abstract: The Atlantic razor clam burrows underground with effectiveness and efficiency by coordinating shape changings of its shell and foot. Inspired by the burrowing strategy of razor clams, this research is dedicated to developing a self-burrowing technology for active underground explorations by investigating the burrowing mechanism of razor clams from the perspective of soil mechanics. In this study, the razor clam was observed to burrow out of sands simply by extending and contracting its foot periodically. This upward burrowing gait is much simpler than its downward burrowing gait, which also involves opening/closing of the shell and dilation of the foot. The upward burrowing gait inspired the design of a self-burrowing-out soft robot, which drives itself out of sands naturally by extension and contraction through pneumatic inflation and deflation. A simplified analytical model was then proposed and explained the upward burrowing behavior of the robot and razor clams as the asymmetric nature of soil resistances applied on both ends due to the intrinsic stress gradient of sand deposits. To burrow downward, additional symmetry-breaking features are needed for the robot to increase the resistance in the upward burrowing direction and to decrease the resistance in the downward burrowing direction. A potential approach is by incorporating friction anisotropy, which was then experimentally demonstrated to affect the upward burrowing of the soft robot. The downward burrowing gait of razor clams provides another inspiration. By exploring the analogies between the downward burrowing gait and in-situ soil characterization methods, a clam-inspired shape-changing penetrator was designed and penetrated dry granular materials both numerically and experimentally. Results demonstrated that the shell opening not only contributes to forming a penetration anchor by compressing the surrounding particles, but also reduces the foot penetration resistance temporally by creating a stress arch above the foot; the shell closing facilitates the downward burrowing by reducing the friction resistance to the subsequent shell retraction. Findings from this research shed lights on the future design of a clam-inspired self-burrowing robot. / Dissertation/Thesis / Video for section A1 of APPENDIX A / Video for section A2 of APPENDIX A / Video for section A3 of APPENDIX A / Video for section B8 of APPENDIX B / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2020

Obtaining new insights into the behavior of free-living marine organisms is fundamental for conservation efforts and anticipating the impact of climate change on marine ecosystems. Despite the recent advances in biotelemetry, collecting physiological and behavioral parameters of underwater free-living animals remains technically challenging. In this thesis, we develop the first magnetic underwater animal monitoring system that utilizes Tunnel magnetoresistance (TMR) sensors, the most sensitive solid-state sensors today, coupled with flexible magnetic composites. The TMR sensors are composed of CoFeB free layers and MgO tunnel barriers, patterned using standard optical lithography and ion milling procedures. The short and long-term stability of the TMR sensors has been studied using statistical and Allan deviation analysis. Instrumentation noise has been reduced using optimized electrical interconnection schemes. We also develop flexible NdFeB-PDMS composite magnets optimized for applications in corrosive marine environments, and which can be attached to marine animals. The magnetic and mechanical properties are studied for different NdFeB powder concentrations and the performance of the magnetic composites for different exposure times to sea water is systematically investigated. Without protective layer, the composite magnets loose more than 50% of their magnetization after 51 days in seawater. The durability of the composite magnets can be considerably improved by using polymer coatings which are protecting the composite magnet, whereby Parylene C is found to be the most effective solution, providing simultaneously corrosion resistance, flexibility, and enhanced biocompatibility. A Parylene C film of 2μm thickness provides the sufficient protection of the magnetic composite in corrosive aqueous environments for more than 70 days. For the high level performance of the system, the theoretically optimal position of the composite magnets with respect to the sensing direction of the sensor has been estimated using finite element modeling software. The magnetic sensing system has been practically implemented for monitoring the belly size of a model fish and for monitoring the behavior of the largest living bivalve, giant clam (Tridacna maxima) in an aquarium. In both of these experiments, the sensing system showed a high performance, indicating its potential for novel marine monitoring applications.

