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Posts from the ‘DNA’ Category

Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases

It’s a pleasure to share the great news that we just published our review in Trends in Molecular Medicine under the title, Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases. We looked at the literature and wrote about whether peripheral blood can be used for the diagnosis of autoimmune diseases or the prediction of the effectiveness of therapies. We also came up with a decision tree and a set of proposed guides in order to facilitate inter-disciplinary collaborations.

The paper is not publicly available, but if you are interested, I’d be happy to send it to you via e-mail.

Gene expression profiling in clinical genomics has yet to deliver robust and reliable approaches for developing diagnostics and contributing to personalized medicine. Owing to technological developments and the recent accumulation of expression profiles, it is a timely and relevant question whether peripheral blood gene expression profiling can be used routinely in clinical decision making. Here, we review the available gene expression profiling data of peripheral blood in autoimmune and chronic inflammatory diseases and suggest that peripheral blood mononuclear cells are suitable for descriptive and comparative gene expression analyses. A gene-disease interaction network in chronic inflammatory diseases, a general protocol for future studies and a decision tree for researchers are presented to facilitate standardization and adoption of this approach.

Electromagnetic signals from bacterial DNA?

Luc Montagnier received the 2008 Nobel Prize in Physiology or Medicine for his discovery of the human immunodeficiency virus (HIV), but now he came up with a more than strange theory. He thinks DNA can teleport from one tube to another via electromagnetic signals. Is this the so-called Nobel-disease?

French virologist Luc Montagnier stunned his colleagues at a prestigious international conference when he presented a new method for detecting viral infections that bore close parallels to the basic tenets of homeopathy.

Although fellow Nobel prize winners — who view homeopathy as quackery — were left openly shaking their heads, Montagnier’s comments were rapidly embraced by homeopaths eager for greater credibility.

Montagnier told the conference last week that solutions containing the DNA of pathogenic bacteria and viruses, including HIV, “could emit low frequency radio waves” that induced surrounding water molecules to become arranged into “nanostructures”. These water molecules, he said, could also emit radio waves

He suggested water could retain such properties even after the original solutions were massively diluted, to the point where the original DNA had effectively vanished. In this way, he suggested, water could retain the “memory” of substances with which it had been in contact — and doctors could use the emissions to detect disease.

Programming DNA

In 2007, Drew Endy (Endy Lab) talked about Programming DNA, a 2-bit language for engineering biology, at the 24th Chaos Communication Congress on biological engineering and synthetic biology.

This talk will introduce current best practice in biological engineering, including an overview of how to order synthetic DNA and how to use and contribute standard biological parts to an open source collection of genetic functions. The talk will also discuss issues of human practice, including biological safety, biological security, ownership, sharing, and innovation in biotechnology, community organization, and perception across many different publics.

(Hat Tip: Biopunk)

Sounds of HIV

A few months ago, Alexandra Pajak, a graduate student at the University of Georgia contacted me about an album of music based on the DNA of the HIV virus she was about to release.  I feel lucky that the album is just on its way to my CD player right now. You can buy the album on Amazon (release date: 26, October). Note that some of the proceeds will go to the Emory Vaccine Center, which conducts research for an HIV vaccine. If you wonder how it was made, here is the explanation:

Sounds of HIV is a musical translation of the genetic code of HIV, the Human Immunodeficiency Virus.  Every segment of the virus is assigned music pitches that correspond to the segment’s scientific properties.  In this way, the sounds reflect the true nature of the virus.  When listening from beginning to end, the listener hears the entire genome of HIV.

In English, the nucleotides Adenine, Cytosine, Uracil/Thymine, and Guanine are abbreviated with the letters A, C, T, and G.  Since A, C, and G are also musical pitches in the Western melodic scale, these pitches were assigned to the matching nucleotides.  To form two perfect fifths (C-G and D-A), “D” was arbitrarily assigned to musically represent Uracil.  I assigned the pitches of the A minor scale to the amino acids based on their level of attraction to water.

On “Sounds of HIV,” depending on the track, only nucleotides and/or amino acids “play” as music.  Tracks 1 and 10 are based on the first and last nucleotides of the RNA chain.  Tracks 2-9 “play” the proteins and sometimes the nucleotides on top of the proteins.

Personalized Genomics in the News

I would like to share three papers, articles that focus on the personalized genomics market with you. Almost 3 years ago, I wrote about that FDA had suggested two genetic markers to be used to determine the minimal starting dose of Coumadin. Later, in a paper, Rosove et al. said that “The value and cost-effectiveness of genetic testing to reduce bleeding or thrombosis rates remain unknown.”

Well, now it seems there is the answer.

Patients who received a test of two genes connected to warfarin sensitivity were 28 percent less likely to be hospitalized for a bleeding episode or blood clot than those whose safe and effective warfarin dosing was determined by traditional trial and error method.

Also researchers have provided the first published example of genome-scale RNA and DNA sequencing of a tumour to aid in clinical decision making and therapeutic choice.

“Utilizing a complete map of the molecular changes within a tumour in a clinical setting represents a world first in the application of this technology,” says Dr. Steven Jones, associate director of the Genome Sciences Centre and professor, Simon Fraser University. “It ushers in the era of personalized medicine in oncology, whereby therapies will be tailored precisely to the genetic make-up of the tumour. I anticipate that in the not too distant future nearly all patient tumours will be characterized in this way as a matter of course.”

And Health Populi reported a very interesting correlation between DTC ads, genetic pre-disposition, and healthy decisions:

A team of researchers now finds that DTC can play an important, positive role in motivating health consumers to adopt healthy behaviors. “The intention to engage in healthy lifestyles was strengthened by exposure to familial risk cues in DTC ads and this effect was mediated through enhanced efficacy to take healthy actions,” the paper concludes. Familial risk cues engendered positive self-efficacy.

DNA Mutations in Real Time: Video

One of my favourite blogs, Spoonful of Medicine, just posted a great video which shows that mutations in E. coli bacteria can be tracked in real time. The method was published in Current Biology.

The key to this approach is using a fluorescent-labeled derivative of MutL, a protein involved in DNA mismatch repair. The accumulation of this fluorescent protein signals the occurrence of a mutation in a population of replicating E. coli bacteria. Even more significantly, this method allows the visualization of mutations that do not result in recognizable phenotypes. That means that it could be used to alert researchers to DNA errors they are not even looking for. The video below shows 180 minutes of E.coli growth compressed to 12 seconds:

Personalized Genomics News: From Virtuality to the Streets

  • DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful.

“Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.”

The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three prominent DTC companies: 23andMe, Pathway Genomics and Navigenics.

  • 23andme: A detailed review of the data the blogger just received from 23andMe.

The family said they received no medical counseling here and are making their own conclusions.  One comment made is that the parents stated they will probably be using more pharmaceuticals, interesting.

A patient analyzes her own 23andMe data:

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