Biological Sciences - Student Works

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9-(2-Phosphonyl-methoxyethyl)-adenine promotes erythrocytic differentiation and disrupts cell replication in chronic myelogenous leukemia K562 cells
(2021) Wiseman, Brittany; Harcombe, Kimberley; Bernstein, Nina
Disruption during cellular differentiation can cause hematopoietic stem cells to proliferate uncontrollably, resulting in the development of cancer. Differentiation therapies are being investigated as a type of cancer treatment which involve inducing agents that promote the differentiation of cancer cells into those with similar properties to normal blood cells. These cells can then undergo apoptosis at an accelerated and controlled rate compared to cancer cells, making this a potential therapeutic technique. In this study, the ability of human chronic myelogenous leukemia K562 cells to undergo cellular differentiation in response to the inducing agent 9-(2-Phosphonyl-methoxy ethyl)-adenine (PMEA) is investigated. PMEA has previously been shown to disrupt cell replication, and promote erythrocytic differentiation in K562 cells. In order to further test the effectiveness of this inducer, cell proliferation was measured with a cell growth curve, hemoglobin presence was measured with benzidine staining, and gamma-globin expression (a protein subunit of fetal hemoglobin) was measured in both induced and uninduced K562 cell cultures via RT-qPCR and western blotting. The results indicate that PMEA slows cell replication, and promotes hemoglobin (and subsequently gamma-globin) expression in treated cells. In summary, the findings support the conclusion that PMEA is able to promote erythrocytic differentiation in K562 cells, and provides information that supports differentiation therapies as a method for cancer treatment.
9-(2-Phosphonyl-methoxyethyl)-adenine promotes erythrocytic differentiation and disrupts cell replication in chronic myelogenous leukemia K562 cells
(2021) Wiseman, Brittany
Disruption during cellular differentiation can cause hematopoietic stem cells to proliferate uncontrollably, resulting in the development of cancer. Differentiation therapies are being investigated as a type of cancer treatment which involve inducing agents that promote the differentiation of cancer cells into those with similar properties to normal blood cells. These cells can then undergo apoptosis at an accelerated and controlled rate compared to cancer cells, making this a potential therapeutic technique. In this study, the ability of human chronic myelogenous leukemia K562 cells to undergo cellular differentiation in response to the inducing agent 9-(2-Phosphonyl-methoxy ethyl)-adenine (PMEA) is investigated. PMEA has previously been shown to disrupt cell replication, and promote erythrocytic differentiation in K562 cells. In order to further test the effectiveness of this inducer, cell proliferation was measured with a cell growth curve, hemoglobin presence was measured with benzidine staining, and gamma-globin expression (a protein subunit of fetal hemoglobin) was measured in both induced and uninduced K562 cell cultures via RT-qPCR and western blotting. The results indicate that PMEA slows cell replication, and promotes hemoglobin (and subsequently gamma-globin) expression in treated cells. In summary, the findings support the conclusion that PMEA is able to promote erythrocytic differentiation in K562 cells, and provides information that supports differentiation therapies as a method for cancer treatment.
A comparison between real and DLA simulated liver lobules using a population density analysis
(2014) Wisk, Sara; Rezania, Vahid
A liver lobule is comprised of networks of sinusoids and hepatocytes. Here, a liver lobule was computationally constructed by using diffusion-limited aggregation (DLA) method. A population density analysis of the sinusoids and hepatocytes was performed and then compared with a real lobule image. The resulting images were compared using a histogram to interpret the ratio of hepatocytes to sinusoids.
Analysis of organic and heavy metal pollutants in marine planktonic organisms from Bamfield, British Columbia by ICP-OES and GC-
(2020) Schaub, Addison; Shaw, Ross; Mugo, Samuel
Plankton form the base of the marine ecosystem (Levinton, J.S., 2017). It is for this reason it is important to understand the interactions between these critical organisms and the pollutants that they encounter. Heavy metals occur naturally in trace amounts and are continuously being released into the atmosphere, hydrosphere, lithosphere, and biosphere of the Earth (Atici et al., 2010; Burada et al., 2014; Callow, P., 1993). The increase in sea water temperatures is increasing the solubility of heavy metals in the water (Levinton, J.S., 2017). Organic pollutants such as pesticides are hydrophobic and lipophilic (Chiuchiolo et al., 2004). Previous results obtained by Kathryn Farmer in 2015 found that an increase in some heavy metals and not others in the four year difference in the Bamfield samples. Analysis of organic pollutants by GC-MS was unable to determine if peaks were the result of pesticides or not and was not able to identify any specific pesticides through the NIST library (Farmer, 2015). This analysis found the majority of the plankton samples showed significant difference between one another for all detected heavy metals. Analysis of organic pollutants was suspended sue to Covid-19 response.
