DEPARTMENT OF BIOLOGY

MEMORIAL UNIVERSITY

HONOURS PROJECT TITLES 2017-2018

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BIGNELL, Dawn SN-1011 dbignell@mun.ca

Secondary Metabolism in Plant-Associated Microbes

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 biosynthesis, regulation and function of these molecules during plant-microbe and microbe-microbe interactions.

Potential projects for honours students include the following:

(1) Construction of Streptomyces scabies gene deletion mutants for characterizing the biosynthesis of phytotoxic secondary metabolites.

(2) Functional analysis of secondary metabolite biosynthetic and regulatory proteins using site-directed mutagenesis.

(3) Development of in vitro plant bioassays for assessing the function of phytotoxic secondary metabolites produced by plant pathogenic Streptomyces spp.

(4) Activation of silent biosynthetic gene clusters for producing secondary metabolites in Streptomyces scabies using chemical, genetic and’/or co- culture strategies.

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CARR, Steve SN3020 scarr@mun.ca

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 scarr@mun.ca

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DEBNATH, Samir Agriculture and Agri-Food Canada samir.debnath@agr.gc.ca

Available projects on berry crop improvement using conventional methods combined with biotechnology:

1. Linkage map and marker-assisted selection in small fruit crops.

2. Morphological and biochemical study of in vitro-derived berry plants.

3. Genetic fidelity in micropropagated lingonberry (partridgeberries) blueberry clones, cultivars and hybrids.

4. Molecular analysis to study epigenetic factors in micropropagated small fruit crops.

5. Bioreactor micropropagation in berry crops.

6. EST-PCR, SSR, ISSR and SNP analyses to study biodiversity in berry crops. .

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DUFOUR, Suzanne SN2086 sdufour@mun.ca

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).

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EDINGER, Evan SN-1012 eedinger@mun.ca

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, eedinger@mun.ca

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FLEMING, Ian Ocean Sciences Centre Contact: 864-3586 or ifleming@mun.ca

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.

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GAGNON, Patrick Ocean Sciences Centre: OS-4016 and OS-4017 Lab website: http//www.ucs.mun.ca/~pgagnon/ pgagnon@mun.ca (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.

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GAMPERL, Kurt Ocean Sciences Centre kgamperl@mun.ca 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 kgamperl@mun.ca

GREGORY, Robert Adjunct Professor Fisheries & Oceans Canada, St. John’s, NL, Canada Robert.Gregory@dfo-mpo.gc.ca (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.

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Hurford, Amy SN-1093 ahurford@mun.ca Projects will involve the derivation and simulation of mathematical models in population biology and evolutionary epidemiology. Evolutionary epidemiology 1. The evolution of feeding bias in mosquitoes. Studies have shown that

mosquitoes are more likely to bite malaria-infected humans. As such, mosquitoes are selective, passing up opportunities to feed on non-malaria-infected hosts. The student will develop and analyze foraging models to understand how this feeding bias could evolve.

2. Modelling coinfections. The student will parameterize and validate a

mathematical model describing Klebsiella coinfections of C. elgans. 3. Predicting regional variability in the body size of sea lice. Individuals with

large body sizes are found in highly variable environments. The student will develop a physiologically explicit mathematical model to predict the size of sea lice for different regions and environmental conditions.

Population biology 1. How do super spreaders move? The student will analyze animal

movement data to look for a relationship between how an animal moves and the number of contacts that individual makes with others. Alternatively, the student will develop a movement model that addresses the same question.

2. Pair approximation for animal movement models. The student will study

the pair approximation method for spatially explicit models and simulate animal movement to understand how the method can be used as a mathematical technique to better understand the output of movement simulation models.

3. Modelling biological invasions and species responses to climate warming.

Potential projects include lobster range expansion in response to climate warming and modelling the spread of red-backed vole in Newfoundland.

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IGAMBERDIEV, Andrei SN-4100 igamberdiev@mun.ca 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. LANG, Andrew SN-3021 aslang@mun.ca 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

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MARINO, Paul SN-3125 pmarino@mun.ca 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.

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MERCIER, Annie Ocean Sciences Centre amercier@mun.ca 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 cparrish@mun.ca Ecological and nutritional projects related to marine lipids.

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PENA-CASTILLO, Lourdes ER-3014 lourdes.@mun.ca 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 craig.purchase@mun.ca A variety of projects related to fish ecology and reproduction are available every year, please see Dr. Purchase to discuss details.

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RONCAL, Julisa SN-4102 jroncal@mun.ca Conservation of Braya in the limestone barrens of Newfoundland I am recruiting an Honours student to work on the genetics aspect of a conservation program for Braya in Newfoundland. The goal of the student thesis will be to characterize the genetic diversity and structure of populations of this endangered plant. With this knowledge, we will be able to provide conservation recommendations to the government by proposing management units. The student will learn basic molecular biology techniques such as DNA extractions, PCR, and electrophoresis, which can be applied to many other disciplines. Data analysis will involve classic population genetics. Fieldwork has been already conducted. The student will be co-supervised by Dr. Luise Hermanutz. For more information about my lab visit my website. https://julissaroncal.wordpress.com/

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SCHNEIDER, Dave Ocean Sciences Centre david.schneider@mun.ca 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].

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SHAHIDI, Fereidoon Biochemistry fshahidi@mun.ca 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.

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SNELGROVE, Paul Ocean Sciences Centre psnelgro@mun.ca 1. Larval ecology 2. Sedimentary biodiversity and ecosystem functioning 3. Ecology of deep-sea ecosystems 4. Biology of juvenile cod in coastal Newfoundland 5. Marine Food Webs STAVELEY, Brian SN-3017 bestave@mun.ca 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. 5. Evaluation of nutraceuticals in Drosophila models of ageing and degeneration.

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TAHLAN, Kapil SN-1007 ktahlan@mun.ca 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.

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VOLKOFF, Helene SN-3009 hvolkoff@mun.ca Project 1. Interactions between appetite regulating peptides in fish The study involves sampling of fish, tissue culture, siRNA and gene expression studies using PCR and qPCR. Project 2. Characterization of appetite-regulating hormones in Characiforeme fish The study involves cloning and gene expression studies using PCR and qPCR. Project 3. The role of neuronostatin and neurokinis in regulating feeding in goldfish The project involves intra peritoneal and brain injections followed by observations of feeding behavior.

WHITNEY, Hugh Chief Veterinary Officer (retired) hughwhitneynl@gmail.com 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.

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WIERSMA, Yolanda SN-4099 ywiersma@mun.ca 1. General landscape ecology research 2. Lichen diversity patterns in the city and surrounding area 3. Citizen science and NL Nature