Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization

The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans, and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioral experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualization of all simulation results using a worm locomotion and neural activity viewer. Models, experiment definitions and results can be exported in a machine-readable format, thereby facilitating reproducible and cross-platform execution of in silico C. elegans experiments in other simulation environments. This is made possible by a novel XML-based behavioral experiment definition encoding format, a NeuroML XML-based model generation and network configuration description language, and their associated GUIs. User survey data confirms the platform usability and functionality, and provides insights into future directions for web-based simulation GUIs of C. elegans and other living organisms. The tool suite is available online to the scientific community and its source code has been made available

The Long-Rage Directional Behavior of the Nematode C. Elegans

Like any mobile organism, C. elegans relies on sensory cues to find food. In the absence of such cues, animals might display defined search patterns or other stereotyped behavior. The motion of C. elegans has previously been characterized as a sinusoid whose direction can be modulated by gradual steering or by sharp turns, reversals and omega bends. However, such a fine-grained behavioral description does not by itself predict the longrange features of the animals’ pattern of movement. Using large (24 cm x 24 cm) Petri dishes, we characterized the movement pattern of C. elegans in the absence of stimuli. To collect trajectories over such a large surface, we devised an imaging setup employing an array of consumer flatbed scanners. We have confirmed quantitatively the results obtained with the scanner-array setup with a camera imaging setup, in a more stringently homogeneous environment. Wild-type worms display striking behavior in the absence of food. The majority (~60%) of the animals’ paths displays persistence in the direction of motion over length scales that are 50-100 times the body-length of C. elegans. The overall direction of movement differs from animal to animal, suggesting that the directed motion we observe might not be interpreted as a taxis to an external cue in the experimental environment. Interestingly, animals appear to exhibit directionality at large scales despite nondirectional motion at smaller scales. We quantified the extent of local directional persistence by computing the autocorrelation function of the velocities. Unexpectedly, correlations in the direction of motion decay over time scales that are much faster than the scales over which directional persistence appears to be maintained. We sought to establish quantitatively that the worm motion is, in fact, biased. To determine whether a null, random walk-like model of locomotion could account for directional behavior, we generated synthetic trajectories drawing from the same angle and step distributions of individual trajectories, and quantified the probabilities of obtaining larger net displacements than the experimental. Such a model fails to reproduce the experimental results. Moreover, the mean square displacements computed for the data display non-diffusive behavior, further demonstrating that the observed directional persistence cannot be explained by a simple random-walk model. To corroborate the hypothesis of biased movement in a model-independent fashion, we employed a geometrical characterization of the trajectories. Isotropic, unbiased walks result in paths that display a random distribution of turning angles between consecutive segments. In contrast, parsing of the worm’s trajectories yields different results depending on the segmentation scale adopted. In fact, increasing the segment size results in increasingly narrow turning angle distributions, centered around the zero. This suggests the emergence of directional coherence at long time scales. In order to investigate whether directional persistence is attained by a sensory mechanism, we analyzed the paths displayed by animals with impaired sensory function. Animals mutant for che-2, which display disrupted ciliary morphology and pleiotropic behavioral defects, exhibited non-directional behavior. Surprisingly however, daf-19 mutants, which lack sensory cilia altogether, displayed residual directionality, albeit at a lower penetrance (~20%) than the wild-type. This result suggests that directionality might implicate sensory modalities that do not require ciliary function, such as AFD-mediated thermosensation or URX-mediated oxygen sensation. Alternatively, the behavior of daf-19 mutants might imply that neural activity, but not sensory inputs, are required to achieve directed motion. Mutations in osm-9, a TRPV channel implicated in several avoidance behaviors in the worm, did not result in an observable phenotype. In contrast, mutations in tax-2/tax-4, a cGMP-gated channel required to transduce a number of sensory stimuli, resulted in loss of directionality. However, specific mutations targeting the signal transduction pathways for thermotaxis, olfaction, phototaxis, and aerotaxis, upstream of TAX-4, did not disrupt directional behavior. To get further insight into the nature of the stimulus directing the animals’ behavior, if any, we performed rescue experiments of TAX-4 function in specific subsets of neurons. In agreement with the results obtained by genetic lesions in the signal transduction pathways for thermotaxis and odortaxis, no rescue of directional behavior was observed when expressing TAX-4 in the thermosensory neuron AFD, or in the olfactory neurons AWB and AWC. Partial rescue of wild-type behavior was obtained by expression of TAX-4 in a set of five cells, which comprised the oxygen-sensing AQR, PQR and URX neurons as well as the ASJ and ASK sensory neurons, which transduce chemical stimuli and responses to dauer pheromone. To address the concern that the animals’ motion might be directed to a chemosensory cue within the plate, we investigated the correlation between path directions displayed by animals that were assayed on a same plate. We did not observe a detectable correlation between path headings, indicating that the worm is not chemotaxing to a plate-specific cue. In conclusion, our results indicate that the motion of C. elegans cannot be assimilated to a random walk, and that directional persistence arises at long times despite local nondirectional behavior. In addition, although we have not conclusively ruled out a sensorybased explanation, the genetic and phenomenological evidence gathered foreshadows the intriguing possibility that C. elegans might be achieving directional motion by relying solely on self-based information

