Where Would DNA Sequencing Be Without Leroy Hood?

There have been many changes in sequencing technology over the course of my scientific career. In one of the research labs I rotated in as a graduate student, I assisted a third-year grad student with a manual radioactive sequencing gel because, I was told, “every student should run at least one in their career”. My first job after graduate school was as a research assistant in a lab that sequenced bacterial genomes. While I was the one creating shotgun libraries for the DNA sequencing pipeline, the sequencing reaction was performed using dideoxynucleotides labeled with fluorescent dyes and amplified in thermal cyclers. The resulting fragments were separated by manual loading on tall slab polyacrylamide gels (Applied Biosystems ABI 377s) or, once the lab got them running, capillary electrophoresis of four 96-well plates at a time (ABI 3700s).

Sequencing throughput has only increased since I left the lab. This was accomplished by increasing well density in a plate and number of capillaries for use in capillary electrophoresis, but more importantly, with the advent of the short read, massively parallel next-generation sequencing method. The next-gen or NGS technique decreased the time needed to sequence because many sequences were determined at the same time, significantly accelerating sequencing capacity. Instruments have also decreased in size as well as the price per base pair, a measurement used when I was in the lab. The long-prophesized threshold of $1,000 per genome has arrived. And now, according to a recent tweet from a Nanopore conference, you can add a sequencing module to your mobile device:

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Choosing a Better Path for Your NGS Workflow

Imagine you are traveling in your car and must pass through a mountain range to get to your destination. You’ve been following a set of directions when you realize you have a decision to make. Will you stay on your current route, which is many miles shorter but contains a long tunnel that cuts straight through the mountains and obstructs your view? Or will you switch to a longer, more scenic route that bypasses the tunnel ahead and gets you to your destination a bit later than you wanted?

Choosing which route to take illustrates a clear trade-off that has to be considered—which is more valuable, speed or understanding? Yes, the tunnel gets you from one place to another faster. But what are you missing as a result? Is it worth a little extra time to see the majestic landscape that you are passing through?

Considering this trade-off is especially critical for researchers working with human DNA purified from formalin-fixed paraffin-embedded (FFPE) or circulating cell-free DNA (ccfDNA) samples for next-generation sequencing (NGS). These sample types present a few challenges when performing NGS. FFPE samples are prone to degradation, while ccfDNA samples are susceptible to gDNA contamination, and both offer a very limited amount of starting material to work with.

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They’re Eating WHAT? Understanding Ecosystems Through Weird Meals

A few days ago, while taking an unplanned distraction break on Facebook, I came across a video of an enormous coconut crab attacking a red-footed booby. The footage was captured by a biologist studying crab behavior in the Chagos Archipelago in the middle of the Indian Ocean. On this trip he had already confirmed that the monstrous crustaceans snacked on large rats, but he never expected to watch one devour a full bird.
This video sent me on a research journey into other interesting meals discovered by animal researchers. Besides providing sensational headlines about what’s eating what, these studies help us understand everything from nutrient exchange to learned behavior. I’ve compiled a short list of observations and discoveries made in the past few months where researchers have used weird meals to understand complex phenomena. Warning: this might get gruesome! Continue reading

Ancient Images of Dogs Include Restraints?

This dog is wearing a leash.

You, like me, may occasionally find youself in need of a canine control device. While I’m not a fan of the dog tie out, I do walk dogs on leash—as is required by our county and city government here in Madison, WI.

If you have read Temple Grandin’s books about dogs, you might feel a tug at your heartstrings while enduring a tug on the leash. Aren’t dogs meant to run freely? Don’t we love to watch them run? Are leashes humane?

When walking dogs I feel the need to protect them, but also a desire to let them live like dogs, sniffing, marking and other behaviors that are all limited when the dog is leashed.

When a report in Science last week showed evidence that our ancient ancestors were using leashes 8,000-9,000 years ago I was: 1) surprised; and 2) felt vindicated from self-imposed dog owner guilt.

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Elephant Endotheliotropic Herpesvirus—A Tiny Virus Threatens the World’s Elephants

My favorite ice-breaker of all time is: “List one fact about you that no one would guess”. It is my favorite because I have an awesome answer (if I do say so myself). My go-to answer is: I spent a summer working with elephants.

It was the summer before I graduated from college, and it was really only one elephant, a five-year-old African elephant named Connie. Connie was intelligent, curious and mischievous—her favorite game with me was trying to untie my shoelaces (hint: double knotting is important). Working with her was one of the most amazing experiences of my life and left me with an abiding love for these creatures.

Elephant Endotheliotropic Herpesviruses threaten captive breeding programs. Copyright.

