MindExpo Abstracts 2021
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Biology
Author(s): Halle Weise
Presentation Title: INVESTIGATION OF MXB AS A RESTRICTION FACTOR OF CYPRINID HERPESVIRUS-3
Faculty Sponsor: Dane Bowder
Field of Study: Biology
Session Type: Oral
Abstract: Cyprinid Herpesvirus-3 (CyHV-3) is a highly contagious agent that causes fatal disease in koi fish and common carp. The rapid spread of this virus, beginning in the 1990s, has caused severe financial losses for both koi and carp industries globally. Human MxB has recently been shown to be a pan-herpesvirus restriction factor, of human and mouse herpesviruses. To date, MxB has not been studied in the context of CyHV-3. In this study, we aimed to determine if MxB has the capability to restrict viral replication in fish cells through overexpression and CyHV-3 challenge experiments.
Author(s): Alexandria Osborn, Erin Doyle
Presentation Title: USING BRED-CONSTRUCTED GENE KNOCKOUTS TO DETERMINE FUNCTIONS OF BACTERIOPHAGE GENES IN THE MYCOBACTERIOPHAGE FUDGETART
Faculty Sponsor: Erin Doyle
Field of Study: Biology
Session Type: Oral
Abstract: Bacteriophage are viruses that infect and kill specific bacteria. Therefore, bacteriophage have the potential to be used as a replacement for antibiotics. This use of bacteriophage is called phage therapy. One limitation to the broader use of phage therapy is that many bacteriophage genomes contain genes with unknown functions. Knowledge of these functions is important because we can better understand the process of infection and potentially engineer more effective bacteriophage for bacteriophage therapy. Bacteriophage Recombineering of Electroporated DNA (BRED) is a technique to mutate specific bacteriophage genes to determine their importance for host infection and to help identify their functions. We used the host bacteria Mycobacterium smegmatis and mycobacteriophage FudgeTart as a case study for BRED. First, we transformed the host bacteria with pJV53, a plasmid that contains the genes for recombinase proteins which allow for replacement of a gene with a mutated version via homologous recombination. Then, we co-transformed the bacteriophage genomic DNA and a DNA oligo containing the desired mutation into the recombineering M. smegmatis. We plated the transformed bacteria and screened the resulting plaques to check for mutations in the specific bacteriophage gene. The goal of this project is to establish an efficient process to perform BRED experiments at Doane University, using Doane’s extensive collection of bacteriophage. If this experiment is successful, we can continue to use BRED on the bacteriophages in Doane’s collection to better understand how bacteriophage work and whether they can be used efficiently for bacteriophage therapy.
Author(s): Grace Su, Brett Schofield
Presentation Title: HOMODIMERIZATION OF SATB1 AND HETERODIMERIZATION OF SATB1 AND SATB2 PRIOR TO NUCLEAR IMPORT
Faculty Sponsor: Brett Schofield
Field of Study: Biology
Session Type: Oral
Abstract: Satb1 and Satb2 are closely related proteins that regulate gene expression through chromatin reorganization. The relative concentrations of Satb1 and Satb2 have been implicated in the regulation of embryonic stem cell differentiation through regulating the expression of Nanog. Satb1 is thought to form homodimers or homo-oligomers through interactions with its N-terminal domain, although it is not yet known if this homodimerization is DNA dependent. The high degree of conservation between Satb1 and Satb2 has led to speculation that they can form heterodimers. We hypothesize that Satb1 homodimerizes and Satb1 and Satb2 heterodimerize with each other in the cytoplasm, prior to their entry into the nucleus. However, the degree of similarity between Satb1 and Satb2 make it challenging to employ traditional biochemical approaches such as co-immunoprecipitation. Here, we propose a set of experiments using fluorescence microscopy to determine if there is interaction between Satb1 and Satb2, and whether this interaction is dependent on the presence of DNA. Pairs of chimeric proteins will be co-expressed in HeLa cells. Each protein will feature a different fluorescent protein, and one of these in each pair will have its Nuclear Localization Sequence (NLS) mutated to a loss of function. This NLS-deficient mutant will only be able to be imported into the nucleus through dimerization with its import-competent partner prior to its import.
