How visual targets are selected for eye movements is a fundamental neural coding problem for all animals that see with a fovea. The strength of the model of the neuron as a coincidence detector suggests neural synchrony is a plausible, if not intrinsic, part of the cortical code. Moreover, synchrony has been proposed as a neural mechanism for the allocation of attention in visual processing. To investigate a synchronous ensemble code for saccadic target selection in the frontal eye field (FEF), the gravity algorithm was applied to simultaneously recorded neurons in a macaque monkey performing color singleton search. In addition to developing an original measure of statistical significance for the gravity method, this thesis demonstrates the existence of synchrony in the search process. The functional influence of synchrony in the distribution of visual attention, however, or in gating broad population responses in FEF, requires further interpretation.

Decision making is pervasive in nature. Organisms from across the phylogenetic spectrum take in information from the external world and pursue courses of action in an attempt to maximize their evolutionary fitness. When faced with several competing alternatives, an individual must decide which option to select or how to distribute their resources amongst the various alternatives. The relatively young field of neuroeconomics has sought to reconcile economics' mathematical tools and formal models of decision processes with physiological measures from the nervous system. How individuals assess the value of competing options and act on internal representations of value is now a major focus of neuroeconomics and systems-level neuroscience. However, experiments in humans and non-human primates face barriers to progress that would be ameliorated in a genetically tractable organism with a compact nervous system. The nematode worm Caenorhabditis elegans has a relatively simple nervous system and a host of genetic tools, making it an advantageous system to elucidate the neural basis of decision making. This dissertation makes several contributions towards establishing C. elegans as a model of value-based decision making. I first develop a behavioral test for C. elegans that parallels paradigms of value-based decision making in human economics. Using microfluidic environments coupled with electrophysiological measures of feeding behavior, I offer worms discrete food choices and monitor how they distribute their 'budget' (i.e., feeding) between the alternatives. By manipulating the relative price (i.e., ease of consumption) of each food, I found that worms alter their spending patterns just as a human consumer does, expanding their consumption of a food as it becomes relatively cheaper. I also found that worms maintain a transitive rank order in their choice preferences, adhering to a classical test of economic rationality. Finally, I show that sensory neuron AWC is necessary for wildtype decision making, and monitor its activity during simulated decision making. AWC is active on the timescale of decision making, but its sensitivity does not fully explain C. elegans food preferences. These results suggest that the representation of value is distributed across a network whose aggregate activity in turn drives value-based decision making in C. elegans. / 10000-01-01

The ability to safely react to dangerous situations, or exploit opportunities within a dynamically changing world is fundamental for our survival. In order to respond to such changes in the environment, sensory information must first be received and processed by the nervous system before an appropriate motor response can be planned and executed. However, relatively little is known about how the central nervous system computes such sensory to motor transformations that are so critical for guiding efficient behavior. This thesis explores some of the neural mechanisms that underlie the visuomotor transformations that guide eye movements. Specifically, this thesis studied saccades (rapid eye movements critical for visual orienting in primates) and examined the relationships between visual and motor signals in the primate Superior Colliculus (SC, a midbrain structure located at the nexus between visual input and motor output that is critical for visual orienting). I recorded extracellular action potentials (spikes) from single neurons related to: 1) the appearance of visual saccade targets; 2) saccade planning and preparation; and 3) the execution of precise saccades that orient to visual targets. In this thesis I present four studies that examine the relationships between visual and motor related responses in the SC during visually guided saccades. In chapter 2 I examined the alignment between visual and motor response fields and concluded that they were well aligned. In chapters 3 and 4 I explored how visual responses were modulated by stimulus intensity and how this modulation influenced saccade behavior. I concluded that luminance modulated multiple properties of the visual response including the timing and maximum discharge rate and these changes were highly correlated to changes in saccade latency and metrics. In the fifth chapter I applied some of the knowledge gained from the previous chapters to develop a neural network model of the SC that was capable of simulating saccadic sensory to motor transformations and predict saccadic reaction time. I concluded that saccade latency was strongly dependant on the spatial interactions of visual and saccade related signals in the SC. Together, these findings provide novel insight into the neural mechanisms underlying saccadic sensorimotor transformations. / Thesis (Ph.D, Neuroscience Studies) -- Queen's University, 2011-03-03 08:36:14.559

