BioInformatics Interesting New News

Week of June 10-June 15, 2007

• Here's an article summarizing a Nature paper which talks about how gene transcription is fundamentally noisy. A nice quote:
  • "The new study finds that essentially every base in the genome shows up in RNA at one point or another. This is despite the fact that most of these bases aren't doing anything: 95 percent of the genome isn't under selective pressure, and most of that 95 percent doesn't appear functional in an evolutionary sense. (...)
    This suggests that regulatory elements around genes act less to specifically start transcription there and more to make gene transcription at the gene more probable than the general background of RNA noise. That said, the study also found clear signals of defined transcription start sites at a rate of nearly ten times the number of genes in the area, suggesting some aspects of the excess transcription are nonrandom."

Week of June 3-June 9, 2007

• Here is an article about sequencing the genome of a single person, James Watson, in two months for less than $1 million. The Human Genome Project took a decade and cose $3 billion. http://www.iht.com/articles/2007/06/01/america/dna.php
• Here's big news -- an article in Nature describing how normal mouse cells can be turned into stem cells, without eggs or embryos involved. It seems like it's "just" a matter of changing four transcription-related genes using retroviruses. This hasn't been successfully done with human cells yet, but the race is on.
• Capping the week off, the BBC reports that genetic variations responsible for a number of major diseases have been identified. It was a large effort: a genome-wide analysis involving 50 research groups, 2000 patients with each of the seven conditions under study, and 3000 healthy controls.
  • Also see this link for more detail on each of the seven conditions: bipolar disorder; coronary heart disease; Crohn's disease; hypertension; rheumatoid arthritis; and type 1 & type 2 diabetes.

Week of May 27-June 2, 2007

• Here are two articles which say that soft drinks are worse for us than we thought. Sodium benzoate has been used as a preservative in sodas for decades, but recent experiments seem to indicate that it harms mitochondrial DNA, knocking out the mitochondria, which causes cell damage. This was observed in yeast; there's no word on what the quantities of sodium benzoate were, or how concerned we should really be, but the BioInfo relevance seemed high. It'd be nice to read more about this in an actual journal.
  • Article 1: Caution: Some soft drinks may seriously harm your health
  • Article 2: E211 Revealed: Evidence highlights new fear over drinks additive
• The cover story this week in Chemical & Engineering News is about nucleic acid quadruplexes, which are peculiarly stable arrangements of DNA and RNA. This isn't about protein folding; it's about the actual genetic information itself, folding into stable structures, moving about the cell, and serving to promote or disable gene expression. Researchers are now designing drugs to specifically target these structures, particularly DNA quadruplexes; most quadruplex research has focused on areas near the telomere, and inhibiting telomere extension implies limiting the number of cell divisions, and this has potential uses in cancer treatments. See the article for more of the story, more links, and pretty pictures. For the bioinformatics types, a quote:
  "Bioinformatics analyses of G-rich gene sequences likely to adopt quadruplex conformations suggest that quadruplexes may be much more prevalent in genomes than was formerly recognized. Using a simple folding rule for possible qudruplex structures, [...] reported that human genes contain as many as 376,000 qudruplex-forming sequences. That means that 43% of human genes could have a quadruplex motif in their promoter regions, which would make this, "one of the most prevalent regulatory motifs known."
• Personal genome analysis: The NYT (free subscription req.) has an article about the complete sequencing of James Watson. It took less than 2 months, and cost less than $1 million, showing how technology has progressed since the beginning of the Human Genome Project. This differs from the reference genome produced by the Genome Project in a number of ways: it can be tied to a particular person, instead of a composite group; the technology for this new project is said to be "bias free", skipping a bacterial amplification step which the author says produced incomplete results because some regions of human DNA may be toxic to bacteria; and, the individual genome captures information from both parents in a way the reference genome doesn't.

