Animals in general, but fish in particular, inhabit environments characterized by dynamic photic conditions that are influenced by cyclical events such as the night-day cycle, or by spatial heterogeneity in the distribution of light. Effects of these dynamic properties on the visual system are compounded in salmonid fishes by migrations that expose individuals to various types of habitats, at various stages of their ontogeny. This dissertation examines some of the adaptations that enable the retina of salmonid fishes to cope with their changes of “visual environment” caused by migration and by the night-day cycle. In the first part of this dissertation, I used a combination of optic nerve response (ONR) recordings and conventional histology of the retina to investigate the ontogeny of sensitivity to ultraviolet (UV) light in salmonid fishes. I found that the UV cone mechanism contributed mostly to the ON response of retinal ganglion cells in rainbow trout (Oncorhpichus mykiss). Furthermore, the presence of UV sensitivity in rainbow trout was associated with the presence of accessory corner cones in the retinal cone mosaic, as both UV sensitivity and these cones were absent in larger (59.5-83 5g) juveniles. These results suggest that corner cones in the salmonid retina are sensitive to UV light, and that their ontogenetic disappearance leads to the loss of UV sensitivity. The changes in the photic environment that occur when mature salmonid fishes return to their natal stream to reproduce mirror those undergone during the first migration. To determine if the accessory comer cones, lost during this first migration, reappear at the time of the return migration, I studied the structure of the photoreceptor layer in sexually mature Pacific salmonids from four species: chinook (O. tschawytscha), chum (O. keta) and coho (O. kisutch) salmon, and rainbow trout. I found accessory comer cones over a large area of the dorso-temporal retina in all four species examined, which provides support for the contention that these cones are the product of late cellular addition. I investigated possible pathways for visual information to various brain centers in rainbow trout by labelling retinal projections and torus semicircularis connections in the same individuals. Double-labelling of neuronal tracts revealed two possible indirect pathways between the retina and the torus semicircularis, through the accessory optic center of the diencephalon and the optic tectum respectively. In the second part of this dissertation, I qualitatively and quantitatively examined the effects of various levels and spectral types of ambient lighting conditions on the sensitivity and time course of multi-unit responses recorded from the optic nerve of juvenile rainbow trout. Change in threshold from the dark-adapted state to progressively brighter ambient light conditions was examined at four wavelengths (380, 430, 540 and 620 nm) and found to be linear over most of the scotopic range, with a slope around 0.8. The results also suggested that, under mesopic conditions, rods and the long-wavelength cone mechanism were active simultaneously, in their respective parts of the spectrum. Implicit time, or time-to-peak of the scotopic responses decreased with stimulus intensity following a logarithmic relationship with a slope of -0.10, suggesting that the scotopic system of trout acts as an 11-stage low-pass filter, a number similar to that inferred in cat and rat, but different from other non-mammalian vertebrates. Similarly, implicit time at threshold decreased logarithmically with background intensity for the scotopic system, with a slope of -0.09 Varying the spectral content of ambient light led to differences in sensitivity and time course of ONRs across the spectrum, suggesting physiological differences between cone mechanisms. Possible implications for the coding of visual information are briefly discussed. In conclusion I provide a qualitative model of light adaptation in the trout visual system. / Graduate