<p>Neurons throughout the auditory pathway respond selectively to the frequency and amplitude of sound. In the auditory midbrain there exists a class of neurons that are also selective to the duration of sound. These duration-tuned neurons (DTNs) provide a potential neural mechanism underlying temporal processing in the central nervous system. Temporal processing is necessary for human speech, discriminating species-specific acoustic signals as well as echolocation. This dissertation aims to explore the role and underlying mechanisms of DTNs through single-unit in vivo electrophysiological recordings in the auditory midbrain of the big brown bat. The durations that DTNs are selective to in echolocating and non-echolocating species are first compared to the durations of each species vocalizations. This comparison reveals that the durations DTNs respond best to correlates to the durations of echolocation calls in echolocating species and to species-specific communication calls in non-echolocating species. The ability of DTNs in the bat to respond to stimulus parameters thought to be important for echolocation processing, such as pairs of pulses and binaural sound localization cues, are subsequently tested. The responses of DTNs to a paired tone spike suppressing paradigm presented monaurally and binaurally are also compared to characterize the role each ear plays in recruiting inhibition known to be involved in duration tuning. The results show that DTNs are able to respond to pairs of pulses at a timescale relevant to bat echolocation, and a majority also responded selectively to binaural sound localizing cues. Nearly half (48%) of DTNs did not show spike suppression to an ipsilaterally presented suppressing tone. When ipsilaterally evoked spike suppression occurred, the effect was significantly smaller than the suppression evoked by a contralateral suppressing tone. These findings provide evidence that DTNs may play a role in echolocation in bats as DTNs are able to respond to the outgoing pulse and returning echoes and localize the echo source and that the neural mechanism underlying duration tuning is monaural in nature.</p> / Doctor of Philosophy (PhD)

<p>A considerable amount of our everyday tactile experience requires interactions between textured surfaces and our fingertips. Such interactions elicit complex vibrations on our skin surface, which are encoded by the mechanosensitive afferents and conveyed to the brain where the perception of the textures emerges seemingly effortlessly. Intuitively, a fundamental question that may be asked is: “what features of the vibration stimuli are behaviourally relevant and what are the neural signatures of these features?” The goal of this thesis is to investigate these questions, which we have done using a combination of theoretical and experimental approaches.</p> <p>Our theoretical approach (in Chapter 2) has been to create an ideal Bayesian perceptual observer that utilizes all the information available in a spike-rate based neural code and makes optimal inferences regarding the amplitude and the frequency of vibration stimuli. Our experimental approach has been to estimate the performance of human participants in vibrotactile detection (in Chapter 3), and in amplitude and frequency discrimination (in Chapter 4) tasks by using psychophysical procedures.</p> <p>The results of these approaches suggest that the human perceptual observer, i.e. the human nervous system, probably uses a rate code to represent vibrotactile amplitude, but a non-rate code, such as a spike timing code, to represent vibrotactile frequency. Additionally, we conclude that humans are capable of inferring and separately perceiving the amplitude and frequency of vibrotactile stimuli; however, depending on experimental tasks, humans might also rely on a feature that combines the amplitude and frequency of vibrotactile stimuli.</p> / Doctor of Philosophy (PhD)

The development of traumatic brain injury (TBI) therapeutics and effective translation to clinic remains stubbornly elusive despite the high prevalence of TBI within the United States and across the globe. Interventions must be devised around testable targets, appropriately timed to intercede on secondary results. Here, we have utilized temporal neuroproteomics as an ideal approach to inform on the complex biochemical processing in order to address the well-recognized temporal evolution of TBI pathobiology and interrogate a novel therapeutic target in a mild-moderate rat Controlled Cortical Impact (CCI) within perilesioned somatosensory cortex. First, our findings revealed 2047 proteins significantly impacted within the first two weeks following TBI. Subsequent artificial neural network analysis revealed a delayed-onset cluster of proteins highly enriched in GABAergic neurotransmission and ion transport to reveal the prototypical target potassium/chloride transport 2 (KCC2 or SLC12A5) for further investigation with the KCC2-specific pharmacologic CLP290. Our tested therapeutic window guided by post-translational processing preceding one-day prior to protein loss revealed effective CLP290 restoration of KCC2 localization. We further demonstrated recovery in functional and behavioral assessments with one-day administration paradigm supporting the effectiveness of CLP290 treatment after brain injury. To better understand the underlying mechanism of CLP290, we utilized proteomic and bioinformatic approaches to tease out the biological response to treatment. Results demonstrate recovery of PKCδ-mediated phosphorylation of KCC2 and recovery of transporter activity. Additionally, findings reveal preservation of tyrosine kinase by reversing ubiquitin-mediated proteasomal degradation. Our functional assessment of secondary injury insults two-weeks following TBI revealed recovery in seizure threshold, reduction in lesion expansion and a decrease in cell loss suggesting maintained recovery of KCC2 and restored E/I balance. In conclusion, the presented studies in these two chapters propose a novel approach for development of therapeutics for TBI and test the selective manipulation via pharmacological intervention. These findings are promising for the development and treatment of other neurological disorders.

