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DEPARTMENT OF BIOLOGY MEMORIAL UNIVERSITY HONOURS PROJECT TITLES 2016-2017 BIGNELL, Dawn SN-1011 [email protected] Research in my lab aims to better understand the ecological roles of natural products (i.e. secondary metabolites) that are produced by Streptomyces and other actinomycete bacteria. As a model, we study the secondary metabolites that are produced by plant pathogenic Streptomyces spp., and our goal is to decipher the function of these molecules in plant-microbe and microbe-microbe interactions. In addition, we currently have an ongoing collaborative project with Dr. Kapil Tahlan and Dr. Suzanne Dufour that aims to characterize the bioactive secondary metabolites that are produced by actinomycetes from marine sediments. Potential projects for honours students include the following: (1) Activation of silent biosynthetic gene clusters for producing secondary metabolites in Streptomyces scabies using chemical, genetic and/or coculture strategies. (2) Characterization of phytotoxic secondary metabolites produced by plant pathogenic Streptomyces spp. isolated in Newfoundland. (3) Isolation and characterization of marine actinomycetes and their bioactive natural products from deep sea sediments. CARR, Steve SN3020 [email protected] Honours projects are available in molecular evolutionary genetics, conservation genetics, and biodiversity genomics. Species of interest include: Atlantic Cod, Wolffish, Harp Seals, Caribou, Salmon, and other marine fish and terrestrial mammals. Potential projects in seabirds and shellfish dependent on funding. Requirements include a strong interest in molecular genetics and evolutionary biology. We have increasing interest in Computational Science programming for analysis of large data sets. Projects in human medical genetics are also conducted in cooperation with the Faculty of Medicine. Genetic studies of an endangered marine species, Atlantic Wolffish Post-glacial origins of Newfoundland Caribou Genomic variation in wild Atlantic Cod fisheries DNA Microarray sequencing: Development of computer algorithms for sequence analysis and pattern identification. Population Genomics (co-supervisor, Dr. D. Marshall) Population Genetics of Newfoundlanders (Co-Supervisor, Dr. D. Marshall) Human Mitochondrial DNA mutations (Co-supervisor, Dr. D. Marshall) See http://www.mun.ca/biology/scarr/research.html for examples of current projects. Contact Dr. Carr at 864-4776 or [email protected] DEBNATH, Samir Agriculture and Agri-Food Canada [email protected] Available projects on berry crop improvement using conventional methods combined with biotechnology: 1. Morphological and biochemical study of in vitro-derived berry plants. 2. Genetic fidelity in micropropagated lowbush, half-high and/or hybrid blueberries. 3. Molecular analysis to maintain genetic purity in cranberry. 4. Bioreactor micropropagation in berry crops. 5. EST-PCR analysis to characterize berry crops. DUFOUR, Suzanne SN2086 [email protected] Marine Chemosymbiosis and Benthic Biology Research projects focusing on the symbiotic relationship between bivalves (Family Thyasiridae) and sulphur-oxidizing bacteria, on adaptations of benthic invertebrates to organically enriched environments, or on bioturbation are available. 1. Description of the gill structure and relationship to bacterial symbiont presence in local populations of thyasirid bivalves. The project involves thin sectioning of bivalve gills, for light microscopy and transmission electron microscopy. 2. Investigation of suspension feeding structures, bacterial symbiont presence and trophic level in bivalves from organically enriched benthic environments (including aquaculture sites). The project can involve a combination of histology, transmission electron microscopy, isotope ratio determinations, and molecular biology (gene sequencing). 3. Study of environmental variability in thyasirid habitats based on long-term in situ data collected at the VENUS underwater observatory. 4. Burrowing behaviour and sedimentary impacts of bioturbating marine animals (in collaboration with Dr. Duncan McIlroy, Earth Sciences). EDINGER, Evan SN-1012 [email protected] 1. Cold-water coral and sponge habitats in the Strait of Georgia, British Columbia (it’s a video analysis project). 2. Biodiversity and biogeography of bryozoans in the Newfoundland and Labrador waters. 3. Biodiversity and conservation of sponges in the Newfoundland and Labrador shelf & slope bioregion. Contact E. Edinger, SN1044, ext. 3233, [email protected] FLEMING, Ian Ocean Sciences Centre Contact: 864-3586 or [email protected] Evolutionary Ecology and Conservation of Fishes. Honours students have the opportunity to potentially undertake projects in the following areas. (i) Invasion Biology and Consequences of the Escape of Cultured Fish – Combining laboratory and field experiments, this work aims to examine the roles of environment (phenotypic plasticity) and genetics (i.e. non-indigenous origins and domestication) in the potential for introduced fishes to establish both within native and non-native ranges, and to assess impacts on the productivity and genetic integrity of wild fish