[tt] advanced nanotechnology - 5 new articles
Eugen Leitl
<eugen at leitl.org> on
Tue Jul 10 14:21:26 UTC 2007
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Date: Tue, 10 Jul 2007 08:36:52 -0400
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Subject: advanced nanotechnology - 5 new articles
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"[2]advanced nanotechnology" - 5 new articles
1. [3]Air pollution index that is tied to health risk
2. [4]DNA synthesis costs and projections
3. [5]Synthetic biology uses viruses to fight biofilms
4. [6]Synthetic biology and synthetic life milestones
5. [7]Ethics and Gene Therapy
6. [8]More Recent Articles
[9]Air pollution index that is tied to health risk
[10]Toronto, Canada is introducing an air pollution index that is
correlated to health risk This is a good way to make the health risks
of air pollution something that people can be aware of on a daily
basis. If this is used globally it could help movitivate replacing or
cleaning up coal and fossil fuel (diesel oil, gasoline) power sources.
The fastest ways are through a combination of conservation, nuclear
power, hydro power and renewable power.
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[14]DNA synthesis costs and projections
[15]DNA Synthesis - Productivity of DNA synthesis technologies has
increased approximately 7,000-fold over the past 15 years, doubling
every 14 months.
Costs of gene synthesis per bases pair have fallen 50-fold, halving
every 32 months. At the same time, the accuracy of gene synthesis
technologies has improved significantly.
If these technologies continue to improve at the exponential rates
achieved historically, the cost of sequencing will fall to less than
$0.01 per base pair by 2010 and the cost of gene synthesis will fall
to less than $0.10 per base pair.
[16]However,George Church in a 2006 interview indicated the following
prices (already lower than the projection for 2010:
Right now the cost of synthesizing a base [using conventional
technology] is about 10 cents. That's the current street price for
raw oligonucleotides. For synthesizing simple genes, it's more like
$1.30 a base. [Our method] can manufacture oligonucleotides at .01
cent per base.
it [DNA sequencing and synthesis] is actually a very fundamental
concept. There is almost no synthesis that doesn't involve
sequencing, and vice versa. And that is why I have really
emphasized this connection in my lab. They are very synergistic.
Projected DNA synthesis costs (halving cost about every 2.5 years)
2006 10 cents per BP
2007 0.01 to 5 cents per BP
2010 0.005 to 2 cents per BP
2013 0.002 to 1 cents per BP
2015 0.001 to 0.5 cents per BP
2017 0.0005 to 0.02 cents per BP
2007 100 BP synthesized for 1 cent
2010 200 BP for 1 cent
2013 400 BP for 1 cent
2015 1000 BP for 1 cent
2017 2000 BP for 1 cent
Projected DNA synthesis maximum lengths (doubling every 14 months)
YEAR Maximum sequence length
2007 45K (common) to 580K BP (record)
2009 200K (common) to 2M BP
2010 400K (common) to 4M BP
2012 1.5M BP to 16M BP
2014 6M BP to 64M BP
2016 25M BP to 250M BP
The global market for DNA sequencing technology and related services
exceeded $7 billion in 2006. The market for synthesis reagents and
synthesis services is nearly $1 billion.
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[20]Synthetic biology uses viruses to fight biofilms
[21]Synthetic biology used to make viruses to combat harmful
'biofilms'
[biofilm-enlarged.jpg]
This diagram shows how an engineered virus,T7, destroys a biofilm
composed of E. coli bacteria. Graphic courtesy / Timothy Lu and James
Collins
In one of the first potential applications of synthetic biology, an
emerging field that aims to design and build useful biomolecular
systems, researchers from MIT and Boston University are engineering
viruses to attack and destroy the surface "biofilms" that harbor
harmful bacteria in the body and on industrial and medical devices.
They have already successfully demonstrated one such virus, and
thanks to a "plug and play" library of "parts" believe that many
more could be custom-designed to target different species or
strains of bacteria.
The work, reported in the July 3 Proceedings of the National
Academy of Sciences, helps vault synthetic biology from an abstract
science to one that has proven practical applications. "Our results
show we can do simple things with synthetic biology that have
potentially useful results," says first author Timothy Lu, a
doctoral student in the Harvard-MIT Division of Health Sciences and
Technology.
They found that their engineered phage eliminated 99.997% of the
bacterial biofilm cells, an improvement by two orders of magnitude
over the phage's nonengineered cousin.
"We hope in a few years, it will be easy to create libraries of
phage that we know have a good chance of working a priori because
we know so much about their inner-workings," says Lu.
Synthetic biology also makes it possible to control the timing of
when a gene is expressed in an organism. For instance, Lu inserted
the DspB genes into a precise location in the T7 genome so that the
phage would strongly express it during infection rather than before
or after.
Though phages are not approved for use in humans in the United
States, recently the FDA approved a phage cocktail to treat
Listeria monocytogenes on lunchmeat. This makes certain
applications, such as cleaning products that include phages to
clear slime in food processing plants, more immediately promising.
