For July 25, 2018
Hi WN@TL Fans,
Biochemists get to work with at least four types of polymers: proteins, carbohydrates (eg, starch, cellulose), lipids (eg, long chain fatty acids), and nucleic acids.
Figuring out the order of the different monomers—the building blocks—of the polymer is a big deal. It’s like to learning to spell words and to decipher sentences.
Sequencing is therefore like spelling. With proteins, carbohydrates and lipids, the leading strategy to sequence them is to start with a whole thing and pull it apart, and figure out the sequence by analyzing the parts.
DNA was also, in early days, spelled out by “degradative sequencing.”
But of the four polymers, only one—the nucleic acids (DNA and RNA)—are also templates that can serve directly to make a complementary copy of the original.
That means you can sequence DNA not by pulling it apart, but by building it up, and noting the order of the new bases (A, T, G or C) being put into place. You can sequence DNA by synthesizing it—not by breaking it, but by making it.
Therein lies the elegance and the opportunity.
This week (July 25) Josh Hyman of the Biotech Center updates us on the latest machines for sequencing DNA, including the new one at the Biotech Center that when fully up & running will be able to crank out a trillion bases a day.
For a little perspective: when I started at the Biotech Center on June 3, 1991 (it was a Monday), the Biotech Center could do about 600 bases a day. By 1999 we had machines that could do about 600,000 bases a day. In 2012, we had two machines that together could crank out about 60 billion bases a day. Last week, Josh unpacked a new machine that cranks out a trillion bases a day.
Sometimes, speed changes just about everything.
So, too, can approaches change everything. The dazzling arrays of ways to sequence different DNAs is a testimonial to chemical and robotic ingenuity. The huge data sets the sequencers crank out both challenge our computer architecture and reward elegance & economy in creating new algorithms to put all the DNA pieces together again.
I have on occasion said that biotechnology is changing how we look at life and how we lead our lives. In few areas of life science is this more true than for the sequencing of DNA. It may be but a four-letter alphabet, but in it is writ nearly all our genetic information. Read DNA, and you read deep insights—and baffling ambiguities.
About the Speaker
Josh Hyman is trained in horticulture and in engineering—a happy combination—and directs the DNA Sequencing Facility (https://www.biotech.wisc.edu/services/dnaseq) at the Biotechnology Center.
The UWBC DNA Sequencing Facility provides cost-effective, cutting edge sequencing resources to the University of Wisconsin-Madison campus as well as colleagues at public and private institutions. We provide comprehensive, fee-for-service support for both Illumina Next Generation and Sanger sequencing projects, from project design and sample preparation through downstream analysis in conjunction with the UWBC Bioinformatics Resource Facility. In addition, we provide DNA extraction, SNP genotyping, and fragment analysis services, and can facilitate custom projects upon request. Our facility is committed to producing high-quality data, maintaining rapid turn-around times, and providing comprehensive support and resources.
By the way, Josh will give us a tour of the DNA Sequencing Lab after the Q&A. It’s not exactly like going to the Terrace to watch the sunset; on the other hand, it’s a chance to see the sunrise of an astonishing new technology.
Next week (Augustus Firstus) Amy Rosebrough, archeologist with the Wisconsin Historical Society, will walk us through the history & current research into Wisconsin’s Effigy Mounds. I am among the people who had learned (wrongly) that the effigy mounds were not burial mounds, and I mentioned this to Amy at her Exploration Station on Picnic Point in April during UW Science Expeditions.
O Contraire, Mon Frere. I was astonished to hear from Amy the other side of the effigy mound story, and I’m looking forward to learning more about the mounds, the people who made them and revered them, and the ways we can keep them part of our mutual patrimonie.
Hope to see you soon at Wednesday Nite @ The Lab.
Biotechnology Center & Cooperative Extension