Department of Biology (Saint John)

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Age validation, size-at-age, size-at-maturity, and age-at-maturity in snow crab (Chionoecetes opilio) from different thermal regimes in Newfoundland
Age validation, size-at-age, size-at-maturity, and age-at-maturity in snow crab (Chionoecetes opilio) from different thermal regimes in Newfoundland
by Nicole Catlin, Calcein dye was used to determine the deposition rate of growth bands on snow crab gastric mill ossicles, although this was unsuccessful due to dye leaching. Annual deposition of growth bands was, however, corroborated based on age estimates from size-frequency histograms. There is limited understanding of the effects of temperature on snow crab growth and sexual maturation. Band counts revealed no significant difference in size-at-age, size-at-maturity, and age-at-maturity between crabs inhabiting “colder” and “warmer” waters around Newfoundland, but a significant difference in size-at-age and size-at-maturity between males (larger) and females (smaller) was found. Some of my findings were consistent and others inconsistent, with the literature, which may have been partly due to a warming trend preceding this study and/or crab movements. Future studies should attempt to relate snow crab growth and maturation to the temperature they experience throughout their lifetime, which should assist fisheries management in a rapidly changing climate., Electronic Only., Electronic Only. "Master of Biology in the Graduate Academic Unit of Biological Sciences"--Title page.
Anti-mycobacterial natural products from Canadian medicinal plants
Anti-mycobacterial natural products from Canadian medicinal plants
by Haoxin Li, The global epidemic of tuberculosis (TB) persists in large part due to the development of resistance against current therapies. One potential source for novel anti-TB drugs is natural products. Plants and the natural products that they produce have long been recognized for their medicinal value and are extensively used as traditional medicines, and therefore they represent an important source of anti-mycobacterial natural products. The objective of this thesis was to investigate anti-mycobacterial natural products from Canadian medicinal plants. Four plants that have been used to treat TB, Aralia nudicaulis, Alnus incana, Empetrum nigrum and Moneses uniflora, were selected after preliminary anti-mycobacterial screening of 13 Canadian medicinal plants. A total of 21 natural products were isolated through bioassay guided fractionation of the four plants. Aralia nudicaulis was selected for the exploration of its endophytic community and the C17 diynes isolated from A. nudicaulis were investigated to identify their anti-mycobacterial modes of action. As it has been demonstrated that some endophytes can produce natural products originally attributed to their host, we considered it worthwhile investigating whether the C17 diynes isolated from A. nudicaulis were biosynthesized from the plant de novo or whether they were produced by endophytes. As such, 88 endophytic fungi were isolated from rhizomes of A. nudicaulis and were screened for their ability to produce falcarinol and panaxydol. Unfortunately, neither of the C17 diynes could be detected in the endophytes from our screening. Microarray analysis was used to determine the transcript responses of Mycobacterium smegmatis when treated with the C17 diynes, falcarinol and panaxydol. Principal component analysis suggested a different mode of action of the C17 diynes when compared with commonly used anti-mycobacterial drugs. Functional enrichment and pathway enrichment analysis revealed that there were gene ontologies and pathways preferentially affected by the C17 diynes treatments. The theoretical bioactivities of the two C17 diynes were estimated through prediction of activity spectra of substances (PASS). Based upon these analyses, it is hypothesized that the C17 diynes inhibit fatty acid biosynthesis, specifically phospholipid synthesis, in mycobacteria.
Assessing potential influence of larval development time and drift on large-scale spatial connectivity of American lobster (homarus americanus)
Assessing potential influence of larval development time and drift on large-scale spatial connectivity of American lobster (homarus americanus)
by Brady Keith Quinn, I used a new larval drift model to investigate potential spatial connectivity of American lobsters at a large scale incorporating most of the species' range. Because temperature-dependent development of lobster larvae might vary across the species' range, I compared a lab study using cold-water larvae with results of previous studies using warm-water larvae, and tested the sensitivity of model predictions to differences in larval development. The relationship between temperature and larval development time differed between warm- and cold-origin larvae, possibly due to adaptation to local thermal regimes. Different larval development scenarios affected the amount of connectivity predicted by the model among areas. The model predicted much potential connectivity among lobster fisheries areas, and predicted retention of larvae in certain areas, and reliance on external larval supply in others. This is important to management, as the amount and direction of connectivity among lobster fisheries can be used to manage them sustainabIy.
