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.
Toxic secrets of the cobra genome
King cobra venom has evolved in an arms race between predator and prey, creating a complex and lethal cocktail of toxic chemicals. These insights revealed from the first genome sequence of the snake, show that regulatory components of the venom system likely evolved from their origin in the pancreas. Comparison with the genome of the only other venomous vertebrate to be sequenced – the platypus – reveals very different signatures of selection, with cobra venom having evolved to rapidly immobilize prey, and the platypus’ for male-male combat.
Vonk et al. PNAS
Reviewing the way we view Reviews
Review articles are disproportionately cited in research articles, with many citations giving inappropriate or inaccurate credit for work. An analysis of the citations received by more than 200 Review articles published in the field of ecology in 2007 reveals that 22 percent of citations were not accurate, and 15 percent gave credit for an original idea to the Review article and not the original research article in which it was found. The authors of this work point out that far from being a victimless crime, misinterpretations and laziness in citation decisions can have severe consequences for researchers who do not receive adequate credit for their work, disproportionately skew the impact factor of journals, and reduce the reliability of published science.
Teixeira et al. PLoS One
How to print a new eye
3D printing may be the latest technology to revolutionize the way we create objects, but it seems that there is still a place for the humble ink jet printer – in printing new cellular structures. UK researchers have developed a method for printing central nervous system cells, as well as those found in the retina, using conventional 2D printing. Although this inventive methodology has been previously demonstrated in more robust embryonic cells, this is the first time the approach has been successfully applied to cells from the central nervous system. It may prove to be a valuable tool in regenerative medicine and the search for a cure for blindness.
Lober et al. Biofabrication
Updating our understanding of plant defences
Plants come under attack from many sources, and have evolved sophisticated chemical and physical defences in response. However, exactly what mechanisms determine why certain defences are expressed in specific tissues is not clear. One such possibility, known as the Optimal Defence Hypothesis, suggests that plant defensive compounds are actively concentrated into regions that provide greatest benefit to the overall reproductive fitness of the plant. Now, a comprehensive review of four decades of research in this area aims to provide an up-to-date framework on which future studies can be based.
Meldau et al. Annals of Botany
Face ape: chimps recognise familiar faces
Chimpanzees display a strong neural response to the faces of other familiar chimpanzees when compared to unfamiliar individuals, but this does not hold true for pictures of familiar humans. Researchers from Japan showed these images to a female chimp named Mizuki, who had been raised in captivity from birth. By comparing electrical signals from her brain – known as event-related potentials – they hope to gain a better understanding of the evolution of facial recognition systems in human and great ape societies.
Fukushima et al. Peer J
How good are your ChiPs?
Forty-five percent of vertebrate transcription factor ChIP-seq datasets in the Gene Expression Omnibus (GEO) are of poor or intermediate quality. A large scale analysis of data deposited in the publicly-available database before April 2012 is the most comprehensive for this method, which is used for identifying genome-scale protein-DNA interactions, and also finds that a significant number of control datasets display characteristics of successful enrichment – indicating a widespread source of potential bias in this data.
Marinov et al. G3: Genes|Genomes|Genetics
Written by Simon Harold, Senior Executive Editor for the BMC Series.