Another potential application: phage-containing drugs for use in
livestock in exchange for or in combination with antibiotics.
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[25]Synthetic biology and synthetic life milestones
[26]Synthetic biology and synthetic life are about to make several
major milestones
Note: the synthesis of 580,000 base pairs of DNA is significant. 3
million base pairs make up a ribosome. Being able to synthesize
580,000 base pairs in 2007 suggests that we could be 1 to 2 years from
synthesizing our own ribosomes. It could also mean that there may not
be serious hurdles to very long synthesizing of millions and billions
of base pairs. There is the question of error rates, but synthesize
sequences could be error corrected. This could be a powerful
bootstrapping method to achieving molecular manufacturing. DNA
nanotechnology would see rapid leaps in capability.
Synthesizing and replacing a bacteria's genome and sequencing DNA
13-15 times longer than previous record:
Scientists at the J. Craig Venter Institute in Rockville, Md., hope
to take a giant stride in synthetic biology by creating a piece of
DNA 580,076 units in length from simple chemicals, chiefly the
material that constitutes DNA's four-letter chemical alphabet. This
molecule would be an exact copy of the genome of a small bacterium.
Dr. Venter says he then plans to insert it into a bacterial cell.
If this man-made genome can take over the cell's functions, Dr.
Venter should be able to claim he has made the first synthetic
cell.
Though human cells effortlessly duplicate a genome of three billion
units, the longest piece of DNA synthesized so far is just 35,000
[I have seen papers claiming 45,000 base pairs] units long.
Synthetic biologists have lofty goals
Adherents of the [synthetic biology] held their third annual
conference last month in Zurich but their creations are still at
the toy rocket stage. A dish of bacteria that generates a bull's
eye pattern in response to the chemicals in its environment. A
network of genes that synthesizes the precursor chemical to
artemisin, an anti-malaria drug. "The understanding of networks and
pathways is really in its infancy and will be a challenge for
decades," says James J. Collins, a biomedical engineer at Boston
University.
That hasn't stopped synthetic biologists from dreaming. "Grow a
house" is on the to-do list of the M.I.T. Synthetic Biology Working
Group, presumably meaning that an acorn might be reprogrammed to
generate walls, oak floors and a roof instead of the usual trunk
and branches. "Take over Mars. And then Venus. And then Earth"
--the last items on this modest agenda.
"The real killer app for this field has become bioenergy," Dr.
Collins says. Under the stimulus of high gas prices, synthetic
biologists are re-engineering microbes to generate the components
of natural gas and petroleum. Whether this can be done economically
remains to be seen. But one company, LS9 of San Carlos, Calif.,
says it is close to that goal. Its re-engineered microbe "produces
hydrocarbons that look, smell and function" very similarly to those
in petroleum, said Stephen del Cardayre, the company's vice
president for research.
FURTHER READING
[27]Cost of DNA synthesis. 10 to 70 cents per base pair in early 2007
(maybe one cent per BP with George Church process) and projected to be
about 1/2000th of one cent per base pair in 2016
it [DNA sequencing and synthesis] is actually a very fundamental
concept. There is almost no synthesis that doesn't involve
sequencing, and vice versa. And that is why I have really
emphasized this connection in my lab. They are very synergistic.
[28]Synthetic biology making viruses that are over 100 times more
effecive at fighting biofilms
[29]DNA factories being made that are anticipating the DNA synthesis
boom
[30]Codon Devices website
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[34]Ethics and Gene Therapy
[35]A New York Times review of THE CASE AGAINST PERFECTION Ethics in
the Age of Genetic Engineering. By Michael J. Sandel.
When norms change, you can always find old fogeys who grouse that
things aren't the way they used to be. In the case of football,
Sandel finds a retired N.F.L. player to support his contention that
today's bulked-up linemen are "degrading to the game" and to
players' "dignity." But eventually, the old fogeys die out, and the
new norms solidify. Sandel recalls a scene from the movie "Chariots
of Fire," set in the years before the 1924 Olympics, in which a
runner was rebuked for using a coach. Supposedly, this violated the
spirit of amateur competition. Today, nobody blinks at running
coaches. The standpoint from which people used to find them
unseemly is gone.
To defend the old ways against the new, Sandel needs something
deeper: a common foundation for the various norms in sports, arts
and parenting. He thinks he has found it in the idea of giftedness.
To some degree, being a good parent, athlete or performer is about
accepting and cherishing the raw material you've been given to work
with.
I view the difference between having gene therapy and not having it:
like 5 card draw which we currently play where we all get random cards
to a change towards Omaha. Choosing the best of two out of four cards
that you are dealt and choosing the best three out of five community
cards. Where we know which cards are best everyone would gravitate
towards taking royal flushes, but just having the genes does not
control the environmental factors. So sometimes it would have been
better to have a full house or four of a kind based on what happens in
the environment. How to judge the cards is still not clearly defined.
If it turns out that low hand wins then a more flexible approach would
be to take a low flush A, 2, 3, 4, 5 a little wheel that is a good low
hand and a good high hand.
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