Assessment of water quality and ecosystem techniques to monitor the environmental effects of salmon aquaculture
Assessment of water quality and ecosystem techniques to monitor the environmental effects of salmon aquaculture
by Jonathan Day, Integrated Multi-Trophic Aquaculture (IMTA) diversifies species culture to produce a variety of products and mitigate nutrient impacts associated with finfish culture. This study examined two biological indicators that could be used to assess IMTA performance with respect to changes in nutrient release. Changes in biocolonization of wild fouling species were examined as an indicator of organic nutrients. Bio-collectors were deployed at different distances from finfish sites to determine if differences in the accumulation of fouling species could be used to detect an aquaculture nutrient source. Biomass accumulation was different with respect to distance from farms and it appears that changes in species composition is responsible. Although there were no measurable differences with respect to distance from salmon cages in environmental conditions such as temperature, salinity, pH, turbidity or chlorophyll, further investigation is suggested to better understand the role of site infrastructure. The relationship between algal colour (lightness, chroma, hue) and nitrogen content within Ulva lactuca, Palmaria palmata, and Poryphyra purpurea was also examined as an indicator of inorganic nutrients. Within each species, colour change corresponded to nitrogen concentration in the thallus, but season and location were significant factors. Palmaria palmata and P. purpurea exhibit less predictable relationships between colour and nitrogen and are harder to identify than U. lactuca and would not be reliable indicators at certain times of year or locations. In both studies the use of wild species responses to nutrient availability was influenced by species type and variability in the coastal environment and require further study before application as tools for IMTA performance monitoring and assessment.
Behavioural and metabolic responses to the cold in winter-dormant fishes: reductions in activity as the key strategy underlying energy savings
Behavioural and metabolic responses to the cold in winter-dormant fishes: reductions in activity as the key strategy underlying energy savings
by Connor Reeve, Metabolic rate depression (MRD) is a reversible downregulation of standard (resting) metabolic rate (SMR) that facilitates survival in energy-limited environments. Previous studies suggesting interspecific variation in the capacity for MRD among winter-dormant fishes may be confounded by unaccounted variation in activity, which affects the accuracy of SMR estimates. When winter activity reductions were controlled for, a recent study on cunner (Tautogolabrus adspersus) found no MRD. I investigated whether inactivity is the central strategy underlying the metabolic phenotype of winter-dormant fishes. I characterized winter-dormant behaviour in four temperate fish species, finding that activity reductions are ubiquitous albeit varying in magnitude. I then investigated the relationship between activity and metabolic rate using video tracking and intermittent respirometry in two species (mummichog, Fundulus heteroclitus; pumpkinseed sunfish, Lepomis gibbosus) during acute cooling and after winter temperature acclimation. Low winter metabolic rates resulted from reduced activity combined with passive physicochemical effects of cooling, not MRD. Inactivity is the key energy saving strategy of winter-dormant fishes.
Bioactive natural products from endophytic fungi
Bioactive natural products from endophytic fungi
by Nicholas J. Morehouse, Natural products are a source of diverse chemical structures with a broad range of bioactivities that provide valuable lead-compounds for drug development. This thesis explores the diversity of natural products biosynthesised by endophytes of marine macroalgae and medicinal plants. Fermentation extracts obtained from four endophytic fungi exhibited significant antimicrobial activity in our bioassay screens and their natural products chemistry was therefore investigated. This resulted in the isolation of poly(3R,5R-dihydroxyhexanoic acid), neobulgarones D, E and F, altenusin, (Z)-6R*,7S*- dihydroxy-2-propyl-2,4-octadien-4-olide, (Z)-6R*,7R*-dihydroxy-2-propyl-2,4-octadien4-olide and punctaporonins A, B, C, T and U. Of these natural products, six were found to possess antimicrobial activity and three were new chemical structures. The discovery of these new bioactivities and new chemical structures adds to the growing evidence that endophytic fungi are a source of chemical diversity and biologically relevant molecules., Electronic Only.