Understandably, I was excited last year when one of my fellow bloggers wrote about Promega helping support the work of Virginia Riddle Pearson, who was working to identify and track strains of elephant endotheliotropic herpesvirus (EEHV) in African Elephant populations. EEHV is associated with the lethal elephant hemorrhagic disease (EHD) (1). This disease is a serious threat to the captive breeding programs of these endangered creatures. Between 1962 and 2007, it accounted for 58% of the deaths of North American captive-born Asian elephants between 4 months and 15 years of age (1). These deaths include the first Asian elephant calves born at the National, Oakland and Bronx Zoos. EHD also claimed the first live-born Asian elephant calves conceived by artificial insemination in both North America and Europe. Continue reading

Some Seriously Funny Science

The other night I was playing volleyball and, during a team huddle, made a joke that the only players working hard were those with two X chromosomes (a playful jab at the male players on my team). The only response I got was a single, delayed smile along with a bunch of blank looks. That joke certainly would have produced a better reaction among my scientific colleagues, even if that simply meant a bunch of immediate groans.

I happen to think science-minded folks like myself have a terrific sense of humor, it’s just tailored to a more niche audience since a lot of the jokes we tell may not be immediately understood by the average person. While I appreciate comedy in all forms, I delight in laughing at and making jokes related to science.

Since I don’t think I am alone, I thought I would share a few events in today’s blog that really highlight the humor that can be found in the scientific community.

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Playing it Forward: Biotechnology Youth Apprenticeship and Mentorship

Amani Gillette’s Story

Amani working in the laboratory of Dr. McFall-Ngai’s as a high school Youth Apprentice

Amani Gillette, a junior from LaFollette High School in Madison, started the Biotechnology Youth Apprenticeship Program (YAP) in Fall Semester, 2010.  An outstanding youth apprentice (YA) throughout her two years in the program, she excelled in both the specialized laboratory course at the BTC Institute and in her work site research under the mentorship of Professor Margaret McFall-Ngai, UW-Madison Department of Medical Microbiology & Immunology.  Amani’s characterization of a gene and protein found in a small tropical squid resulted in her first scientific publication and poster presentation.

Fast forward— after receiving a B.S. in Biomedical Engineering at Michigan Technological University (which included working in a tissue engineering lab and two summers interning at Promega Corporation under the supervision of Dr. Dan Lazar to help develop an assay for autophagy), Amani is now back in Madison. She is in her second year of graduate school and, working with Dr. Melissa Skala at the Morgridge Institute for Research, is currently mentoring Biotechnology YA Ava VanDommelen (senior from DeForest High School). Following in Amani’s footsteps, Ava will present her research nationally this January at the SPIE conference (the International Society of Optics and Photonics). Continue reading

H7N9 Influenza Virus: A Perfect Pathogen?

Artist’s rendition of a virus particle.

It’s late October and here in Wisconsin, like many of you, we are experiencing a change of seasons, with the associated drop in temperatures, changes in leaf color and later this week, Halloween.

Another thing that comes with fall is the start of cold and flu season. By “flu”, I mean influenza, caused by avian influenza viruses of the H-N type. Recent research results by teams at UWI-Madison and in Japan, makes the coming influenza season potentially more scary than usual.

In a recent Cell Host & Microbe paper, M. Imai et al. study a seemingly more virulent version of H7N9 avian influenza virus that is startling in its ability to spread from infected to healthy animal models. Based on a current epidemic of H7N9, human-to-human transmission with this strain is increasing. Continue reading

Coffee and Science–A Cartoon Perspective

Although never actually on the lab bench,  coffee makers have had a prominent place in every laboratory I have worked in. It is because of my laboratory coffee experiences that I am able to drink coffee at any temperature and at any time of the day. The credit for my preference for really strong coffee (with cream, I confess)  goes to two Russian labmates who insisted on making the coffee every morning and went through two bags of beans a week (we had a very wide awake lab).

In all the labs, keeping track of whose turn it was to buy the coffee supplies was just as important as keeping track of whose turn it was to defrost the freezers. I am sorry to say we never thought of a log book because that might have saved me some frantic early morning trips to the store.

Does your lab have coffee rules or traditions? I’d love to hear what they are.

Rwanda – Africa’s Next Biotech Hub – Welcomes Promega

Promega sponsored a preconference workshop for grad and undergrad students at the University of Rwanda’s biotechnology campus in Huye, the capital city of Rwanda’s Southern Province.

More than twenty years after the Rwandan genocide when some 800,000 people were killed in just 100 days by ethnic extremists, Rwanda is on a path to not only healing and order, but also technological advancement. Now politically and functionally stable, which is an exception to the rule in east Africa, the country is recognizing that biotechnology is one of the key drivers to help improve the health and well being of its citizens. Rwanda is focusing on providing the resources and training needed to grow its capabilities in biotechnology, and could be on track to become an African biotech hub.

Rwanda, and its biotech push, caught the attention of Promega by way of customers working with its Belgium-Netherlands-Luxembourg (BNL) branch office. Researchers who are also African ex-patriots working at Université libre de Bruxelles (ULB), a French-speaking private research university in Brussels, Belgium, invited Promega to attend a conference in Rwanda earlier this month organized by the Society for the Advancement of Science in Africa (SASA) and the Rwanda Biotechnology Association focusing on translational science and biotechnology advances in Africa. Promega was a main sponsor of the conference along with US medical device manufacturer Medtronic. Continue reading