Most of what is known about the ways in which strongly interacting species affect ecological communities stems from changes to community structure revealed in contemporary research. However, trophic downgrading has limited the temporal extent to which inferences can be drawn. The aim of my Dissertation was to expand on the strongly interacting species concept by examining species interactions at a historical scale, in a textbook example of a strongly interacting and keystone predator. The sea otter, Enhydra lutris, was driven to near-extinction but is recovering in parts of its range, providing a mosaic of areas with and without sea otters. This mosaic allowed for a series of natural experiments, which I conducted using behavioural observations, genetic tools, and archaeological methods, to examine sea otter effects spanning contemporary (last ~40 yrs.), and late-Holocene (~3500-150 yrs. ago) timeframes, and on an evolutionary scale that inferred middle-Pleistocene interactions. In Chapter 2, my coauthors and I found that sea otter use of clam-based niches increased as occupancy-time increased, and that bachelor groups of male otters primarily inhabited these niches, findings that informed and inspired subsequent questions. In Chapter 3, we found that where sea otters were established for 20-30 years, the disturbance to eelgrass (Zostera marina), caused by sea otters digging for clams and other infaunal prey, was correlated with ~25% greater eelgrass allelic richness than where otters were present <10 yrs, or absent. We posit that sea otter digging has long-influenced the genetic diversity and resilience of eelgrass – perhaps since the middle Pleistocene. In Chapter 4, we asked how two strongly interacting species – people and sea otters – co-existed for millennia where they both consumed clams. We used assemblages of live and otter-cracked butter clams (Saxidomus gigantea), to confirm the ecological effects that sea otters exert today. We measured clams from archaeological assemblages in areas densely populated with clam gardens – terraced beaches that enhance clam habitat and productivity – and found that sea otters reduced the sizes of ancient clams, acting as ecologically effective predators in the mid-to-late Holocene. However, clam harvests were stable for thousands of years, with or without otters. We suggest that clam gardening supported coexistence of people and otters in the past, and could function the same way today. Collectively, we found that a few, perhaps long-forgotten, interactions increased the breadth of the strongly interacting species concept. In Chapter 5, I suggest that such rediscoveries could occur in other systems. Many large vertebrates have suffered population declines, but the most insidious losses accompanying these, are the losses of ecological interactions that become unknowable, and thus cannot be intentionally restored. By searching out ancient interactions, long-forgotten relationships have the potential to be recovered, and to inform our understanding of contemporary systems. / Graduate / 2022-09-10

No description available.

Marine shellfish play a vital role in intertidal ecosystems and coastal communities, but many of these fisheries are small-scale and lack the necessary monitoring to ensure long-term sustainability. Effective management often requires information on key demographic parameters, such as population status, reproduction and growth. Pismo clams (Tivela stultorum) are a culturally important and iconic species in California, which supported a thriving commercial and recreational fishery throughout much of the 1900’s. However, Pismo clam populations have declined statewide in recent decades and are attributed to human harvest and predation by California sea otters (Enhydra lutris); However, no studies have examined their populations, population drivers, or life history for at least 40 years. Managers require updated and expanded information on populations, habitat associations, reproduction and growth rates to effectively manage, regulate, and recover Pismo clam in California. In Chapter 1, we investigated current Pismo clam population levels in California and examined the role of abiotic and biotic factors as correlates of clam abundance. We quantified Pismo clam presence, density and biomass at 38 sites in California during 2018 and 2019. Our results indicate that while human population density does not appear to drive clam populations, median sediment grain size is an important predictor for Pismo clams on open coast beaches. As median grain size increases, the probability of clam presence, density, and biomass decreases, suggesting that the composition of beach habitat is a critical factor regulating Pismo clam populations. Additionally, clam density and biomass are significantly higher on beaches north of Point Conception compared to beaches south. This suggests that Pismo clam population declines are more complicated than conventional wisdom suggests. Overall, Pismo clam densities are lower and size structures are shifted towards smaller sizes than historical accounts. This study is the most comprehensive set of population surveys to date and identifies key factors associated with Pismo clam abundance, which may be used to inform management and guide restoration and recovery of this once iconic species. In Chapter 2, we examined life history characteristics of Pismo clams in California. Specifically, we investigated the annual reproductive cycle of Pismo clams in California, pairing multiple metrics within a single study to describe the sex ratio, gonad development stages, body condition index, and length at sexual maturity. Further, we examine age-length relationships across California to provide estimates of age structure and growth rate, which will better inform recovery timelines for the recreational fishery in California. Our results indicate that the sex ratio is 1:1, peak spawning occurred in late summer, and clams can spawn in their first year (<20 >mm). Cycles of body condition were influenced primarily by mean monthly sea surface temperature, but mean monthly chlorophyll-a concentration, photoperiod, clam size, and year were also important. Body condition was significantly correlated with the proportion of clams in the Ripe stage. Thus, body condition has the potential to be a rapid, inexpensive proxy for monitoring reproduction in Pismo clams, potentially providing useful information about changes in reproductive patterns. Finally, examination of age-length relationships for Pismo clams suggest that clams may require over 13 years to reach a legally harvestable size (114 mm across most of California). The estimated age at legal size is substantially older than historical estimates, which suggested that Pismo clams could reach legally harvestable size in as few as 6 years. Collectively, this work represents a significant advance in our knowledge of the biology and ecology of this iconic and culturally important species. Furthermore, it provides vital information on the current population status, reproduction, and growth rates to inform management, regulation, and potential recovery of Pismo clams in California.

No description available.

No description available.