Week of May 20-26, 2007

• Here's an article on Did Lincoln have Smallpox?
• Google invests in Genetics firm: http://news.bbc.co.uk/2/hi/business/6682451.stm
• Sharks reproduce asexually http://www.belfasttelegraph.co.uk/news/local-national/article2574083.ece

• Make some beautiful music. "Music made from Genetic Patterns" on Discovery.com: http://dsc.discovery.com/news/2007/05/24/proteinmusic_tec.html?category=technology&guid=20070524091500

Week of May 13-19

• Quoting straight from Science, April 20th, 2007:
  Short of a personal tutor who's willing to devote weeks or months to your training, a video might be the best way to learn the subleties of a lab procedure. This pair of sites can help biologists find or swap video how-to's.
  At the Journal of Visualized Experiments, you'll find step-by-step demonstrations of more than 30 lab techniques, including how to isolate blood-forming stem cells or extract embryos from a mouse uterus. Launched last winter by former postdoc Moshe Pritsker and computer scientist Nikita Bernstein, the site features videos shot by professionals and vetted by scientists.
  For a YouTube-style site on subjects such as genetics and bioinformatics, go to the new LabAction from grad student Siddharth Singh of Devi Ahilya University in India. Although it has only a handful of clips so far, it aims to be fun as well as educational, with a category set aside for amusing takes on campus life.
  • Journal of Visualized Experiments: http://www.jove.com/
  • LabAction: http://www.labaction.com/

Week of April 22-28

• This morning, Nature has a short article about a natural peptide which resists HIV. The first paragraph is key: "A natural component of human blood has been found to block the HIV virus from infecting cells. And fortunately, tweaking just a few of the amino acids that form the molecule somehow makes its effects 100 times more potent."
• There's a lot of news lately about honeybees, as scientists and farmers try to figure out why they're mysteriously vanishing. This seems to be an occasional phenomenon, documented at least back to the 19th century, but it's never been understood. The New York Times has an article (free registration required) summarizing the latest news, which includes this tidbit for us: "Computers can decipher information from DNA and match pieces of genetic code with particular organisms. Luckily, a project to sequence some 11,000 genes of the honeybee was completed late last year at Baylor University, giving scientists a huge head start on identifying any unknown pathogens in the bee tissue. “Otherwise, we would be looking for the needle in the haystack,” Dr. Cox-Foster said."
  • Update! It appears that the honeybee's "sudden colony collapse" syndrome has been linked to a fungus. Maybe we can stop blaming cell phones now.
• A mammal that's a "living fossil"? A small fragment of the genome of a Laotian rock rat has been sequenced and compared with every other major rodent species in existence, and the evidence indicates that it split off from the rest of the rodents 44 million years ago. Ars Technica has a good article on this, including links to the background, to videos, and to the recent paper published in PNAS which describes the genomic work.

Week of April 15-21 (back-dated)

• Here's another article about the primate genome, although it's not related to last week's sequencing of the rhesus monkeys. People have been looking at the differences between the chimp and human genomes for a while now. According to a team at the University of Michigan, chimps have picked up more positively selected changes than humans have since the genetic split some 6 million years ago. Several possible reasons for this are given in the article; check it out.

Week of April 8-14, 2007

• Here's an article on retrieving protein information from T-Rex bones. This helps support the theory that dinosaurs and birds are closely related.
• Science magazine is about to say that the macaque (fully, "rhesus macaque monkey") genome is complete sequenced. This is only the third primate genome to be sequenced. They've put up a special page with papers, an "interactive poster", material for high school biology teachers, and more. link

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-- MichaelHannemann - 28 May 2007
-- MichaelDavis - 24 May 2007
-- DaveAngulo - 24 May 2007
-- DaveAngulo - 23 May 2007
-- MichaelHannemann - 13 May 2007
-- MichaelHannemann - 27 Apr 2007
-- MichaelHannemann - 26 Apr 2007
-- MichaelHannemann - 25 Apr 2007
-- MichaelHannemann - 24 Apr 2007
-- DaveAngulo - 14 Apr 2007
-- MichaelHannemann - 12 Apr 2007
-- DaveAngulo - 27 Mar 2007