The aim of the work reported in this thesis is to investigate a methodology for studying perception by building and testing robotic models of animal sensory mechanisms. Much of Artificial Intelligence studies agent perception by exploring architectures for linking (often abstract) sensors and motors so as to give rise to particular behaviour. By contrast, this work proposes that perceptual investigations should begin with a characterisation of the underlying physical laws which govern the specific interaction of a sensor (or actuator) with its environment throughout the execution of a task. Moreover, it demonstrates that, through an understanding of task-physics, problems for which architectural solutions or explanations are often proposed may be solved more simply at the sensory interface - thereby minimising subsequent computation. This approach is applied to an investigation of the acoustical cues that may be exploited by several species of tone emitting insectivorous bats (species in the families Rhinolophidae and Hipposideridae) which localise prey using systematic pinnae scanning movements. From consideration of aspects of the sound filtering performed by the external and inner ear or these bats, three target localisation mechanisms are hypothesised and tested aboard a 6 degree-of-freedom, binaural, robotic echolocation system. In the first case, it is supposed that echolocators with narrow-band call structures use pinna movement to alter the directional sensitivity of their perceptual systems in the same whay that broad-band emitting bats rely on pinnae morphology to alter acoustic directionality at different frequencies. Scanning receivers also create dynamic cues - in the form of frequency and amplitude modulations - which very systematically with target angle. The second hypothesis investigated involves the extraction of timing cues from amplitude modulated echo envelopes.

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Thesis (Ph. D.)--Washington State University, December 2007. / Includes bibliographical references.

Unfortunately, chemists can never experimentally unravel a full reaction pathway. Even our ability to define key aspects of mechanisms, such as short-lived intermediates and the even more ephemeral transition states, is quite limited, requiring subtle experiments and subtle interpretations. Arguably the most important knowledge to be gained about the mechanism of a reaction is the structure and geometry of the transition state at the rate-limiting step, as this is where a reaction’s rate and selectivity are generally decided. The Singleton group has developed a methodology for predicting the combinatorial kinetic isotope effects (KIEs) at every atomic position, typically carbon or hydrogen, at natural abundance. A combination of experimental isotope effects and density functional theory (DFT) calculations has greatly aided our ability to predict and understand a reaction’s pathway and transition state geometries. Precise application of this method has allowed for the mechanistic investigation of a myriad of bioorganic, organic, and organometallic reactions. The technique has been applied in the analysis of the catalytic borylation of arenes via C-H bond activation, dynamic effects in the enyne allene cyclization, palladium catalyzed allylic alkylation, the nature of proton transfer in orotate decarboxylase, and the epoxidation of enones with t-butyl hydroperoxide.

Under challenge by a dietary soybean cysteine protease inhibitor (scN), cowpea bruchids overcome the inhibitory effects by reconfiguring the expression profiles of their major digestive enzymes, the cathepsin L-like cysteine proteases (CmCPs). In addition, cowpea bruchids activate transcription of the counter-defensive cathepsin B-like cysteine protease (CmCatB). I undertook an interest in understanding the molecular mechanisms utilized by bruchids to differentially regulate cysteine proteases in response to plant inhibitors. First, to investigate the functional significance of the differential regulation of CmCPs, I expressed CmCP proprotein isoforms (proCmCPs) in E. coli, and characterized their activities. Among proCmCPs, proCmCPB1 exhibited the most efficient autocatalytic processing, the highest proteolytic activity, and was able to degrade scN in the presence of excessive CmCPB1. Second, to dissect the molecular mechanisms behind the differential function of CmCPs, I swapped domains between two representative subfamily members B1 and A16. Swapping the propeptides did not qualitatively alter autoprocessing in either protease isoform. Incorporation of either the N- or C-terminal mature B1 segment into A16, however, was sufficient to prime autoprocessing of A16. Bacterially expressed isolated propeptides (pA16 and pB1) showed that pB1 inhibited B1 enzyme less than pA16 due to its protein instability. Taken together, these results suggest that cowpea bruchids selectively induce specific cysteine proteases for their superior autoprocessing, proteolytic efficacy, and scNdegrading activities, and modulate proteolysis of their digestive enzymes by controlling cleavage and stability of propeptides to cope with plant inhibitors. Third, to understand the transcriptional regulatory mechanisms of CmCatB hyperexpression that underlies bruchid adaptation, I cloned a portion of its promoter and demonstrated its activity in Drosophila S2 cells using a CAT reporter system. Gel shift assays identified cowpea bruchid Seven-up (CmSvp, chicken ovalbumin upstream promoter transcription factor homolog) in scN-unadapted insect midgut, and cowpea bruchid HNF-4 (CmHNF-4, hepatocyte nuclear factor 4) in scN-adapted insect midgut. When transiently expressed in S2 cells, CmSvp repressed, while CmHNF-4 activated CmCatB expression. CmSvp antagonized CmHNF-4-mediated transactivation when they were present simultaneously in the cell. Thus, the data suggest that transcriptional regulation of CmCatB in response to plant inhibitor depends, at least partly, on the cellular balance between positive and negative regulators.