Recent Changes

Monday, October 27

  1. page space.menu edited [[include component="navigation"]]
    [[include component="navigation"]]
    (view changes)
    12:56 pm

Tuesday, July 22

Monday, February 3

  1. page The Phoenix Virus. edited ... Abstract Human Endogenous Retroviruses are expected to be the remnants of ancestral infection…
    ...
    Abstract
    Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral “progenitor” element of one of the most recently amplified family—the HERV-K family—and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.
    {phoenix-200.jpg}
    I'll start with an analogy to help explain what the Phoenix virus is about and what it tells us. Instead of a stretch of DNA, we'll look at a piece of text.
    There is no need to do more than skim the next two paragraphs, but see if you can spot a few mistakes before moving on to the next section.
    (view changes)

Sunday, January 26

  1. page Were Retroviruses Created Good? A Critique. edited The evidence from retroviruses provides powerful evidence for different kinds of creatures having h…
    The evidence from retroviruses provides powerful evidence for different kinds of creatures having had common ancestors.
    ...
    ancestry, as ignores itignore it, and instead
    The article uses technical terms that mean little to the reader who has not already studied the subject. However, the facts behind these technical terms are very easy to understand. Dr. Liu provides a brief glossary, but in my opinion, it is inadequate for the general reader. To familiarize yourself with the subject of retroviruses, please click on this introductory course which will open in a new window or tab. For further assistance, I have attempted to explain and clarify Liu's writing (which is indented here) at the same time as critiquing it. I will also be adding links throughout this page, both in my quotes of the AiG article, and in my own notes. All such links will be my own.
    We begin by examining Dr. Liu's abstract.
    (view changes)
  2. page Were Retroviruses Created Good? A Critique. edited ... {HorseInAStable.jpg} A xenotropic ERV is an ERV that is unable to infect the cells of the spec…
    ...
    {HorseInAStable.jpg} A xenotropic ERV is an ERV that is unable to infect the cells of the species it is inhabiting. We will go into this 'problem' for the endogenization theory (the theory that ERVs are remnants of infections of germ cells) in more detail later. The problem amounts to the same sort of problem one might have if one fails to understand how a horse can come to be in a stable, because the stable door is shut. (The solution involves recognizing that the stable door was not necessarily always shut.)
    ... and essentiality of some ERVs in host physiology. Syncytins, products of the env gene of HERV-W and HERV-FRD, contribute to human placenta development. Similar genes are also found in mouse and sheep. Indeed, the sheep ERV genes have been shown essential for sheep reproduction. Furthermore, regulation of the human syncytin-1 gene involves a complex regulation network including both viral and host factors.
    ...
    the target cell. This makescell, and they can cause the fusion of more cells to create a syncytium, which is a "supercell" containing multiple nucleii. HIV, for example, combat's T-cells by "swallowing" them into syncytia. This such env proteins are thus ideal candidates for being cooptedco-opted by the
    ...
    as syncytin proteins, which bindproteins for their own purposes, binding certain cells of the placenta with thoseto create the syncytial cell layers of the uterus.placenta. 2) No
    Conclusion: While intact ERVs with positional polymorphism are likely germline copies of exogenous viruses, ERVs with fixed locations and conserved beneficial genes may have been incorporated into the host genome at the time of creation. Exogenous retroviruses may have been created to help the ERVs and to transfer useful genes between hosts.
    'Positional polymorphism' just means 'found in different locations'. The koala retrovirus, KoRV, for example, has been inserted into germ cells in different DNA locations in different groups of koalas. Each example, however, is heritable, and appears in the same location in every cell of the offspring that inherit it. Liu tries to contrast these with "ERVs with fixed locations and conserved beneficial genes", neglecting to mention their non-conserved nonfunctional genes and neglecting to mention ERVs and ERV remnants with fixed locations and no conserved beneficial genes at all - only around 200,000 of them in our genomes. As has already been noted, ERVs with beneficial genes are hardly star witnesses for design anyway.
    (view changes)

Saturday, May 18

  1. page The Phoenix Virus. edited ... The "Phoenix Virus": an explanation of an experiment Reference: Identification of a…
    ...
    The "Phoenix Virus": an explanation of an experiment
    Reference: Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
    Abstract
    Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral “progenitor” element of one of the most recently amplified family—the HERV-K family—and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.

    I'll start with an analogy to help explain what the Phoenix virus is about and what it tells us. Instead of a stretch of DNA, we'll look at a piece of text.
    There is no need to do more than skim the next two paragraphs, but see if you can spot a few mistakes before moving on to the next section.
    (view changes)

More