Celebration Schedule 2015 (Friday)

Full presentation schedule for Celebration, Friday, May 1, 201

Dopaminergic and Activity-Dependent Modulation of Mechanosensory Responses in Drosophila Melanogaster Larvae

A central theme of this dissertation is nervous system plasticity. Activity-dependent plasticity and dopaminergic modulation are two processes by which neural circuits adapt their function to developmental and environmental changes. These processes are involved in basic cognitive functions and can contribute to neurological disorder. An important goal in modern neurobiology is understanding how genotypic variation influences plasticity, and leveraging the quantitative genetics resources in model organisms is a valuable component of this endeavor. To this end I investigated activity-dependent plasticity and dopaminergic modulation in Drosophila melanogaster larvae using neurobiological and genetic approaches. Larval mechanosensory behavior is described in Chapter 2. The behavioral experiments in that chapter provide a system to study mechanisms of plasticity and decision-making, while the electrophysiological characterization shows that sensory-motor output depends on neural activity levels of the circuit. This system is used to investigate activity-dependent plasticity in Chapter 3, i.e., habituation to repetitive tactile stimuli. In Chapter 4, those assays are combined with pharmacological manipulations, genetic manipulations, and other experimental paradigms to investigate dopaminergic modulation. Bioinformatics analyses were used in Chapter 5 to characterize natural genetic variation and the influence of single nucleotide polymorphisms on dopamine-related gene expression. The impact and suggested future directions based on this work are discussed in Chapter 6. Dopamine also modulates cardiomyocytes. Chapter 7 describes biochemical pathways that mediate dopaminergic modulation of heart rate. The final two chapters describe neurobiology research endeavors that are separate from my work on dopamine. Experiments that have helped characterize a role for Serf, a gene that codes for a small protein with previously unknown function, are described in Chapter 8. In the final chapter I describe optogenetic behavioral and electrophysiology preparations that are being integrated into high school classrooms and undergraduate physiology laboratories. Assessment of student motivation and learning outcomes in response to those experiments is also discussed

A Mechanism for Spatial Orientation Based on Sensory Adaptation in Caenorhabditis Elegans

During chemotaxis, animals compute spatial information about odor gradients to make navigational choices for finding or avoiding an odor source. The challenge to the neural circuitry is to interpret and respond to odor concentrations that change over time as animals traverse a gradient. In this thesis, I ask how a nervous system regulates spatial navigation by studying the chemotaxis response of Caenorhabditis elegans to diacetyl. A behavioral analysis demonstrated that AWA sensory neurons drive chemotaxis over several orders of magnitude in odor concentration, providing an entry point for dissecting the mechanistic basis of chemotaxis at the level of neural activity. Precise microfluidic stimulation enabled me to dissociate space from time in the olfactory input to characterize how odor sensing relates to behavior. I systematically measured neuronal responses to odor in the diacetyl chemotaxis circuit, aided by a newly developed imaging system with flexible stimulus delivery and elevated throughput. I found reliable sensory responses to the behaviorally relevant range of odor concentrations. I then followed odor-evoked activity to downstream interneurons that integrate sensory input. Adaptation of neuronal responses to odor yielded a highly sensitive response to small increases in odor concentration at the interneuron level, providing a mechanism for efficient gradient sensing during klinokinesis. Adaptation dynamics at the sensory level were stimulus-dependent and cell-autonomously altered in several classes of mutant animals. Behavioral responses to different concentrations of diacetyl resulted from overlapping contributions from multiple sensory neurons. AWA was specifically required for orientation behavior in response to small increases in odor concentration that are encountered in shallow gradients, demonstrating functional specialization amongst sensory neurons for stimulus characteristics. This work sheds light on an algorithm underlying acute behavioral computation and its biological implementation. The experimental results are presented in two parts: Chapter 2 describes the development of a microscope for high-throughput imaging of neuronal activity in Caenorhabditis elegans. I present a characterization of chemosensory responses to odor and its correlation with behavior. This work has been published (Larsch et al., 2013). Chapter 3 describes the functional architecture of the AWA chemosensory circuit and the role of adaptation in maintaining sensitivity over a wide range of stimulus intensities. This work is currently being prepared for publication

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

13th 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 as well as from 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 thirteenth annual Undergraduate Student Symposium