DNA Seen Through the Eyes of a Coder

With a background in computer programming and an undergraduate degree in molecular genetics, its interesting to see the comparisons at multiple levels – and it looks fairly accurate to me at quick glance. There are some other interesting things that could be covered such as methylation patterns and supercoiled DNA (from a genetics point of view), but hopefully the author will keep updating his page — check it out:
DNA seen through the eyes of a coder.

Bioengineering Gene Expression

A recent article at Sciencedaily called Bioengineers Devise ‘Dimmer Swith’ To Regulate Gene Expression In Mammal Cells discusses new technology being developed that combined a targeted DNA repressor protein, and a custom-designed RNAi strand. The repressor is thought to prevent most transcription, but in the event not all genes are repressed, the RNAi is thought to hunt out those transcripts, and destroy them.

Another chemical called Isopropyl-รข-thiogalactopyranoside acts as a “dimmer” that can block the repressor protein. Thus by altering the amount of this chemical, repressor and RNAi, they can regulate a gene’s expression. Cool.

10 new genes linked to 7 diseases

The largest study ever conducted on genes and disease turned up 10 new genes that may predispose someone to 7 of the most highly acclaimed disease conditions. Diseases include type 1 and type 2 diabetes, coronary artery disease, hypertension, Crohn’s disease, rheumatoid arthritis, and bipolar disorder. More at: Biggest ever haul of genes linked to diseases.

Bacterial Cancer Therapeutics? Maybe.

A company called EnGeneIC in Sydney, Australia have created a targeted drug delivery platform based on “mini bacteria”, or as they call it, EnGeneIC Delivery Vehicles (EDVs). These vehicles look and behave like bacteria, including cell division — albeit, without chromosomes. I may need to dig a little deeper into the science of this one!

In any case, these EDVs have been shown to target tumorigenic tissue, being fed by blood vessels; 30% of an IV dosage reached the cancerous region within 2 hours. It has so far been proven safe in dogs with advanced non-Hodgkin’s lymphoma, as well as in pigs and monkeys.

The study also suggests that these EDVs can carry RNAi or siRNA-based products to their destination, as delivery of these nucleic acids has been proven difficult due to nuclease/enzymatic degredation before reaching its target.

Adapted from [NewScientist] from [Cancer Cell (vol 11, p431) “Bacterially Derived 400 nm Particles for Encapsulation and Cancer Cell Targeting of Chemotherapeutics”]

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Personalized Medicine: Legal Update

Up until now, there has been a big problem in the realm of personalized medicine, with respect to pharmacogenomic analysis, record keeping and access to information. Previously, according to US law, anybody could have access to that information. Meaning: employers and insurance companies could scan your results, or look at your specific genotypes that pre-dispose you to specific illnesses or conditions and discriminate against you for fear of taking on too much risk financially. See my post on ethics of personalized medicine.

As of April 25th, the US House of Representatives voted 420 to 3 in favour of passing the Genetic Information Nondiscrimination Act (GINA), and the senate along with President Bush are expected to approve the act in a few weeks. Undoubtedly, this will be a huge step for the world of personalized medicine. We are already seeing the use of pharmacogenomic markers such as Cytochrome P450 (including the 2C9 and 2D6 variants), warfarin and others that screen for efficacy of drugs such as Herceptin.

It is good timing for this news to come as genotyping is becoming evermore affordable.

Everyone should thank the NHGRI Director Francis Collins for pushing to get this act passed! The act has been shot down twice previously by the senate; hopefully, as the saying goes, the third time will be the charm.

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Essential Gene Clusters

I just came across a very interesting article that talks about essential gene clusters and some speculation from a lab out of the Baylor College of Medicine.

Scientists say they found a cluster of essential genes on mouse chromosome 11, which is also found to be conserved in other organisms including humans, possum, cow, dog and chimp.

“When we saw that there were all these essential genes in this region, we wondered if the reason that the chromosome remained together (and is not easily broken apart or recombined with other parts of this or other chromosomes) is that it had all these densely packed essential genes. The reason this part of the chromosome has remained intact is that it has densely packed essential genes. If the chromosome broke anywhere, the organism would not develop,” said Dr. Monica Justice, the associate professor of molecular and human genetics at Baylor.

View full scientific publication at PLoS Genetics.
View full review article at ScienceDaily.com.

Prostate Cancer Update: New Gene

A genetic pattern (variation) found on human chromosome 8 has been found to have an association with a 5x risk increase for developing prostate cancer. It is thought to cause 2/3 of African-American cases and 1/3 of Caucasian-American cases of the disease.

Another biomarker might be coming! Pharmacogenomics companies: ready … go!

Full story at Geneticsandhealth.com.

Gene Therapy: Eye-Eye Doc!

Twelve patients are in the middle of a first-of-its-kind trial in the UK. They are undergoing gene therapy to correct a genetic gene deficiency; a gene called RPE65. It is supposed to be expressed at the beack of the eye, in the retina, and without that gene expression the eye won’t interpret images.

Currently in one patient, Robert Johnson, he can now see outlines during the day, but little at night – he has had genes inserted into one eye. The procedure itself requires extensive precision, including a risk of tearing the retina. (See image to the right; Source: Moorfields Eye Hospital)
Story adapted from BBC.
See full story here.

At a Glance: RNAi Companies

I have stumbled upon a new blog, authored by Dirk Haussecker, a Stanford post-doc in RNAi-releated research. He put together a nice view of the companies operating within the RNAi space. Check it out.

Of all the companies, he highlighted Alnylam Pharmaceuticals for having a healthy IP portfolio surrounding their work in RNAi and microRNAs in humans. Keep on the lookout.

Metagenomics – Emerging Field

Metagenomics is defined as the study of genomes recovered from environmental samples as opposed to from clonal cultures (wikipedia). The National Research Council says that these new capabilities in genomics will revolutionize understanding of the microbial world.

The Research Council report was requested by several federal agencies interested in the potential of metagenomics and how best to encourage its success. In particular, the committee was asked to recommend promising directions for future studies. It concluded that the most efficient way to boost the field of metagenomics overall would be to establish a Global Metagenomics Initiative that includes a few large-scale, internationally coordinated projects and numerous medium- and small-size studies.

Metagenomics studies begin by extracting DNA from all the microbes living in a particular environmental sample; there could be thousands or even millions of organisms in one sample.

Please see the article at Science Daily for more information.