life inspired

A Turing machine inside a Turing machine?

"The enormous scale of the invasion of vertebrate genomes by viral sequences has become apparent through analyses of complete genomes. Sequences derived from many kinds of RNA and DNA viruses have found a convenient resting place in host genomes during evolution, and the process is ongoing. Retroviral genomes, the major and best understood viral insertions, alone account for 6 to 14% of the genomes analyzed to date, including ∼8% of human DNA. These endogenous retroviruses (ERVs) comprise more genomic DNA than that encoding the host proteome. The functionality or otherwise of this "junk" DNA has become the focus of an intense debate. Here we consider a number of consequences of ERV acquisition (see the figure"). Full paper @ Scienve

Labels: dna, evolution, Turing machine, virus

"Traces of genetic material from non-retroviruses have unexpectedly turned up in the genomes of several mammal species, including humans." See commentary @ The Scientist. The actual report:

Horie1, M. et al [2010]. "Endogenous non-retroviral RNA virus elements in mammalian genomes". Nature 463, 84-87.

Labels: evolution, RNA, virus

"Tailed bacterial viruses (bacteriophages) are ubiquitously distributed in nature and are likely the most abundant organisms on the biosphere ( 1 1 ). Spending most of their time outside of the host, a bacterial cell, in often hostile external environments, they come to “life” upon encountering the receptor molecules on the host cell surface. The virus consists of a head (capsid) into which the DNA (genome) is packaged and a tail that delivers the genome into the bacterium. The capsid is pressurized because of packing of highly negatively-charged, relatively rigid dsDNA to near-crystalline density (≈500 μg/mL). The internal capsid pressure, ≈6 MPa or >10 times that of bottled champagne ( 1 2 ), provides a driving force for delivery of viral genome into host cell. One of the longstanding questions in phage biology has been how these viruses contain the DNA pressure and trigger release only upon recognition of a specific host cell. In this issue of PNAS, a study by Lhuillier et al. describes the pseudoatomic structure of a DNA gate from the Bacillus subtilis bacteriophage SPP1, which “zips” the capsid after the genome is packaged and unzips it when the virus is ready to infect the host. It is a compelling story, which began with the first in vitro virus assembly experiments described by Edgar and Wood >40 years ago ( 1 4 ) and is applicable not only to phages but also to large eukaryotic viruses such as herpes viruses." Full commentary @ PNAS

The paper: "Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating".

Labels: molecular machinery, virus

Researchers have discovered the first virus to infect another virus, according to a study appearing tomorrow in Nature. The new virus was found living inside a new strain of the viral giant, mimivirus. Full story @ The Scientist : NewsBlog : A virus's virus [6th August 2008]

Labels: virus

This Virtual Virus is the first simulation of an entire life form (from LiveScience.com)

Labels: simulation, virus, whole-organism modeling