Biological Sciences - Student Works

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https://hdl.handle.net/20.500.14078/47

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Identifying unknown soft coral species of Anthelia (Octocorallia) with multilocus DNA barcoding
(2023) Pataria, Mannraj; Shaw, Ross; Miller, Joshua M.
There are an estimated 1-9 million species of corals yet to be discovered. Anthelia is a species of soft coral that belongs to the Xeniid ae family within Octocorallia. The Xeniidae family of soft corals are of interest due to their ability to rapidly recolonize disturbed reefs, which have become more prevalent with global warming. Octocorallia also contains some of the most valuable corals used in jewelry. Identifying corals not only contributes to its conservation and our knowledge of its evolution, but also prevents fraudulent coral jewelry and the overharvesting of coral beds. However, morphologically identifying corals is very difficult and is further exacerbated with global warming or when it is polished and carved into jewelry. Instead, multilocus DNA barcoding can utilize the genetic material of corals to reveal an accurate classification of species and prevent its exploitation. Specifically, genetic loci in the mitochondrial or nuclear genes can be used to tag and classify corals, with referencing done to genetic databases such as GenBank or NCBI. We identified the soft corals Anthelia glauca, Sarcophtyon tro cheliophorum, and a Sinularia spp. that was mistaken for a species of Nepthea.
Neurodevelopmental effects of teratogens on chick embryos: a model organism for human health
(2022) Slade, Sophia A.; Davis, Monica
The chick embryo (Gallus gallus domesticus), and its extraembryonic membranes, have been a commonly used model organism in developmental biology due to it being relatively easy to manipulate, inexpensive, and widely available. Chickens are one of the most valuable model organisms for medical and biological research and have profoundly influenced developmental biology since the 20th century. After 24 hours of development (during gastrulation), the process of neurulation begins, with the cephalic region progressing faster than the caudal region. Signalling centres release morphogen transcripts to determine axis formation of the neural tube. Complete neurulation is essential for the proper development of the brain and spinal cord. Chickens share many morphological, genetic, and biochemical similarities with humans, making them an appropriate model organism to examine teratogenic actions and effects on human development. This paper examines the impact of teratogens of differing origins: viral infection (Zika virus), environmental pollutants (cadmium), and recreational drugs (alcohol) on neural development in early chick embryos. Due to the similarities between human and chick embryonic development, researchers can correlate the findings of neural tube alterations in chickens following teratogen exposure with human congenital malformations, providing insight into their causes and mechanisms.
Is true informed consent achievable?
(2022) Matz, Miya
Imagine you have just found out that a loved one, such as a parent, sibling, or close friend, suffers from a rare and deadly genetic disorder. There are currently no successful mainstream treatments for this disorder. However, the doctor mentions a highly experimental treatment that would involve removing bone marrow from a healthy donor once a month for a full year and could potentially cause permanent damage to them. It turns out that you are a match. How would you make your decision regarding treatment? Most individuals would suggest leaving it to the doctor’s discretion, but because it is your body, it is ultimately your choice. You attempt to do further research on the internet but end up confused and frustrated. How will you ultimately decide as to whether you should give informed consent for the procedure?
The development of the chick embryo heart and using it as a model for atrial septal research
(2022) Vignjevic, Mimi; Davis, Monica
As an essential model organism, chicks can be used to study embryonic development. Information obtained by experiments can be applied to human development to understand how humans develop, processes and mechanisms that occur during human development, and possible sources of developmental disorders. Due to the rapid development of chick hearts, and similar developmental mechanism to human hearts, experiments performed on chick hearts can be applied to human heart development and be used to study human developmental disorders. Atrial septal defect is a common heart defect present at birth in humans, causing a hole in the septum of the heart. Using chicks, researchers can identify how heart structures move to form the septal hole, what genetic mutations or teratogens produce the defect, and potential mechanisms and treatments that can be used to prevent or treat atrial septal defect. Ultimately, chick heart research provides a more in depth understanding of human heart development which further provides the scientific community a greater understanding of general embryonic development.
Recovery ability of thermally stressed captive Coral Anthelia spp., as measured by dinoflagellate density
(2022) Dunbar, Dana; Shaw, Ross
Warming ocean temperatures are leading to an increase in coral bleaching events. These rising temperatures are fatal to coral species as they disrupt the symbiotic relationship between corals and dinoflagellates. Among other factors, thermal stress results in dinoflagellate damage and the loss of these symbionts. The recovery ability of corals exposed to this stress is a small area of research within the larger body of coral conservation. This study aims to add to that field by examining how soft corals, specifically Anthelia spp., react to thermal stresses. Over a nine- week period, 4 different experimental tanks will be raised from 28o to 32oC before returning to 28C to observe recovery potential. Dinoflagellate density was examined twice per week using a maceration method on tissue samples, viewed under a compound microscope. These densities were used as an indication of coral health and successful recovery. Expanding the knowledge of the recovery ability of soft corals is imperative to continuing the existence of these species.
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.
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).
Sand armour: how it provides plants with an edge up in survival
(2021) Roth, Jennifer
Plants have evolved a dizzying array of morphological and biochemical defenses; a deceptively simple one involves sand. Some plants actively coat themselves in sand, termed psammophory, as an ingenious adaptation for survival. While the functional significance of psammophory is understudied, experimental data from Abronia latifolia and Navarretia mellita suggests that it acts as a mechanical defense against herbivory within dune habitats. This defense stems from both the damaging and non-nutritive properties of sand and the lasting detrimental effects it has on herbivore physiology. While sand armour may seem like an unusual adaptation, it certainly can deter herbivores by giving them something to chew on.
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.
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?
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).