Bioactive natural products from marine macroalgal endophytes from the Bay of Fundy, Canada
Bioactive natural products from marine macroalgal endophytes from the Bay of Fundy, Canada
by Andrew J. Flewelling, We are approaching a time where antimicrobial drugs may no longer be effective due to the growing global antimicrobial resistance crisis, coupled with the lack of antimicrobial drug discovery and development. New antimicrobial therapies are needed, and endophytes from marine macroalgae have been highlighted as an important biological reservoir for the identification of novel antimicrobial molecules. A preliminary investigation of marine macroalgae from the Bay of Fundy, New Brunswick, Canada for their endophytes indicated this location to be an excellent source of endophytic fungi possessing antimicrobial activity. One hundred and forty fungal endophytes were isolated from 20 species of marine macroalgae collected from the Bay of Fundy. Fifty-four endophytes were identified to the genus or species level, and include eleven fungi not previously isolated as endophytes of marine macroalgae. The identity of 86 isolates could not be confirmed through DNA sequencing due to an inability to amplify or sequence DNA or due to low sequence homology with entries in GenBank. These isolates were designated codes according to their morphology. Each endophyte was fermented to obtain an extract in order to facilitate the discovery of new natural products. In order to prioritise the extracts obtained from these endophytic fungi, an antimicrobial bioactivity profiling technique was developed using nine microorganisms and a panel of 17 antimicrobial standards to not only attempt to identify new antimicrobial natural products, but also those that possess unique antimicrobial targets or modes of action. Principal component analysis of the extract bioactivity profiles revealed that the profiles of 37 extracts were unique within the library. Hierarchical cluster analysis using the profiles of the 37 unique extracts and the 17 antimicrobial standards showed that 26 extracts possessed bioactivity profiles that were distinct from the antimicrobial standards and thus warranted further investigation. Subsequent bioassay guided fractionation of four fungal extracts led to the isolation of six antimicrobial natural products: penicillic acid, methylenolactocin, fumagillin, fumigatin oxide, poly(3R,5R-dihydroxyhexanoic acid) and (P/M)-maximiscin. These natural products, while being known chemical entities, are all reported to possess antimicrobial activity and may play an important role in future antimicrobial drug discovery and development.
Comparing genetic variation among Atlantic cod (Gadus morhua) off Newfoundland and Labrador following the stock collapse
Comparing genetic variation among Atlantic cod (Gadus morhua) off Newfoundland and Labrador following the stock collapse
by Ty Gormley, Following the collapse of the Northern cod stock, there has been much debate regarding the population structure of Canada’s Northern Atlantic cod (Gadus morhua). The objectives of the study are: 1) to determine whether the stock exhibits structure or panmixia and 2) to compare historic cod chromosomal inversion frequency (LG01) to among historic and modern cod. A whole genome scan on 119 historic cod captured between 2001 and 2003 was conducted from four locations spanning the range of the stock and two locations outside the stock. Population structure analysis using 3,907 SNPs suggests that the stock is a single panmictic population. However, additional analyses on only LG01 (15) revealed that historic cod had a higher inversion frequency than modern cod. Taken together, these results provide support for the metapopulation hypothesis and provide novel information on putative adaptive inversion allele changes over a short timeframe.
