Integrating biophysics and the gut microbiota.
Integrating biophysics and the gut microbiota.
I am a JSMF postdoctoral fellow in Dr. Sonnenburg’s lab at Stanford University. In my PhD I developed a deep understanding of the molecular biophysics of bacteria; in my postdoctoral work I am translating this approach to studying complex communities of microbes.
My goal is to determine the interplay between the gut environment, microbial colonization and disease, and to apply the principles that I elucidate to effectively reprogram diseased host habitats.
Born in Italy, Provincia di Cuneo, I moved to Canada in 2001 and graduated from UBC Biophysics in May 2008; I attended Stanford University as a PhD student in the School of Medicine's Biophysics program and graduated in 2014.
My goal is to become a faculty member at an institution supportive of interdisciplinary research as well as teaching, where I can combine my passion for medical research with my objective of mentoring the next generation of quantitative biologists and bioengineers. While there has recently been a remarkable expansion of investigations into the gut microbiota’s connection to human health, many fundamental mechanistic principles are being neglected. Physical perturbations such as temperature, osmolality, or pH have profound effects on both the gut microbiota as well as host physiology, but have been largely overlooked. My investigations bring a novel biophysical perspective to the microbiota field, integrating approaches from the physical and biological sciences. My line of studies has provided me with a unique framework which integrates biophysical analyses, mathematical modeling, cutting-edge in vitro technologies such as microfluidics with quantitative imaging, and in vivo experiments in animal models.
Living a well-rounded life is very important to me, I enjoy many activities outside of academics including cooking, ballroom dancing, beach volleyball, skiing, rock climbing, golfing, reading and horseback riding.
Two to five billion cases of diarrhea occur each year in humans, primarily due to infections; however, little is known about the long-term effects of diarrhea on the health of our intestinal flora. Using computational tools, high-throughput sequencing, transcriptomics and metabolomics combined with imaging of the gut, we seek to understand how the intestinal microbiota responds to periods of osmotic stress, and importantly, how the recovery progresses after a large portion of the microbiome has been depleted.
I am developing a microfluidic system to test how chemical and osmotic perturbations affect gut microbe species in the absence of host interactions. The ability to monitor the real-time dynamics of a complex microbial community during physical perturbations will allow us to characterize relevant members and key metabolic pathways involved during disruption of the normal equilibrium. To achieve fine-scale microfluidic control we use an Elveflow controller.
Mechanical properties of the mucosal layer can apply selective growth pressures to gut microbes involving entire macromolecular complexes such as the cell wall and membrane. Therefore, I am interested in studying how the host creates a primary line of defense by establishing and shedding mechanical barriers such as the intestinal mucus, whose physical and chemical characteristics select for a specific and stable set of commensal microbes. We are performing microrheology on mucus and assaying the effects of changes in mechanical properties to microbes in collaboration with the Spakowitz lab at Stanford.
With the widespread availability of information online, the mandate of university classes is shifting away from rote knowledge transfer, and toward the goal of teaching students tools that highlight the scientific method. Asking the right questions, reading scientific literature, and critically analyzing data are increasingly required, particularly now that data acquisition is rarely a limiting factor in science. I am committed to training the next generation of quantitative biologists to tackle challenging research questions using systems-based approaches, in part by integrating biology with computational modeling and bioinformatics. Merging theoretical biology with practical data analysis and model generation ideally prepares students for the challenges of research, as well as for the modern data-driven work environment.
As science becomes more collaborative, I believe that the next generation of researchers will be increasingly quantitative. Training these new scientists will require a strong understanding of physical and mathematical principles, and will involve integrating these approaches with a large variety of disciplines. Having trained in a unique environment where cutting-edge technologies from engineering and physics are applied to important questions in basic science, I am qualified to impart both the rigor as well as the breadth of knowledge required for a successful interdisciplinary education.
Cheetah3D is a great animation program and pretty intuitive to learn. To add a little visuals to my talks I have started animating a few concepts, such as the life-cycle of Caulobacter crescentus above. Once you start it is hard to stop! It’s easy to get carried away and start animating too much. Email me if you would like the full-version files!
Being a woman in the physical sciences comes with challenges. About only 20% of physics degrees are granted to women, which leads to a lack of role models and entrenches gender stereotypes. My undergraduate physics class was no different, and while the lack of other women created a close-knit community, it also isolated us. In my second undergraduate year at UBC I was fortunate to take a class with Dr. Mona Berciu, a professor in physics and an amazing role model. Dr. Berciu was well aware of these gender issues and was planning an event for high school women to meet other women in physics. That year I volunteered for the first event of “Welcome women to physics” (WOW) and enjoyed it immensely: the event created a support system and reinforced awareness that women succeed in the physical sciences. I decided to organize it the following year and improve the format based on what we had learned the previous year. The event was a great success and WOW is still running to this day, helping recruit bright women students to the UBC physics department.
If you are interested in a very comprehensive manual on the topic I recommend Molecular Cloning by Sambrook and Russell. I compiled this document utilizing material from a number of resources, in particular the molecular biology workshop at UBC, invitrogen, NEB, my lab notebook, Molecular Cloning: A Laboratory Manual, CSH protocols and notes from Russell Monds and Tiffany Vora. If you find any typos or inconsistencies please email me so that I can keep this document up to date and as useful as possible.
Science should not be only limited to scholars. Most scientific journals and textbooks require a significant degree of background; hopefully you will find the topics presented here accessible no matter what your training is!
Living la vida LOCa. A brief insight into the world of the "Lab on a chip" and microfluidics.
Diffusion equation tutorial. Requires some basic linear algebra and derivatives background.
Even though there are numerous other seminar series occurring at any university, in most cases they are oriented towards individuals that are either actively researching, or have a substantial education in the topics being presented. This structure can be very discouraging to undergraduate students interested in discovering possible future employment opportunities, learning about cutting edge research, or simply attending a lecture for interest. Due to the nature of much of the active research, lectures are mainly presented at international conferences – venues that are inaccessible to undergraduate students.
I decided to start The Adventures in Science seminar series to try and break down these barriers and provide a venue for UBC students to find out about new and exciting aspects of science by exposing them to research early in their undergraduate career. The series consisted of 12 talks, 6 per term. The invited speakers were all top-notch researchers at UBC who were chosen for both the quality of their research as well as their effectiveness as a speaker. In 2007-2008 Dr. Andre Marziali, Dr. Patricia Schulte, Dr. Douw Steyn, Dr. Brett Finlay and Dr. David Ng, Dr. Michael Bennett, Dr. Keith Benson, Dr. Bill Unruh, Dr. Carl Hansen, Dr. Mark Halpern and Dr. Neil Cashman more gave lectures on topics ranging from biology to biotechnology to physics, to science outreach and even history of science. This event hosted approximately up to 100 science undergraduates and is still continued at UBC by a very talented team of students that are part of the UBC Biophysics Student Society.
AIS not only allows students to learn about new research, it can also direct them towards a specialization in their studies by giving them a new or more specific direction. Due to the large breadth of topics covered, this seminar series can affect directly all science undergraduates, most of which have only experienced science in classes and therefore can hardly judge what they would like to do in the future. From the point of view of COOP and more generally internships in laboratories this can be a great way by which students find out more about the laboratories that are at UBC; from the perspective of the speaker this is a great way to recruit possible research assistants thereby fostering collaborations and internships.
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