The visual biology and its relevance to orientation was examined in fishes in the subfamily Salmoninae (salmon, trout, and char) by characterising the spectral and polarisation sensitivity of their visual systems. Integrated spike activity of axons from the optic nerve was used as a measure to determine the polarised-light sensitive mechanism underlying the ability of rainbow trout (Oncorhynchus mykiss) to orient in down-welling, linearly-polarised light. Relative sensitivity curves were then obtained for the five types of photoreceptor cells in this trout's retina: rods, ultraviolet sensitive cones (UV), short wavelength cones (blue-sensitive) (S), medium wavelength cones (green-sensitive) (M), and long wavelength cones (red-sensitive) (L). Under scotopic conditions (dark adapted), no sensitivity to e-vector was apparent. Under photopic conditions (light adapted), trout parr exhibited on-responses with e-vector sensitivity in two orthogonal channels. No evidence of polarisation sensitivity was observed in the on-responses of larger fish (50–78 g smolts) under UV-isolating background conditions, whereas the off-responses were unchanged.M and L cones, in contrast, retained their unimodal response. The decrease in UV-polarisation sensitivity in larger fish was found not to be attributable to size-related changes in the ability of the ocular media of the eye to transmit polarised light. Rainbow trout was used as a model species and spectral and polarisation sensitivity were compared with steelhead (an anadromous form of O. mykiss), cutthroat trout (O. clarki), kokanee (land-locked form of O.nerka), and brook char (Salvelinus fontinalis ). Visual pigment templates from rainbow trout were corrected for ocular media absorbance and overlaid on the spectral sensitivity curves for the purposes of comparison. Some differences in sensitivity were observed among species. In particular, on-responses were dominated by L-cones in most species.However, in kokanee, the M- cone was dominant.These differences may be related to the photic environments from which these fish originate. The first physiological evidence of near-UV sensitivity in the genus Salvelinus is also provided. It was therefore concluded that UV sensitivity is ubiquitous in the subfamily Salmoninae. Polarisation sensitivities in the above species were modelled using periodic regression analysis. Comparisons suggest that all of these species have a similar dual-channel polarisation detection system. The effect of the tuberculostatic drug Ethambutol on the visual physiology of rainbow trout was also examined. This drug appears to cause a decrease in sensitivity analogous to chromatic adaptation. Fish were fed daily for one month and then spectral sensitivity and polarisation sensitivity of Ethambutol-treated fish were compared to control fish. Relative to controls the visual systems of treated fish were dominated by the M-cone mechanism. Spectral and polarised light sensitivity of UV and L-cones were reduced. Finally, orientation responses of juvenile rainbow trout, steelhead, and brook char to a polarised-light stimulus were examined under controlled laboratory and semi-natural field conditions. Trained fish of all species oriented to the plane of polarised light, whereas untrained fish could not. Fish trained in the lab were tested at twilight and were found to be able to orient under natural skylight. Under semi-natural conditions, fish in floating net-pens in a lake were provided food rewards at a specific compass bearing. Their orientation responses were assessed under various natural and artificial conditions. When the sun was visible the fish typically had a unimodal distribution. However, they were typically not oriented when presented with only brightness and spectral cues at Zenith or on cloudy days. In contrast, both steelhead and sockeye were oriented correctly at civil twilight if the horizon was not obscured by heavy cloud or if blue sky was visible at Zenith. / Graduate

Indiana University-Purdue University Indianapolis (IUPUI) / The 20S proteasome, a multi-subunit protease complex, present in all domains of life and some orders of bacteria, is involved in degradation of the majority of cellular proteins. Structurally, it is made of α and β subunits arranged in four heptameric rings, with inner two β-rings sandwiched between outer two α-rings. The 20S proteasome in prokaryotes usually has one type of α and one type of β subunits, whereas eukaryotes have seven distinct types of α and seven distinct types of β subunits. Unlike the highly conserved structure of proteasome, its assembly pathway is different across the domains. In archaea and eukaryotes, proteasome assembly begins with α subunit interactions leading to the α-ring formation. By contrast, bacterial proteasome assembly pathway bypasses the α-ring formation step by initiating assembly through an α and β subunit interaction first. These early interactions are not well understood due to their highly rapid and dynamic nature. This dissertation focused on understanding the early events in proteasome assembly and contributed three significant findings. First, the archaeal proteasome assembly can also begin without formation of α-rings, demonstrating the coexistence of a bacterial-like assembly pathway. Second, a novel assembly intermediate was identified in yeast, and its composition argues for the presence of a similar α-ring independent assembly pathway. Third, the assembly chaperone Pba3-Pba4 prevents the formation of high molecular weight complexes arising from spontaneous and non-productive interactions among the α subunits. These findings provide a broader understanding of proteasome biogenesis and suggest considering proteasome assembly event as a network of interactions rather than a linear pathway. The results also shed light on assembly chaperone’s contribution in increasing the efficiency of proteasome assembly by streamlining the productive interactions. / 2020-12-07

Biological and environmental factors contribute collectively to the development of human cancers. The primary focus of this research project was to investigate the impact of germline gene mutations, as a significant biological factor, on 29 major primary human cancers. For this I obtained data from multiple databases, including the Genetic Association Database (GAD), Sanger database (COSMIC), HGMD database, OMIM data and PubMed literature. Using the Extraction Transform and Load (ETL) process, 424 genes were obtained with 8,879 cancer mutation records. By integrating these gene mutation records a Human Cancer Map (HCM) was constructed, from which several sub-maps were derived based on particular mutation classes. Furthermore, a Protein-Protein Interaction Map (PPIM) was constructed based on the encoded proteins of the 424 gene set. Several key questions were addressed using the HCM and its sub-maps including the following: (i) Are individual groups of primary cancers associated with specific subset of genes (within the 424 full set)? (ii) Are groups of primary cancers associated with particular mutation classes? (iii) If both questions prove to be true, are groups of cancers associated with particular mutation class of target genes? This project also explored whether a corresponding Protein-Protein Interaction Map, derived from the Missense/Non-sense Mutation portion of the HCM gene set, would provide further information on gene associations between primary cancers in terms of the consequent identical amino acid changes involved. Results showed that: (1) closely-connected human cancers in the HCM exhibited a strong association with a particular mutation class; (2) Missense /Nonsense and Regulatory mutations played a central role in connecting cancers (i.e. via primary nodes) and so significantly influenced the construction of the HCM; (3) Genes with Missense/Nonsense and Regulatory mutations tended to be involved in cancer-associated pathways; (4) Using the kappa test to measure the extent of agreement between two connected primary cancers in the sub-HCMs, BRCA1, BRCA2, PALB2, MSH2, MSH6, MLH1, CDKN2A, and TP53 showed highest agreement for 5 of 10 mutation classes; (5) From the PIPM, it was evident that BRCA1, MSH6, BARD1, TP53, MSH2 and CHEK2 proteins best connected Breast, Ovarian, Prostate and Bowel primary cancers, and so the latter could represent ¿driver proteins¿ for these cancers. In summary, this project has approached the analysis of gene involvement in human primary cancers from the starting position of the mutation class that harbours the specific gene mutation. Together with their downstream resultant alterations in the associated proteins, this analysis can provide insights into the relatedness of primary human cancers and their potential gene hierarchies. These data may therefore help us to understand more fully the etiology, diagnosis and potentially personalized treatments for cancer.

