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Comment: Re:With all this progress on HIV, (Score 3, Insightful) 64

by structural_biologist (#47513047) Attached to: Researchers Successfully Cut HIV DNA Out of Human Cells
Here is probably the biggest difference in terms of a drug-development perspective: HIV relies on enzymes that are not normally found in the human body, so it is relatively easy to find drugs that can target these proteins without causing significant side effects. Cancer cells, however, are human cells themselves, so the proteins that drive tumor growth and malignancy are found in healthy cells as well. Thus, developing anti-cancer drugs is not just a matter of finding and inactivating the proteins that drive cancers, but also making sure that inactivating these targets does not harm other non-cancerous cells in the body.

Comment: Re:The problem is... (Score 3, Interesting) 190

We have had the ability for quite some time to synthesize viruses from scratch (the first report in the scientific literature came from the laboratory of poliovirus from scratch, published in 2002). So, there is no reason to keep smallpox stocks around because we can just synthesize the virus if we need it. While this technology means that anyone with sufficient resources could download the (publically available smallpox genome, and synthesize it, the same technology also enables scientists to more rapidly generate vaccines without having to start with a physical sample of the virus.

+ - How to Genetically Modify an Ecosystem

Submitted by structural_biologist
structural_biologist (1122693) writes "Genes normally have a 50-50 chance of being passed from parent to offspring, but scientists may have figured out a way to create genes that show up in offspring with a much higher frequency. "One type of gene drive influences inheritance by copying itself onto chromosomes that previously lacked it. When an organism inherits such a gene drive from only one parent, it makes a cut in the chromosome from the other parent, forcing the cell to copy the inheritance-biasing gene drive—and any adjacent genes—when it repairs the damage." When introduced into the wild, organisms containing gene drives would breed with the population, quickly spreading the modified genes throughout the ecosystem. While the technology could help prevent the spread of malaria and manage invasive species, many scientists worry about the wide-ranging effects of such a technology and are calling for its regulation."

Comment: Re:DNA Data Storage (Score 1) 204

by structural_biologist (#45126139) Attached to: Billion Year Storage Media
When I mentioned DNA from millenia ago, I was referring to scientists being able sequence DNA from the remains of dead, extinct animals (like the woolly mammoth genome). In the Science paper, they print the DNA onto a microchip which can be easily read out with standard DNA sequencing machines. Storing information in the DNA of a living organism would, of course, not work very well because of the low but significant error rate of DNA replication.

Comment: DNA Data Storage (Score 3, Interesting) 204

by structural_biologist (#45122297) Attached to: Billion Year Storage Media
Last year George Church and colleagues published a paper in Science describing data storage using DNA (Church, Gao, and Kosuri. 2012. Next-Generation Digital Information Storage in DNA. Science 337: 1628. doi:10.1126/science.1226355) . While perhaps not lasting billions of years, given that we've been able to read DNA from creatures that existed millenia ago (whose DNA was definitely stored in non-ideal conditions), DNA data storage could potentially preserve data for very long periods of time.

Comment: Happend with the papaya in Hawaii (Score 2) 358

by structural_biologist (#44408429) Attached to: GMO Oranges? Altering a Fruit's DNA To Save It
A similar situation occurred with the papaya ringspot virus threatening to devastate the papaya industry in Hawaii. However, in 1998, researchers developed a genetically modified papaya resistant to the virus, and this scientific development has been credited with saving Hawaii's papaya industry. Perhaps this offers some hope for a good outcome in using genetic modification to solve the problem of citrus greening.

Comment: Re:Why was that viral gene inside in the first pla (Score 5, Informative) 391

by structural_biologist (#42664313) Attached to: Hidden Viral Gene Discovered In GMO Crops

1. Why is that viral gene in there?

When you insert a new gene (such as an herbicide resistance gene in Monsanto's Roundup Ready crops) into a plant, you also need to insert a piece of DNA called a promoter that tells the plant to turn the gene on. The scientists who created the GMOs chose to insert the promoter from the cauliflower mosaic virus (CaMV), as it is particularly good at this task and is very well studied. This promoter also happens to include part, but not the entirety, of gene VI from the virus.

