Modeling and simulation of Caenorhabditis elegans chemotaxis in response to a dynamic engineered bacteria

Parasitic helminthes remain important causative agents of human, plant and animal diseases. Helminthes seek out food sources and navigate toward potential hosts using olfaction of simple chemical cues in a process called chemoattraction. While several studies have examined how nematodes, including Caenorhabditis elegans, behave in response to a chemoattractant, how the characteristics of the chemoattractant affect worm behavior has yet to explored. In this manuscript, we develop a mathematical model to examine how characteristics of common chemoattractants affect movement and behavior in the model nematode C. elegans. Specifically, we model a scenario where a toxic, engineered bacteria designed to express a chemoattractant influences the behavior of a population of worms. Through the model we observe that, under static conditions, the diffusion rate of the chemoattractant is critical in influencing choice of C. elegans. Here, the higher diffusion rate, the more the worms are attracted to the chemoattractant. We then show that if the worms learn that the chemoattractant is associated with toxicity, choice index is counterintuitively more strongly reduced with increasing diffusion rate. Finally, our model predicts a tradeoff between pulse period and attractant strength when the chemoattractant is dynamically pulsed in the environment. Our results reveal unique tradeoffs that govern chemoattraction in worms and may have implications in designing novel strategies for preventing or treating infections with parasitic worms

Neural Architecture of Hunger-Dependent Multisensory Decision Making in C. elegans

Little is known about how animals integrate multiple sensory inputs in natural environments to balance avoidance of danger with approach to things of value. Furthermore, the mechanistic link between internal physiological state and threat-reward decision making remains poorly understood. Here we confronted C. elegans worms with the decision whether to cross a hyperosmotic barrier presenting the threat of desiccation to reach a source of food odor. We identified a specific interneuron that controls this decision via top-down extrasynaptic aminergic potentiation of the primary osmosensory neurons to increase their sensitivity to the barrier. We also establish that food deprivation increases the worm's willingness to cross the dangerous barrier by suppressing this pathway. These studies reveal a potentially general neural circuit architecture for internal state control of threat-reward decision making

Improvements in optical techniques to investigate the behavior and neuronal network dynamics over long timescales

Developments in optical technology have produced an important shift in experimental neuroscience from electrophysiological methods for observation and stimulation to all-optical solutions. One expects this trend to continue as future developments continue to deliver, and improve upon, the original promises of the technology: 1) minimally invasive actuation and recording of neurons, and 2) a drastic increase in targets that can be treated simultaneously. Moreover, as the high costs of the technology are reduced, one may expect its larger-scale adoption in the neuroscience community. In this thesis, I describe the development and implementation of two alloptical solutions for the analysis of behavior, neuronal signaling, and stimulation, which improve on previous state-of-the-art: (1) A minimally-invasive, high signal-to-noise twophoton microscopy setup capable of simultaneous, live-imaging of a large subset of sensory neurons post activation, and (2) a low-cost tracking solution to stimulate and record behavior. I begin this thesis with a review of recent advances in optical neuroscience techniques for the study of neuronal networks with the focus on work done in Caenorhabditis elegans. Then, in chapter 2, I describe my implementation of a two-photon temporal focusing microscopy setup and show significant improvements through the use of a high power/ high pulse repetition rate excitation system, enabling live imaging with high resolution for extended periods of time. I model temperature increase during a physiological imaging scenario for different repetition rates at fixed peak intensities and find range centered around 1 MHz to be optimal. Lastly, I describe the low-cost tracking setup with the ability to stimulate and record behavior over the course of hours. The setup is capable of two-color stimulation of optogenetic proteins over the area of the behavioral arena in combination with volatile chemicals. To showcase the utility of the system, I demonstrate behavioral analysis of integration of contradictory cues. In summary, I present a set of techniques for the interrogation of neural networks from animal behavior to neuronal activity, over timescales of potentially hours and days. These techniques can be used to address a new dimension of scientific questions.Okinawa Institute of Science and Technology Graduate Universit

14th Annual Undergraduate Student Symposium

The Undergraduate Student Symposium, sponsored by the Farquhar College of Arts and Sciences, presents student projects through presentations, papers, and poster displays. The event serves as a “showcase” demonstrating the outstanding scholarship of undergraduate students at NSU. The symposium is open to undergraduate students from all disciplines. Projects cover areas of student scholarship ranging from the experimental and the applied to the computational, theoretical, artistic, and literary. They are taken from class assignments and independent projects. The projects do not have to be complete; presentations can represent any stage in the concept’s evolution, from proposal and literature review to fully completed and realized scholarly work. As in past symposia, the definition of scholarship will be sufficiently broad to include work presented in the biological and physical sciences, the social and behavioral sciences, computer science, mathematics, arts and humanities, education, and business. This is the fourteenth annual Undergraduate Student Symposium