Author(s): Madison Sladky
Presentation Title: USING BACTERIOPHAGE RECOMBINEERING OF ELECTROPORATED DNA (BRED) TECHNIQUE TO MARK ESSENTIAL AND NONESSENTIAL GENES FOUND IN A BA
Faculty Sponsor: Erin Doyle
Field of Study: Biology
Session Type: Oral
Abstract: A bacteriophage is a virus that has the ability to infect specific bacteria. With the epidemic of antibiotic-resistant bacteria, understanding how bacteriophages infect bacteria and what genes are specific to that process is crucial for the future medical treatment for bacterial infections. Using the Bacteriophage Recombineering of Electroporated DNA (BRED) technique can help identify key genes found in bacteriophages that can be useful for phage therapy. I have selected a sequenced bacteriophage named Jabith that infects the host bacteria Mycobacterium smegmatis. The phage Jabith is lysogenic, meaning it incorporates its DNA into the host bacteria’s genome for replication. Changing infection behavior by engineering Jabith’s genome using BRED by deleting a gene could make the phage infect in a lytic life cycle. I hypothesize that if we deleted an essential gene then the bacteria infected would not produce plaques. The phage DNA was isolated and used for transformation into a recombineering M. smegmatis to control for transformation efficiency. Currently, we are identifying important genes for lysogenic growth in Jabith’s genome. We will use this gene sequence to guide the construction of oligos. The next steps after constructing an oligo is to use BRED to knock out a gene. This will illustrate what genes are vital for its lysogenic growth to understand what genes are specific to for infecting and killing M. smegmatis. By finding what genes cause a change from lysogenic to lytic lifestyle in Jabith using BRED, can help with the availability of phage therapy treatment.
Author(s): Kade Wehrs
Presentation Title: SATB1 DIMERIZATION DOMAIN
Faculty Sponsor: Brett Schofield
Field of Study: Biology
Session Type: Oral
Abstract: Chromatin reorganization is one of the many factors that influence gene regulation, and Satb1 is one of the few proteins that has been implicated in this process. This conformational change is used to switch cell behavior in a number of important ways, including being a factor in determining whether embryonic stem cells differentiate. Satb1’s mode of activity is uncertain, but it contains three DNA-binding domains that bind to AT-rich sequences. Many DNA-binding proteins dimerize in order to recognize longer stretches of DNA, but there is conflicting evidence whether this is true for Satb1. Here we show that a fluorescently-tagged Satb1 is able to drag a nuclear-import deficient mutant of Satb1 into the nucleus. This demonstrates that Satb1 forms homodimers in a DNA-independent manner and that they are stable enough to persist through nuclear import. Truncations of Satb1 are currently being tested to identify which region of Satb1 is responsible for homodimerization.
Author(s): Trevin Alberts
Presentation Title: YEAST ASSAY OF POTENTIAL INSULATOR PROTEINS
Faculty Sponsor: Brett Schofield
Field of Study: Biology
Session Type: Oral
Abstract: Insulator proteins serve as boundary markers that stop the spread of gene-repressing heterochromatin. The only mammalian protein that has been identified as having insulator properties is CTCF, however, it is likely that other proteins have undiscovered insulator activity. Here we test whether an insulator assay in Saccharomyces cerevisiae could be used to discover novel mammalian insulator proteins. This assay directs chimeric candidate proteins to a binding site between a telomere and a sub-telomeric gene that is usually silenced by the position effect. Insulator proteins will halt the spread of heterochromatin, thereby allowing this gene to activate. Several human candidate proteins have been tested, including Satb1, Satb2, MeCP2, and HDAC1. These candidate proteins have all been implicated in chromatin reorganization at some level. None of the tested proteins have demonstrated insulator activity in the assay. However, this method may act as a template for testing new candidate proteins in the future.
Author(s): Josie Hughes, Ramesh Laungani, Tanner Sand, Ayden Benavides, Sadie Finnegan, Tessa Durham-Brooks
Presentation Title: EFFECTS OF BIOCHAR ON ZEA MAYS AND MICRONUTRIENT CONCENTRATION
Faculty Sponsor: Ramesh Laungani
Field of Study: Biology
Session Type: Poster
Abstract: Since 1970, CO2 emissions have increased by about 90% (US EPA, 2016). With rising levels of atmospheric CO2, protein concentrations in plants have been negatively altered (Taub, 2010) and could potentially begin to affect human health. Biochar could be one solution to sequestering atmospheric CO2, as it has the ability to store carbon and the potential to retain water and nutrients. Thus, its effects on various plants has been widely studied as well as its effects on certain micronutrients. Micronutrient studies are increasingly important as micronutrient deficiencies have been linked to increasing the risk for development of chronic diseases (Woodside et al., 2005). However, there is a lack of information relating biochar’s effects on Zea mays productivity and micronutrient concentrations. In this we examined the impact of biochar on variation in micronutrient concentrations in Zea mays.
