November 7 at Cambia Grove: Manipulating Microbial Communities Through Artificial Selection
Product Creation Studio — in partnership with Fred Hutchinson Cancer Research Center’s Shou Lab — is hosting an event based on their research of microbial communities on November 7 at Cambia Grove.
Learn from – and network with – Seattle’s Biotech and Research Community!
Thursday, November 7, 2019
4:00 – 7:15 p.m.
Agenda
Introduction to approaches of modulating functions of microbial communities, Dr. Li Xie
Improving Microbial Community Functions through artificial selection, Dr. Li Xie
Automate Your Experiments with a Robotic System, Dr. David Skelding
Networking and Refreshments
Seattle was recently identified as the fastest-growing life science market in the top 10 from 2014 to 2017, showing tremendous growth in collaborations between the research community and biotech companies.
Product Creation Studio — in partnership with Fred Hutchinson Cancer Research Center’s Shou Lab — is hosting an event based on their research of microbial communities.
For this event, Dr. Li Xie and Dr. David Skelding will cover both the theoretical and practical progress in the current research conducted in Dr. Wenying Shou’s lab. The Shou Lab is exploring the use of artificial selection, also known as directed evolution, to improve “community functions.” Some community functions are extremely useful, such as fighting off pathogens, synthesizing pharmaceuticals and degrading environmental pollutants.
In this 3-part presentation, you will learn:
Various approaches for improving desirable functions of microbial communities
How to “breed” desirable microbial communities through artificial selection
How mathematical analysis and computer simulation can guide the design of experiments
How to automate your experiments, …lessons learned through robotic systems development in the Shou Lab
The newest research and findings from Shou Lab to discuss with like-minded professionals
Whether you’re a scientist or a biotech engineer looking to solve problems using microbiomes or artificial selection, you’re sure to gain value from this unique opportunity. This series is designed for senior biotech engineers and scientists who design and carry out research at their companies.
Presentation #1:
Dr. Li Xie, Introduction to approaches of modulating functions of microbial communities
Successful microbiomes are no longer a guessing game.
Multispecies microbial communities often display “community functions” that are useful to us, such as fighting off pathogens, synthesizing pharmaceuticals and degrading environmental pollutants. Community functions often arise from complex interactions among member species and therefore can be difficult to modulate.
In this first part of the three-part presentation, Fred Hutch Postdoctoral research fellow, Li Xie, provides a primer for scientists and engineers interested in engineering microbial communities, including:
Reviewing various approaches explored by scientists to improve the functions of different microbial communities
Pre-requisites for several approaches of engineering microbial communities
How artificial selection may improve community functions
Presentation #2:
Dr. Li Xie, Improving Microbial Community Functions through artificial selection
To use artificial selection to improve some function of a microbial community, one repeatedly chooses communities with the highest function to reproduce by partitioning each into multiple “Newborn” communities for the next cycle. This approach does not require a detailed understanding of a microbial community or techniques of genetic modification, and thus can be applied to a wide range of communities.
However, advances using artificial community selection can be challenging, often requiring studies that are carefully executed, controlled, and reproducible. A trial-and-error approach can be slow, costly and often generate inconclusive results. To avoid these shortcomings, we use mathematical analysis and computer simulation to guide experimental design.
In this talk, you will learn:
Pre-requisites for using artificial selection to improve community functions
How mathematical analysis and computer simulation can facilitate designing effective selection schemes
Factors important for successful selection (e.g., promoting species coexistence, suppressing noncontributors, increasing inter-community variations, and reducing stochastic fluctuations that interfere with selection)
Plans for future investigations
Presentation #3:
Dr. David Skelding, Automate Your Experiments with a Robotic System
Evolutionary experiments involve growing populations of organisms for many generations. The addition of an artificial selection of communities necessitates a highly flexible system in order to automate experiments.
To achieve this goal, we have developed a robotic system using the Hamilton Star liquid handling system, by combining the native Hamilton scripting language with an SQL database.
In this talk, Dr. Skelding will share:
An overview of Hamilton’s prepackaged operations
How the SQL database provides the perfect environment to make decisions based on the previous history of an experiment
Strategies for working around implementation difficulties that arise from the inevitable quirkiness of a proprietary scripting language
Practical solutions for managing communities of living organisms
Seattle’s Microbiome Event - Speakers
Li Xie, Ph.D
Postdoctoral Research Fello
Shou Lab
Basic Sciences Division
Fred Hutchinson Cancer Research Center
Li Xie is a postdoctoral research fellow at Basic Sciences Division of the Fred Hutchinson Cancer Research Center. She is interested in tackling problems through an approach that integrates quantitative experiments with mathematical modeling and numerical simulation. After receiving her degree in biophysics from University of Pittsburgh, she joined Dr. Wenying Shou's lab, which seeks to quantitatively predict how ecological and evolutionary processes shape microbial communities. Her current project aims at “breeding” microbial communities for desirable functions. Besides answering fundamental scientific questions, Li is also interested in applying her research to solve real life problems.
David Skelding, Ph.D
Professional Support Specialist
Shou Lab
Basic Sciences Division
Fred Hutchinson Cancer Research Center
After completing a Ph.D. in experimental high energy physics at the University of Washington, I entered the software industry. I wrote software for scientific and medical instruments at Bruxton Corporation for a couple decades. I enjoyed writing software and making it work with hardware, but not as much as I enjoy doing science. During an economic downturn, the software business was a little slow, so when I saw an ad on Craigslist for interdisciplinary work in biology, physics and chemistry at the Fred Hutchinson Cancer Research Center, I took the opportunity to become involved directly in scientific research again. I have spent much of my time at Fred Hutchinson building and perfecting experimental devices, while participating in the scientific community that is the Shou Lab, the Basic Sciences Division and the Fred Hutchinson Cancer Research Center. My work involves mechanical fabrication, software control, electronics construction and biological technique. In collaboration with others, I have developed a robotic system for automating evolutionary experiments with communities of organisms, and currently this is the primary focus of my work.