands, Executive Editor for the BMC Series
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