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Browsing Undergraduate Research by Subject "Biology"
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Item A comparison between automated and manual detection methods for detecting bird species richness in audio recordings(University of New Brunswick, 2018) Hines, Jeff; Houlahan, JeffUnderstanding long-term human impacts over large areas of the environment requires large-scale biological monitoring programs and efficient ways to analyze the volume of data that will be generated. Automatic recording devices (ARDs) can be deployed in the field to record sounds over long periods and are useful for monitoring vocal animal populations. The data can be analyzed by searching through portions of the audio species vocalizations (manual detection) or having software perform the search (automatic detection). Here we compare manual and automated techniques for detecting the presence of 43 bird species over 7 sites based on the vocalizations each method detected in field recordings. Results show that an automated method detected significantly more species than the manual method. Automated detection is, therefore, a viable option to efficiently analyze large audio datasets to determine bird species richness.Item A retrospective assessment of marine ecological research using optimal α(University of New Brunswick, 2020) Zhao, Chuhan; Houlahan, JeffNull hypothesis significance testing (NHST) is and has been for many decades broadly applied across disciplines, NHST’s shortcomings have been identified and discussed since its introduction. Optimal alpha is a better method for setting statistical thresholds in NHST because it minimizes the overall probability of making errors. However, we don’t know how often using optimal α would result in a different conclusion than NHST. I calculate optimal α for 433 tests from 2009-2018 published marine biology papers and compare conclusions with NHST. I find totally 24 % of conflicting results (small ES: 22 %; medium ES: 22 %; large ES: 29 %). For disagreement, optimal alpha has 97 % significant results at small ES, 54% at medium and 24% at large. Low observed p value tends to have disagreement. These results mean that failing to use optimal alpha may be inflating the probability of making wrong conclusions in marine biology.Item Change in occupancy and density of nesting Atlantic puffins and razorbills on Machias Seal Island between 2011 and 2019(University of New Brunswick, 2020) Elisseou, Meredyth; H. MajorAt Machias Seal Island (MSI), populations of nesting Atlantic Puffins (Fratercula arctica) and Razorbills (Alca torda) are stable and increasing (respectively). The purpose of my study was to determine whether the increasing Razorbill population has caused a change in the spatial distribution of nesting puffins on the island. I hypothesized that the larger, more competitive Razorbills outcompete puffins for nesting space, resulting in the movement of puffins to alternative regions of the island. Using data from Alcid surveys that occurred in 2011, 2015, 2016, and 2019, I assessed occupancy and density of puffins and Razorbills in each of 1,753 surveyed quadrats. Using generalized linear models in an information theoretic approach, I found no changes in occupancy or density of either species. However, I note the short timespan (eight years) covered in my study and suggest that continued monitoring and analysis of changes in puffin and Razorbill occupancy and density.Item Changes in body size of Atlantic Puffins at Machias Seal Island (MSI) from 1995-2019(University of New Brunswick, 2020) Georgantopoulos, Joy; Major, HeatherBody size of fledging Atlantic Puffins (Fratercula arctica) at Machias Seal Island have been decreasing over the past 25 years (1995-2019) likely due to climate change. Using fledging size data archived in the Microsoft Access data base “seabird finder” I asked three questions: 1) have puffin fledgers gotten smaller in size (wing chord and mass) over the last 25 years, 2) can small fledgers continue to grow (in wing chord) after leaving the island, and 3) are adult Atlantic Puffins decreasing in size (wing chord). Using linear regressions, I found support for the hypothesis that fledgers are getting smaller with time and that small fledgers grow more after leaving the island than large fledgers. Finally, I found a marginally insignificant result suggesting that adult size is changing in response to fledging size (i.e., adults are becoming smaller with time).Item Comparing the effectiveness of protein coding genes to the ITS gene as DNA barcode markers for species-level identification of Penicillium and Aspergillus fungal isolates(University of New Brunswick, 2020) Po, Hui Ting; Gray, Christopher; Johnson, JohnPenicillium and Aspergillus are important genera of fungi in the order Eurotiales that are species-rich and are found living ubiquitously. The ability to identify these fungal species allows researchers to collate and access valuable information associated with these fungi. In recent years, a molecular technique known as DNA barcoding has become a common method used for fungal identification. The internal transcribed spacer (ITS) gene was described in 2012 as the universal DNA barcode marker for fungal identifications but has limited sequence variability to identify species of Penicillium and Aspergillus. Protein coding genes; benA and calmodulin may be more effective barcode markers for identifying Penicillium and Aspergillus species, respectively, due to higher interspecific variations in the gene sequences. In the present