synthetic biology

by

Catalyzing Solutions with Synthetic Biology

Computer-generated model of a virus.

The keynote speaker for this year’s International Symposium on Human Identification (ISHI), Andrew Hessle, describes himself as a catalyst for big projects and ideas (1). In biology, catalysts are enzymes that alter the microenvironment and lower the energy of activation so that a chemical reaction that would proceed anyway happens at a much faster rate—making a reaction actually useful to the biological system in which it occurs.

In practical terms, Andrew Hessel is the person who helps us over our inertia. Instead of waiting for someone else, he sees a problem, gathers an interested group of people with diverse skills and perspectives, creates a microenvironment for these people to interact, and runs with them straight toward the problem. Boom. Reaction started.

One of the problems he has set his mind toward is that of cancer drug development. Continue reading →

by

iGEM: Saving the World with Science

The University of Chicago 2016 iGEM team group photo (Photo credit: Julia Byeon)

Every year, groups of teenagers gather together and brainstorm ways to save the world—with science. The International Genetically Engineered Machine (iGEM) Foundation is a non-profit organization that is dedicated to educating young scientists and enhancing open community and collaboration in the field of synthetic biology. They hold a competition every year with hundreds of teams participating from around the world.

Last year, Promega provided cloning reagents to the University of Chicago iGEM team, and they received a bronze medal for their work. We asked two of the team members, Steve Dvorkin and Julia Byeon, about their experience. Steve is a junior and majors in biology; he is co-president of the team this year. Julia recently graduated and works in public policy. Continue reading →

by

iGEM: Building Living Machines

Life forms are often compared to machines, whether you are referring to a single cell or a complex organism. This concept is the basis for the International Genetically Engineered Machine (iGEM) Competition. Each year, high school and university students around the world assemble teams that create genetically engineered systems. In addition to the building work, teams document their process and progress through wikis that are assessed by judges at the end of the competition.

teamfoto-900x250

Some members of iGEM 2016 Team Duesseldorf.

In order to synthesize these living machines, iGEM teams use standard biological parts called biobricks—each biobrick is a sequence of DNA encoding a particular biological function. Teams receive a kit of standard biobricks and work over the summer to build and test biological systems in living cells. These basic units are put together to make more complex parts which can then be grouped together to make “devices” that can function within living cells. Continue reading →

by

Manipulating Microbiota: A Synthetic Biology Exploration of the Gut

33553646_lMicrobial cells outnumber the cells of our own bodies approximately 10:1, these microbes that live on our skin and along the epithelial linings of our internal tubes make up our microbiota*, and they can have major effects on our health. Most of our microbiota are commensal organisms, living in harmony with our body, but if you suppress our immune system or greatly reduce their populations with large doses of antibiotics, and you will soon see the effects of disrupting our microbiota.

There is much interest in the microbiota that inhabit our bodies. For instance several studies have indicated that intestinal microbes can play a big part in obesity, with changes in the makeup of the microbiota being a major risk factor (1). But many of these organisms are hard to learn about—the ones that inhabit the deep folds of our gut thrive in moist, warm, anaerobic conditions with lots of specialized nutrients, conditions that are very hard to replicate in the laboratory. For that reason, we don’t know much about many of the microbes that are the most abundant within us.

The Human Microbiome Project begun in 2008 by the National Institutes of Health (2) seeks to understand human microbiota and their relationship to human health. To do this, the researchers leading the project took a metagenomic approach—using advanced DNA sequencing technologies to sequence the genomes of human microbiota and get a look at the human microbiome—without culturing the microbes.

But to truly understand their biology, and to perhaps exploit what we learn to enhance human health we need to be able to manipulate these organisms. In particular, biologists who are interested in synthetic biology would like to use these micro-organisms to monitor what is going on in our bodies, particularly our guts. What better monitor for these hard-to-access places than an organism that is already well adapted to live there?  Continue reading →

by

Designer Bacteria Detect Cancer

Every day scientists apply creative ideas to solve real-world problems. Every so often a paper comes up that highlights the creativity and elegance of this process in a powerful way. The paper “Programmable probiotics for detection of cancer in urine”, published May 27 in Science Translational Medicine, provides one great example of the application of scientific creativity to develop potential new ways for early detection of cancer.

The paper describes use of an engineered strain of E.coli to detect liver tumors in mice. The authors (Danino et al) developed a potential diagnostic assay that uses a simple oral delivery method and provides a readout from urine, all of which is made possible by some seriously complex and elegant science. Continue reading →

by

Synthetic Biology: Reaching Back 20 …Make that 50 Years

Recently I had the opportunity to meet emeritus professor Dr. Waclaw Szybalski from the University of Wisconsin- Madison, who has worked at the McArdle Laboratory for Cancer Research since 1960.  

During an interview we discussed Dr. Szybalski’s amazing exit from his native Poland in 1946 following the alternating German and Soviet occupations, his education in the early days of genetic engineering, and finally the foundational work he has done in both prokaryotic and eukaryotic genetic engineering.

Photo of award from Polish government for Szybalski's research contributions.

Doctor Honoris Causa awarded to Waclaw Szybalski. Szybalski, in his laboratory, background. Photo: Maciek Smuga-Otto.

At age 90 Szybalski continues to maintain a laboratory with postgraduate students. At the same time (and with Promega’s assistance) he continues to support research in Poland. In May 2011, Szybalski was honored by the President of Poland with the highest order, Grand Cross of Polonia Restituta, celebrating his many scientific contributions, including: 1) establishment of the genetic basis of antibiotic resistance in bacteria;
2) multidrug therapy for bacterial pathogens and leukemia; and 3) the ability to sensitize mammalian cells to radiation. Continue reading →