Antimicrobial properties of medicinal teas and their interactions with antibiotics
(2020) Maziarz, Sydney; Harcombe, Kimberley
The rise of antibiotic-resistant bacteria has greatly increased the need for new drugs to be developed. These drugs may be new antibiotics, or synergists of existing antibiotics. Plants have been identified as a valuable source of new drugs, as plants produce secondary metabolites that have antimicrobial and synergistic activity. In addition, plants are the basis of many natural health products and dietary supplements, and public interest in these products continues to increase. The increasing popularity of natural health products also increases the possibility for antagonistic interactions to occur when these products are used in conjunction with antibiotics. The present study investigated the antimicrobial properties of aqueous extracts of three medicinal teas and their interactions with common antibiotics. The antimicrobial properties of the aqueous extracts of Bronchitis tea, Eyebright tea, and Hyssop tea were assessed via disk diffusion. It was found that both Eyebright tea and Hyssop tea extracts have antimicrobial properties, likely due to the phenolic acids and flavonoids found in extracts of these plants. Interactions between the tea extracts and antibiotics were assessed using a double disk diffusion method, where it was found that all three tea extracts interact antagonistically with sulfadiazine. Additionally, Eyebright tea extract was found to interact antagonistically with chloramphenicol. While further research is required to determine the mechanism of this interaction and the specific compounds involved, this research has identified that these teas should potentially be used with caution in combination with antibiotics. In addition, the antimicrobial properties of both Hyssop and Eyebright tea extracts warrant further research as these extracts may be the basis for new antimicrobial drugs in the future.
Antimicrobial screening of phytochemicals produced by Albertan invasive weeds
(2021) Supina, Brittany; Bott, Tina; Harcombe, Kimberley
Antibiotic resistance has rendered many clinically-used antibiotics ineffective, creating an urgent need for new antimicrobial agents. Phytochemicals (secondary metabolites produced by plants) are produced in response to environmental stressors, and can inhibit the growth of bacteria, fungi and surrounding plants. Therefore, these phytochemicals offer an alternative source of antimicrobial compounds. The diversity and abundance of phytochemicals produced by plants can increase during the invasion of new habitats, making invasive weeds strong candidates for antimicrobial discovery. Despite this increase in phytochemical production, invasive plant species are often overlooked in favour of medicinal and edible plants, and few studies have characterized their antimicrobial activity. In this research, we used successive Soxhlet extractions with hexane, ethyl acetate, and methanol to extract the phytochemicals from Albertan invasive weed species collected from the Edmonton area. Using Kirby-Bauer disk diffusion assays, extracts were assessed for their ability to inhibit the growth of tester bacterial species including Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, and Staphylococcus aureus, which represent a range of common pathogens and bacterial types. Preliminary characterizations of extracts from multiple plant species, including common tansy (Tanacetum vulgare) and woolly burdock (Arctium tomentosum), showed promising inhibitory activity against several bacterial species, warranting further investigation. This study provides a starting point for further bioactivity and chemical characterizations of Albertan invasive weeds and highlights these invasive plant species as potential leads for the development of new antimicrobial treatments.
Are we too clean? A history and analysis of the hygiene hypothesis
(2020) Steed, Riley
Since the second half of the 20th century, the incidence of atopic disease has been on the rise. Allergies and rhinitis have become so common that some have called it an epidemic (Strachan, 1989). Initial research into the reasons for the rapid increase was done by David P Strachan, and he proposed the “hygiene hypothesis,” a theory claiming that early childhood infections can protect us against atopic diseases later in life (Strachan, 1989). Subsequent research found an interaction between T-helper 1 and T-helper 2 cells that, for many years, was considered to be the mechanism by which the hygiene hypothesis functioned (Romagnani, 1992). Eventually, it was discovered that this interaction did not work exactly as previously thought, and Graham A. Rook introduced a new theory to match the more recent research. Rook proposed the “old friends” hypothesis, which suggested that certain microbes, which evolved alongside humans, were responsible for protecting us against atopic disease (Rook et al., 2004). According to Rook, modern lifestyles have eliminated many of those microbes from our normal flora, and that explains the recent rise in atopic disease (Rook et al., 2004). The “old friends” hypothesis is now the prevalent atopic disease theory in epidemiology, and has helped improve both public and scientific understanding of the relationship between infection, hygiene, and atopy (Stiesma, et al., 2015).