study, we compare whether it is more effective to identify Penicillium and Aspergillus fungal isolates to the species level using protein coding genes or the ITS gene as barcode markers.Item Confirmation of the absolute stereochemistry of a polymeric natural product from a macroalgal endophyte(University of New Brunswick, 2018) Morehouse, Nicholas J.; Gray, Christopher; Johnson, JohnThe bioactive biopolymer, poly(3,5-dihydroxyhexanoic acid), was previously isolated from an unidentified fungal endophyte of the marine macroalga Scytosiphon lamentaria. Literature reports for this compound failed to provide adequate details about poly(3,5-dihydroxyhexanoic acid) to allow for its complete characterization, thus requiring additional methods to be employed to determine the absolute stereochemistry of poly(3,5-dihydroxyhexanoic acid). Saponification of poly(3,5-dihydroxyhexanoic acid) yielded the lactone, 4-hydroxy-6-methyltetrahydro-2H-pyran-2-one. Nuclear magnetic resonance spectroscopy and polarimetry confirmed that the lactone was the 3R, 5R enantiomer, thus, the biopolymer isolated was confirmed to be poly(3R,5R-dihydroxyhexanoic acid).Item Contribution of variability in embryo development rate and status at hatch to the protracted hatch period of female American lobster Homarus americanus(University of New Brunswick, 2018) White, Lydia; Rochette, Rémy; Zou, LiwenFemale American lobsters typically hatch their embryos over protracted hatch periods of 15-32 days. To investigate the mechanisms underlying this intra-brood variation in hatch time, I reared individual embryos from June to September 2017 at a constant temperature of 9°C, took photos of them at the beginning of the study and prior to hatch, and measured their eye size as a proxy of their development status. A multiple linear regression model explained 74% of the variability in hatch day, and indicated that embryos that hatcher earlier in the summer are (i) more developed come spring (44% of explained variance), (ii) less advanced in development (28%), and (iii) develop at a faster rate (27%). This study suggests that the process of hatching is not strictly associated with a particular role of the brooding female, but rather is perhaps mostly a function of processes or attributes of individual embryos.Item Critical thermal maximum and hematology of Atlantic sturgeon (Acipenser oxyrinchus) after repeated exposure to thermal challenge separated by three different recovery times(University of New Brunswick, 2018) Kaser, Miranda; Kieffer, JamesTo determine the effect of a thermal stress in the form of a critical thermal maximum test (CTmax) on the subsequent critical thermal maximum and hematology of Atlantic sturgeon, fish acclimated to 19 °C were exposed to either no thermal stress (i.e., control; n=6), one CTmax test only (n=6) or two CTmax tests separated by a 1 hour (n=6), 2 hour (n=7) or 24 hour (n=6) recovery period. The critical thermal maximum of the first test (CTmax 1) was not significantly different from that of the second test (CTmax 2) across all recovery periods. Similarly, the hematological values tested (hematocrit, plasma osmolality, and plasma lactate, chloride, glucose, and protein concentrations) did not display strong sensitivity to thermal stress. It is proposed that the high acclimation temperature may mask the effect of CTmax 1 on CTmax 2, or that Atlantic sturgeon are not strongly sensitive to repeated thermal stress.Item Cultivation of endophytic fungi inhabiting Abies balsamea using two techniques: a comparative study(University of New Brunswick, 2018) Fitzherbert, Tyson; Gray, Christopher; Johnson, JohnTwo cultivation techniques: leaf segment cultivation and dilution-series cultivation, were compared for recovery of endophytes from needles of Abies balsamea collected in Saint John, New Brunswick, Canada. Endophytes were cultured on 2% malt extract agar and morphology of the endophytic growth was used to aid identification of distinct isolates. Endophytes were isolated from A. balsamea needles using the leaf segment cultivation method at a frequency of 13%, all replicates of two distinct isolates. Endophytes were isolated form eight of 25 prepared isolation plates for the dilution-series method. All endophytic growth from the dilution-series method was single-celled yeast species, while the endophytic growth from the leaf segment method was exclusively filamentous fungal species; thus, dichotomy was seen between the two methods of isolation.Item Determination of a link between the taxonomic relationship of Canadian medicinal plants and the exhibited antibiotic activity of their crude extracts(University of New Brunswick, 2019) Therrien, Julie K.; Gray, ChristopherChemotaxonomy is effective in determining the expected chemical compounds found in extracts from different organisms. However, this is time-consuming and costly, as it is based on purified fractions of a chemical extract. Utilizing biological activity data of extracts and relating it to the taxonomic relationship of plants may be a more effective approach. The aim of this study was to determine if a link exists between the taxonomic relationship of plants and the exhibited antibiotic activity of their extracts. The antibiotic activity of methanolic extracts of 90 plants were evaluated against eight microorganisms. Bioactivity profiles were created and analyzed, using two separate methods. It was found that the lowest taxonomic level that correlated with the bioactivity profiles of the extracts was family.Item Does land-use affect bird abundance?