Department of Biology (Fredericton)

Pages

The aromatic amino acid responsive TyrR transcription factor of Enterobacter cloacae UW5 : its role in regulation of indole-3-acetic acid biosynthesis and the identification of an expanded regulon using RNA-sequencing
The aromatic amino acid responsive TyrR transcription factor of Enterobacter cloacae UW5 : its role in regulation of indole-3-acetic acid biosynthesis and the identification of an expanded regulon using RNA-sequencing
by Thomas J.D. Coulson, The control of transcription is an important process in all living cells. In the bacterial family Enterobacteriaceae, the transcription factor TyrR controls genes for aromatic amino acid uptake and biosynthesis. In this thesis, I explore the control of genes by TyrR in Enterobacter cloacae UW5, a soil bacterium commonly associated with plant roots that confer beneficial effects on its host and is also an inhabitant of human intestinal microflora and an opportunistic pathogen. Chapter 1 provides a general introduction to bacterial activities in the plant rhizosphere and transcriptional regulation, especially by TyrR. In Chapter 2, I investigated the regulation of two divergently transcribed genes, ipdC and akr, by TyrR. The ipdC gene encodes indolepyruvate decarboxylase for the production of the plant growth hormone indole-3-acetic acid, which plays an important role in the plant beneficial behavior of E. cloacae. TyrR is required for activation of ipdC by binding a single DNA element upstream of the promoter. All three aromatic amino acids act as cofactors for TyrR to induce ipdC expression. Expression of akr, encoding a putative aldo-keto reductase, was repressed by TyrR independently of aromatic amino acids and involved TyrR binding an atypical DNA site within the promoter. In Chapter 3, I assembled the E. cloacae UW5 genome sequence, which revealed genes and pathways that contribute to its plant-associated lifestyle and served as a reference for mapping RNA-sequencing data. In Chapter 4, I delineated the TyrR regulon by comparing transcription profiles in wild-type and tyrR mutant strains of E. cloacae generated through RNA-sequencing. Broad changes in gene expression were identified and several new TyrR members confirmed, including dmpM encoding a methyltransferase that is highly upregulated by tyrosine and phenylalanine, and cpxP and cpxR, which encode components of the envelope stress response. Additionally, pathways for aromatic metabolism, anaerobic respiration, and motility were altered in the tyrR mutant. Chapter 5 summarizes this research that suggests that the E. cloacae TyrR regulon has expanded from that of E. coli to include genes for survival in the diverse environments that this bacterium inhabits and illustrates the expansion and plasticity of transcription factor regulons.
The biogeographic history and contemporary origins of north american arctic marine macroalgae
The biogeographic history and contemporary origins of north american arctic marine macroalgae
by Trevor T. Bringloe, Arctic coastal communities are expected to change in response to warming climate trends, and yet basic information is lacking in these systems. Marine macroalgae provide an opportunity to examine historical migration pathways into the Arctic, and may serve as a model system for future changes. In this thesis, phylogeographic and population level biogeographic patterns were examined in Arctic marine macroalgae. Multiple markers were used to examine phylogeographic patterns in 14 trans-Arctic lineages of red marine macroalgae and determine what role the opening of the Bering Strait and Pleistocene glaciation had on contemporary biogeographic distributions. Results confirmed the opening of the Bering Strait resulted in a predominantly Pacificto- Arctic/Atlantic movement of species, while Pleistocene glaciation did not appear to play a significant role in promoting trans-Arctic speciation events. The Last Glacial Maximum, however, is hypothesized to have extirpated marine coastal populations in the Northwest Atlantic, with subsequent recolonization out of the Northeast Atlantic. DNA barcode data were used to determine if trans-Atlantic populations of brown and red macroalgae were consistent with this hypothesis. Contrary to the historical consensus, isolation times in 60% of the species examined suggested populations were not recently derived from Europe. Sequence data were also used to assess recolonization pathways of marine macroalgae into the Arctic following the Last Glacial Maximum. Of the 100 species with Arctic populations examined (including brown, green, and red macroalgae), 39 had uncertain origins, 46 had origins in the North Atlantic, five had origins in the Pacific and the Atlantic, while the remaining 10 had origins in the North Pacific. Pacific contributions to Arctic recolonization, however, were inferred in 9 of the 12 best sampled species. Surprisingly, 18 genetic groups and some Arctic haplotypes in 28 species were not assignable to Atlantic or Pacific populations. The results from this thesis indicated that the Pacific Ocean has played a major role in establishing Arctic and North Atlantic lineages/populations of marine macroalgae. In addition, some marine populations may have survived glaciation in the Arctic basin, reducing the role of recolonization pathways out of the Atlantic and/or Pacific.
