Thursday, December 09, 2004

Do We Also Taste Just Like Chicken?


Fantastic news in science:

Researchers compare chicken, human genomes
http://www.eurekalert.org/pub_releases/2004-12/nhgr-rcc120804.php


Some highlights:

Chicks have less junk DNA:





In their paper published in Nature, members of the International Chicken Genome
Sequencing Consortium report that the chicken genome contains significantly less
DNA than the human genome, but approximately the same number of genes.
Researchers estimate that the chicken has about 20,000-23,000 genes in its 1
billion DNA base pairs, compared with the human count of 20,000-25,000 genes in
2.8 billion DNA base pairs. The difference in total amount of DNA reflects a
substantial reduction in DNA repeats and duplications, as well as fewer
pseudogenes, in the chicken genome.


Of course, core cellular functions are better conserved than recent adaptations:






About 60 percent of chicken genes correspond to a similar human gene. However,
researchers uncovered more small sequence differences between corresponding
pairs of chicken and human genes, which are 75 percent identical on average,
than between rodent and human gene pairs, which are 88 percent identical on
average. Differences between human and chicken genes were not uniform across the
board, however. Chicken genes involved in the cell's basic structure and
function showed more sequence similarity with human genes than did those
implicated in reproduction, immune response and adaptation to the environment.

The analysis also showed that genes conserved between human and
chicken often are also conserved in fish. For example, 72 percent of the
corresponding pairs of chicken and human genes also possess a counterpart in the
genome of the puffer fish (Takifugu rubripes). According to the researchers,
these genes are likely to be present in most vertebrates.



Obviously: chicks have feathers, we have hair. We have milk and teeth - chicken do not. No pheromones in chicken, either.





As might be expected, genomic researchers determined that chickens have an
expanded gene family coding for a type of keratin protein used to produce
scales, claws and feathers, while mammalian genomes possess more genes coding
for another type of keratin involved in hair formation. Likewise, chickens are
missing the genes involved in the production of milk proteins, tooth enamel and
the detection of hormonal substances called pheromones, which researchers say
may mirror the evolution of the mammary glands and the nose in mammals and the
loss of teeth in birds. But other results of the analysis caught even the
researchers by surprise.


I always thought the birds could smell better than usually believed - the tests used (the odorant chemicals) are inappropriate for birds. Also, it appears that the chicken do not taste just like humans:




The analysis showed that a group of genes that code for odor receptor proteins
is dramatically expanded in the chicken genome – a finding that appears to
contradict the traditional view that birds have a poor sense of smell. And, as
it turns out, birds might not have such a great sense of taste. When compared
with mammals, chickens have a much smaller family of genes coding for taste
receptors, particularly those involved in detecting bitter sensations.


This is technically very important:





Alignment of chicken and human genes indicate that approximately 2,000 human
genes may actually start at different sites than scientists thought. The
discovery of these "true" start sites, which appear to lie inside the previously
hypothesized boundaries of the genes, may have implications for the
understanding of human disease and the design of new therapies.


This is waaaay cool! We make bone the way birds make eggshells! On the other hand, formation of bone started in bony fish, while calcification of eggshells started in some reptiles and birds, thus one would think that it was birds who exapted the bone-forming machinery to make shells, not the other way round.

Chicken genes that code for eggshell-specific proteins, such as ovocleidin-116,
have mammalian counterparts that play a role in bone calcification. Previously,
such genes were not known outside of birds. However, the analysis also showed
that, in contrast to chickens, mammals are missing key genes coding for proteins
involved in egg production, such as egg whites and yolk storage.


This will bring in lots of NIH money - OK a larger proportion of the tablescraps NIH will get from Bush:





Chickens have a gene that codes for interleukin-26 (IL-26), a protein involved
in immune response. Previously, this immune-related gene was known only in
humans. The discovery means that the chicken may now serve as a model organism
in which researchers can investigate the function of IL-26.


Photosensitive proteins? Photopigments for circadian (extraretinal) photoreception? Which ones? I will have to look into the paper itself...





Chickens possess genes coding for certain light-dependent enzymes, while mammals
have lost those genes. It is thought losses reflect a period in early mammalian
history in which mammals were active mainly at night.


This may explain why it was so easy to turn Red State chicken (see picture below) into a Blue State chicken, while it is so difficult to domesticate Red State people into Blue State people: we get blue in the face somewhat differently.




The avian genome contains a gene that codes for an enzyme involved in generating
blue color pigments, while mammals are lacking that gene.


More cool stuff:




Besides providing insights into gene content and evolution of genes, the
consortium's analysis offers new perspectives on the evolution of portions of
the genome that do not code for proteins. Less than 11 percent of the chicken
genome consists of interspersed segments of short, repetitive DNA sequences,
compared with 40 to 50 percent of mammalian genomes. With genes comprising
another 4 percent of the chicken genome, researchers say that leaves them with
no explanation for the function of more than 85 percent of the chicken genome.
They hypothesize this genetic "dark matter" may contain previously unrecognized
regulatory elements, but also may include ancient DNA repetitive elements that
have mutated beyond recognition. Furthermore, researchers said it appears that
the 571 non-coding RNA "genes" that they identified in the chicken genome may
use different duplication and/or translocation mechanisms than do regular
protein-coding genes, opening the door to a whole new realm of scientific
inquiry.


Since every chicken gene is 95-100% orthologous with a quail gene, sequencing the chicken is like sequencing the quail, and quail hatches in 17 days and matures in six weeks at about 150g - talk about more prolific breeding than lab mice! A hundred breeding female mice can give you, at best 4000 offspring per year. In the same period of time, a hundred female quail will produce about 26000 offspring. Perhaps I should stay with my lab model. Quail and chicken surely taste better than mice:
http://www.theonion.com/news/index.php?issue=4049&n=1

Not to mention how great it is to do developmental biology in the embryo that is contained inside an egg because eggs are outside of jurisdiction of the Institutional Animal Care and Use Committees. As long as the IACUC approves your breeding colony, you can do whatever you want with embryos - try THAT with mice!


And here is the Red Jungle Fowl - the wild cousin (presumed ancestor?) of the domestic chicken:




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