Master of Science

thesisPrevious studies indicate that the brain tissue reaction to implanted silicon recording microelectrode arrays involves hyperplasia of macrophages, microglia and astrocytes, and that these reactions are accompanied by a decrease in the density of neurons immediately surrounding the implant. It is generally believed that the foreign body response is a major factor in the inconsistent recording performance observed with these devices. To gain insight into the earliest events, we used immunohistochemical methods to characterize the cellular responses adjacent to implanted microelectrodes at 1 ,3 , and 7 days after implantation using single shank planar Michigan-style silicon microelectrode arrays implanted into the cortex of adult male Sprague Dawley rats (225-300g) with N=12 per time point. Electrodes were implanted using stereotactic positioning at +0.2 mm bregma, 3 mm lateral, and 2 mm deep and were anchored with photo-cured adhesive into a polyurethane grommet. As a control, stab wounds were created in the same method, with N=6 at 3 and 7 days. Animals were sacrificed by transcardial perfusion and serial sectioned with a vibrotome. Significant variability existed in the amount of surface hemorrhage and the presence of infracted blood vessels along the implantation tract. Activated macrophages were attached to explanted probes at all postimplantation periods. Activation o f perivascular macrophages and extravasation of ED1+ cells at the site of injury was evident by 1 day postimplantation. Macrophages were found at the implant-tissue interface at all time points and were most prevalent at 3 days. At as early as 1 day, GFAP+ astrocytes were absent from the implantation site to about 50 |im, which was maintained at days 3 and 7. There was a significant decrease in neuronal soma within 0-50 jiin of the electrode track for stab wound and implanted animals. However for implanted animals, the area of neuronal loss had increased to 0150 |itn at 7 days, suggesting that secondary neuronal cell death is part of the early phase of the foreign body response. Future studies may use pharmacological approaches to understand if these early events can be modulated to improve the longterm functionality o f microelectrodes for neuroprosthetic devices

Comparing Migratory Patterns and Survival Between Wild and Wild Fish Surrogate Juvenile Spring Chinook Salmon (Oncorhynchus tshawytscha)

Anadromous salmonid populations in the Pacific Northwest have declined over the past 150 years. In 1999, wild spring Chinook salmon (Oncorhynchus tshawytscha) were federally listed as threatened within the Willamette Basin, OR. Currently, practices to restore wild populations in the upper Willamette Basin involve trapping wild adults at the base of high-head dams and hauling them upstream to historic spawning locations. Their resulting progeny must migrate downstream past the dams, highlighting the necessity of effective juvenile passage. Ideally, studies evaluating downstream juvenile passage structures would use wild fish, but this is often not feasible because of the large number of fish required for reliable estimates. The Wild Fish Surrogate Project at Oregon State University rears juvenile spring Chinook salmon as substitutes for wild-origin fish that are intended to behave similarly to wild ones and emulate wild juvenile migratory phenotypes in the Willamette Basin. We compared survival and movement of wild and wild fish surrogate juvenile Chinook salmon using a combination of PIT-tag detections at interrogation stations and seining recaptures in the McKenzie River Basin. We estimated survival with multi-state Cormack-Jolly-Seber models and compared survival between the two groups through time. Overall, detections and movements of wild and surrogate juveniles were similar, although wild fish surrogates tended to move earlier than their wild juvenile counterparts. Surrogate juveniles had a greater probability of movement within the upper Willamette River Basin compared to wild juveniles. This was likely due to the wild fish surrogates experiencing a novel environment and searching for suitable resources within the river system. Movement both within the upper Willamette River Basin and past Willamette Falls increased as the mean 7-day maximum temperature decreased, reflecting seasonal changes. Apparent survival differed between the two groups, and varied with maximum temperature. Surrogate fish had greater apparent survival at warmer temperatures compared to wild juveniles. This difference may have been a result of surrogate juveniles rearing at warmer temperatures prior to release and also being more likely to move downstream soon after being introduced into the McKenzie River

Global Extinction Risk for Seahorses, Pipefishes and Their Near Relatives (Syngnathiformes)

Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species

Clarinet Ensemble Recital

Program listing performers and works performe

Resetting predator baselines in coral reef ecosystems

What did coral reef ecosystems look like before human impacts became pervasive? Early efforts to reconstruct baselines resulted in the controversial suggestion that pristine coral reefs have inverted trophic pyramids, with disproportionally large top predator biomass. The validity of the coral reef inverted trophic pyramid has been questioned, but until now, was not resolved empirically. We use data from an eight-year tag-recapture program with spatially explicit, capture-recapture models to re-examine the population size and density of a key top predator at Palmyra atoll, the same location that inspired the idea of inverted trophic biomass pyramids in coral reef ecosystems. Given that animal movement is suspected to have significantly biased early biomass estimates of highly mobile top predators, we focused our reassessment on the most mobile and most abundant predator at Palmyra, the grey reef shark (Carcharhinus amblyrhynchos). We estimated a density of 21.3 (95% CI 17.8, 24.7) grey reef sharks/km2, which is an order of magnitude lower than the estimates that suggested an inverted trophic pyramid. Our results indicate that the trophic structure of an unexploited reef fish community is not inverted, and that even healthy top predator populations may be considerably smaller, and more precarious, than previously thought

Senior Recital

List of performers and performances

Predatory journals and their practices present a conundrum for systematic reviewers and evidence synthesisers of health research: A qualitative descriptive study

Predatory journals are a blemish on scholarly publishing and academia and the studies published within them are more likely to contain data that is false. The inclusion of studies from predatory journals in evidence syntheses is potentially problematic due to this propensity for false data to be included. To date, there has been little exploration of the opinions and experiences of evidence synthesisers when dealing with predatory journals in the conduct of their evidence synthesis. In this paper, the thoughts, opinions, and attitudes of evidence synthesisers towards predatory journals and the inclusion of studies published within these journals in evidence syntheses were sought. Focus groups were held with participants who were experienced evidence synthesisers from JBI (previously the Joanna Briggs Institute) collaboration. Utilising qualitative content analysis, two generic categories were identified: predatory journals within evidence synthesis, and predatory journals within academia. Our findings suggest that evidence synthesisers believe predatory journals are hard to identify and that there is no current consensus on the management of these studies if they have been included in an evidence synthesis. There is a critical need for further research, education, guidance, and development of clear processes to assist evidence synthesisers in the management of studies from predatory journals.</p

Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific

Corals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals

A Novel Anti-Inflammatory and Pro-Resolving Role for Resolvin D1 in Acute Cigarette Smoke-Induced Lung Inflammation

Introduction: Cigarette smoke is a profound pro-inflammatory stimulus that contributes to acute lung injuries and to chronic lung disease including COPD (emphysema and chronic bronchitis). Until recently, it was assumed that resolution of inflammation was a passive process that occurred once the inflammatory stimulus was removed. It is now recognized that resolution of inflammation is a bioactive process, mediated by specialized lipid mediators, and that normal homeostasis is maintained by a balance between pro-inflammatory and pro-resolving pathways. These novel small lipid mediators, including the resolvins, protectins and maresins, are bioactive products mainly derived from dietary omega-3 and omega-6 polyunsaturated fatty acids (PUFA). We hypothesize that resolvin D1 (RvD1) has potent anti-inflammatory and pro-resolving effects in a model of cigarette smoke-induced lung inflammation. Methods: Primary human lung fibroblasts, small airway epithelial cells and blood monocytes were treated with IL-1β or cigarette smoke extract in combination with RvD1 in vitro, production of pro-inflammatory mediators was measured. Mice were exposed to dilute mainstream cigarette smoke and treated with RvD1 either concurrently with smoke or after smoking cessation. The effects on lung inflammation and lung macrophage populations were assessed. Results: RvD1 suppressed production of pro-inflammatory mediators by primary human cells in a dose-dependent manner. Treatment of mice with RvD1 concurrently with cigarette smoke exposure significantly reduced neutrophilic lung inflammation and production of pro-inflammatory cytokines, while upregulating the anti-inflammatory cytokine IL-10. RvD1 promoted differentiation of alternatively activated (M2) macrophages and neutrophil efferocytosis. RvD1 also accelerated the resolution of lung inflammation when given after the final smoke exposure. Conclusions: RvD1 has potent anti-inflammatory and pro-resolving effects in cells and mice exposed to cigarette smoke. Resolvins have strong potential as a novel therapeutic approach to resolve lung injury caused by smoke and pulmonary toxicants