Eye on DNA » DNA Lab Talk

Flickr on DNA: BeadArray Gene Reading Panels

Hsien-Hsien Lei, PhD — Mon, 10 Dec 2007 09:10:00 +0000

Esther Dyson’s Flickr photostream is one of the few photo feeds I subscribe to because she’s all over the place participating in all sorts of amazingly smart events! Last week, she visited Illumina in San Diego.

The fascinating thing is how much the whole business of sequencing and reading genomes is a physical process, even though it is based on leading-edge science. On the one hand there are all the issues around millions of tiny beads, each of which is designed to detect a specific SNP (genetic variation); on the other, there’s the need to be absolutely, positively accurate in tracking a sample from arrival (with a unique but anonymous identifier) to the data that is read and analyzed at the end. Illumina does this by fanatical use of bar codes and automation; nothing is labeled or identified by a human. (Humans move things that are labeled, but machines identify each item at each step.)

Tags: genetics, genes, dna, illumina, arrays, snp, esther dyson

2007 Nobel Prize in Medicine Goes To Mice Geneticists

Hsien-Hsien Lei, PhD — Mon, 08 Oct 2007 11:23:30 +0000

Congratulations to Mario R. Capecchi, Oliver Smithies, and Sir Martin J Evans who won the 2007 Nobel Prize in medicine today! The announcement was made just minutes ago and their pictures aren’t even up on the Nobel Prize site yet.

The 2007 Nobel Prize in Physiology or Medicine goes to Mario R. Capecchi, Martin J. Evans, and Oliver Smithies for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.

The three Nobel Laureates pioneered gene targeting in mice which can be used to inactivate single genes to create “knockout” mice. Over ten thousand mouse genes have been knocked out and studied thus far and over five hundred different mouse models of human disorders have been created.

More about the fascinating gene-targeting experiments in the Nobel Prize Press Release.

Photo: Knockout mice from Wellcome Images under Creative Commons

Tags: genetics, genes, dna, mice, knockout mice, gene targeting, mario capecchi, oliver smithies, sir martin evans, nobel prize, medicine, science

Eye on DNA Links for 3 July 2007

Hsien-Hsien Lei, PhD — Tue, 03 Jul 2007 15:32:40 +0000

Grand Rounds is up at over my med body! Don’t miss the great quips that accompany each link.
The ever prolific scientists at deCODE Genetics have found two variants on chromosome 17 that increase prostate cancer risk, one in TCF2 that protects against type 2 diabetes, and other variants on chromsome 4 that increase the risk of atrial fibrillation. Next step – commercial DNA tests.
Together with deCODE, Illumina has commenced shipment of the Human1M DNA Analysis BeadChip that has more than one million single-nucleotide polymorphisms (SNPs) on a single chip and includes novel copy number variation (CNV) sites that are not currently found anywhere else. So who’s ordering?
Applied DNA sciences has teamed up with Supima to develop DNA authentication technology that can confirm the cotton content of branded apparel and home fashion products. Only 1% of world’s cotton is of high enough quality to be labeled Supima.
The New York Times interviews cell biologist Dr. Elizabeth Blackburn who studies telomeres, telomerase, and aging. Dr. Blackburn won the 2006 Albert Lasker Award for Basic Medical Research and is rumored to be the next woman to be awarded the Nobel Prize in Medicine. Hurrah!

Tags: decode genetics, genetics, genes, dna, elizabeth blackburn, genome, genomics, supima

Nanosphere DNA Test Using Gold Nanoparticles

Hsien-Hsien Lei, PhD — Sat, 23 Jun 2007 09:50:13 +0000

A biotech company in Illinois is hoping they have the Midas touch. Nanosphere has created DNA probes made of gold nanoparticles. The Verigene System is meant to “make molecular diagnostic testing simple, accessible, and flexible, but still provide the high sensitivity, accuracy, and rapid multiplex target detection required by these applications.” The benchtop system is currently under FDA review and incoporates the Verigene Reader, Verigene Processor, and Verigene Test Cartridges. Each analysis costs about $30 and takes 90 minutes to complete compared with other commercial tests which run up to $500 and require several weeks from start to finish.