Temporal Processing by Caenorhabditis elegans Sensory Neurons

Caenorhabditis elegans is a promising organism for trying to understand how nervous systems generate real-time behavior. Its low neuron count suggests that we may be able to observe all of the constituents of the computation of sophisticated sensorimotor behavior. However, its appropriateness as a system for quantitative dynamical study has yet to be established. We show that C. elegans chemosensory neurons can operate in a highly deterministic and low-noise mode, and they act as reliable linear filters of their input. We then use dynamical systems analysis in combination with classical genetic perturbation to uncover cellular and circuit mechanisms of temporal processing. This work should firmly establish C. elegans as a viable platform for applying quantitative dynamical systems methods to understanding how a nervous system processes sensory information, integrates it with an evolving internal state, and produces goal-directed, coordinated behavior

Developing whole-cell biosensors for microbiome engineering applications

It is becoming increasingly apparent that the microbiota has a profound effect on human health and disease. Modern synthetic biology provides tools that can be used to engineer new diagnostic and therapeutic circuits- facilitating microbiome engineering and the creation of engineered biotherapeutics. These engineered biotherapeutics have the potential to expand our knowledge of microbial communities, host-microbe interactions and human health. However, to achieve these ambitious goals several challenges remain to be solved. These involve the creation of novel model systems and design strategies that can be used to characterise and improve these engineered strains. The primary focus of this thesis are whole-cell biosensors, that can be used to monitor molecules relevant to human health. Within this work I develop a novel model system, based on the Caenorhabditis elegans nematode that can be used to characterise biosensor strains in vivo. Through the developed protocols I use the nematode model to show that ratiometric biosensors can detect and report on changes within the C. elegans digestive tract. This model could be used to improve engineered biosensor strains, while also expanding our understanding of nematode biology and host-microbe interactions. In addition, I engineer a range of new ratiometric plasmids that can be used in conjunction with the C. elegans model system in future. Finally, I develop a range of acetoacetate-inducible biosensors; while also exploring methods of rationally improving two-component system biosensors. Two component systems are a common sensing mechanism that can be used to create a range of biosensors, therefore methods of rationally improving these biosensors would be an invaluable tool. Overall, it is hoped that the tools developed within this thesis can be used to further engineer whole-cell biosensors, which may help expand our knowledge of host-microbe interactions and human health

2019 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Schedule and abstract book for the Eleventh Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: November 16-17, 2019Location: UT Conference Center, KnoxvilleKeynote Speaker: Sadie Ryan, Medical Geography, Univ. of Florida; Director, Quantitative Disease Ecology & Conservation Lab (QDEC Lab)Featured Speaker: Christopher Strickland, Mathematics, Univ. of Tennessee, Knoxvill

PAS Signaling Mechanisms in Aer and Aer2

PAS domains are widespread signal sensors that share a conserved three-dimensional αβ fold that consists of a central β-sheet flanked by several α- helices. The aerotaxis receptor Aer from Escherichia coli and the Aer2 chemoreceptor from Pseudomonas aeruginosa both contain PAS domains. Aer senses oxygen (O2) indirectly via an FAD cofactor bound to its PAS domain, while Aer2 directly binds O2 to its PAS b-type heme cofactor. The Aer and Aer2 PAS domains both interact with a signal transduction domain known as a HAMP domain. The PAS-HAMP arrangement differs between Aer and Aer2, with Aer- PAS residing adjacent to its HAMP domain, and Aer2-PAS being sandwiched linearly between three N-terminal and two C-terminal HAMP domains. The differences between these PAS-HAMP architectures raise the possibility of two different PAS-HAMP signaling mechanisms: a lateral PAS-HAMP signaling mechanism for Aer, and a linear PAS-HAMP signaling mechanism for Aer2. This dissertation focuses on uncovering the PAS-HAMP transduction mechanisms and clarifying the signaling of conserved residues in Aer and Aer2 PAS. In Aer, I determined that a region on the PAS β-scaffold was sequestered by direct interaction with the HAMP domain. These data support a novel lateral PAS-HAMP arrangement that is crucial for Aer signaling. In Aer2, I demonstrated that unique PAS domain residues are involved in heme-binding, oxygen-binding and PAS signal initiation. My data provide the first functional corroboration of the Aer2 PAS signaling mechanism previously proposed from structure. The work presented in this dissertation demonstrates two variations of PAS-HAMP signaling mechanisms, both involving a global conformational change of the PAS domain that is transmitted from the PAS β-scaffold to the HAMP domain. My Aer and Aer2 studies provide the first direct evidence that HAMP domains can be activated by either linear or lateral interaction with a sensor module. Studying PAS-HAMP signaling mechanisms will help in understanding how sensing domains activate chemosensory systems that are involved in the survival of both commensal and pathogenic bacteria