Helminth therapy: a promising approach to treating Crohn’s disease and asthma
(2020) Szaszkiewicz, Joshua
Increasing rates of autoimmune diseases, such as asthma and Crohn’s disease, have become a major concern in industrialized countries. One potential cause for the rising rates of autoimmune diseases in humans, is the disconnected relationship to parasites due to better hygiene. The extensive history between parasites and humans has resulted in the evolution of immunomodulating characteristics in parasites that may prevent the development of autoimmune diseases in humans. Here, I discuss the evolutionary reason for the protective effect against autoimmune diseases provided by parasites, explain the hygiene hypothesis as it relates to parasites, and propose the immunological mechanisms of parasites that might confer protection from autoimmune diseases. I will also give evidence for the protective effect and indicate the current state of helminth therapy and its challenges. While helminth therapy may be an effective treatment and prevention method for autoimmune diseases, much more research needs to be conducted in order to determine the specific mechanisms of action on our immune systems, and how these could be used medically to treat autoimmune diseases.
Lifestyles of the rhiz and not-so famous: a poetic introduction to the rhizosphere
(2020) Rayner, Lyndsay
The rhizosphere is a dynamic place where plant roots interact with soil, along with all of the living things that occupy this very small, yet very important space. Plants are often viewed as the foundation sustaining all living things on terrestrial Earth. But what about the components that sustain and impact our beloved chlorophyll companions? What helps them thrive? Where do the nutrients come from? What may potentially harm them? This collection of poems will help shine light onto the essential role that the microbial community plays on plant life and ecosystems at a global level.
The smart plant: a look into the controversy behind plant intelligence
(2020) Fermaniuk, Coral Lynn
Plants have long been excluded from the conversation regarding intelligent functioning in living things. This mindset dates back to ancient times, when plants were assigned a low-functioning and unintelligent rung on the scala naturae. In comparison to animals, plants have evolved to respond to their environment with a modular body plan, which lacks a nervous system and ‘intelligent’ organ, such as a brain. Despite this, research has demonstrated that plants are able to sense their environment, transmit sensory information throughout the entire organism, and respond to this sensory information with appropriate physiological responses. Also, plants have been shown to demonstrate aspects of learning and memory -cognitive functions once thought to be restricted to ‘intelligent’ beings (i.e. animals). The argument against plant intelligence is largely semantic-based, and stems from the concept that the word ‘intelligence’ cannot be applied to organisms which lack organs responsible for intelligent functioning. To truly appreciate the intelligent functioning of plants, we must eliminate this semantic barrier through a re-evaluation of our conventional understanding of intelligence. Perhaps this would require us to view intelligence, not as a quality unique to animals, but as a biological property, which in varying degrees is present in all life forms.
Is young blood the cure to aging?
(2020) Lacombe, Kennedy
Recent studies on parabiosis between young and old animals have discovered that young blood has a powerful rejuvenating effect on skeletal and cardiac muscles, as well as on the brain of older animals. These results suggest that there is something in the young systemic environment that may possess anti-aging properties. The results have recently been attributed to a circulating protein by the name of GDF11. Recent controversies, related challenges, and a futher outlook are highlighted and examined further.
Population analysis of Carcharodon carcharias in localized areas surrounding South Africa using semi-automated dorsal fin identification
(2021) Flathers, Erin; Shaw, Ross; Andreotti, Sara
The great white shark (Carcharodon carcharias) is a marine apex predator with a global distribution. In recent years, the number of white sharks has drastically declined as a consequence of anthropogenic activities such as illegal/targeted fishing, bycatch, and habitat disruption. Until recently, research on sharks has been lacking, resulting in an information gap on shark populations. This study aims to analyze the current population distribution of white sharks in the wild, to fill the research gap on white shark data, and to use this information to inform policies makers for improvements in white shark conservation measures. White shark population distribution between Gansbaai and Mossel Bay, South Africa, were estimated using semi-automated and manual dorsal fin identification techniques. Dorsal fin photos from Mossel Bay were organized into a both a coded database, and an edge pattern database, then matched to a pre-existing Gansbaai database to identify population dynamics between the two sites. The anticipated outcome of this study is an indication of the population dispersal along the South African coastline, to promote knowledge based improvement of existing marine conservation and fishing management strategies.
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.
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.
Identifying the nuclear localization signal of the Arabidopsis thaliana MADS box transcription factor Flowering Locus C
(2021) Wiseman, Brittany; Hills, Melissa
The goal of this project is to design a research strategy to identify the Nuclear Localization Signal (NLS) of the Arabidopsis thaliana MADS box transcription factor Flowering Locus C (FLC), and to make plant transformation components that are necessary for the creation of controls for this objective. An NLS is required for the nuclear localization of nuclear proteins, and though previous work on Arabidopsis has established conserved structural-functional domains within FLC, the NLS has not yet been characterized. To complete the objectives of this project, primers were designed and used to modify FLC to be compatible with the GreenGate cloning system. FLC was cloned, sequenced, and glycerol stocks were created and stored. Future projects will use this FLC to create an FLC:GFP fusion to serve as a control where protein localization is expressed in the nucleus. Electrocompetent Agrobacterium tumefaciens were made and a pGFPGUSPLUS plasmid was introduced. Glycerol stocks were stored to be used in Agrobacterium mediated transformation in the future, which will establish another control line of Arabidopsis expressing GFP proteins that are not nuclearly localized. Finally, a literature review was completed to explore the existing understanding of NLS structure in general and in MADS box transcription factor proteins, to propose mutations that might disrupt the NLS sequence within FLC. This work aims to fill a knowledge gap in regards to the mechanism of nuclear localization of FLC and will ultimately contribute to our understanding of nuclear localization in plants and MADS box proteins in general.
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.

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