(University of New Brunswick, 2019) Prosser, Jacob; Houlahan, JeffOver the last 50 years many species have seen negative population trends and scientists have identified habitat loss, change, and fragmentation as possible causes. I investigated the ability of random forest and boosted trees models to predict bird abundances based on land-use throughout the United States. Bird abundance data was acquired from the North American Breed Bird Survey (BBS) and land-use data was gathered by the Multi-Resolution Land Characteristics (MRLC) consortium. The models had a mixed transferability between the training and test data with 14 of 21 models better fit the training data. The models were mixed in their ability to accurately predict abundances based on land-use compared to the mean; 14 of 21 models more accuracy predict abundance compared to the mean suggesting an effect of land-use on abundance. Six models were classified as “good,” 11 as “cautious,” and 4 as “poor.”Item Effects of environmental conditions on egg-laying dates in Atlantic puffin Fratercula arctica(University of New Brunswick, 2019) Fana, Natalia; Major, H.L.; Whidden, S.E.Climate change trends may have an impact on the timing of seasonal activities, and in particular the phenology of Atlantic Puffins. The purpose of this study was to investigate if changes in environmental conditions, such as Sea Surface Temperature (SST), are responsible for the observed delay in egg laying at Machias Seal Island (MSI), New Brunswick. I used monthly means for SST and egg laying dates over a period of 24 years (1995-2018) from MSI. I used general linear models in an AICc framework and found a positive relationship between egg laying dates and SST over time. I suggest continued long-term monitoring to assess future changes and the puffin’s ability to continue to adapt to those changes.Item Effects of ocean acidification on respiration and burrowing behaviour of infaunal marine invertebrates in the Bay of Fundy.(University of New Brunswick, 2018) Walsh, Sindy; Hunt, HeatherCoastal acidification alters the physiology and behaviour of invertebrates. pH-driven behavioural changes may be mediated by GABAA receptors. I examined whether water column pH affects respiration rate, and whether GABAA receptors are the mechanism behind burrowing behaviour changes at reduced pH. Respiration of clams (Mya arenaria), snails (Tritia obsoleta), and crustaceans (Corophium volutator) was measured after 6 weeks in ambient-pH or reduced pH. In a second experiment, effects of sediment pH and a GABAA neuroinhibitor on burrowing of T. obsoleta and C. volutator were tested. Respiration rates were higher in reduced pH water but did not differ significantly between treatments. Burrowing by C. volutator decreased in reduced pH, but not when treated with the neuroinhibitor, and T. obsoleta showed no difference among treatments. Results suggest that reduced water column pH stresses animals and GABAA is the mechanism behind burrowing behaviour for C. volutator but maybe not T. obsoleta.Item Human behavioural ecology in the middle palaeolithic : a comparative study based on how we quantify the use of raw material(University of New Brunswick, 2020) Mears, Peter; Wilson, Lucy; Browne, ConstanceResource Selection Function (RSF) analyses can be used to understand what variables influenced hominin choices for selection of lithic raw materials. Previous work examined stone tool assemblages from the Bau de l’Aubesier (Vaucluse, France), quantifying raw material use by the number of lithics from a particular source area. My study compares this to quantifying use by the weight of those pieces, using Generalized Linear Models that describe the sources of raw material used in each archaeological layer. Independent variables describe raw material characteristics or the surrounding terrain. In the older layers of the site, terrain variables contribute more towards source area use. In the younger layers, raw material characteristics drive source use, but less so in models that quantify lithics by their weight. k-fold cross-validation analyses suggest the best method of quantifying lithic artefacts for use in RSFs may vary depending on the hominin behaviour that led to the assemblage.Item Identification and DNA taxonomic analysis of a library of endophytic fungi(University of New Brunswick, 2019) Stack, Ryleigh A.; Gray, Christopher; Johnson, JohnEndophytes represent a largely untapped source of natural products. Despite a growing body of research, data and knowledge relating to endophyte biology and chemistry, one of the difficulties in endophyte research remains the accurate identification of endophytes. The advancements and development of molecular methods have provided researchers with tools that allow them to obtain an identification based on the endophyte’s DNA sequence, rather than its morphological and/or phenotypic characteristics. In the present study, the DNA extracted from 155 endophytes was analyzed following a DNA taxonomy methodology and compiled to give phylogenetic trees to obtain identifications based on the molecular properties of the endophytes, rather than their morphology. Of the 155 endophytes; 57 were identified to the species level, 65 to genus, 5 to class, 2 to subdivision, 10 to order, 15 to family, and 1 to subclass.Item Investigating the genetic structure of Atlantic Cod (Gadus morhua) spawning populations following the collapse of the northern cod stock(University of New Brunswick, 2019) Gormley, Ty; Pavey, ScottThe Atlantic cod (Gadus morhua), within the Northern cod stock, once served as the economic pillar for Newfoundland and Labrador. After years of overfishing and reduced ocean temperature, the stock population collapsed in 1992, driving many to question the genetic structure for its recovery. Currently, the metapopulation and isolation hypotheses have been proposed to describe the genetic structure of the stock, but there is much debate on which is reliable. The stocks genetic structure will be determined using fin clips obtained from 2001- 2003, from various spawning populations, to indicate whether the stock exhibits panmixia. A double-digest restriction site associated DNA technique was used to identify 846 single nucleotide polymorphisms, and the population structure was determined using the Fixation Index (FST). The FST analysis found no significant differences, therefore, spawning populations of the stock are panmictic. Further research is necessary to obtain a more robust genetic structure for extensive ecological management.Item Investigation of antimicrobial activity of Canadian medicinal plant extracts(University of New Brunswick, 2018) Dao, Khoi Thien; Gray, Christopher; Johnson, JohnMethanolic extracts of seven Canadian medicinal plants were investigated for antimicrobial activity against a Gram-positive bacterium (Staphylococcus aureus), a Gram-negative bacterium (Pseudomonas aeruginosa), and a fungal organism (Candida albicans). Chamerion angustifolium extract was highly bioactive against S. aureus and P. aeruginosa; Crataegus sp. extract was moderately bioactive against S. aureus, but had a low bioactivity against C. albicans. The extract from Betula papyrifera had a low bioactive against both S. aureus and C. albicans. The active constituents of C. angustifolium, Crataegus sp., and B. papyrifera were detected via separation using two-dimensional thin layer chromatography followed by testing against S. aureus using bioautography. This is the first study to report antimicrobial activity of Crataegus sp. native to Canada and first study to find the antimicrobial constituents of C. angustifolium and B. papyrifera.Item Ionoregulation in the cold: a possible barrier to freshwater colonization?(University of New Brunswick, 2018) Dougay, Brett; Speers-Roesch, BenTo test if ionoregulation in winter cold is a barrier to freshwater colonization at high latitudes in fishes, I investigated the ionoregulatory responses of euryhaline marine-adapted Mummichogs (Fundulus heteroclitus) and freshwater-adapted Banded killifish (Fundulus diaphanus) held in freshwater at 14°C and 0, 4, 14, and 28 days of exposure to winter temperature of 4°C. I predicted that the Banded killifish would be able to maintain their ionoregulation better then Mummichogs in the cold freshwater. I measured maximal activities of gill Na+-K+-ATPase and H+-ATPase, two key ionoregulatory enzymes, and plasma chloride concentrations as a measure of osmotic status. There were no significant differences between species and no effect of cold acclimation on plasma chloride or enzyme activities. The lack of ionoregulatory perturbation by winter cold in either species, especially the seawater-preferring mummichog, do not support the hypothesis that ionoregulation in winter is a barrier to freshwater colonization in fishes.Item Is there geographic variation in development rate of American lobster (Homarus americanus) embryos?(University of New Brunswick, 2018) Mawer, Kalen; R. Rochette; L. ZouAmerican lobster fisheries in Canada are managed via Lobster Fishing Areas, which are divided based on sociopolitical considerations rather than biological stocks. Bio-physical models use physical and biological parameters to predict larval dispersal and contribute to understanding the identity of stocks, and the connectivity between management areas. Hatching time of lobster embryos is an important parameter of these models, as it impacts the survival and transport of larvae. This study aims to determine whether embryo development functions used to predict hatch need to be “location-specific”. We sampled eggs from six locations in eastern Canada, reared them in the lab, and photographed them weekly to track embryo development based on changes in eye size. The results suggest that embryo development functions do not need to be developed for individual fishing ports, but that distinct development functions for larger marine systems may improve larval dispersal modelling and sustainable management of fisheries.Item Isolation and identification of the bioactive natural product A-26771B from an endophytic Penicillium expansum isolate(University of New Brunswick, 2020) Forgrave, Kirstyn A.; Gray, ChristopherNatural products are an important source of bioactive compounds and endophytic fungi derived from marine algae represent an under-investigated source of natural products. The objective of this research was to isolate and confirm that an extract from an endophytic Penicillium expansum contained the natural product A-26771B. The natural product was tentatively detected, using high-resolution electrospray ionization mass spectroscopy data, in a methanolic extract from the endophyte. Despite repeated rounds of high performance liquid chromatography and multiple fermentations of the endophyte, the compound was isolated in sub milligram quantities and identified using proton nuclear magnetic resonance data. However, prior to obtaining carbon nuclear magnetic resonance data that would confirm the identification of A-26771B the natural product degraded. Future work should include isolating more of the molecule A-26771B to determine the bioactivity of the molecule against Mycobacterium tuberculosis and Mycobacterium smegmatis.