Crowdsource and crowdfunding are everywhere these days.
Jimmy Lin, a medical student at Johns Hopkins University, and other young scientists created the Rare Genomics Institute, a non-profit that leverages falling DNA sequencing costs and rising online giving to support medical research. Great idea!
In mid-July, the institute announced that it had completed its first crowdfunded gene sequencing and discovered what it believes is the root cause afflicting 4-year-old Bronx resident Maya Nieder. The girl can’t speak, and doctors are unsure whether she can hear. They had likewise failed to determine why she has missed so many developmental milestones. Lin’s team posted Nieder’s story online, and within hours donors had given the $3,500 needed to sequence key slices of the Nieder family’s DNA. (Yale University covered the rest of the costs.) The results, RGI says, point to a flaw in a gene crucial to fetal development.
Moreover, my friend, Lucien Engelen just published the results of his genomic analysis at 23andme. He aims at crowdsourcing potentially underlying genetic consequences of his genome.
What do you think? Was it a good idea? Would you make such information public?
Björk, the extraordinary singer, released a new music video with her son Hollow which features a DNA animation created by biomedical animator Drew Berry. Enjoy!
The video for the song could be a documentary of a strange alien world or the beginning of life on Earth. Every frame is bursting with hyperactive life. It’s an odd feeling, watching DNA strands twist and form as small bits of proteins scurry around in the background. This is the unceasing chaos that is going on inside every one of us. The video could be a piece of a museum explaining our biological process were it not for the strange molecular face that appears near the end. That little addition adds a touch of mysticism to the piece and puts a small bit of humanity in a universe of mindless chemical processes.
There is a very interesting thread on Quora. Users want to find the most iconic scientific image ever. It might sound like an easy job but it’s truly not. My vote is for the Watson-Crick DNA double helix photo. What is yours?
Some months ago I wrote about Alexandra Pajak, a graduate student at the University of Georgia, who released an album of music based on the DNA of HIV. And now here is the Genetic Music Project, an open source genetic art project combining music and science where everyone is art and everyone can be an artist.
Since all genetic information can only come in the language of four nucleotides (A Adenosine C Cytosine G Guanine T Thymidine) it is fairly easily conveyed in musical form. Another way of thinking about it is that each and every one of us and all life on this planet is made of music.
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.
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.
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.
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.
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.”
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.
“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.
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: