A brief introduction to the new Center for Microbiome Sciences & Therapeutics at the University of Washington

CMIST IS CURRENTLY UNDER CONSTRUCTION
CMIST IS CURRENTLY UNDER CONSTRUCTION
A note from Will Innovation Services CMiST Art+Science
A note from Will Innovation Services CMiST Art Science
A note from Will There is an entire ecosystem of bacteria, fungus and virus that resides within each of us. This complex community of microbes, who call our intestines home, is collectively referred to as the microbiome. As scientists and clinicians uncover more about the biology of the microbiome we are finding that changes in this community may have a role in causing or worsening intestinal diseases such as Inflammatory Bowel Disease (IBD), diabetes, gastrointestinal cancers, and even neurological diseases like Autism and Multiple Sclerosis. We are just beginning to scratch the surface in the understanding of the microbiome and its role in disease. It is my belief that this microbial world harbors a number of important potential discoveries that can help us treat these diseases. These next few pages will introduce you to the work that my laboratory is pursuing, research that I feel is important, thoughtful and will one day bring real solutions to complex diseases. I believe firmly in transparency and openness, particularly in science, so before you continue reading about my scientific endeavors, I would like to introduce myself. It is important to me that you know a little about who I am not only as Dr. William DePaolo “the scientist,” but also as Will, a son, a brother, a husband and a friend. Growing up Italian I was born in Portland, Maine into a large Italian-American family. Being only third generation American those strong Italian traditions of family are ideals I still hold very close. I grew up in the kitchens of my grandparents. If I wasn’t helping out at my grandfather’s pizzeria then I was in the kitchen with my grandmother making spaghetti sauce. I remember how they always told me that I had to go to college, that I had to become
A note from Will There is an entire ecosystem of bacteria, fungus and virus that resides within each of us. This complex c...
educated so that unlike my family who came to America, poor and struggling, I could have a strong future. These memories did inspire me to go to college, to become the first DePaolo to get a college degree and then the first DePaolo to get a PhD. None of my grandparents were able to celebrate these accomplishments with me. I lost all four of my grandparents to cancers and heart disease and diabetes before I graduated from college. I lost them to diseases that should be treatable, that we should be able to cure. I talk a lot, but I also listen I was one of those loud, talkative, curious children who was always less interested in what they were supposed to be doing, and more interested in how what they were supposed to be doing was going to affect activities the next day. I grew up to be a loud, talkative, curious adult who is also more interested in how today’s findings will impact science or life in the future. I have always been a talker, I used to talk so much that my school teachers would send me home with my unfinished lunches and notes saying “Your son did not eat lunch today, he was too busy talking.” Sometimes, I was made to stand against a wall at recess because I was distracting other students during class. I still talk a lot, but I also listen. I am able to relate to those people around me. As an adult this skill has allowed me the opportunity to establish important connections, to bridge different disciplines in science, and to initiate fruitful collaborations that otherwise may not have occurred. In the end, all of that time in the kitchen talking and cooking with my grandparents, and all of that talking during class helped to shape me a scientist and as a man. -Will
educated so that unlike my family who came to America, poor and struggling, I could have a strong future. These memories d...
Innovation Services Microbial Isolation & Cultivation CMiST will synergize with existing resources within the University of Washington, Department of Medicine, to establish a unique set of tools and reagents that can be used by clinicians and researchers to address the complex relationship between intestinal microbiota and host tissues in diseases such as Inflammatory Bowel Disease (IBD). Specifically, we will: Isolate bacterial species within the microbiota of patient samples using standard culturing paired with automation. Identify isolated bacteria using MALDI-TOF mass spectrometry. Establish a repository for clinical and research isolates obtained from patients and healthy controls. Equipment & innovations: Link isolates to clinical patient data and/or existing tissue in the GI biorepository, which will enable investigators to study the disease phenotype, tissue status and bacterial response from the same patient. Cultivate and prepare isolates and/or commercially available probiotics strains for in vivo and in vitro testing. Provide resources and training to investigators who want to expand their microbiology programs. SHEL LAB Bactron anaerobic bacterial chamber, MALDI-TOF mass spectrometer
Innovation Services Microbial Isolation   Cultivation CMiST will synergize with existing resources within the University o...
Bruker MALDI-TOF microflexTM Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique used in mass spectrometry that allows for the analysis of both biological molecules (such as DNA, proteins, peptides and sugars) and large organic molecules (such as polymers, dendrimers and other macromolecules). Though the MALDI-TOF microflexTM is fairly compact, just a little bigger than a PC tower, its capabilities are huge. With this piece of highly specialized equipment, we will be able to identify single bacterial species in just a few minutes. SHEL LAB BACTRON900 anaerobic chamber With the capacity to house 900 plates, the BACTRON900 will allow us to successfully cultivate a number bacteria species, often difficult to grow, that live only within the confines of our intestine.
Bruker MALDI-TOF microflexTM Matrix-assisted laser desorption ionization time-of-flight mass spectrometry  MALDI-TOF MS  i...
Host & Microbe Interaction With this service, we will explore the immunological and genetic consequences of the microbiome when in contact with human cells. Normally, we co-exist with the 100 trillion bacteria that call our bodies home. However, genetics and/or extrinsic factors (e.g. infection, diet) can influence this relationship and cause changes leading to the development or exacerbation of inflammatory intestinal diseases. Understanding the complex tug-of-war between host and microbe is critical in our ability to develop therapies to treat disease. Specifically, we will: Provide functional assays examining the response of human cell lines and human/mouse organoid cultures against purified bacterial isolates, metabolic by-products and/or mixed bacterial populations from stool. Generate or acquire fluorescent probes against specific bacterial members of the microbiota in order to visualize their relationship with each other as well as with the intestinal tissue using fluorescent microscopy. Screen potential drugs and microbiome-derived biotherapeutics using functional assays. Determine gene induction of host and microbiota using fluorescence microscopy paired with laser capture technology. Equipment & innovations: Novel assays, Leica fluorescent microscope, organoids developed from IBD and healthy intestinal tissue, 16S fluorescent in situ hybridization (FISH)
Host   Microbe Interaction With this service, we will explore the immunological and genetic consequences of the microbiome...
Organoids With just a tiny tissue sample, we have the ability to actually grow three-dimensional intestinal organoids or “mini-guts” as they are known here in the lab, in less than a week. These mini-guts retain key features of the intestinal epithelium, including all of the major epithelial cell types, making them an ideal tool to help us isolate and understand the different mechanisms at play in IBD versus healthy intestinal tissue. Day 0 Day 1 Day 4 Day 5 Novel functional assays –omics data predicts biological “function” of the microbiome based upon theoretical models, which may potentially ascribe incorrect characteristics to a community. Our lab has developed assays that can determine the immunological signature induced by the microbiota. These assays can also be used to test potential biotherapeutics or synthetic drugs on blocking microbiota-host immune interactions.
Organoids With just a tiny tissue sample, we have the ability to actually grow three-dimensional intestinal organoids or  ...
Other equipment available LI-COR Odyssey CLx Imaging System Two OMNI Bead Ruptors The Odyssey CLx Imaging System utilizes near-infrared fluorescence (NIR) light, a relatively recent optical imaging method, to provide digital images that are at both consistent and reproducible. Because this imaging technique offers great sensitivity, it produces images of very high quality, giving us the ability to confidently analyze samples more clearly and completely. The OMNI Bead Ruptor is simply a bead mill used to homogenize tissue samples for molecular extraction. While simple in function, it is the most advanced homogenizer on the market. With the capacity to hold 24 samples at once, the Bead Ruptor gives our researchers the ability to grind and lyse samples effectively and efficiently. CMiST Associated Facilities and Services GI Division biorepository Gnotobiotic facility
Other equipment available LI-COR Odyssey CLx Imaging System  Two OMNI Bead Ruptors  The Odyssey CLx Imaging System utilize...
CMiST Art+Science Microbiome, probiotics and stool transplants have entered pop culture and the mainstream media, but is correct and accurate information being circulated? In an era where Tweets reach hundreds and thousands of people instantly, and where information is at the tip of our fingers, it is critical that the information regarding health, disease and the microbiome come from legitimate sources providing factual information. We will establish relationships with UW arts and film departments in order to educate local communities about health and the microbiome using art, film and writing. An emphasis of this initiative is to reach under-served populations regarding the importance of the microbiome and nutrition and health Introducing Bioartist Kathy High As part of our art and science initiative world-renowned bio-artist, Kathy High, will be doing an artist residency in DePaolo Lab during winter 2016. Kathy is an artist, but also a person who suffers from inflammatory bowel disease. Her passion for trying to understand this complex disease is part of her art. Kathy has been commissioned to do an art exhibition in Fall of 2017 with a focus on IBD and the microbiome. As part of her experience she will be joining the DePaolo lab and CMiST as an artist in residence during the winter of 2016. Kathy has shown her work across the US, as well as Australia, Germany, Poland, Spain, Ireland and the UK, and is a Guggenheim fellowship recipient.
CMiST Art Science Microbiome, probiotics and stool transplants have entered pop culture and the mainstream media, but is c...
Our Values think deeply embrace creativity cultivate relationships facilitate discovery “Don't keep forever on the public road, going only where others have gone, and following one after the other like a flock of sheep. Leave the beaten track occasionally and dive into the woods. 'Every time you do so you will be certain to find something that you have never seen before. Of course it will be a little thing, but do not ignore it. Follow it up, explore all around it; one discovery will lead to another, and before you know it you will have something worth thinking about to occupy your mind. All really big discoveries are the results of thought.” -Alexander Graham Bell
Our Values  think deeply embrace creativity cultivate relationships facilitate discovery     Don t keep forever on the pub...