The diversity and taxonomy of Ulva species (Ulvales, Chlorophyta) in the Bay of Fundy (New Brunswick, Canada)
The diversity and taxonomy of Ulva species (Ulvales, Chlorophyta) in the Bay of Fundy (New Brunswick, Canada)
by Kirby Morrill, Species in the green algal genus Ulva have simple morphologies with few diagnostic features for species identification, and characters used for identification are often subject to high intraspecific variability and plasticity in response to environmental conditions. Routine Ulva species identification using morphological characteristics is therefore challenging even for seasoned phycologists. Molecular techniques (namely, DNA barcoding) are useful for species recognition when morphological investigation alone is inadequate, but molecular work must be accompanied by taxonomic study for accurate morphospecies name application. In this thesis I employed molecular techniques along with observations on biogeography, ecology, and morphology in order to assign meaningful morphospecies names to species of Ulva present in the Bay of Fundy (New Brunswick, Canada). Ten unique genetic groups were identified from the Bay of Fundy: eight genetic groups were assigned existing morphospecies names and the remaining two were assigned provisional species names pending publication.
The effect of acclimation temperature and triploidy on hypoxia tolerance in brook charr, Salvelinus fontinalis
The effect of acclimation temperature and triploidy on hypoxia tolerance in brook charr, Salvelinus fontinalis
by Rebecca Rae Porter, Triploid fish could be beneficial to aquaculture sustainability due to their effective sterility preventing escaped farmed fish from mating with wild fish. However, experience to date has suggested that they are less tolerant of environmental stressors. The goal of this study was therefore to determine whether acclimation to warm temperature improves the performance of both diploid and triploid brook charr (Salvelinus fontinalis) under conditions of high temperature and hypoxia. A preliminary experiment tested fish of both ploidies acclimated to two different temperatures (15 and 18°C) at a range of test temperatures (ambient, 20, 22, 24, 26, 28, 30°C) to determine the oxygen tension (PO2) at loss of equilibrium and time taken to reach loss of equilibrium, during progressive hypoxia. A follow-up experiment involved first acclimating fish to the same two temperatures and then reacclimating the 18°C fish to 15°C before using the same protocol to test hypoxia tolerance at a narrower range of temperatures (ambient, 24, 26, 28, 30°C). Warm acclimation (18°C) improved high temperature and hypoxia tolerance in both ploidies, but this improvement did not last after reacclimation to cooler temperatures. Triploids had slightly lower hypoxia tolerance in both experiments. This study shows that (1) while increasing acclimation temperature improves tolerance of fish regardless of ploidy in high temperature and hypoxic conditions, the effect is not long-lasting, and (2) the difference in tolerance between ploidies may not be great enough for triploids to have a negative impact on the aquaculture industry and instead should be used to minimize negative impacts caused by farmed salmon mating with wild populations of Atlantic salmon. However, further research needs to be done to optimize this approach for use in the aquaculture industry.
The effect of triploidy on postprandial metabolism and ammonia excretion in brook charr, Salvelinus fontinalis
The effect of triploidy on postprandial metabolism and ammonia excretion in brook charr, Salvelinus fontinalis
by Nicole Jennifer Daigle, Many studies have attempted to find physiological differences between sterile (triploid) and normal (diploid) salmonids with the goal of increasing triploid performance for aquaculture. The objective of this thesis was to study the effects of triploidy on specific dynamic action (SDA) and net total ammonia nitrogen (TAN) excretion by measuring aerobic metabolic rate (MR) and TAN excretion of brook charr, Salvelinus fontinalis, from 48h before to 48h after being fed a single ration (measured as % body mass; BM). A first experiment determined an appropriate ration size (0.4% BM) and validated the tube-feeding procedure. The process of tube-feeding itself only affected the MR factorial scope, which was significantly higher (by 5%) in the sham-fed group. The second experiment compared the same parameters between ploidies and demonstrated that triploids had significantly lower standard metabolic rates and a higher net TAN excretion than diploids when fed 0.4% BM.
