The ocean covers most of Earth’s surface and plays a crucial role in global biogeochemical cycles. Phytoplankton growing in the open ocean surface account for approximately half of all annual carbon fixation. Therefore, we need a robust accounting of the drivers of phytoplankton growth and mortality, particularly their responses to changing environmental regimes, in order to model the Earth’s carbon cycle. The new flood of insights molecular technologies have provided into marine microbial adaptations to the hostile and nutrient-bereft open ocean surface calls for a fresh look at the role of dynamical ecosystem models in microbial oceanography. Here we will cover a few vignettes exploring (1) the response of the entire microbial ecosystem to the day/night cycle, linking physiological changes to bulk ecosystem properties, (2) the coevolutionary dynamics between a phytoplankton host and its virus under nutrient limiting conditions, adding theory to the proposed ‘Ferrojan Horse Hypothesis’, and (3) preliminary progress on fledgling work seeking to understand the role of viral infection in organic particle formation and export. 

The seminar will be hosted at this bluejeans link.

Bacterial gene expression and regulation mainly involves coupled processes of transcription, translation and degradation of messenger RNAs (mRNAs) and proteins. Limited efforts have been made to quantify the combined effects of these gene regulatory events globally. Here we aim to understand genome-wide gene expression control and to evaluate if RNA level is a good proxy to predict protein abundance in model organisms. I first analyzed the correlation of mRNA and protein abundance in Pseudomonas aeruginosa (PA). Our PA data suggest that mRNA abundance alone cannot precisely predict protein abundance (~60%). I also measured mRNA and protein expression profiles in Aggregatibacter actinomycetemcomitans (Aa) using RNA-seq and mass spectrometry approaches, and will integrate with their half-life dynamics for thousands of genes (work in progress). These studies provide a quantitative analysis of the cellular abundance and turnover dynamics of mRNA and protein and help us understand the underlying principles of gene expression control.

The seminar will be hosted at this bluejeans link.

Elongate animals (e.g., snakes, nematodes) propagate waves of body curvature to generate propulsion in dissipative environments. In particular, the nematode worm C. elegans lives in environments (e.g., rotting fruit) where maneuverability is crucial to overcome heterogeneities and post-interaction deformations. To search for steering control principles in undulatory locomotion, we studied C. elegans traversing both agar, liquid buffer, and lattices. These worms generate a time-dependent omega-like shape for reorientation to achieve high body rotation independent of the environment. Principal component analysis (PCA) revealed the worms use four principal components during turning, superimposing two body traveling waves with two spatial frequencies. A geometric mechanics framework rationalized the observed turning dynamics by properly coupling the amplitude and the phase of the two body traveling waves. These results and robophysical experiments, implementing the behavior, suggest that omega turns are a robust strategy for turning in diverse environments.

The seminar will be hosted at this bluejeans link.

The addition of therapeutic phage to treat Multi-Drug Resistant (MDR) pathogens imposes a strong selective pressure for the emergence of phage-resistant bacteria. Modeling and in vivo experiments have established that phage-resistant bacteria proliferate in Myd88-/- (immunodeficient) mice, corresponding to a failure of phage therapy. This work aims to develop evolutionarily robust phage therapy in immunodeficient hosts. First, we consider a model where bacteria evolve in an abstract discrete phenotypic space against different types of phages present in a therapeutic phage library. Second, we formulate a single-dose optimization problem subject to the proposed eco-evolutionary dynamics. The goal is to minimize the total bacterial population while penalizing the treatment costs by optimizing the phage therapy administrations. Finally, we extend single-dose treatment to multi-dose treatment and find the optimal policy via control theory. 

This seminar will be hosted at this bluejeans link.

Many bacterial species have multiple quorum sensing systems. Could these seemingly redundant systems improve on the performance of a single system? And if so, how would the different systems interact with each other?

In Australia, it is common knowledge that the bare-nosed wombat forms cubic scat, yet there has been little research on how this happens. From dissections, we find that the cubes form within the wombat’s intestines, prior to the anus. Through material testing, numerical simulations, and experiments with mimic wombat intestines, we investigate how the unique flat sides and rounded corners of the wombat’s feces form.

Dobzhansky-Muller sites play very important roles in hybrid incompatibility and speciation over evolution. However, its effect on organismal fitness and population genome structure remains elusive. In this talk, I’ll talk about a detailed study of Dobzhansky-Muller site that is a toxin/antidote system. Using quantitative assays and forward evolution simulation, I’ll show how could this site spread through population and have changed genome structure of the whole population. 


The students of the Georgia Tech Ph.D. in Quantitative Biosciences and Program Director Joshua Weitz invite you to a two-day hands-on modeling workshop on microbial games. During the workshop, attendees will learn the basics of programming using MATLAB and Python. They will also learn about microbial games and how to build their own simulations.  (Registration is now closed).

https://www.qbios-workshop-2019.com/

Event Date/Time: 

Monday, May 13, 2019 - 08:30

Event End: 

Tuesday, May 14, 2019 - 15:00

Do you want to build computational models of living systems but are not 
sure where to start? If so, the students of the Quantitative Biosciences 
program here at Georgia Tech (with program director Dr. Joshua Weitz) are 
pleased to invite you to a two-day Hands-On Modeling Workshop on 
evolutionary dynamics.

During the workshop, attendees will:

• Learn the basics of Matlab and/or Python programming languages (NO previous
  coding experience required!).
• Discuss quantitative principles of evolutionary dynamics.
• Build a simulation of evolution in action over experimental time-scales.
• Evaluate potential ways to incorporate computational models of evolutionary
  dynamics into your research.

Programming Languages: Matlab or Python

Skill Level: No prerequisites

During the workshop, attendees will:

• Learn the basics of Matlab and/or Python programming languages (NO previous coding experience required!).
• Discuss quantitative principles of evolutionary dynamics.
• Build a simulation of evolution in action over experimental time-scales.
• Evaluate potential ways to incorporate computational models of evolutionary
  dynamics into your research.

Programming Languages: Matlab or Python

Skill Level: No prerequisites