Assessing the spread and establishment of Prussian carp (Carassius gibelio) in northern Alberta
(2021) Jessen, Erika; Shaw, Ross; Das, Mrinal
The Prussian carp (Cassasius gibelio) is an exceptionally dangerous invasive freshwater fish species. Native to Asia and eastern Europe, it has come to dominate many freshwater bodies across Eurasia through anthropogenic activities, causing extensive ecological damage by outcompeting native taxa and degrading environmental conditions. Within the last two decades, the Prussian carp has been introduced into Alberta, and has since spread into the rivers and lakes of the province. To date, most research relating to Prussian carp in North America has focused exclusively on southern Alberta. My research project aimed to expand research into northern Alberta, specifically the Edmonton region, with the objective to determine if Prussian Carp have spread into northern Alberta. Twelve lakes and ponds in the Edmonton area were surveyed using an underwater drone to collect footage. Four of these sites were further subjected to eDNA analysis. The results of the drone footage picked up a mixture of native and invasive fish species, with two being positive for goldfish. The eDNA analysis picked up neither goldfish or Prussian carp DNA at any of the test sites, likely due to low eDNA concentrations. Overall, these results highlight the need for ecological management to mitigate the spread of invasive fish species in Alberta.
Bed bugs (cimex lectularius): biology, control methods, and their role as pests
(2014) Fedor, Dreann Nicole
Bed bugs (Cimex lectularius) are blood feeding ectoparasites that have evolved as human pests due to their unique biology and reproduction. Common side effects of bed bug bites include: skin lesions, localized inflammation, itchiness and anxiety. There are numerous control methods to reduce bed bug populations such as vacuuming, steaming, laundering, exposure to extreme temperatures and chemical eradication methods. Bed bugs have become resistant to pyrethroid insecticides and DDT, supporting the cosmopolitan reemergence of bed bugs in the last couple decades.
Behavioural and mechanical isolation in the Great Grig, Cyphoderris monstrosa
(2020) Dennis, Miranda; Judge, Kevin
The Great Grig (Cyphoderris monstrosa) is a species that has shown evidence of possibly being in the early stages of speciation. This study uses mating trials to determine the degree of isolation between the Alberta and British Columbia populations behaviourally and looking at the morphology of the populations to determine the possibility of mechanical isolation in C. monstrosa, possibly representing pre-zygotic mating barriers. If C. monstrosa is in the early stages of speciation, then it is predicted that there will be distinct differences between the grigs, specifically behavioural differences seen when attempting to mate the two groups, and morphological differences in their genitalia. Analyses of behaviour and morphology showed that the two populations were significantly different in aspects of size and form of genitalia, with the Alberta grigs being larger than the British Columbia grigs. This finding is concurrent with other studies, indicating the possibility of speciation between the populations, as per the biological species concept. This study helps to answer questions regarding species concepts and speciation in the Great Grig, as well as indicates the need for future work with these insects.
Biochemical characterization of DNA repair enzyme inhibitors, molecules with possible applications to improving cancer treatment
(2020) Hamel, Jolie; Bernstein, Nina
Polynucleotide kinase-phosphatase (PNKP) is a critical DNA repair enzyme responsible for processing DNA damage caused by radiation. A loss of function in this enzyme results in increased cell susceptibility to radiation-induced DNA damage and subsequent cell death. As radiation therapy is commonly used in cancer treatment, targeted inhibition of PNKP has been proposed to increase the effectiveness of radiation therapy at lower doses. We characterized two previously identified PNKP inhibitors, Candesartan and S4, by their effects on the kinase activity, kinase substrate binding, and phosphatase substrate binding of Caenorhabditis elegans and mouse PNKP. The binding assays were conducted using electromobility shift assays (EMSA), while in vitro kinase assays were performed to assess kinase activity. Both inhibitors had an effect on both domains of PNKP, but were more effective at displacing the phosphatase substrate than the kinase substrate. Comparisons of kinase activity inhibition by new and older samples of inhibitors showed that both Candesartan and S4 degrade over a span of 3-4 months and lose their effectiveness. These inhibitors show promise for applications in cancer treatment, but further research is needed.
