Frontiers in Plant Science
Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses
Within the genome of each species, there are thousands of stretches of DNA that undergo little change in position and sequence over millions of years, but do not code for any proteins. Some of these evolutionarily stable sequences, so-called conserved noncoding sequences (CNSs), are known to regulate the expression of other genes or the condensation of chromosomes, but the function of many CNSs remains unknown. Michael Freeling and colleagues from Berkeley here present their new open-source program "CNS Discovery Pipeline 3.0" which has taken three programmers six years to develop and can automatically find CNSs in newly sequenced genomes. The authors show that the program gives highly accurate results in a short time, requiring only 30 minutes to find the same number of CNSs as two trained biologists could do in two years. By helping us to understand how key genes are regulated, the program's output can boost medicine and the breeding of new crops.
URL: http://www.frontiersin.org/Plant_Genetics_and_Genomics/10.3389/fpls.2013.00170/abstract
Source code for CNS Discovery Pipeline 3.0 at: https://github.com/gturco/find_cns
Instructions for installation at: https://github.com/gturco/find_cns/blob/master/INSTALL.rst
Researcher contact
Prof Michael Freeling
Department of Plant & Microbial Biology
University of California at Berkeley
Email: freeling@berkeley.edu
Frontiers in Behavioral Neuroscience
Spatial learning of female mice: a role of the mineralocorticoid receptor during stress and the estrous cycle
In a stressful situation, rodents produce the stress hormone corticosterone. This helps the animal, because spatial learning is promoted when corticosterone binds to one of the stress hormone receptors (mineralocorticoid receptors) in the hippocampus, a region of the brain. Judith ter Horst and colleagues from Leiden University here show that female mice that lack the gene for the mineralocorticoid receptor in the forebrain have difficulty finding their way home through a maze, especially shortly before ovulation. The interaction between female sex hormones and stress hormones could result in worsening of spatial learning. There was also an interaction with stress: it was easier for mutant females to find their way home after they had been briefly and gently restrained, probably due to an increase in corticosterone levels in the blood. Ter Horst and colleagues conclude that mineralocorticoid receptors are necessary for efficient spatial learning by female mice.
URL: http://www.frontiersin.org/Behavioral_Neuroscience/10.3389/fnbeh.2013.00056/abstract
Researcher contact:
Dr Judith ter Horst
Division of Medical Pharmacology
Leiden Academic Center for Drug Research and Leiden University Medical Center
Leiden University
Tel: +31 205257719
Email: j.p.f.terhorst@uva.nl
Frontiers in Neuroscience
Abrupt changes in the patterns and complexity of anterior cingulate cortex activity
It simply feels good to regain your bearings after getting lost, especially when you are hungry and had been looking for a particular restaurant. Jeremy Seamans and colleagues from the University of British Columbia, Canada, here show that hungry rats experience a similar abrupt neural change when they stumble upon food in an unfamiliar environment. They recorded patterns of activity in the medial prefrontal cortex of the brain, an area implicated in the regulation of behavior and emotion. When the rats first realized that food had to begun to literally drop from above, their patterns of brain activity changed abruptly and dramatically from preceding patterns, characteristic of hungry rats that are busy exploring a new enclosure. Not only were the patterns completely different after finding the food, but they were also simpler. Seamans et al. conclude that whenever a critical goal is realized, the medial prefrontal cortex can change abruptly from a "search state", where many outcomes are possible, to a simpler "consumption state" that needs to consider fewer outcomes: principally, the outcome of digging into tasty food.
URL: http://www.frontiersin.org/Decision_Neuroscience/10.3389/fnins.2013.00074/abstract
Researcher contact
Prof Jeremy K. Seamans
Department of Psychiatry
Brain Research Centre
University of British Columbia
Tel. : +1 6048227759
E-mail: Jeremy.seamans@ubc.ca
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