The genetic and evolutionary basis for somatic cell differentiation in the multicellular alga Volvox carteri: investigations into the regulation of regA expression
The genetic and evolutionary basis for somatic cell differentiation in the multicellular alga Volvox carteri: investigations into the regulation of regA expression
by Stephan Konig, The evolution of life is characterized by a series of major transitions in the complexity of biological systems. One such transition was from unicellular to multicellular organisms and involved the evolution of sterile somatic cells-a premier example of cooperation. The goal of this thesis was to investigate the genetic and evolutionary basis for somatic cell differentiation in Volvox carteri, a simple multicellular green alga composed of ca. 2,000 somatic cells and up to 16 reproductive cells (gonidia). In V carteri, the terminal differentiation of small somatic cells involves the expression of regA, a gene coding for a transcription factor thought to repress nuclear genes required for chloroplast biogenesis and, thus, for cell growth and division. regA induction is likely dependent on cell size, but the molecular mechanism whereby cell size is translated into regA expression remains to be elucidated. This study focused on the regulation of regA expression by employing mechanistic and evolutionary approaches. Using a regA-/gonidialess double mutant strain characterized in this study, I showed for the first time that in addition to its developmental expression, regA can be induced by environmental stimuli, and this induction is also dependent on cell size. These findings provide support for a previously proposed hypothesis that regA evolved from an ancestral stress-response gene. Furthermore, in mutants expressing a non-functional RegA protein, the conditions that trigger regA expression also induce programmed cell death, which points towards a dual function for regA in cell fitness: to decrease cell reproduction (by repressing cell growth) and to increase cell survival (by conferring resistance to stress). Genes with antagonistic pleiotropic effects on fitness have been proposed to stabilize cooperation, and regA is the first such example in multicellular organisms with unitary development (i.e., developed from a single cell). To identify transcription factors binding to cis-regulatory elements of regA I have used yeast one-hybrid assays. No potential candidates were identified, suggesting that cooperative binding of proteins or multi-protein complexes are involved in the regulation of regA. Overall, this study provides novel insights into our understanding of somatic cell differentiation, from both a mechanistic and an evolutionary perspective., Scanned from archival print submission.
The geography of diet: diversity in diet and foraging behavior in herring gulls (Larus argentatus) across Atlantic Canada
The geography of diet: diversity in diet and foraging behavior in herring gulls (Larus argentatus) across Atlantic Canada
By Katherine R. Shlepr, Changes in food availability are thought to be the primary driver of Herring Gull (Larus argentatus) species decline, but empirical evidence linking gull diet to population dynamics is lacking. First, I test the ability of new GPS tracking technology to provide representative data on Herring Gull movement, analyzing the effect of tag deployment on adult behavior and reproductive output. I found that effects were short-term. Secondly, I analyze data from GPS tags deployed on Herring Gulls at two colonies in the Bay of Fundy, Canada, and combine results with those from a more established diet methodology, stable isotope analysis. I found that variation in individual foraging strategy is high, but colony-level differences in diet and foraging location do emerge. This study provides the foundation for understanding how differences in individual foraging strategy may lead to variation in individual reproductive success and the ability to adapt to a changing environment.
The importance of marine-derived nutrients from anadromous fishes to Atlantic rivers
The importance of marine-derived nutrients from anadromous fishes to Atlantic rivers
by Kurt M. Samways, With the dramatic declines in Atlantic anadromous fishes over the past century it is important to identify the relative roles marine-derived nutrients (MDNs) delivered by these fishes play in influencing freshwater food web dynamics. Rivers in New Brunswick and Nova Scotia, Canada containing Atlantic salmon (Salmo salar), alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax), or sea lamprey (Petromyzon marinus) as the primary anadromous species, were chosen to study their effects on i) primary production/productivity; ii) trophic interactions; and iii) resource quality. To understand the linkages between freshwater and marine ecosystems, observational studies, experimental frameworks, and analytical techniques (including stable isotope and fatty acid analysis) were employed. Biofilm communities followed a predictable response pattern to MDN inputs, regardless of the fishes spawning strategy, timing, or MDN load being delivered. Biofilm community standing crop and gross primary productivity were greater in sites receiving MDN subsidies than reference sites. The 13C and 15N data showed that MDNs were incorporated into all trophic levels (biofilm, invertebrates, and salmon parr) across streams with anadromous fish spawning. Community-wide niche space (i.e. the trophic diversity among food webs) shifted toward the marine-nutrient source, however the total ecological niche space (i.e. magnitude of trophic diversity) did not always increase with MDN inputs. Exposure to MDN resources from spawning Atlantic salmon led to improved nutritional quality for all biota, as indicated by increased lipid stores in all trophic levels and incorporation of fatty acids. The variability in fatty acid profiles was accredited to inherent differences between trophic groups combined with assimilation of marine-derived fatty acids in the MDN treatments. Precipitous declines in fish populations have resulted in a net loss in MDN loading to a point that may no longer sustain elevated levels of productivity needed for sustaining large fish populations. The current trend of declining anadromous fish populations in Atlantic Canada means fewer nutrient-rich marine subsidies for stimulating trophic production in these river systems. Marine-derived subsidies (nutrients and lipids) benefit multiple trophic levels of freshwater organisms as well as provide a cross-ecosystem spatial subsidy. In order to maintain ecosystem function and productivity, it is critical to include MDNs for effective ecosystem management and river restoration strategies.