Biochemical characterization of the kinase activity of DNA repair enzyme, PNKP from C. elegans
(2015) Oladogba, Oluwatosin; Bernstein, Nina
DNA damage by genotoxic agents such as ionizing radiation or reactive oxygen species is likely to occur in the DNA of all living organisms. Therefore the cells of living organisms have developed complex protein networks overtime to help discover and repair DNA damage (Bernstein et al. 2005). Polynucleotide Kinase/Phosphatase (PNKP) is an enzyme that plays a crucial role in repairing a type of DNA damage known as DNA strand breaks (Bernstein et al. 2005). This enzyme has 3 domains, a kinase domain at the C-terminal, a phosphatase domain at the center, and an FHA domain at the N-terminal (Figure 1) (Bernstein et al. 2008). The kinase and phosphatase domains are responsible for directly repairing DNA strand breaks while the FHA domain is responsible for binding PNKP to other DNA repair enzymes (Bernstein et al. 2008). The general objective of this study is to analyze the kinase activity of PNKP derived from C. elegans (CePNKP) in comparison to PNKP derived from humans (hPNKP) by conducting kinase assays. A long term goal for this research is to characterize useful orthologs of PNKP for structural studies of an inhibitor binding to this enzyme. Results from this research showed that the kinase activity of CePNKP is more selective for the recessed 5’ terminus compared to the kinase activity of hPNKP, and this suggests that it might possibly be a good model for hPNKP.
Breathing easy in an oligoxic world: Vampyroteuthis infernalis (Phy. Mollusca, Cl. Cephalopoda) adaptations to the oxygen minimum zone
(2015) Steckler, Deanna
This review explores the existing literature on the Vampire Squid from Hell, Vampyroteuthis infernalis (Phylum Mollusca, Class Cephalopoda, Order Vampyromorpha). They are largely unstudied deep water cephalopods found in the oxygen minimum zone (OMZ) throughout the world’s temperate and tropical oceans. Their unique morphology and genetic ambiguity has contributed to scientific debate regarding their phylogenetic relationships, to which there is still no definitive answer. Vampyroteuthis are so well adapted to life in the OMZ that foraging, locomotion and antipredator behaviours are entirely unique among cephalopods and perfectly well-adapted to the oxygen-starved environment. Despite a lack of direct research, inferences are made to determine the effects of anthropogenic disturbance on the vampire squid.
Brittle stars: a story of success in biodiversity
(2015) Beatty, Alex
The brittle star is found in a wide range of habitats all over the world. The regenerative and adaptive capabilities have allowed them to diversify. Huge photo evidence has determined several species to be invasive as they disperse into new habitats.
Cloning and purification of a glycerol-specific alditol oxidase for biosensor construction
(2022) Barroma, Chrissa; Kryjak, Amanda; Bernstein, Nina
Wine production is dependent on ethanol, but also on optimal glycerol concentrations, both of which are produced by S. cerevisiae fermentation. Wine characteristics like sweetness levels are influenced by glycerol concentrations. Additionally, elevated glycerol levels can be an indication of abnormal blood sugar levels. In both situations, close observations of glycerol levels are essential. One proposed method of measuring glycerol concentrations is through enzymatic oxidation with a glycerol biosensor. Alditol oxidase (AldO) is a recently discovered carbohydrate oxidase in S. coelicolor. Despite specificity for longer-chained polyols, studies have proposed that AldO can be used as a glycerol oxidase. Using random point mutations, an AldO mutant was isolated and had increased specificity for glycerol. These results suggest that potential for AldO with glycerol biosensor development. This project aimed to produce a glycerol specific alditol oxidase to be used as a biosensor. A synthetic alditol oxidase (AldOG) gene was used to produce AldOG via cloning methods. We plan to overexpress and purify the AldOG protein to use in construction of a glycerol biosensor in collaboration with Dr. Samuel Mugo (MacEwan University).
CRISPR: a revolutionary technique… For humans?
(2020) Barroma, Chrissa
CRISPR/Cas9 is a revolutionary technique that carries the possibility of altering the genomic sequence of an organism. Discovered in a bacterial immune system, CRISPR/Cas9 has been a popular topic of discussion since its first publication in 2012. In this essay, the opposing arguments on the use of CRISPR/Cas9 are discussed, based on the practical uses in human genetic engineering. First, the technique is described along with the comparison of other successful gene editing techniques. Secondly, the ethical and clinical implications are also discussed, and the effects of CRISPR use on human germline and somatic cells. This essay aims to answer whether CRISPR/Cas9 should be used to edit the genome of humans?
Determining recovery success in Anthelia sp. after exposure to varying levels of thermal stress
(2020) Hender, Rebecca; Shaw, Ross
Coral bleaching is a phenomenon caused by anthropogenically increased ocean temperatures, and may lead to the eventual death of massive reef systems. Bleaching is the result of corals expelling dinoflagellate endosymbionts in order to compensate for thermal stress. However, the loss of symbionts leads to a subsequent reduction in fluorescence intensity emitted by the coral. Substantial research has been done on coral bleaching due to environmental stressors, but little knowledge has been acquired about coral recovery after thermal stress. The present study aimed to determine how Anthelia species recover after being exposed to varying levels of temperature stress. Corals were exposed to varying levels of heat stress and subsequently brought back down in temperature to promote recovery. Using fluorescence microscopy, a relatively new method of quantifying coral health, and health-colour indices, recovery ability after thermal stress was determined. Analyses concluded that corals were able to successfully recover after thermal stress of 31°C, and exhibit a thermal compensation point around 30°C. However, beyond 31°C, recovery was not achievable. The findings of this study are beneficial to the larger coral research field because they indicate that corals do possess recovery ability up until reaching a fatal thermal maximum.