The analysis of DNA or RNA targets follows this procedure:

1. Genomic DNA is loaded into a single-use “Test Cartridge.” Sonication shears the genomic DNA into 300 to 500 base-pair fragments so that they’re small enough to be probed.

2. The genomic DNA fragments hybridize (stick) to capture probes that are attached to a solid support base. Then, gold nanoparticles with oligonucleotide probes attached are added.

3. The entire complex is washed and gold nanoparticle probes that did not find a complementary genomic DNA fragment are removed.

4. Elemental silver is deposited onto the gold nanoparticle probes which hybridized to a complementary DNA fragment. This amplifies the signal.

A video is also available for viewing.

According to Nanosphere CEO Bill Moffitt, approximately 35 million tests can be performed using the same amount of gold as the average wedding band. Nanosphere technology can be used in genetic diagnostics, pharmacogenetics, infectious diseases, and oncology.

More from CNNMoney.com
via Resource Investor

Tags: genetics, genes, dna, nanosphere, gold nanoparticles, verigene, genomics, genome, biotechnology

Geeky Lab T-Shirt – NIH Summer Tour

Hsien-Hsien Lei, PhD — Tue, 15 May 2007 20:11:53 +0000

Anyone who’s ever worked in a lab has gotten at least one or two free t-shirts from companies selling lab equipment or some event being held on campus. Here’s an old t-shirt of mine from the summer I spent at the National Institutes of Health in Bethesda, Maryland working in a malaria research lab. (Click on the images to see a larger verson.)

Some of the seminars I attended:

Prospects for Gene Therapy given by Dr. R. Michael Blaese
The Molecular Biology and Pathophysiology of Hypertrophic Cardiomyopathy given by Dr. Neal D. Epstein
Molecular Regulation of Breast Cancer Progression given by Dr. Patricia S. Steeg
Nucleic Acid Presentation and Packaging Regulates Gene Expression given by Dr. Alan P Wolffe

Where’s your t-shirt? I’d love to feature yours and if you’re wearing it all the better. Email your photos to hsien [AT] eyeondna [DOT] com!

Tags: t-shirts, fun, lab, laboratory, nih, genetics, genes, dna, health, medicine, genome

Lab Help at Your Fingertips – OpenWetWare

Hsien-Hsien Lei, PhD — Sat, 28 Apr 2007 22:53:36 +0000

Laboratories are intimidating places. The glaringly bright fluorescent lights reflecting off the cold linoleum floors, large machines doing things that no mere mortal understands, black countertops scarred by acid and other chemicals, freezer after freezer of samples marked with biohazard signs…. Imagine yourself there on your first day without a clue where to stand so that you don’t contaminate something. You can prepare yourself by visiting OpenWetWare first.

Started at MIT by the Endy and Knight labs, OpenWetWare is a wiki that is open to everyone interested in laboratory procedures and exchange of scientific information. For instance, there’s a page on avoiding RNase contamination that says you should use separate sets of pipettors and avoid touching the barrel or metal ejector to the side of the tubes. Anyone can add to or edit the information already there just like The Free Encyclopedia Wikipedia. Much of the existing content at OpenWetWare could use some fleshing out and there is much that hasn’t been included yet.

If you’re currently working in a lab involved in some form of biology, what are you waiting for? OpenWetWare is a great place to ask questions, share what you know, and congregate with other lab rats. Maybe I should go add what I know about electroporating malaria parasites, Plasmodium falciparum. Zap!

HT: Jason

Tags: openwetware, wiki, MIT, genetics, genome, dna, genes, molecular biology, laboratory, labs

Geeky Lab T-Shirt – PCR Beads and Me

Hsien-Hsien Lei, PhD — Wed, 25 Apr 2007 13:38:33 +0000

We’re ready to go.

From a Pharmacia Biotech (now GE Healthcare Life Sciences) t-shirt I got during my lab days when I used PCR beads 90% of the time to perform a bajillion genotypes.

Tags: pcr, pcr beads, genotyping, genotypes, genetics, genes, health, medicine, dna, genome