Wednesday, April 16, 2014

Aotus monogamy

Observations suggest that Azara's Owl Monkey is monogamous, which is rare in the animal kingdom.  they are the first primate to be documented as being monogamous.
**Note: I saw this blurb in the NY Times Science Times a few weeks back and forgot to post it--sorry for the delay!  The NY times blurb and the original paper are linked here:

Tuesday, April 15, 2014

Correlated evolution of sensory structures and sensory genes in mammals

An article by Garrett & Steiper just published in Proceedings of the Royal Society B looked at anatomical correlates of main olfactory system (ethmoid) and vemoronasal system (vemoronasal organ, VNO) across mammals as well as the size of the related gene families (OR, V1R, and V2R) in mammalian genomes. They found that absolute ethmoid area is correlated with the proportion of functional ORs and that the relative size and complexity of the VNO is correlated with proportion of functional V1R genes in mammalian genomes. These results show nice concordance between anatomical and molecular evolution and may indicate a role for natural selection in the evolution of these genes families.

Monday, April 14, 2014

Genome wide association of methylation with BMI

A recent issue of The Lancet featured an epigenome wide association study (EWAS) of methylated CpGs associated with BMI. Sites were identified in an initial cohort of 479 Europeans and, after filtering data for false positives, inspected in a replication cohort of 339 people. Sites still significant were tested in a larger second replication cohort of 1789 individuals. Five sites were identified as significantly associated with BMI, three of which fall within the first intron of the gene HIF3A, which encodes a subunit of the Hypoxia Inducible Transcription Factor (HIF). Chromatin state at this intron indicates regulatory activity. For all these cases, increasing methylation is linearly correlated with increasing BMI. Notably, the association is tissue specific, manifesting in blood and adipose tissues, but not skin.

Sunday, April 13, 2014

Alu elements found to function similarly to enhancers

In a recent issue of Cell authors Su et al. carried out genome-wide analyses of genomic distribution, evolutionary conservation, histone positioning and epigenetic profiles to examine the characteristics of Alu elements. They found that Alu elements in multiple tissues and cell-lines resemble those of putative transcription enhancers. They also find that Alus show long-range interactions with gene promoters, and their similarity to enhancers becomes more prominent with their age in the human genome. The authors conclude that some Alu elements can function as enhancers, and, further, that many more Alus may be proto-enhancers that serve as a repertoire for the de novo birth of enhancers.

A critical period discovered in development of the olfactory bulb

Authors Tsai and Barnea report in the most recent issue of Science that a critical period exists during which an olfactory “sensory map” becomes established. Previous findings show that the olfactory system exhibits enhanced plasticity that is maintained throughout life due to continuous neurogenesis of sensory neurons in the nose and olfactory bulb. However, the authors found evidence in mice that there is less plasticity than originally thought and that a sensory map is created during a developmental critical period. Specifically, the authors were able to test the neural pathways of transgenic mice, finding that perinatal expression of the transgenic odorant receptor (i.e. before the sensory map is established) led to activation of new axons. In contrast, expression of the transgenic receptor after the sensory map was established did not activate new axons.

Sunday, April 6, 2014

A review of methods for DNA methylation analysis

Peter Laird, in a 2010 issue of Nat. Rev. Genet., reviews the technology of genome-wide DNA methylation analysis. The review gives the pros and cons of each methodology, as well as the principle behind the analyses. Additionally, he provides information on statistical issues and a list of bioinformatics resources for DNA methylation analysis.

Positive selection of hair, skin and eye pigmentation in Europeans over the last 5000 years

In the current issue of PNAS Wilde et al. find evidence for positive selection of skin, hair and eye pigmentation in Europeans during the last 5000 years. They looked at selection acting on three polymorphic sites that been previously identified in GWAS and fine-mapping SNP association as related to pigmentation in Europeans. They used ancient DNA and computer simulations to estimate the strength of selection on these genes. Their results and analyses indicate that positive selection on pigmentation variants associated with depigmented hair, skin and eyes has been operating within western Eurasia for the past 5000 years. The authors propose two hypotheses for the selection on hair and eye color, in particular. They hypothesize that changes in hair and eye pigment may be byproducts of a selection on skin pigment, or they propose that selection for depigmented eyes and hair may be driven by mate preference.

Saturday, April 5, 2014

An In-depth look at gene expression in the developing brain

Miller et al. published a paper in this week's Nature describing the group's study of gene expression in the brain across tissue types during gestational weeks 15-21. RNAs were analyzed from over 300 anatomical regions and in situ hybridization was used to localize expression of elements of interest. Several genes show differential patterns of expression in humans compared with the mouse. Genes nearby human-accelerated noncoding regions show high differential expression among different regions of the neocortex. Notably, FOXP2 expression is enriched in putative language areas. More about the paper's many analyses and findings can be heard on the Nature podcast.