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Links 1 through 10 of 23 by Charlie Schick tagged molecularbiology

"Molecular diagnostics and molecular biology in general are becoming more pervasive every day in a range of applications but are still seen by many as being an arcane science. Many undergraduate science curricula cover only the basics of theoretical components without exposure to laboratory practice, due to perceived cost and complexity of laboratory facilities needed. With this in mind, I recently set out on a quest to see whether a non-specialist, $500 complete molecular biology laboratory was possible."

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"The traditional view of mRNA as a pure intermediate between DNA and protein has changed in the last decades since the discovery of numerous RNA processing pathways. A frequent RNA modification is A-to-I editing, or the conversion of adenosine (A) to inosine (I)."

Hah. One more inflection point in the complexity of molecular biology. I think the reality is that life doesn't give a hoot about the individual organism, but is one gigantic randomization engine (or should I say, purposeful variation), sampling adjacent possibles, giving rise to genomic variants of all sorts, with some variants tending towards even greater complexity and randomization techniques. [Hm, that's a brain wave developing there...]

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"Researchers have invented a new form of secret messaging using bacteria that make glowing proteins only under certain conditions. In addition to being useful to spies, the new technique could also allow companies to encode secret identifiers into crops, seeds, or other living commodities."

Cool.

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We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation."

We regularly talk about errors in replication, much less so about errors in transcription. This is indeed an unexplored aspect of genome variation. Furthermore, we have no easy way to visualize errors in translation, either. Right now, so many of our tools look en-masse and only see averages. With advances in single-cell techniques, might we start seeing individual molecules and understand the effect of chance and variability in life? I hope so, don't you?

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"At least 17 incidences of viral contamination in biologics have been reported, but industry insiders say that many more go unreported. Rather than risk negative publicity and lawsuits, companies have largely chosen to keep the details of contamination, and even their occurrence, secret — even, at times, from government regulators. Genzyme's experience, which legally had to be made public because it caused a significant drug shortage, may have only deepened industry's fears of going public."

This has triggered a few thoughts about the future of biotech. I guess I'm primed by the "Windup Girl" book I read recently. Yet, if this were as prevalent and dark as the article suggests, we would have heard more on this. I can't think that Genzyme is the only one who had to fess up about contamination of an existing product (though there might be contaminated products in biotech pipelines).

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"The scientists used a so-called homing-endonuclease gene (HEG), a selfish gene found in fungi, plants, and bacteria that has the ability to create a second copy of itself in individuals that have only one. This ensures that all offspring have the gene as well, and it's one of the fastest ways genes can spread in nature, says insect geneticist Jason Rasgon of the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland, who was not involved in the new study."

Why does the idea of releasing a genetically modified animal into the wild as a way to control a wild-type population make me uneasy. Uh, GM release? Uh, controlling organism by introducing one that isn't native?

Shiver. How many generations will it take before we are comfortable with that?

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"The researchers found 14 that did the trick, but one molecule—named RNPA1000—was especially effective against S. aureus. RNPA1000 killed cells from all 12 major strains of methicillin-resistant S. aureus (MRSA)."

Biochemistry and molecular biology informing anti-bacterial targets. Quite cool.

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Cool. Codon usage modulates trasncription speed and subsequent post-translational modification. The paper.

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Cool. Codon usage modulates trasncription speed and subsequent post-translational modification.

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"These findings join a growing body of evidence that the classic "central dogma" of genetics is incomplete. In the central dogma, chromosomal DNA is transcribed into RNA, which is then translated by the cell into proteins. In recent years, however, scientists have found that not all transcribed RNA molecules become translated into proteins. In fact, studies have shown that whole swathes of the genome are transcribed for unknown reasons."

Heh. siRNAs, snoRNAs, now long ncRNAs. Add to that funky splicing of RNA and proteins and the Central Dogma seems like an oversimplification. I was never taught Central Dogma thinking, and cringed when folks would use it in presentations. Biology is messy and the Central Dogma really doesn't capture it. :-)

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