Saturday, January 25, 2014

New Domestic Organism Genome: The Sugar Beet

This Nature paper announces the genome sequence of the sugar beet, a domestic crop that provides ~30% of the world’s sugar. The completed sequence was ~567Mb with over 27,000 predicted genes and 3,000 predicted ncRNAs. The researchers used a combination of 454 and Illumina platforms, as well as Sanger sequencing. The functional categories of defense and response to stress were enriched among gene families showing gain and loss. Resequencing of the genomes of several other sugar beet specimens revealed large “variation deserts,” most likely reflecting domestication. 

Thursday, January 23, 2014

Future goals for genome analysis

This recent commentary article discusses how scientists should collaborate on genome analysis projects to provide the most comprehensive analysis of Mendelian disorders and share the wealth of data.  In addition, the author suggests that published genomic data should be thoroughly reviewed in a systematic way to ensure completeness of the data.

Wednesday, January 22, 2014

Optogenetic and Electrical Microstimulation Systematically Bias Visuospatial Choice in Primates

Hi all, this article explains the successful use of optogenetics to control neural activity in primates. I learned a little bit about optogenetics in my biochemistry lecture during the fall, and it was fascinating to come across this article.  Optogenetics employs using neurons that have been genetically modified to express membrane proteins that are sensitive to light.  Current methods involve electrical microstimulation to control neural activity, but recent studies like the one here show that optogenetics might be a better alternative.  These studies have been successfully done in other mammals such as rodents, but this is the first study to successfully accomplish using optogenetics to control primate behavior.

Change in diet can rapidly change the human gut microbiome

This study from today’s Nature provides strong evidence for the quick-acting impact of diet on the gut microbiome. To address hypotheses suggesting that diet has a role in shaping the human microbiome, and especially in industrialized societies where diet has changed considerably in the last century, David et al. put subjects on either an animal-based or plant-based diet and sampled their microbiomes. They found that microbial community structures were altered as soon as one day after the first meal of the diet reaching the distal gut. The microbial communities of those consuming the animal-based diet increased in bile-tolerant bacteria and decreased in species performing carbohydrate fermentation. This study demonstrates the impressive plasticity of the human gut microbiome and may suggest a link between animal-protein-rich diets and diseases like inflammatory bowel disease.