Weitz Group

Investigating how viruses transform human health and the fate of our planet

Investigating how viruses transform human health and the fate of our planet.      

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Daniel successfully defends his dissertation, earning his Ph.D. in Quantitative Biosciences.

June 10, 2022 by adavidson38

On June 9th, 2022, Daniel Muratore successfully defended his dissertation entitled “Emergence of Marine Biogeochemical Dynamics Across Scales Drive by Complex Microbial and Viral Communities,’’ earning his Ph.D. in quantitative biosciences.

Congratulations, Daniel!

To learn more about Daniel’s dissertation, read the abstract below.

Marine microbial populations are subject to the dual pressures of bottom-up nutrient limitation and top-down infection by abundant viruses. However, top-down and bottom-up controls do not act independently. Environmental conditions also have a large impact on the ecology and evolution of viral populations. This thesis explores the mutual feedbacks between the bottom-up and top-down drivers of marine microbial ecosystems.

The first part of this thesis studies two Lagrangian field campaigns conducted in oligotrophic gyres – one in the North Pacific and one in the Sargasso Sea. Emergent ecosystem-level diel cycles in nutrient uptake and assimilation show partitioning of key limiting resources. We also identify diel coordination of viral gene transcription across vast viral diversity.

The second part studies eco-evolutionary responses of marine virus infection strategies and variable environmental conditions. A comparative metagenomic study of genomic and proteomic nitrogen content across the Eastern Tropical North Pacific oxygen minimum zone identifies genome streamlining in bacteria, archaea, and viruses across nitrogen gradients. Then, we construct and analyze a game theoretic model of the evolution of strategies for viruses and their hosts in iron-limited environments, where viruses can use specialized host iron uptake mechanisms to facilitate infection. We identify conditions for the coexistence of hosts with and without this iron uptake capacity, and viruses that do or do not leverage it for infection.

Filed Under: Accomplishment Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

Register for the 6th annual Quantitative Biosciences hands-on modeling workshop

April 14, 2022 by adavidson38 Leave a Comment

Applications are now open to register for the 6th annual QBioS hands-on modeling workshop. This in-person, hands-on workshop, organized by the first-year cohort of Quantitative Biosciences PhD students, the first-year cohort of InQuBATE PhD students, Prof. Joshua Weitz, and  Prof. J.C. Gumbart, serves to introduce scientists of all experience levels to the process of modeling stochastic gene expression.

The workshop will include an opening lecture by group member and postdoctoral researcher, Adriana Lucia-Sanz, and a Plenery lecture by Professor Ido Golding, University of Illinois at Urbana-Champaign (UIUC). There will also be hands-on tutorials on implementing computational stochastic models of gene expression using Python or Matlab – no experience necessary!

To learn more or apply, visit https://workshop2022.qbios.gatech.edu

Filed Under: Education Tagged With: Foundations of quantitative viral ecology

Winter school, “Quantitative Viral Dynamics Across Scales,” comes to a close

April 11, 2022 by adavidson38 Leave a Comment

Paris Sciences et Lettres (PSL) University hosted a winter school centered around Quantitative Viral Dynamics Across Scales. Organized by Prof. Weitz, the school ran for one week (March 21-25, 2022) in Paris, France, and aimed to “bring thought leaders in dialogue with the next generation of early-career scientists to advance the integrative study of quantitative viral dynamics across scales.” Prof. Weitz also served as a lecturer and Scientific Committee Chair. Other guest lecturers include Weitz Group research scientist David Demory, postdoctoral fellow Jacopo Marchi, and several group collaborators.

Filed Under: Education, Science Communication Tagged With: Education, Foundations of quantitative viral ecology, Science communication

New paper published in Ecology Letters

January 31, 2022 by adavidson38 Leave a Comment

Look for our new paper out in Ecology Letters, titled “Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing.” This work is was done in collaboration with researchers from the University of California in San Diego as well as former group members Shengyun Peng and Chun Yin Leung.

Filed Under: Publication Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

Ashley successfully defends her dissertation, earning her Ph.D. in Physics.

November 22, 2021 by adavidson38 Leave a Comment

On November 18th, 2021, Ashley Coenen successfully defended her dissertation entitled “Inferring ecological interactions from dynamics in phage-bacteria communities,’’ earning her Ph.D. in physics.

To learn more about Ashley’s dissertation, read the abstract below.

Characterizing how viruses interact with microbial hosts is critical to understanding microbial community structure and function. However, existing methods for quantifying bacteria-phage interactions are not widely applicable to natural communities. First, many bacteria are not culturable, preventing direct experimental testing. Second, “-omics” based methods, while high in accuracy and specificity, have been shown to be extremely low in power. Third, inference methods based on time-series or co-occurrence data, while promising, have for the most part not been rigorously tested. This thesis work focuses on this final category of quantification strategies: inference methods.

In this thesis, we further our understanding of both the potential and limitations of several inference methods, focusing primarily on time-series data with high time resolution. We emphasize the quantification of efficacy by using time-series data from multi-strain bacteria-phage communities with known infection networks. We employ both in silico simulated bacteria-phage communities as well as an in vitro community experiment. We review existing correlation-based inference methods, extend theory and characterize tradeoffs for model-based inference which uses convex optimization, characterize pairwise interactions in a 5×5 virus-microbe community experiment using Markov chain Monte Carlo, and present analytic tools for microbiome time-series analysis when a dynamical model is unknown. Together, these chapters bridge gaps in existing literature in inference of ecological interactions from time-series data.

Filed Under: Accomplishment Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

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The Weitz Group

Investigating how viruses transform human health and the fate of our planet

310 Ferst Dr
School of Biological Sciences
Georgia Institute of Technology
Atlanta, GA 30332, USA

Website developed by Audra Davidson for the Weitz Group, 2021. For more information on the group, contact Dr. Gabi Steinbach: gabi.steinbach (@) physics.gatech.edu

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