The goal of this dissertation is to advance our understanding of perceptual decisions. A perceptual decision is a decision that is based on sensory evidence. For example, a monkey must choose whether to eat a food item based on sensory information such as its color, texture or odor. Previous research has identified regions of the brain involved in the encoding of sensory information as well as areas involved in transforming encoded representations of stimuli into signals useful for forming decisions about those stimuli. Researchers carried out much of this work by painstakingly observing the firing of single neurons or small groups of neurons while a subject performs a task, and used this information to propose and evaluate models of the decision process. However, previous studies have also shown that sensory stimuli are encoded in a distributed fashion across populations of neurons rather than in individual or small groups of neurons. Thus it is likely that populations of neurons, rather than individual neurons, are responsible for the formation of a decision. Here I directly address the question of how decisions are formed through the collective activity of populations of cortical neurons. I used voltage-sensitive dye imaging, a technique that allowed me to simultaneously monitor millions of neurons in sensory cortex, while primates performed a simple yet challenging binary decision task. I also used psychophysical techniques and computational modeling to address fundamental questions about the nature of perceptual decisions. Here I provide new evidence that choice-related neural activity is distributed across a broad population of neurons, and that most of the decision-related neural activity occurs as early as primary sensory cortex. I propose a physiological and computational mechanism for the subject’s decision process in our task, and demonstrate that this process is likely sub-optimal due to intrinsic uncertainty about sensory stimuli. Overall, I conclude that in our task, perceptual decisions are likely to be limited primarily by the quality of evidence that resides in populations of neurons in sensory cortex, secondarily by sub-optimal decoding of these sensory signals, and to a much lesser extent by additional downstream neural variability. / text

We developed a spatially-tracked single neuron transcriptomics map of an intrinsic cardiac ganglion, the right atrial ganglionic plexus (RAGP) that is a critical mediator of sinoatrial node (SAN) activity. This 3D representation of RAGP used neuronal tracing to extensively map the spatial distribution of the subset of neurons that project to the SAN. RNA-seq of laser capture microdissected neurons revealed a distinct composition of RAGP neurons compared to the central nervous system and a surprising finding that cholinergic and catecholaminergic markers are coexpressed, suggesting multipotential phenotypes that can drive neuroplasticity within RAGP. High-throughput qPCR of hundreds of laser capture microdissected single neurons confirmed these findings and revealed a high dimensionality of neuromodulatory factors that contribute to dynamic control of the heart. Neuropeptide-receptor coexpression analysis revealed a combinatorial paracrine neuromodulatory network within RAGP informing follow-on studies on the vagal control of RAGP to regulate cardiac function in health and disease.

The corticospinal tract (CST), which carries commands from the cerebral cortex to the spinal cord, is vital to fine motor control. Spinal cord injury (SCI) often damages CST axons, causing loss of motor function, most notably in the hands and legs. Our preliminary work in rats suggests that CST circuitry is complex: neurons whose axons project to the lower cervical spinal cord, which directly controls hand function, also send axon collaterals to other locations in the nervous system and may engage parallel motor systems. To inform research into repair of SCI, we therefore aimed to map the entire projection pattern, or “connectome,” of such cervically-projecting CST axons. In this study, we mapped the corticospinal connectome of the Rhesus macaque - an animal model more similar to humans, and therefore more clinically relevant for examining SCI. Comparison of the Rhesus macaque and rat CST connectome, and extrapolation to the human CST connectome, may improve targeting of treatments and rehabilitation after human SCI. To selectively trace cervically-projecting CST motor axons, a virus encoding a Cre-recombinase-dependent tracer (AAV-DIO-gCOMET) was injected into the hand motor cortex, and a virus encoding Cre-recombinase (AAV-Cre) was injected into the C8 level of the spinal cord. In this intersectional approach, the gCOMET virus infects many neurons in the cortex, but gCOMET expression is not turned on unless the nucleus also contains Cre-recombinase, which must be retrogradely transported from axon terminals in the C8 spinal cord. Thus, gCOMET is only expressed in neurons that project to the C8 spinal cord, and it proceeds to fill the entire neuron, including all axon collaterals. Any gCOMET-labeled axon segments observed in other regions of the nervous system are therefore collaterals of cervically-projecting axons. gCOMET-positive axons were immunohistochemically labeled, and axon density was quantified using a fluorescence microscope and Fiji/ImageJ software. Specific regions of interest were chosen for analysis because of their known relevance in motor function in humans, and for comparison to results of a similar study in rats. Results in the first monkey have revealed both similarities and differences between the monkey and rodent CST connectome. Analyses of additional monkeys are ongoing. The final results will provide detailed information about differences between rodent and primate CST, will serve as a baseline for examining changes in the CST connectome after SCI, and will provide guidance for studies targeting treatment and functional recovery after SCI.

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.