Functional magnetic resonance imaging (fMRI) is a noninvasive technique that can measure blood oxygenation level dependent (BOLD) signal changes in a large field of view with high spatial resolution. The objective of this dissertation is to explore and integrate novel and noninvasive fMRI methods at 7 Tesla to investigate the auditory and visual functions. First, different fMRI methods and stimulation paradigms were employed to explore some basic auditory functions such as sound pressure level (SPL) dependence in different brain structures, and periodotopy and tonotopy in the inferior colliculus (IC). BOLD signal changes increased significantly with SPL and the dependence was monotonic in the IC and lateral lemniscus (LL). The external cortex of IC (ECIC) had higher BOLD signal change than the central nucleus of IC and LL at high SPLs. This study indicates that sparse temporal sampling that is used to reduce the adverse effects of scanner noise may not be a prerequisite in auditory fMRI studies of the IC. Periodotopy and tonotopy in the IC was investigated using continuous imaging with passband balanced steady state free precession (bSSFP) sequence instead of sparse temporal sampling and echo planner imaging (EPI). The spatial gradients of best amplitude modulation frequency (referred to as periodotopy) and characteristic frequency (referred to as tonotopy) varied across the IC, but were approximately perpendicular at different locations. These findings enhance our understanding of how auditory information is preserved in the midbrain. Second, higher order function of behaviorally relevant sounds response selectivity in subcortical structures was investigated. The IC was found to exhibit a stronger response to forward vocalization than to the temporally inverted one. Moreover, blocking cholinergic projections to the IC by atropine injection was observed to significantly reduce the IC response selectivity to the 22 kHz vocalizations. These findings demonstrate the IC response selectivity to vocalizations and suggest that the cholinergic projection contributes to IC responses selectivity to the 22 kHz vocalization. This study provides further understanding about the higher order auditory processing and may have implications for the neural mechanisms underlying human speech perception Third, BOLD fMRI was applied to measure the brain response to stationary and apparent motion visual stimulation. The response of superior colliculus (SC) was weaker under dim light and saturates at higher intensities. Further, the BOLD signal changes and number of activated voxels were both significantly lower during 164 ˚/s apparent motion stimulation compared to stimuli at slower speeds. The results suggest that the SC was more sensitive to slow moving visual stimuli. This is the first fMRI study to investigate motion responsiveness and stimulus speed dependence in the rat SC. Results from these studies complement current knowledge and demonstrate the sophisticated role of subcortical structures such as IC and SC, which may have strong clinical significance to the field of auditory and visual research. Findings from the animal studies should open up new avenues of research and lay the ground work for future human studies. / published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

The precautionary principle has emerged as one of the most contentious international norms within international environmental law. Yet, despite the vexing conceptual uncertainties confronting the precautionary principle, it is repeatedly invoked by policy makers and incorporated within international and domestic environmental law and agreements. This thesis explores how the international norm of precaution comes to be translated from the international sphere to domestic public policy. The research utilizes the pathways framework, which suggests that there are three additional pathways in additional to the direct implementation of international rules in national law and policy - international norms and discourse, markets and direct access - through which actors, institutions and interests can influence domestic and firm-level policy change. The findings propose an explanation of why Canada came to adopt a particular version of the precautionary principle, also revealing the complex nature of norm transfer, the significance of multiple causal pathways of influence and the interactions arising along these pathways.

published_or_final_version / Physiology / Doctoral / Doctor of Philosophy

published_or_final_version / Physiology / Doctoral / Doctor of Philosophy

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No description available.