Evolution of N. gonorrhoeae in response to host adaptive immunity
Evaluating equity of sewer connection in wastewater-based epidemiology
A scalable method for inferring genetic drift in pathogen transmission
- QinQin Yu, Joao Ascensao*, Takashi Okada*, Olivia Boyd, Erik Volz, Oskar Hallatschek. Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission. bioRxiv (2022). [link]
Evolution of genetic drift in microbial populations
Genetic drift is the change in a population’s composition due to the random nature of birth and death events. The strength of genetic drift directly impacts a population’s evolutionary trajectory by modulating the rate of diversity loss and rate of adaptation.
Changes in strength of genetic drift in a population are conventionally thought to be due to changes in population size and to occur over long time scales. I expanded our understanding of genetic drift by discovering that in microbial colonies, single mutations can affect the strength of genetic drift over short timescales by altering colony morphology. This result suggests that genetic drift can be an evolvable trait of a population. In other words, mutations can affect not only fitness and mutation rate, but also the strength of genetic drift, and this effect in turn affects the evolutionary trajectory of the population.
In collaboration with Joao Ascensao, a graduate student in the Hallatschek Lab, I extended this study to well-mixed cultures, where we hypothesized that phenotypic stochasticity in single cell traits modulates the offspring number variance, which together with the population size determines the strength of genetic drift. We measured the offspring number variance in strains from the E. coli Long Term Evolution Experiment (LTEE) to assess changes in genetic drift over evolutionary time.
Publications:
- QinQin Yu, Matti Gralka, Marie-Cécilia Duvernoy, Megan Sousa, Arbel Harpak, and Oskar Hallatschek (2021), Mutability of demographic noise in microbial range expansions, in press, ISME Journal. [link] [bioRxiv link].
Interplay of self-organization and evolution in microbial biofilms
Biofilms are the most common form of microbial life and can be found in environments ranging from the human gut to thermal hot springs. Biofilms form complex spatial structures which are hypothesized to impact evolutionary dynamics.
However, we currently have an incomplete understanding of how complex structures, such as three-dimensional growth, cellular nematic ordering, and extracellular matrix production impact biofilm evolutionary dynamics. In collaboration with Hallatschek lab graduate students Aditya Prasad and Joao Ascensao and the lab of Dr. Na Ji, I developed experimental methods to interrogate the impact of biofilm structure on evolutionary dynamics. I developed a molecular system for inducing and visualizing synthetic mutations in V. cholerae biofilms. I also developed imaging and microfluidics techniques.
Publications:
- Jona Kayser, Carl F. Schreck, QinQin Yu, Matti Gralka and Oskar Hallatschek. Emergence of evolutionary driving forces in pattern-forming microbial populations (2018). Phil. Trans. R. Soc. B 373: 20170106. http://dx.doi.org/10.1098/rstb.2017.0106. [link].
Pre-PhD dissertation work
During my undergraduate and graduate rotations, I worked on a variety of physics topics including atomic, molecular and optical physics, astronomy, and condensed matter physics.
As a graduate rotation student in Dr. Naomi Ginsberg’s group, I built a laser-based autofocus system for a new stroboscopic scattering microscope. The autofocusing setup allowed observations on the microscope to be made on both short and long timescales and the setup was used for studying exciton migration in novel materials.
- Milan Delor, Hannah Weaver, QinQin Yu, and Naomi Ginsberg. Imaging material functionality through three-dimensional nanoscale tracking of energy flow (2020). Nature Materials. [link]
For my undergraduate thesis with the lab of Dr. Vladan Vuletic, I wrote simulations to characterize atomic trajectories in a two-color (i.e. dual-wavelength) magneto-optical trap. The two-color scheme allowed us to cool and trap atoms at lower magnetic field strengths, and this setup was incorporated into a broader experiment to create a spin-squeezed atomic clock.
- QinQin Yu. Characterization of a two-color magneto-optical trap for a spin-squeezed optical lattice clock (2015) [Bachelor’s thesis].
- Akio Kawasaki, Boris Braverman, QinQin Yu, Vladan Vuletic. Two-color magneto-optical trap with small magnetic field for ytterbium (2015). Journal of Physics B. [link]
A major open question in astrophysics is how the elements were formed in the early universe. Working with Dr. Anna Frebel, I collected spectroscopic data of old stars using the Magellan Telescopes in Chile and analyzed the spectra using peak-fitting software to quantify elemental abundances. We discovered a star with very low abundances of the heavy elements, which helped to constrain the yields in a known process (r-process) that gives rise to these elements.
- Anna Frebel, QinQin Yu, Heather R Jacobson. A new r-process star with low abundances of r-process elements (2016). Journal of Physics: Conference Series. [link]