* 2. Was it put there by accident or by purpose? * 2(a). If by accident, how, when, what happened? * 2(b). If by purpose, why, and by whom?

As stated above, the fragment of gene VI was placed into the GMOs on purpose. Because fragments of genes are generally inactive, the presence of the gene fragment is not expected to be problematic and showed no evidence of causing problems during the testing of the GMOs. Furthermore, because cauliflower mosaic virus is a naturally occurring virus, the full gene VI can be found in many non-GMO crops (for example, see this 2004 study).

3. How come the American scientists never detected this viral gene? * 3(a). Was it because of incompetence, or was it because the American scientists were not allowed to publish their finding, if they had found it before the Europeans?

These findings were not published before because we already knew that many GMOs contain a fragment of CaMV gene VI. In fact, in the Podevin and du Jardin study, the authors "found" the gene VI fragments by simply querying a database. A more substantial finding would have been if they found evidence that the gene VI fragments are actually made into functional protein (a prerequisite for the gene VI fragment to cause any deleterious effects), but this study did not investigate this issue. Rather, the study simply looked at what proteins might be produced in the worst case scenario and concluded that any possible proteins made from the gene VI fragments are unlikely to be human allergens or toxins. The authors speculate these possible proteins could be harmful to the plant itself, but because many of these GMOs are very productive plants that produce high yields in commercial settings, this possibility seems unlikely.

Comment: Paradigm shifts in Biology (Score 2) 265

by structural_biologist (#42524187) Attached to: Does All of Science Really Move In 'Paradigm Shifts'?

Sydney Brenner, who won the Nobel Prize in Physiology or Medicine for his work on programmed cell death, wrote a nice essay in the journal Science (subscription required) describing what he saw as a major paradigm shift in the 1950s and 60s that created modern molecular biology. Prior to the discovery of the structure of DNA by Watson and Crick, biologists had been focusing on how DNA and its associated proteins might be carrying out the functions of the cell. The discovery of the structure of DNA, however, fundamentally changed how researchers approached these questions by revealing that DNA is really just carrying information. Brenner writes:

"We can now see exactly what constituted the new paradigm in the life sciences: It was the introduction of the idea of information and its physical embodiment in DNA sequences of four different bases. Thus, although the components of DNA are simple chemicals, the complexity that can be generated by different sequences is enormous. In 1953, biochemists were preoccupied only with questions of matter and energy, but now they had to add information. In the study of protein synthesis, most biochemists were concerned with the source of energy for the synthesis of the peptide bond; a few wrote about the “patternization” problem. For molecular biologists, the problem was how one sequence of four nucleotides encoded another sequence of 20 amino acids."

Indeed, following this paradigm shift, Watson and others quickly worked out the question of how the information encoded in DNA gets read by the cell and their work now forms the central dogma of modern molecular biology. Therefore, Kuhn's concept of paradigm shifts does indeed apply to biology.

Comment: Re:I hope.. (Score 1) 304

by structural_biologist (#40732271) Attached to: Patent Troll Claims <em>Minecraft</em> Infringement
William Press and Freeman Dyson recently published a very interesting paper showing that the optimal IPD strategy depends on whether your opponent is mindlessly following a particular algorithm or is actually sentient. In particular, if you who can figure out your opponent's algorithm, you can then game the opponent's algorithm for your benefit. You may find reading the paper (http://www.pnas.org/content/109/26/10409) and the accompanying commentary by Stewart and Plotkin (http://www.pnas.org/content/109/26/10134) to be useful.

Comment: Re:I work for one of these companies... (Score 2) 153

by structural_biologist (#40137669) Attached to: The Race To $1,000 Human Genome Sequencing
You've got it backwards. The cost of materials for sequencing is dropping to $1k, but the data analysis (stitching together all of the short DNA reads to assemble a full genome sequence) still costs well in excess of $1k. For example, a 2011 Chemical and Engineering News article suggests that the cost of the analysis was still ~$100k.

Never tell people how to do things. Tell them WHAT to do and they will surprise you with their ingenuity. -- Gen. George S. Patton, Jr.

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