Refining Human DNA Mutation Rate Estimates

NEW YORK (GenomeWeb News) – In a paper appearing online yesterday in Current Biology, British and Chinese researchers reported that they have refined the estimates for human DNA mutation rates.

The team, led by investigators at the Wellcome Trust Sanger Institute, used a combination of high-throughput and Sanger sequencing to hone in on base substitutions in the same Y chromosome sequence from two distantly related men.

New Catalysts Cleave DNA With Water Molecule

Newly discovered deoxyribozymes (catalytic DNA) with significant potential as sequence-specific DNA cleavage reagents may soon provide better tools for manipulating DNA in the lab.   The researchers discovered the new deoxyribozymes while searching for artificial sequences of DNA that could cleave proteins. The newly found catalysts function in a fashion similar to restriction enzymes, although to date by cleaving only single-stranded DNA. The new DNA catalysts require two metal ions – manganese and zinc – to carry out their catalysis.  Read more in Nature Chemical Biology.

A 3D Atlas of C. elegans

Nature Methods
Published online: 16 August 2009 | doi:10.1038/nmeth.1366

 A 3D digital atlas of C. elegans and its application to single-cell analyses

Fuhui Long1,3, Hanchuan Peng1,3, Xiao Liu2, Stuart K Kim2 & Eugene Myers1

 Abstract

We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.

 1. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

 2. Department of Developmental Biology, Stanford University Medical Center, Stanford, California, USA.

3.  These authors contributed equally to this work.

Correspondence to: Eugene Myers1 e-mail: myersg@janelia.hhmi.org

New Method Kills Rare, Aggressive Breast Cancer Stem Cells

ScienceDaily, August 17th, 2009.  A team of Boston-area researchers has discovered a chemcial that kills mouse breast concer stem cells.  Researchers do not know whether the chemical holds therapeutic potential in humans.  The finding is significant because it demonstrates that it is possible to identify chemicals that specifically kill cancer stem cells.  The results appear in the August 13 advance issue of Cell.