David Kirkpatrick

May 28, 2010

Nanotech and DNA sequencing

Put the two together and you’ve got a solution for a major problem with the genome sequencing technique called nanopore translocation. And yet another application is found for graphene.

From the link:

But how do you measure the electrical properties of a single subunit among many tens or hundreds of thousands?

One of the most promising ideas is to make a tiny hole through a thin sheet of material and measure the amount of current that passes from one side of the sheet to another.

Next, pull a strand of DNA through this hole and measure the current again. Any difference must be caused by the nucleotide base that happens to blocking the hole at that moment.

So measuring the way the current changes as you pull the strand through the hole gives you a direct reading of the sequence of nucleotide bases in the strand.

Simple really. Except for one small problem. Even the thinnest films of semiconducting materials used for this process, such as silicon nitride, are between 10 and 100 times thicker than the distance between two nucleotide bases on a strand of DNA.

So when a strand of DNA passes through the hole, it’s not a single nucleotide base that blocks it but as many as 100. That makes it hard to determine the sequence from any change in the current.

Today, Grégory Schneider and buddies at the Kavli Institute of Nanoscience in The Netherlands present a solution to this problem. Instead of a conventional material, this team has used graphene, which is relatively easy to produce in sheets just a single atom thick.

Graphene is like a sheet of chicken wire made of carbon atoms. These guys have drilled holes of various diameters through just such a sheet using an electron beam to smash carbon atoms out of the structure.

February 15, 2010

Synthetic biology marches on

Filed under: Science, Technology — Tags: , , , , , — David Kirkpatrick @ 3:36 pm

Via KurzweilAI.netSynthetic biology is here to stay and is branching out.

DNA 2.0: A new operating system for life is created
New Scientist Life, Feb. 14, 2010

University of Cambridge scientists have created a new way of using the genetic code, allowing proteins to be made with properties that have never been seen in the natural world.

The breakthrough could eventually lead to the creation of new or “improved” life forms incorporating these new materials into their tissue. For example, they could help make drugs that can be taken orally without being destroyed by the acids in the digestive tract, or produce entirely new polymers, such as plastic-like materials; organisms made of these cells could incorporate the stronger polymers and become stronger or more adaptable as a result.

In the genetic code that life has used up to now, there are 64 possible triplet combinations of the four nucleotide letters; these genetic “words” are called codons. Each codon either codes for an amino acid or tells the cell to stop making a protein chain. The researchers have created 256 blank four-letter codons that can be assigned to amino acids that don’t even exist yet.
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October 2, 2009

Synthetic biology in the marketplace

Synthetic biology is one of those technologies you’re going to be hearing more and more of in the near future. That is if you haven’t already run across the field after this article was published in the September 28, 2009, issue of the New Yorker. Here’s some news about Ginkgo BioWorks, a company in the marketplace right now creating well, synthetic biological material.

From the final link:

In a warehouse building in Boston, wedged between a cruise-ship drydock and Au Bon Pain’s corporate headquarters, sits Ginkgo BioWorks, a new synthetic-biology startup that aims to make biological engineering easier than baking bread. Founded by five MIT scientists, the company offers to assemble biological parts–such as strings of specific genes–for industry and academic scientists.

“Think of it as rapid prototyping in biology–we make the part, test it, and then expand on it,” says Reshma Shetty, one of the company’s cofounders. “You can spend more time thinking about the design, rather than doing the grunt work of making DNA.” A very simple project, such as assembling two pieces of DNA, might cost $100, with prices increasing from there.

Synthetic biology is the quest to systematically design and build novel organisms that perform useful functions, such as producing chemicals, using genetic-engineering tools. The field is often considered the next step beyond metabolic engineering because it aims to completely overhaul existing systems to create new functionality rather than improve an existing process with a number of genetic tweaks.

February 6, 2009

Synaesthesia and cheaper fuel cells through nanotech

Filed under: Science, Technology — Tags: , , , , , — David Kirkpatrick @ 4:40 pm

From KurzweilAI.net — I’m going old school (old school for this blog) today with post containing multiple bits from today’s KurzweilAI e-newsletter.

First up is a story on the genetic roots of synaesthesia — the condition of seeing sounds and tasting colors and other mixed up signals from the five senses. The second is on carbon nanotubes making fuel cells more cheap and longer lasting.

Genetic roots of synaesthesia unearthed
New Scientist Health, Feb. 5, 2009

The regions of our DNA that wire some people to “see” sounds have been discovered. So far, only the general regions within chromosomes have been identified, rather than specific genes, but the work could eventually lead to a genetic test to diagnose the condition before it interferes with a child’s education.
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Cheaper Fuel Cells
Technology Review, Feb. 5, 2009

University of Dayton researchers have shown that arrays of vertically grown carbon nanotubes could be used as the catalyst in fuel cells.


The carbon nanotubes, which are doped with nitrogen, would be much cheaper and longer lasting than the expensive platinum catalysts used now, with four times higher current densities.

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December 26, 2008

Top 10 genetics articles from 2008

Filed under: Science — Tags: , , , , — David Kirkpatrick @ 1:25 pm

From KurzweilAI.net — The list comes from New Scientist Health and covers subjects such as human genetic modification and MicroRNAs.

Genetics: Top 10 articles from 2008
New Scientist Health, Dec. 24, 2008

The top 10 best features on genetics in New Scientist include Me and my genome, Genetically modified humans: Here and more coming soon, and MicroRNAs: The cell‘s little emperors.

NewScientist.com is now making free all in-depth articles from the past 12 months.

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