This thesis focuses on the traditional cultivation of an edible root species by Kwaxsistalla, Clan Chief Adam Dick, of the Qawadiliqalla Clan, of the Dzawada ēnuxw, a subgroup of Kwakwaka’wakw, occupying the Kingcome Inlet area on the Central Coast of British Columbia. Kwaxsistalla is a traditionally trained Clan Chief and potlatch speaker with recognized authority to share his detailed knowledge and experiences of his clan’s food production system. This research is centered on his Clan’s tekkillakw (estuarine salt marsh root garden) root gardens of the Kingcome River estuary, and the long-standing practices associated with the large-scale production of tleksem Pacific silverweed [Argentina egedii (Wormsk.) Rydb.; syn. Potentilla pacifica (L.) Howell.], is one of the four cultivated root species. Kwaxsistalla has shared his hands-on knowledge of how root garden cultivation fits into his family’s seasonal patterns of food production as well as detailed accounts of how to construct and use tools for cultivating, weeding, harvesting, and cooking estuarine roots. He has also provided information that has been instrumental in developing a model of aboriginal management of estuarine root gardens (Deur 2005). This thesis builds on Deur’s model by attempting to experimentally replicate tekkillakw management in order to better understand the management effect on the abundance, size, and flavour of Argentina egedii roots. Over the course of the 2008 growing season I randomly subjected 60 ¼ square meter patches of Kwaxsistalla’s fallow tekkillakw to either a “till” or “till + weed” treatment and allocated 30 similar patches as a control. I applied a roto-tilling treatment just prior to the growing season, a weeding treatment mid-summer, and harvested the roots near the end of the growing season. While the short duration of my study and use of a roto-tiller limit the inferential power of my results, I found that tilling and weeding significantly increased the abundance or A. egedii but significantly decreased the root size. Throughout the same 2008 field season I also collected root specimens for analysis of their bitter and sweet constituents and found (bitter) tannins concentrations to be highest in the late summer and lowest in the spring and fall. / Graduate

Thesis (M.A.)--Memorial University of Newfoundland, 2006. / Bibliography: leaves 105-114. Also available online.

À partir des ovocytes de la palourde Spisula solidissima, un ADNc codant un récepteur nommé Spi-OAR a été cloné et séquencé. Une analyse de la séquence en acides aminés a indiqué que ce nouveau récepteur possède une forte similarité avec les récepteurs β-adrénergiques et les récepteurs à octopamine. En effet, il est étroitement lié à la classe des récepteurs à octopamine « β-adrénergique-like » couplés à une protéine Gs. L’ADNc de Spi-OAR a été introduit dans un vecteur d'expression (pCEP4) et un épitope reconnaissable par un anticorps commercial a été ajouté au segment N-terminal. Cette construction a été transfectée dans des cellules hôtes (HEK 293) et des études d’immunofluorescence ont montré une expression efficace du récepteur au niveau membranaire. Également, des mesures d'AMPc pour les cellules exprimant Spi-OAR ont révélé une augmentation de ce messager secondaire lors de l'ajout de l'octopamine, et dans une moindre mesure, la tyramine, tandis que la dopamine, la sérotonine et l'histamine n’ont engendré aucun effet. Une légère activité constitutive de ce récepteur dans les cellules hôtes a été observée. De plus, une analyse RT-PCR avec des oligonucléotides spécifiques a révélé l'ARNm de Spi-OAR non seulement dans les ovocytes, mais aussi dans les gonades, le cœur, les muscles adducteurs, les branchies et les ganglions suggérant que ce récepteur soit exprimé de façon ubiquitaire dans divers tissus et dans différents stades embryonnaires chez la palourde. En outre, des études avec des ovocytes isolés n'ont montré aucun effet de l’octopamine sur la réactivation méiotique. Des études éventuelles pourront finalement confirmer le rôle fonctionnel de Spi-OAR. / A cDNA encoding for an octopamine receptor named Spi-OAR was cloned and sequenced from the surf clam Spisula solidissima oocytes. An analysis of its predicted amino acid sequence showed a high degree of similarity with β-adrenergic and octopamine receptors. This receptor qualifies as a novel receptor closely related to the proposed class of insect octopamine « β-adrenergic–like » receptors coupled to Gs protein. This cDNA was introduced into an expression vector (pCEP4), with an added N-terminal FLAG tag sequence, and transfected in host cells (HEK 293). Immunofluorescence studies showed expression of the receptor with a proper localization to the plasma membrane. Measurements of cAMP in transfected cells revealed that addition of octopamine, and to a lower extent, tyramine induced a rise in cAMP while dopamine, serotonine and histamine had no effect. Overexpression of Spi-OAR in mammalian cells induced slight constitutive increase of cAMP. An RT-PCR analysis with specific oligonucleotides revealed the presence of the receptor mRNA not only in oocytes but also in whole gonads, heart, adductor muscle, gills and ganglia suggesting that this receptor is likely ubiquitously expressed. Expression of Spi-OAR was also detected at different embryonic stages. Despite the demonstrated expression of Spi-OAR in oocytes, octopamine had no effect on meiotic reinitiation. Further studies will examine the function of Spi-OAR.