Environmental determinants of invertebrate community structure and nutrient storage in aquatic invertebrate larvae
Environmental determinants of invertebrate community structure and nutrient storage in aquatic invertebrate larvae
by Heather Loomer, Aquatic invertebrates play a key ecological role in riverine biogeochemical cycles, transferring nutrients incorporated from diverse food sources (e.g.algae or terrestrial detritus) to resident and migratory predators within aquatic and riparian ecosystems. Agricultural land use affects stream aquatic invertebrate communities, generally reducing their diversity and the prevalence of sensitive taxa as a result of the introduction of agro-chemicals (nutrients and pesticides) and other environmental stressors (fine sedimentsand flow). This thesis aims to understand how agricultural land use affects aquatic invertebrate communities and the role these communities play in the storage and transfer of nutrients within stream food webs. To accomplish this, streams in northwestern New Brunswick were sampled over a three-year period (2010 –2012) for water nutrient concentrations, site characteristics, and aquatic invertebrate biomass and nutrient content. The first study established associations between agricultural land use and stream water nutrient concentrations (positive), aquatic invertebrate community diversity and sensitivity (negative), and total community biomass (negative).The second study determined that the nitrogen and phosphorus content within aquatic invertebrate communities decreased and increased, respectively, as aquatic invertebrate communities lost diversity and sensitive taxa. Using data from a subset of these sites and additional ones sampled in 2012, the final study validated the results of the previous studies and showed similar effects of agricultural land use on aqueous nutrient concentrations, aquatic invertebrate communities, and community nutrient content. Further, this study showed that the quantity of nitrogen stored within the aquatic invertebrate community decreased with increasing agricultural land use while the quantity of phosphorus was unaffected. Together these results demonstrate that as aquatic invertebrate communities change their composition in response to increasing agricultural land cover in the catchment, the amount of nutrients stored by the community decreases. This reduction in nutrient storage capacity likely results from shifts in life history strategies in the aquatic invertebrate community. More broadly, these findings suggest that agriculture affects how aquatic invertebrates cycle nutrients in riverine food webs, which may in turn impact aquatic and terrestrial predators that rely on these communities.
Genetic biomarkers for personalized treatment in multiple myeloma
Genetic biomarkers for personalized treatment in multiple myeloma
by Ming Han, Multiple myeloma is an incurable haematological cancer characterized by the accumulation of monoclonal plasma cells inside the bone marrow. Melphalan and Thalidomide are two drugs that have dramatically improved patient survival. However, a significant subpopulation of myeloma patients does not respond to these drugs; in addition, some patients are predisposed to drug-related toxicities, which remains unpredictable. Using samples from the MY.10 randomized clinical trial with an observation arm, the present study found several single nucleotide polymorphism (SNP) genetic biomarkers to be predictive of thalidomide treatment benefit and thalidomide related toxicity (peripheral neuropathy). In addition, the present study also confirmed previous findings where several SNPs were also found to be predictive of melphalan response. Lastly, novel SNPs were found to be associated with myeloma prognosis. These findings contribute to the growing body of evidence that genetic biomarkers can be useful in predicting drug response and prognosis in myeloma. Further studies are needed to confirm our findings., Entered as "Graduate Academic Unit of Biology, UNBSJ", doesn't make much a difference, but wanted to note
Influence of sediment acidification on the burrowing behaviour, post-settlement dispersal, and recruitment of juvenile soft-shell clams (Mya arenaria l.)
Influence of sediment acidification on the burrowing behaviour, post-settlement dispersal, and recruitment of juvenile soft-shell clams (Mya arenaria l.)
by Jeff C. Clements, Ocean acidification (OA) is expected to elicit biological impacts in the near future by impacting the behaviour and physiology of marine animals, potentially leading to decreased fitness and survival. While acidification in the water column has received much attention, sediment acidification has received relatively little, although conditions in sediment porewater can already reach conditions far beyond those of near-future OA projections. This dissertation assesses some impacts of porewater acidification on the burrowing behaviour, post-settlement dispersal, and recruitment of juvenile soft-shell clams (Mya arenaria), and attempts to elucidate the biological mechanism for observed burrowing responses. In addition, this thesis attempts to assess the potential impact of sediment acidification on burrowing behaviour in the context of another ocean climate driver – ocean warming. In laboratory and field experiments, burrowing was depressed and post-settlement dispersal was increased by sediment acidification (low sediment pH) comparable to conditions often experienced by clams in the Bay of Fundy. In the lab, increasing temperature appeared to partially alleviate the effect of sediment acidification on burrowing, and GABAA-like neurotransmitter interference under low pH conditions was found to be the mechanism for hindered burrowing responses. In a field study, air temperature and sediment pH were good predictors of juvenile clam abundance, explaining 68% of the variability in clam abundance, although other factors such as rainfall appeared important. Coupled with previous studies, this thesis suggests that bivalve burrowing and recruitment will likely be impacted by near-future OA in areas where sediments will become more acidic as overlying seawater pH drops.

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