Open Reading Frame: jumping genes, better biofuels and acid signalling

Posted by Biome on 4th April 2014 - 0 Comments


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.

 

African clawed frog (crop)_Flickr_Liz WestXenopus frogs take another leap forward for biology
You may not know it, but the African clawed frog (Xenopus laevis) is something of a pioneer in biology. The first vertebrate to be cloned, the first organism from which a gene was isolated and subsequently sequenced, and now the organism with the largest proteomic dataset. The proteome consists of all the proteins expressed in any particular organism, tissue or cell; using a technique called iTRAQ that labels specific peptides in the protein sequence so that they can be tacked and quantified, researchers identified around 4000 proteins from developing frog embryos. Observing how each set of proteins clusters around different stages of embryo development has allowed them to pinpoint major events in the process of development into adulthood, especially the role that these proteins play in the development of specific organs and tissues.
Sun et al. Scientific Reports

 

How balanced are your reviews?
As the volume of published scientific research steadily increases, so too does the burden on peer-reviewers. But without an established etiquette on how much to review relative to how much you submit, how does anyone keep track of whether researchers are doing their fair share of reviewing?  By analysing the reviewing habits of researchers publishing in journals supported by the British Ecological Society, it seems that – at least for now – we may not have to worry too much. Extracting a subset of data from the society’s reviewer database, Owen Petchey and colleagues find that  12-44 percent of peer-reviewers contributed substantially more reviews than would be required to balance their submissions over the seven year time period that was analysed. Although the authors caution that the analysis is restricted to a select group of  journals in this field, they argue that these findings are likely to reflect broader reviewing patterns in the biological sciences, and call for better data collection on reviewing habits in the future.
Petchey et al. PLoS ONE

 

Switchgrass Panicum virgatum (crop)_Flickr_Matt LavinRainforest yields crucial genes for better biofuels
The development of advanced biofuels from non-food crops is one approach for tackling future energy needs, but is proving difficult to produce on industrial scales since the high lignin content of grasses makes sugar extraction difficult. It is these sugars that are needed for engineered microbial hosts, like bacteria and yeasts, to produce the biofuel. The most common approach to tackle this problem is to treat grass with ionic liquids, which act as solvents to release sugars from the grip of lignin. However, these ionic liquids may also inhibit microbial growth. Now, a solution to this problem may have been found in the rainforests of Puerto Rica through a soil bacterium called Enterobacter lignolyticus. This unique microorganism is known to be able to tolerate exposure to ionic liquid conditions, via the control of two key genes not found in other microbes. In light of this finding, researchers have now engineered the transfer of these genes into industrial strains of E. coli bacteria. These newly engineered strains are able to tolerate previously inhospitable ionic liquid conditions, and demonstrate enhanced production of biofuel products on a large scale.
Ruegg et al. Nature Communications

 

Calyx filled w Lucifer yellow_Highstein et al,PNAS,2014,March 25The acid test for a novel neurotransmitter
A new mechanism of nervous system signalling has been identified in the inner ear, which may play a key role in the way that organisms sense gravity. Previously, only two chemical mechanisms were known to transmit signals between synapses (the junctions between neurons): one in which neurotransmitter molecules cross the divide between synapses in small packages, and one in which gases like carbon monoxide freely pass through cell membranes. Now, by delving a little deeper into previous research that demonstrated a signalling role for acids  in the contraction of nematode worm muscles, researchers have found that acidic protons also act directly as neurotransmitters in the inner-ear of these worms, allowing a continuous stream of signals to be transmitted. This is in contrast to signalling molecules that are released in packages, which may be susceptible to depletion over long time-periods. The continual need for organisms to monitor gravity-sensing makes this mechanism much more suitable for low-level signalling, and may be widespread in other neuronal systems that require continual feedback.
Highstein et al. PNAS

 

Horizontal jumping genes in plants
Transposable elements are often called ‘jumping genes’ because of their high mobility within genomes. These shifting stretches of DNA are found in all living organisms, where they are transferred vertically across generations. In higher organisms (Eukaryotes) this vertical inheritance is thought to limit the spread of elements across different lineages, whereas in Prokaryotic microorganisms horizontal transfer may also occur within generations, in a process thought to be especially important in their genome evolution. Few such horizontal transfers have been documented in Eukaryotes, and so their impact on the evolution of genomes in this domain is less well understood. However, a new analysis of 40 eukaryotic genomes representing the major plant families has found that this type of transfer may actually be far more widespread than previously thought, with 65 percent of the genomes studied having at least one instance of horizontal transfer of a transposable element.
El Baidouri et al. Genome Research