The information insects leave behind: spatial and temporal variation of benthic assemblages using novel non-invasive methods
The information insects leave behind: spatial and temporal variation of benthic assemblages using novel non-invasive methods
by Zoe Gabrielle O’Malley, Rare and elusive benthic macroinvertebrate (BMI) taxa are difficult to detect and sampling methods often require preserving live specimens, a concern for monitoring species-at-risk. Here, we aim to understand spatial and temporal variation in BMI communities within a complex, understudied river-wetland system using exuviae (shed exoskeletons), environmental DNA (eDNA) water samples and bulk-sequenced benthic samples. Samples were collected across wetland, tributary, and mainstem habitats within the lower Saint John River and Grand Lake Meadows, New Brunswick. Using exuviae, we demonstrate that terrestrial factors (e.g. riparian vegetation community) affect emergent dragonfly community composition more than aquatic factors (e.g. water temperature). Further, BMI communities identified via eDNA water samples did not differ from bulk-sequenced benthic communities, except during higher flow conditions in larger systems. Using non-invasive methods to capture biodiversity allowed us to explore ecological linkages, crossing boundaries between life stages and ecotones, to elucidate mechanisms between spatial and temporal drivers of BMI communities in a complex river-wetland system.
The role of habitat and dispersal in shaping the biodiversity of riverine insect assemblages
The role of habitat and dispersal in shaping the biodiversity of riverine insect assemblages
by Colin Curry, Given limited resources, biomonitoring progrrum are touted as a source of biodiversity information for conservation planning in riverine ecosystes. However, the degree to which patterns revealed by biomonitoring are reflected in unsampled mesohabitats and undersampled taxonomic groups has not been fully addressed. Differences in dispersal capacity among taxonomic groups, in particular, may result in divergent patterns of biodiversity at landscape and regional scales. I sought to address the suitability of biological monitoring data in freshwater biodiversity assessment, and to test the prediction that the degree of spatial structuring in aquatic insect assemblages is inversely related to their dispersal capacity. My thesis comprises four articles. The first addresses whether macroinvertebrate biodiversity patterns in riffles, the target mesohabitat of Canada's national aquatic biomonitoring program, are reflective of those in riverine wetlands. The second addresses whether biodiversity in a group of insects that is abundant in biomonitoring samples (Trichoptera) reflects that of an underrepresented group (Odonata). The third tests the above prediction by comparing the degree of spatial structuring in the weakly dispersing Trichoptera and the stronger dispersing Odonata. The final article investigates regional and national aquatic insect biodiversity patterns utilizing the national biomonitoring dataset, and seeks to evaluate the influence of scale on the observation of spatial structuring aquatic insect assemblages. Several key findings emerged from this work: 1) Patterns of invertebrate taxon richness and beta diversity in riftles poorly reflect those in riverine wetlands. 2) Odonata and Trichoptera biodiversity were not always congruent, however, differences in abundance among groups may account for weak correlations. 3) Both Odonata and Trichoptera assemblages demonstrate relatively weak spatial structuring at a landscape (ie. 5th order catchment) scale. The weak explanatory ability of spatial variables was also apparent at a regional scale, as just one of the Water Survey of Canada sub drainages within the Pacific drainage demonstrated a significant spatial component in aquatic insect assemblage variation These findings suggest caution in the application of biomonitoring data to conservation planning. Although landscape and regional scale structuring of aquatic insect communities may be weak, it does not preclude the existence of smaller scale spatial structuring driven by local dispersal processes., Electronic Only., Ph.D. University of New Brunswick, Department of Biology, 2014.