populations and the ecosystems they inhabit. (ii) Captive Breeding and Fish Conservation – Our research in this area aims to address whether captive breeding programs can successfully contribute to the recovery of populations, and under what circumstances. Using field and laboratory experiments we explore how captive rearing can generate an array of behavioural, life history and morphological changes that impede the success of fish after release. (iii) Maternal effects – This research explores the evolutionary significance of maternal effects (i.e. female differences in egg size, breeding time and location) on offspring performance (growth and survival). We work primarily with salmon and trout. GAGNON, Patrick Ocean Sciences Centre: OS-4016 and OS-4017 Lab website: http//www.ucs.mun.ca/~pgagnon/ [email protected] (709) 864-7663 Research in my laboratory, the Cold Ocean Benthic Ecology Lab (COBEL) located at the Ocean Sciences Centre, aims to elucidate the structure and function of subtidal marine ecosystems in subarctic and temperate regions with current emphasis on shallow rocky ecosystems of eastern Canada. It investigates how environmental variability (including anthropogenic disturbances) affects recruitment, growth, survival, and interactions in native and invasive invertebrates and seaweeds. Our approach combines field and laboratory experiments and observations using SCUBA diving*, underwater photography and videography, wave tanks, remote sensors (airborne and satellite), and GIS tools to extract and merge ecological data across spatial and temporal scales. Honours projects are available in the following areas: 1. Effects of environmental variability on species interactions and population dynamics. 2. Ecology and ecosystem impacts of marine invasive species. 3. Mapping and study of shallow marine communities at broad spatial and temporal scales. * Honours students are not expected to dive for their projects, though projects can be tailored to include diving depending on qualifications. GAMPERL, Kurt Ocean Sciences Centre [email protected] A position is available in my lab at the Ocean Sciences Centre for a 4th year honours student to investigate how temperature or reductions in water oxygen levels (hypoxia) affect fish physiology. All candidates for the honours B.Sc. in Biology must take both Biology 499A and 499B, and the program requires students to undertake an independent research project that takes approximately 12 hours per week (160 hours per course). If you are interested in this project, or have an idea for a dissertation topic in the area of fish physiology/biology, please contact 864-2692 or email [email protected] GREGORY, Robert, Adjunct Professor Fisheries & Oceans Canada, St. John’s, NL, Canada [email protected] (709)772-4491 1. Growth and survival of Atlantic cod in coastal habitats (field and non-field components are possible). 2. Juvenile fish distribution in coastal nursery habitats (field components). 3. Fish associations with marine seabed habitats on offshore banks (non-field project; analysis of existing data). Applicants should have an interest in pursuing studies on fish behaviour and ecology during the late spring or summer periods. Previous employment or volunteer experience working outdoors on a daily basis would be an asset. IGAMBERDIEV, Andrei SN-4100 [email protected] 1. Anaerobic operation of plant mitochondria: can plants respire without oxygen? 2. Pathways of nitric oxide synthesis and scavenging in plant cells. 3. The role of plant bioactive compounds in protection from oxidative stress in brain cell cultures (in collaboration with the School of Pharmacy). 4. Antioxidant metabolism of cool season berry crops (in collaboration with Agric. Can). 5. Plant hemoglobins and their functions. INNES, Dave SN-4114 [email protected] 1. Genetics of sexual and asexual Daphnia 2. Evolution and genetics in a mussel hybrid zone 3. Mussel aquaculture genetics 4. Spider mating LANG, Andrew SN-3021 [email protected] 1. Bacterial genetics: role of viruses in bacterial evolution regulation of gene expression by signal transduction pathways 2. Avian influenza viruses: genomics and evolution prevalence and diversity in wild birds global movements of viruses by wild birds 3. Marine microbiology: viruses and gene exchange in the ocean diversity and biogeography of marine bacteria marine microbes as sources of novel bioactive compounds 4. Virus discovery: Identification of new viruses in different animal species Identification of new viruses infecting bacteria MARINO, Paul SN-3125 [email protected] Marino’s research in ecology and evolution focuses on understanding the mechanisms behind which plants attract insects by examining the ecology and evolution of spore dispersal in Splachnaceae mosses. Spores are dispersed by flies and the sporophytes of these species are highly modified and promote the dispersal of their spores. Potential projects include: 1) characterization of sporophyte odour chemistry, and 2) exploring the relative importance of visual vs odour cues in attracting flies to particular species of mosses. 