Open Reading Frame: from big cat genomes to cell locomotion

Posted by Biome on 27th September 2013 - 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.


What makes a popular pooch?
An analysis of breed statistics from the US Kennel club database, containing records of more than 50 million dogs registered over the past 80 years, finds that some traits which might be considered favourable – such as longevity, health and a good temperament – are not correlated with overall popularity, measured by ownership. Instead, breed popularity over the past century is more likely to have been driven by changing fashions and fads, than by function.
Ghirlanda et al. PLoS One


Big data from big cats: Genome sequence of the Amur tiger
The first tiger genome sequence assembly and annotation reveals a 95.6 percent similarity to the domestic cat from it which diverged 10.8 million years ago. Comparative analysis with the genomes of other big cats like the snow leopard and African lion finds possible genetic signatures for their carnivorous lifestyle and powerful muscle strength, and could prove to be a valuable resource for future conservation efforts of these threatened species.
Sung Cho et al. Nature Communications


New methods to study how cells do the locomotion
How cells interact with one another when they come in to contact can be an important part of many biological processes; for example, directing the wound healing responses of epithelia. By contrast, regulatory failure of these contact processes can lead to malignancy, manifest in the invasiveness of cancerous cells. This concept is known as ‘contact inhibition of locomotion’, but due to the infrequency and unpredictability of some contact collisions, has so far proved difficult to study. Now a new assay to restrict such collisions to a one-dimensional surface guides cells into microscale furrows on an assay plate, in order to better manipulate their motility.
Scarpa et al. Biology Open


“It is essential that plant data are made available”
The vast amount of data generated by new high-throughput methods means that far more data is generated in the course of most experiments than is often needed for their final analysis. Developments in the fields of transcriptomics, metabolomics and proteomics means that large, open-access databases are readily available in which to make this data discoverable and re-usable  for all scientists. However, understanding what data should be deposited and where can be something of a minefield. A Commentary article in the Journal of Experimental Botany aims to summarise the current state of these fields for practising plant scientists, guiding them through the available options. The authors conclude that community-driven initiatives to improve access to data are essential to foster growth in the plant sciences and related disciplines.
Leonelli et al. Journal of Experimental Botany


Apes go for grapes when given a choice
In the wild, chimpanzees live in complex groups in which social interactions may mediate foraging decisions. However, the extent to which individuals are influenced by the perceived success of their social partners may vary among different species of non-human primates. In a reward-based feeding experiment in which chimps were offered the choice of high-value items like grapes versus low-value items like celery, individuals attempted to maximise their own rewards when they had previously received low-value items, regardless of the level of reward that they had seen other chimps given. However, they would only do so if they could be certain of receiving a high-value item. When food rewards could not be improved, individuals agreed to low-value items only when their test partners were also perceived to be obtaining the same low-value items, suggesting that some form of social facilitation does operate in this species.
Hopper et al. PeerJ


Identifying the master switch in fungal spore formation
In order to reproduce successfully, filamentous fungi such as Streptomyces send out aerial spores. A protein called WhiA  plays a critical role in initiating this sporulation, with mutant fungi lacking the protein being unable to proceed to the aerial phase of spore formation. Intriguingly the protein is also found in all Gram-positive bacteria, even those that do not sporulate. Understanding the regulatory networks that switch spore formation on and off will therefore provide valuable insights into the evolution of this feature of the fungal life-cycle. Previous work on this system has been hampered by logistical problems in obtaining sufficient fungal biomass in the spore phase to be able to use genomic techniques such as CHIP-seq. However, an emerging model species, Streptomyces venezuelae is able to overcome this by sporulating entirely in liquid culture. Applying the CHIP-seq techniques to this new system has now allowed researchers to confirm WhiA as a transcription factor and characterise the genes involved in spore formation that are under its control.
Bush et al. mBio