First transgenic primates

Four marmosets, whose parents were given a gene to create green fluorescence, have been born with the gene. That makes them the first artificially transgenic primates. `

The image shows These marmosets are the first transgenic primates. Here are the baby pictures of a: Hisui (Jade), b: Wakaba (Young Leaf), c: Banko, d: left, Kei; right, Kou. Insets show one of each baby’s paws (right) beside the paw of a nontransgenic marmoset under ultraviolet light. Except for Banko, the transgenic animals make green fluorescent protein in their skin.
(Image credit: E.Sasaki et al., 2009, in Nature)

Origin of the Immune System

Science 1 May 2009:
Vol. 324. no. 5927, pp. 580 – 582
DOI: 10.1126/science.324_580

On the Origin of the Immune System
John Travis

“The elucidation of VDJ recombination gradually exposed immunology’s big bang, recalls David Schatz of the Yale School of Medicine. By 1990, he and other colleagues then working in David Baltimore’s lab at the Whitehead Institute for Biomedical Research in Cambridge had identified two genes essential to VDJ recombination, RAG1 and RAG2 (for recombination-activating genes). Sharks and all the other jawed vertebrates with adaptive immunity have these genes, but all the evidence at the time indicated that hagfish, lampreys, and invertebrates didn’t. So, where did RAG1 and RAG2 come from?

Several clues, including that the two genes are located immediately next to each other, prompted Schatz and his colleagues to wonder whether the pair had once been part of a DNA recombination system in fungi or viruses that got incorporated into vertebrates. As immunologists teased out what the proteins encoded by the two did, they realized the molecules are the scissors and knitting needles that cut out all but one V, D, and J and stitch those remaining three gene segments together.

In 1995, Craig Thompson, then at the University of Chicago in Illinois, formally proposed that the DNA now encoding RAG1 and RAG2 was once a mobile genetic element called a transposon. Transposons can cut themselves out of one DNA sequence and stick themselves back in another, so immunologists could envision those skills being co-opted to recombine V, D, and J gene segments. In this “transposon hypothesis,” Thompson suggested that at some point after jawed and jawless vertebrates split into two branches, about 450 million years ago, a transposon invaded the former lineage, perhaps brought in by a virus that infected a germ cell. Boom—the enzymes that would ultimately provide adaptive immunity, by creating diverse antibodies and T cell receptors, were now in place and could mutate into that new role.

Many research teams began trying to verify the transposon hypothesis. In 1998, for example, Schatz’s team and one led by Martin Gellert of the National Institute of Diabetes and Digestive and Kidney Diseases in Bethesda, Maryland, independently showed that the enzymes encoded by RAG1 and RAG2 could, in addition to cutting out DNA sequences, actually insert one stretch of DNA into another. In a commentary in Nature, immunologist Ronald Plasterk of the Netherlands Cancer Institute in Amsterdam expressed the awe of many at this solid evidence of the transposon hypothesis. “We may owe our existence to one transposition event that occurred 450 million years ago,” he wrote.”

VDJ are different variable, diversity, and joining genes that generate incredible diversity in immunoglobulin (Cellular Immunology blog) and thus in our immune systems. RAG1 and RAG2 are recombination activating genes.

The VDJ recombination mechanism in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Although no transposase sequence similar to RAG1 or RAG2 has been found, the approximately 600-amino acid “core” region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. It has been demonstrated that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs.[r] These findings refute one of [Michael] Behe’s claims for irreducible complexity of complex biochemical features.

Blue sparrow seen in Australia

In April, GrrlScientist posted a picture of a blue house sparrow seen in April among normal colored birds. She commented on the nature of its mutation.

Passer domesticus, var. blue

Birds and butterflies aren’t blue because of pigment but because of their surface texture of their feathers or scales, so I’m guessing that this is a structural change in the feathers.

It would be very interesting to get the local university to put up a mist net, band their catch, and perhaps pluck a feather or two. I’m curious about the genetics of family members — I wonder if some of the brown ones are heterozygous for blue feathers and how many ordinary sparrows it would take to find out. And will the chicks dig it?

GrrlScientist has a follow-up and more photos from the one who spotted this bird in Sydney, Australia, in April.

Genetic analysis confirms pattern of sheep domestication

Manx Loaghtan sheep, from the Isle of Man, have 4 – 6 horns

Blogger Abbie Smith at ERV has the story: “Bah bah black sheep, have you any ERVs?”.

The gist of it is that ERVs are viral genomes which read themselves into an individual’s DNA. If the infected cells are in the eggs or sperm, the ERV is passed on to all descendants, who have the same virus at a unique location in their chromosome.

ERVs mutate rapidly, which makes it possible to trace different lineages of the same original ERV and put them into a tree diagram showing who broke off first and who’s descended from the breakaway group vs. the original group.

The evidence thus gathered confirms historical evidence about the domestication of sheep in southwest Asia in two waves. In some remote places, farmers kept on breeding the older types. The details are interesting and the explanation is amusing.

Simple arithmetic washes out Flood story

The Talk Origins post of the month for February is by Lenny Flank: “Is present human diversity possible if only eight people survived Noah’s Flood?”

The first stumbling block is how much genetic variation got off the boat. Lenny points out that with eight people and two genes each for each gene location, the whole family, even if none of them shared a single gene, could carry only 16 alleles (variations) for each gene. Larry writes:

today we find human genetic loci (such as hemoglobin or the HLA complex) that have well over *400* different alleles (indeed some have over *700* different alleles). Hmmmm. Since there could have only been 16 possible on the Big Boat, and since there are over 400 now, and since 400 is more than 16, that means that somehow the GENETIC INFORMATION INCREASED from the time they got off the Big Boat until now.

And he goes on from there.

Read “Is present human diversity possible if only eight people survived Noah’s Flood?“

God drowns children because their parents displease Him

Mark Twain wrote:

Then at last, Noah sailed; and none too soon, for the Ark was only just sinking out of sight on the horizon when the [dinosaurs] arrived, and added their lamentations to those of the multitude of weeping fathers and mothers and frightened little children who were clinging to the wave-washed rocks in the pouring rain and lifting imploring prayers to an All-Just and All-Forgiving and All-Pitying Being who had never answered a prayer since those crags were builded, grain by grain, out of the sands, and would still not have answered one when the ages should have crumbled them to sand again.