Developing a measure of fatigue for deaf and hard of hearing students
(2020) Maziarz, Sydney; Hayward, Denyse V.; McQuarrie, L.; Zarezadeh kheibari, S.; Rohatyn-Martin, Natalia K.
Fatigue is a prevalent issue in school-aged children and has been shown negatively impact well-being and academic performance. This is especially the case for deaf and hard of hearing (D/HH) students, who must produce greater auditory and visual efforts than their hearing peers, leading to greater levels of cognitive and physical fatigue. At present, there exists no standardized measure of fatigue that can be used in schools to specifically evaluate fatigue in students, let alone those who are D/HH. Such a measure would be incredibly valuable as it would allow for accurate identification of fatigue, allowing for supports and interventions to be implemented. The present research aimed to identify strengths and weaknesses of existing measures of fatigue in order to inform the construction of a measure that would specifically address fatigue in D/HH students. It was found that fatigue has largely been determined to be best assessed using a unidimensional measure with responses based on a 5- or 7-point Likert scale. Additionally, it was found that the development of measures usually follows the same general process. Items included in measures are typically generated based on focus-group interviews, then preliminary items are administered to a test group. Statistical tests are conducted based on the data generated to reduce the number of items, as well as to ensure reliability and validity. The next steps of this research will be to conduct focus group interviews to aid in generating preliminary items.
Developing microsatellite markers for Cypripedium passerinum (Sparrow’s egg lady’s slipper)
(2022) Lim, Lina; McFadyen, David A.
Natural and anthropogenic disturbances contribute to increased habitat loss and fragmentation and subsequently, species loss. Integrated conservation approaches combine both in-situ and ex-situ approaches whereby natural habitats of endangered species are conserved, and the genetic diversity of the threatened population is retained outside of their natural habitat. Therefore, an essential component of an effective conservation strategy is to assess genetic variation to ensure that the conservation approach employed is effective in preserving the diversity of the whole population. Microsatellites, highly polymorphic repetitive DNA sequences in the genome of all organisms, have proven to be a valuable tool in the assessment of genetic diversity. This project aimed to isolate microsatellite markers from Cypripedium passerinum, a native North American terrestrial orchid at risk of extinction. Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) was employed to generate a genomic DNA library enriched for AT, AC, and AAG microsatellites. Clones were selected from the libraries and bidirectionally sequenced to identify those which contain microsatellites. A total of 158 microsatellite loci were identified, of which 83% were perfect microsatellites. PCR primers were developed using the unique sequences flanking the identified microsatellites and were evaluated for their utility. Primers amplifying polymorphic loci can be used to assess the genetic diversity of C. passerinum populations both within the Wagner Natural Area, Alberta, Canada and elsewhere in its range of distribution. The project findings will contribute to the integrated conservation efforts to protect species found in Wagner Natural Area and contribute to our understanding of C. passerinum.
DNA barcoding of Masdevallia orchids using the matK locus
(2018) Drever, Josh; McFadyen, David A.
Maintaining global biodiversity is becoming more of a focus as the quality of this biodiversity declines. Conservation efforts need to be targeted at areas where this loss of biodiversity is most critical. Orchids are a family of plant facing significant survival pressures. Masdevallia is a genus of neotropical orchids which is poorly represented in orchid studies. When not flowering, individuals of this genus are morphologically indistinguishable from each other. DNA barcoding will assist in targeting conservation efforts by genetically identifying unknown species in threatened ecosystems. Many different loci in the orchid genome have been examined for use as a barcode, and the matK locus has had the best results. The objective of this study is to use the matK locus to create a DNA barcoding system which distinguishes between individuals of the Masdevallia genus. DNA has been isolated from samples and PCR has been done to amplify the matK locus. PCR products were sequenced using ABI sequencing, and the resulting sequences were aligned to create a phylogenetic tree. This tree contains unedited sequencing data, so while not conclusive, it indicates that this DNA barcoding system is sufficient to distinguish between samples at the species level. This will contribute to a DNA library, so unknown orchid individuals may be better identified in threatened ecosystems.

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