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Updates in DNA studies along with Anthropological Notes of general interest with a particular emphasis on points pertinent to the study of Ancient Israelite Ancestral Connections to Western Peoples as explained in Brit-Am studies.
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BAMAD no. 49
Brit-Am Anthropology and DNA Update
1 April 2009, 7 Nisan 5769
Contents:
1. Public profiler/world names
2. Brit-Am Right Again??
DNA Changed by Chemicals!! May be Determined by Diet!!
3. EPIGENETICS:
Interesting Video Clips
1. Public profiler/world names
http://www.publicprofiler.org/worldnames/
A very useful tool.
2. Brit-Am Right Again??
DNA Changed by Chemicals!! May be
Determined by Diet!!
Fertilizers shape plant genomes
http://www.the-scientist.com/templates/trackable/display/blog.jsp?type=blog&o_url=blog/display/55500&id=55500
Posted by Elie Dolgin
Extracts Only
Spraying plants with nitrogen-rich fertilizers does more than just make crops
grow bigger; it also molds the chemical composition of their genomes and
proteomes, according to a study published online last week (Mar. 2) in the
journal Molecular Biology & Evolution.
"This tells us how modifications in the environment can have a big effect on a
species and its genome, and how quickly it can happen," said Sudhir Kumar, an
evolutionary biologist at Arizona State University's Biodesign Institute in
Tempe who led the study.
Nitrogen is a scant resource in nature. So Kumar and his postdoc Claudia
Acquisti set out to test whether plants conserve the essential element by opting
to use nitrogen-poor nucleic acids such as thymine, which only contains two
nitrogen atoms, as opposed to guanine with its whopping five N atoms. All told,
an AT nucleotide combo equates to a single nitrogen molecule "savings" compared
to a GC duo. Thus, if nitrogen limitation has shaped plant genomes, one would
expect to find more AT-rich regions, especially in highly transcribed parts of
the genome, which use a lot of molecular resources.
Kumar and Acquisti analyzed the Arabidopsis genome and found that 95% of the
transcribed genome had lower nitrogen content than the genome-wide average. In
contrast, humans and fruit flies, which get plenty of nitrogen from their diets,
had near-identical nitrogen compositions genome-wide and in their transcribed
regions.
The researchers then compared the genomes of Arabidopsis, a wild weed, and
domestic rice (Oryza sativa), the world's third largest crop, and showed that
the rice genome had significantly more nitrogen-rich nucleic acids, although
still less than animals. The researchers also inspected the proteomes of seven
other plant species and found that domesticated species, as well as plants
harboring nitrogen-fixing bacteria, used more nitrogen-rich amino acids. Because
nitrogen is no longer a limiting resource when humans introduce fertilizers into
the soil, "there is a release of selection pressure for nitrogen conservation"
in farmed plants, Acquisti told The Scientist.
Researchers have known for centuries that strong selection "leads to tremendous
changes in phenotypes," noted Kumar. And now it's becoming apparent that "it can
lead to tremendous changes in the genome as a whole."
"If it's true, then it's really interesting because it ties in something as
fundamental as genome structure with diet," said Michael Purugganan, a plant
genome researcher at New York University who was not involved in the study. He
noted, however, that he "would have liked to have seen more comparisons" -- for
example, between wild rice and cultivated rice species. That would confirm
whether the rice genomic nitrogen content has, indeed, shifted over the course
of less than 20,000 generations of domestication, or whether rice differs from
Arabidopsis for other reasons. Purugganan and others are currently working to
sequence and annotate parts of the wild rice genome, so "in less than a year
that comparison can be made," he said.
Purugganan was also "intrigued" that Acquisti and Kumar may have discovered a
reason why plant introns are much more AT-rich than animal introns. This
difference "has been known for 20 years, but no on had an explanation," said
Purugganan. "[The finding] will fuel a lot of debate into whether it's real or
not, and really open the way for more comparisons," he added.
comment:
Other explanations
by null null
This leaves a lot of unexplored explanations.
The most obvious rejoinder is that genome size and so total nitrogen (and
phosphorus) requirement varies enormously between species, by factors of 10 and
100, and would have a much bigger effect on nitrogen requirement than a small
change in AT:GC ratio. That aside, there are other confounding factors.
1/ C.G is more stable (higher melting temperature) than A.T so a higher GC ratio
might be predicted in organisms living at a higher temperature (mammals and
e.coli for example).
