Sunday, May 31, 2009

PSYORG Article: Stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome!


Quoted from: http://www.physorg.com/news162753069.html May 28th
VIB researchers linked to K.U.Leuven and Harvard University show that stretches of DNA previously believed to be useless 'junk' DNA play a vital role in the evolution of our genome. They found that unstable pieces of junk DNA help tuning gene activity and enable organisms to quickly adapt to changes in their environments. The results will be published in the reputed scientific Journal Science.

Junk DNA

'Most people do not realize that all our genes only comprise about 3% of the total . The rest is basically one large black box', says Kevin Verstrepen, heading the research team. 'Why do we have this DNA, what is it doing?'.

Scientists used to believe that most of the DNA outside of genes, the so-called non-coding DNA, is useless trash that has sneaked into our genome and refuses to leave. One commonly known example of such 'junk DNA' are the so-called tandem repeats, short stretches of DNA that are repeated head-to-tail. 'At first sight, it may seem unlikely that this stutter-DNA has any biological function', says Marcelo Vinces, one of the lead authors on the paper. 'On the other hand, it seems hard to believe that nature would foster such a wasteful system'.

Unstable repeats
The international team of scientists found that stretches of tandem repeats influence the activity of neighboring genes. The repeats determine how tightly the local DNA is wrapped around specific proteins called 'nucleosomes', and this packaging structure dictates to what extent genes can be activated. Interestingly, tandem repeats are very unstable - the number of repeats changes frequently when the DNA is copied. These changes affect the local DNA packaging, which in turn alters gene activity. In this way, unstable allows fast shifts in , which may allow organisms to tune the activity of genes to match changing environments -a vital principle for survival in the endless evolutionary race.

Evolution in test tubes
To further test their theory, the researchers conducted a complex experiment aimed at mimicking biological evolution, using yeast cells as Darwinian guinea pigs. Their results show that when a repeat is present near a gene, it is possible to select yeast mutants that show vastly increased activity of this gene. However, when the repeat region was removed, this fast evolution was impossible. 'If this was the real world' the researchers say 'only cells with the repeats would be able to swiftly adapt to changes, thereby beating their repeat-less counterparts in the game of evolution. Their junk DNA saved their lives'.

Source: VIB (the Flanders Institute for Biotechnology)

Saturday, May 23, 2009

CodeCon09 SynthBio Tutorial Handout

Sung Won Lim recently posted this excellent resource on SynthBio from CodeCon 2009. Some of the data has already been posted on this blog, but here it is in a nice neat package.
      0000_DOWNLOAD_ALL_Co..> 19-Apr-2009 13:52   38M 
01 Adventures in Syn..> 20-Aug-2008 18:49 11M
02 Foundations for e..> 08-Jun-2006 10:55 291K
03 Genetic parts to ..> 16-Aug-2007 12:34 451K
05 Setting the Stand..> 21-Aug-2008 08:27 408K
06 Refinement and St..> 21-Aug-2008 08:26 1.2M
07 Engineering BioBr..> 21-Aug-2008 08:29 407K
08 Synthetic biology..> 21-Jun-2007 14:58 510K
09 Laying the Founda..> 03-Apr-2009 16:00 141K
README - ANNOTATED B..> 18-Apr-2009 13:10 2.2K
appendix1 - Primer f..> 20-Aug-2008 12:49 5.5M
appendix2 - A Comput..> 12-Oct-2007 11:40 5.6M
appendix3 - GinkgoBi..> 18-Apr-2009 12:58 15M

A blog about building a DIY Lab inexpensively

Here is a great blog that deals with trying to build a DIY lab very inexpensively. In it, Lawrence walks us through each step as he builds his own science lab. Thanks Lawrence!
http://citsci.blogspot.com/



Homemade Centrifuges
Converted Old Light Bulbs into Flasks

Homemade Oscilloscope
Parts For a MicroBio Lab

and more!

Synthetic Biology Resources


http://syntheticbiology.org/
Image:SB Primer 100707.pdf
Berkeley Intro to Synthetic Biology (PDF)
Jason Kelly's Measurement Kit Video
Targeted Development of Registries of Biological Parts (Peccoud lab
Adventures in Synthetic Biology comic

Bioinformatics Tutorials Series (BITS)
A collaboration of the MIT Engineering and Science Libraries and Harvard's Countway Library

BIT 1.1: UCSC Genome Browser: Getting DNA Sequence (3:57)
BIT 1.2: UCSC Genome Browser: Using Annotation Tracks (5:47)
BIT 1.3: UCSC Genome Browser: Locating Intron-Exon Boundaries (4:56)
BIT 1.4: UCSC Genome Browser: Searching with BLAT (6:14)

BIT 2.1: Do I need to BLAST? The Use of BLAST Link (7:24)
BIT 2.2: Do I need to BLAST? The Use of Related Sequences (6:53)
BIT 2.3: Nucleotide BLAST (5:46)
BIT 2.4: Nucleotide BLAST: Algorithm Comparisons (6:14)