The role of the Rubisco small subunit in Arabidopsis thaliana
The role of the Rubisco small subunit in Arabidopsis thaliana
by Amanda Pearl Cavanagh, Life on Earth almost exclusively depends on the reduction of inorganic atmospheric carbon dioxide (CO2) into organic molecules, via photosynthesis. Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) catalyzes the first irreversible enzymatic step of this process: the addition of CO2 to a 5-carbon molecule (ribulose-1, 5-bisphosphate, RuBP). Rubisco's abundance belies its kinetic shortcomings, which include a slow catalytic rate and a tendency to confuse its substrate, CO2, with O2. Biochemical and structural limitations constrain the evolution of the enzyme, but our understanding of the structure-function relationships of Rubisco is in its infancy. In land plants and green algae, Rubisco is a multimer of eight large and small polypeptide subunits (LSu and SSu, respectively). Because it houses the catalytic site, the LSu has been widely researched and characterized. Conversely, the role and origin of the SSu is unclear, although its structure and molecular biology are both well characterized. In this thesis I explore the impact of an altered SSu complement on Rubisco activity and photosynthetic performance. In Chapter 1, I show that temperature-induced changes in Rubisco performance can have a significant impact on photosynthetic carbon gain. These changes are associated with altered rbcS gene expression in some species, and in chapter 2 I demonstrate that the expression of two rbcS genes vary with growth temperature, but not CO2 in A. thaliana. In Chapter 3, I show that these changes in rbcS gene expression are associated with differences in SSu protein accumulation, and that changes in the SSu complement from warm-grown plants are associated with the production of a Rubisco that is more specific for CO2 at elevated growth temperatures. In Chapter 4, using whole plant gas-exchange, I show that SSu associated kinetic differences improve photosynthetic nitrogen use efficiency in the growth environment, likely by producing a more efficient enzyme. In total, this work characterizes the evolution of the genes, peptides, and function of the SSu of Rubisco, and will expand our understanding behind the evolution of the world’s most abundant enzyme.
The utility of growth form for predicting and evaluating aquatic plant nutrient relations
The utility of growth form for predicting and evaluating aquatic plant nutrient relations
by Christopher Dean Tyrrell, My dissertation focuses on the role of agricultural nutrient enrichment in structuring aquatic plant communities in Southern Manitoba, Canada, and changes in nutrient cycling resulting from changes in vegetation structure. Built around the “holy grail” framework of community ecology, which describes connections between the environment and ecosystem services or function as mediated by the traits of the biotic community, I explore the linkages between nutrient enrichment and aquatic plants of prairie streams focusing on species growth form (morphology) as a proxy for a suite of co-varying individual traits. I found that plant morphology interacted with environmental factors to determine which growth forms predominated in a stream: plant community shifts from being dominated by species with a submerged morphology to a community dominated by an emergent morphology as nutrient concentrations increase. I show how this pattern allows plant growth form to be used as an indicator of stream nutrient status. Further, I found that plants with similar growth forms share similar physiological features. Emergent plants have lower tissue nutrient concentrations per unit biomass and thus transfer fewer nutrients per unit biomass from the sediment to the water column than submerged plants. My work also includes a phylogenetic thread that brings novel insight: species at sites with higher nutrients all tend to be clustered in a few branches of the plant phylogeny whereas stream sites with lower nutrients have species from a diverse mixture of phylogenetic lineages. I used plant phylogeny to examine whether evolutionary history is related to tissue nutrient concentration and found the influence is mostly attributable to phenotype. These findings hint at the possibility of alternative stable states for prairie stream vegetation: a high nutrient emergent community and a low nutrient submerged community. These alternative states are comparable to those found in shallow lakes, where high nutrient conditions are dominated by algal growth and bring about turbid water, whereas lower nutrients are characterized by clear water and abundant macrophyte growth. The nutrient transferring functionality of these two vegetation states should also differ, but specific quantities transferred would dependent on the proportion of biomass of each growth form., Electronic Only. (UNB thesis number) Thesis 9589. (OCoLC)959237866., Ph.D. University of New Brunswick, Department of Biology, 2015.

Pages

Zircon - This is a contributing Drupal Theme
Design by WeebPal.