3) comparing spore dispersal ability among different fly taxa. 4) exploring competitive interactions among different species of Splachnaceae mosses. MARSHALL, Heather Dawn SN-2102 [email protected] 1. Phylogeography of red and Arctic foxes in Northern Canada and the relationship to spread of rabies. 2. Investigation of immune system genetic diversity in Newfoundland red foxes and coyotes susceptible to French Heartworm. 3. Using mitogenomics to test the nearly neutral theory of molecular evolution in European chaffinches. MERCIER, Annie Ocean Sciences Centre [email protected] 1. Biology of deep-sea invertebrates. This research involves the use of microscopy and imaging analysis techniques for the study of preserved specimens (possibly new or poorly known species). It may also involve collection of specimens (ship time) and assessment of feeding and reproductive cycles in live animals. 2. Breeding strategies of echinoderms (e.g. spawning periodicity and synchrony, ecology of brooding, fecundity, etc.). This research is based on behavioural observations, experimental trials in controlled environments, histology/microscopy, image analysis, and biochemical analysis. 3. Biology and management of the sea cucumber Cucumaria frondosa. This research focuses on the study of the Newfoundland populations of sea cucumbers with respect to an emerging fishery and potential aquaculture program. It involves the study of growth patterns, tagging and aging methods, diets, prey-predator interactions and various other aspects of the biology and ecology of the species. 4. Various other projects on the general biology and ecology of marine invertebrates (e.g. symbioses, trophic ecology, competition, behaviour, morphology, etc.). PARRISH, Chris Ocean Sciences Centre [email protected] Ecological and nutritional projects related to marine lipids. PENA-CASTILLO, Lourdes ER-3014 [email protected] The research in my group focuses on the application and development of bioinformatics resources. Honours students who enjoy working with computers and are looking for a dry lab project, have the opportunity to undertake projects mostly in the analysis of large-scale omics data and network analysis. If this is of interest to you - come and see me, or send me an email. PURCHASE, Craig SN-4103 [email protected] A variety of projects related to fish ecology and reproduction are available every year, please see Dr. Purchase to discuss details. RONCAL, Julissa SN-4102 [email protected] “Towards a molecular phylogeny of the vascular plants of Newfoundland” Honors thesis project in the Plant Diversity and Evolution Lab under the supervision of Dr. Julissa Roncal This thesis project aims to reconstruct a molecular phylogenetic tree of all vascular plant genera in Newfoundland (ca.200). This phylogenetic tree will be useful to determine measurements of plant diversity among the different ecological regions of Newfoundland. To reconstruct this tree we will use DNA sequences, most of them are already available from public databases but we are missing approximately 15 genera. The student will conduct DNA sequencing for these missing genera from herbarium specimens or live plants. Therefore the student will learn basic molecular laboratory techniques like DNA extractions, PCR, and DNA sequencing. Different methods like maximum parsimony and Bayesian will be used to infer the tree. More information on the research we conduct in my group can be found on my webpage http://julissaroncal.wordpress.com/ SCHNEIDER, Dave Ocean Sciences Centre [email protected] All four topics are potentially publishable in the refereed literature. Funding available for students during summer prior to final year. Marine and Aquatic Birds 1. Long term variation in osprey reproductive success in Labrador. BACI design. [Environmental science journal] 2. Long term trends in migratory shorebirds at Gulf Islands National Seashore, Florida. Potential for field work at GINS. [Ornithology journal] Oceanography 1. Annual primary production due to episodic coastal upwelling in the northwest Atlantic. Compute gross production (carbon fixation) from rate of injection of nitrogen into the euphotic zone by episodic upwelling. Verify model from literature. [Oceanography journal]. Natural Selection 2. Frequency dependent selection on polymorphic molluscs at multiple spatial scales. Field work at Heart’s Delight (Thais), and possibly Florida (Donax). Ten years of data from Florida. [Journal of Natural History]. SHAHIDI, Fereidoon Biochemistry [email protected] Plant Phenolics, Antioxidants, Lipids and proteins Phenolics are ubiquitous components in all plants and exist as structural components and for playing biological roles in the plant with respect to anti-hebivory, protection from oxidative stress under sunlight, as wound-healing components and as attractants for polinators, among others. We are interested in such compounds as antioxidants, free radical scavengers and as nutraceuticals for disease risk reduction and health promotion. Studies of interest include extraction, evaluation of antioxidant and biological activity of the extracted materials and structure elucidation of active components. Derivatization of ployphenols for enhancing their bioavailability and for their beneficial effects in