Human endogenous retroviruses: markers of evolution?

As published in the latest issue of Molecular Biology and Evolution…

The human genome hosts numerous endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population, to date there has been no report on their prevalence in the US population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the USA, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in African Americans compared to Caucasians (K113 9% and K115 6%) within the US. We also report the presence of three single nucleotide polymorphism (SNP) sites in the K113 5′ long terminal repeats (LTR) and four in the K115 5′ LTR that together constituted four haplotypes for K113 and five haplotypes for K115. HERV insertion times can be estimated from the sequence differences between the 5′ and 3′ LTR of each insertion, but this dating method cannot be used with HERV-K115. We developed a method to estimate insertion times by applying coalescent inference to 5′ LTR sequences within our study population, and validated this approach using an independent estimate derived from the genetic distance between K113 5′ and 3′ LTR sequences. Using our method we estimated the insertion dates of K113 and K115 to be a minimum of 800,000 and 1.1 million years ago, respectively. Both these insertion dates pre-date the emergence of anatomically modern Homo sapiens.

PMID: 19666991 [PubMed – as supplied by publisher

My forgotten Dreamcatcher

You know about the things that we get and forget right? We do that all the time. I bought a dreamcatcher once in a Mexican arts and craft store where I went to shorten my wrist-watch’s metal band. I did not know what a ‘dreamcatcher’ was at that time. According to Wikipedia,

According to Terri J. Andrews, “Only good dreams would be allowed to filter through . . . Bad dreams would stay in the net, disappearing with the light of day.”[4] Good dreams would pass through and slide down the feathers to the sleeper.

The store operator told me…or I understood it so that a dreamcatcher brings your dreams come true…so, I bought one… it was made out of leather, red leather on the outside, yellow on the inside with one long white feather and another short one on top of it. It looked beautiful. I bought it for its aesthetic appeal rather than its associations with dreams.

In any case, I placed it above the computer of my laptop dock on my desk and it probably fell behind the screen and I forgot about it. At that time, I was a recent graduate with shameful grades and struggling finances and therefore a low self-esteem of all times. In those days I used to dream about having my own project, my own publications and going to graduate school…which is where I am today.

Today is my last day at work. As I was cleaning my desk to head out to Africa tomorrow and then to Chicago for my PhD, I found my dreamcatcher behind the computer screen. May be it was there this whole time catching me good dreams and making my dreams come true. I had an option to chug it or take it with me…guess what I did….you guessed it right. Its in the box with “The most valuable things” scribbled on it.

Matt Ridley finally proven right!

The Red Queen

(Image obtained from here)