2/ Mammals, at least, are well known for having CpG islands at the start of
about half their genes and in mammals the CG content of coding regions is much
higher than in regions with low gene density. This seems to contradict the
comparison referred to above.
3/ cytosine is often methylated to 5methyl cytosine which deaminates to uracil
which can be repaired to thymine and leads to a transition from C.G to T.A,
reducing the frequency of GC in the parts of the genome where such mutations are
not harmful.
4/ Plants are known to use repeat induced gene silencing (RIGS) to mutate and
inactivate transposable elements. This involves systematic methylation of
cytosine in repeated sequences facilitating deamination of C to U and then
replacement by T. This could help explain the high level of AT in plant
transposons. It predicts more AT in larger genomes with more junk transposons.
5/ Animals that feed exclusively on plants, most obviously aphids, are as
nitrogen-limited as their food. The hypothesis predicts that wheat aphids will
have more CG than their relatives restricted to wild-grass.
Maybe I could go on, but this research so far has barely scratched the surface,
and while it is entirely plausible, it certainly does not support any valid
conclusions.
Hugh Fletcher.
comment:
WHOLE WORK OF MINE OVER LAST 10 YEARS FINDS IT ULTIMATE LOGIC!!!
by Jag Rawat
[Comment posted 2009-03-16 01:36:53]
I, as a the-then-International Coordinator of 'International Network of Students
for Environment, Education and Development (www.angelfire.com/pa/INSEED/)
had a spirited debate within Department of Evolutionary Biology of Liverpool
Univrsity (1998 probably) on the issue of 'NPK working as selection pressure on
plant varieties and therefore, it could have been exerting a selection pressure
and varieities eventually were selected, could be categorised as 'NPK intensive
varieities or cultivars'. In this selection, those which would have rather
responded to organic sources of supply of nutrients, got rejected.
Making this hypothesis, I argued that "In this way, all cultivars resposnive to
NPK were being selected over all these years and those responding to organic
sources, got ignored by mainstream plant breeding research".
That kind of historical bias brought all such NPK intensive cultivars and
varieities leading to polluted soils on one hand, while rejection of 'organic
responsive varieties', led the researchers to only research for NPK intensive
varieites.
At that time, I said it was a great tragedy of our times and we launched
'Strengthening Organic Farming Initiative' or SOFI at that time. That was the
time, I being veterinarian, still got intrigued and interested in the field of
evolutionary biology and thought that there could be something which I needed to
do to bring all those 'organic responsive cultivars' back into reckoning of
plant breeding research, improve them and then, challenge all NPK-intensive
varieties. Could we do that? Answer has been rather positive and resounding
success.
Well, a that time also, my spirited debate convinced the Professor in Liverpool
university on the rationality of the thought but still he was not sure of any
evidence of my hypothesis.
Now, that hypothesis stands confirmed and still more work would have to be done
to know that so much alteration and shaping of genome has happened that we would
have to take recourse to original or wildtype genomic sources and trace those
varieties which would be responsive to organic or sustainable inputs. That kind
of approach would not only solve productivity problems but also sustainabability.
Our own success in that field has been tremendous over some 8 years and our
cultivars have been selected precisely on this premise.
Our not-for-profit organisation named HABITAT INDIA (www.meragaonmeradesh.co.cc)
has a very good reservoir of such cultivars for rice, wheat and Arhar.
I think we would be happy to work in field situations and further establish some
of the other issues which are getting more and more understood in the light of
the above discovery.
Kudos to Dr Sudhir Kumar!
Jagveer Rawat
Associate Professor, CCS Haryana Agri University, Hisar INDIA
and Chief Advisor
HABITAT INDIA (www.meragaonmeradesh.co.cc)
The results are interesting as well as intriguing.If fertilizers can affect the
genome then scientists have a wonderful tool to work in this field.It may also
lend more credit to organic farming.
Gian Singh Aulakh
3.
EPIGENETICS:
Interesting Video Clips
The Ghost In Your Genes - Part 1
http://www.youtube.com/watch?v=GOid4jrCeFE&feature=related
The Ghost In Your Genes - Part 2
http://www.youtube.com/watch?v=tg_XpcnoBaM&feature=related
The Ghost In Your Genes - Part 3
http://www.youtube.com/watch?v=VaCepg2avKA&feature=related
The Ghost In Your Genes - Part 4
http://www.youtube.com/watch?v=Cewwd0RPrhk&feature=related
http://www.youtube.com/watch?v=KkScrdldW68&feature=related
The Ghost In Your Genes - Part 5
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