reaching mitochondria is also intended. Furthermore, such compounds protect lipids against oxidation. Oxidative stability of lipids is important because their deterioration leads to generation of toxic degradation products as well as flavour reversion. Oxidative stability of lipids is generally dictated by the degree of unsaturation of their fatty acid constituents. However, recent research in our laboratory has shown that factors such as minor components in the oil as well as presence of the lipids in the bulk or in an emulsion system might exert effects that could possibly reverse the expected trends. The work of interest includes study of stability and stabilization of selected plant/food material. As an example, disease prevention and health promotion activities of such products will be examined by testing their effects on prevention of human LDL oxidation and DNA breakage, among others. In collaboration with other researchers, studies on selected cell lines or animals may be performed for demonstrating the efficacy of commodities of interest that include cereals, grains, small fruits, nuts as well as fish and fish by-products. Studies on preparation of so-called structured lipids, including phenolipids, using lipid biotechnology, to examine their characteristics and potential use in diseases prevention/amolioration are also of continued interest. In addition, hydrolysis of protein leads to the formation of peptides, some of which are biologically active and provide many health benefits as supplements or for use in food and cosmetics or for aquaculture feed application. Therefore, there will be ample opportunity to select a project that concentrates on one of the above areas. SNELGROVE, Paul Ocean Sciences Centre [email protected] 1. Larval ecology 2. Sedimentary biodiversity and ecosystem functioning 3. Ecology of deep-sea ecosystems 3. Biology of juvenile cod in coastal Newfoundland STAVELEY, Brian SN-3017 [email protected] 1. Isolation and characterization of new insulin receptor pathway genes. 2. Characterization of genes involved in programmed cell survival signal transduction. 3. Development of genetic models of human degenerative diseases. 4. Study of mitochondrial integrity genes in Drosophila models of human disease STOREY, Anne Psychology [email protected] Honours projects may be available to study the behavioural ecology of seabirds. Potential projects include: 1. Field projects on mating and parental behavior of Common Murres and Atlantic Puffins 2. Laboratory projects examining the costs of seabird parental behavior. For example, a project might focus on how individual differences in parental behavior are related to levels of stress hormones. TAHLAN, Kapil SN-1007 [email protected] 1. Genetics and biochemistry of antibiotic producing bacteria: This project involves studying the production on pharmaceutically important natural products in industrially used Streptomyces species. 2. Screening for novel bioactive compounds: On an ongoing basis our laboratory has projects on screens to identify bacteria from different environments that produce bioactive natural products. The projects also involve genetic manipulations to produce new natural products which could have applications in medicine and industry. We also have collaboratirve projects where we test chemically synthesized compounds for antimicrobial activities. 3. Identification of agents and targets active against mycobacteria: The project involves the use of genetics and biochemistry to look at the mechanism of action of bioactive compounds (synthetic and natural) using non-pathogenic mycobacterial models as a surrogate for M. Tuberculosis, which causes tuberculosis in humans. 4. Studies on bacterial pathogens of concern to veterinary medicine: This project is focused on the identification bacterial pathogens that cause animal diseases in Newfoundland. It also involves the use of genetics and biochemistry to study antibiotic resistance, virulence mechanisms and pathogenicity in these organisms. VOLKOFF, Helene SN-3009 [email protected] Project 1. Interactions between appetite regulating peptides in goldfish and piranha. The study involves sampling of fish, tissue culture and gene expression studies using PCR and qPCR. Project 2. Characterization of amylin in cunner, skate and flounder. The study involves cloning and gene expression studies using PCR and qPCR. Project 3. The role of neuronostatin in regulating feeding in goldfish. Neuronostatin, a recently discovered peptide derived from the somatostatin preprohormone, significantly inhibits food intake when administered in adult male rats. The project involves intra peritoneal and brain injections followed by observations of feeding behavior. WHITNEY, Hugh NL Forestry and Agrifoods Agency (Animal Health) [email protected] Topics related to diseases of wild and domestic animals, particularly those of public health or economic importance. This could be for students interested in a career in veterinary medicine or as a research scientist. WIERSMA, Yolanda SN-4099 [email protected] 1. General landscape ecology research 2. Lichen diversity patterns in the city and surrounding area 3. Citizen science and NL Nature