Author(s): Ayden Benavides, Ramesh Laungani, Tanner Sand, Josie Hughes
Presentation Title: IMPACT OF BIOCHAR WITHIN SOIL UNDER DIFFERENT TREATMENTS OF H20 PRECIPITATION
Faculty Sponsor: Ramesh Laungani
Field of Study: Biology
Session Type: Poster
Abstract: Climate change has caused more harm to ecosystems all over the world and the largest cause is human activity, but there are ways of reversing these detrimental effects. With higher emissions of greenhouse gases leading to an increase in global temperature, it is important to look into what may slow down the amount of carbon being released into our atmosphere. Drought is another result of climate change and will determine how much water availability individual’s will have in their household in later years and could possibly affect crop yield. These two changes are highly influential for farmers and how they will proceed with treatment for their crops. Biochar, additions to soil, is one proposed solution to climate change. Biochar is a charcoal like substance produced from plant matter, which has been deoxygenated and burned within a furnace. Biochar is used in soil, most commonly for farming and gardening to boost soil fertility and stimulate plant growth. The main purpose of adding biochar in soil is to reduce the amount of carbon compounds released from soil that’s generated by microbes and bacteria which reside in soil. However it is vital to understand how drought and biochar additions to soil impact the release of carbon from soil by microbes. The experiment consisted of an incubation experiment examining the relationship between precipitation and carbon release. By limiting the amount of carbon released into the atmosphere we could slow the rising temperatures across the globe but still maintain healthy carbon concentrations within the soil.
Author(s): Jaime Troester, Dane Bowder
Presentation Title: RELATIONSHIP BETWEEN BEEF CONSUMPTION AND S. EPIDERMIDIS ANTIBIOTIC RESISTANCE
Faculty Sponsor: Dane Bowder
Field of Study: Biology
Session Type: Poster
Abstract: Antibiotic resistance is an issue that is becoming increasingly problematic in our world today. Bacterial species such as S. aureus and other species are becoming increasingly resistant to antibiotics, which will be a significant problem in the future, as alternative treatments to antibiotics may need to be developed and implemented. Additionally, of the total number of antibiotics administered, eighty percent of them are administered to livestock, especially tetracycline, in the case of conventionally raised cattle. This research aims to draw parallels between S. aureus and its less pathogenic relative, Staphylococcus epidermidis, a common bacteria found on the human skin. In this senior research project, we aimed to determine whether a correlation exists between the frequency of one’s beef consumption and S. epidermidis antibiotic resistance to tetracycline, among other commonly prescribed antibiotics. This will be achieved through sampling Doane University staff and students’ skin bacteria (S. epidermidis) and testing each sample’s resistance to multiple antibiotics. Based on previous research studies, we expect a higher frequency of beef consumption to correlate to increased S. epidermidis antibiotic resistance to tetracycline. We need to find alternatives to antibiotics, pertaining to their role in livestock production, for cattle in particular. The results we collect from this research will be used to determine if a correlation between S. epidermidis antibiotic resistance and frequency of beef consumption does, indeed, exist in the Doane community.
Author(s): Tanner Sand, Dr. Ramesh Laungani, Ayden Benavides, and Josie Hughes
Presentation Title: EFFECTS OF NITROGEN ON THE EFFICACY OF BIOCHAR TO SEQUESTER CO2
Faculty Sponsor: Dr. Ramesh Laungani
Field of Study: Biology
Session Type: Poster
Abstract: Unprecedented temperatures, natural disasters and greenhouse gas levels have pushed climate change to an existential issue in the world today. With constantly rising CO2 emissions, innovations are actively searched for in order to sequester excess carbon. One potential solution, biochar, is organic carbon that is pyrolyzed to produce a highly porous, stable form of carbon that is proposed to sequester carbon in the soil resulting in a net loss of carbon to the atmosphere. However, inconsistent results have drawn attention to the efficacy of biochar to mitigate CO2 flux from soil respiration. Another real world problem, nitrogen deposition, is exacerbated through synthetic fertilizer use and can result in an increase in other greenhouse gases, such as nitrous oxides and ozone. The effects of nitrogen on the efficacy of biochar to store carbon are inconclusive. Our objective in this study is to analyze the interactions between biochar and nitrogen, and measure the impact on soil CO2 flux.
Author(s): Catie Welty
Presentation Title: IDENTIFICATION OF OVERREPRESENTED TRANSCRIPTION FACTOR BINDING SITES IN ROOT-ASSOCIATED GENE PROMOTERS
Faculty Sponsor: Dr. Erin Doyle
Field of Study: Biology
Session Type: Poster
Abstract: Roots are an understudied part of the plant because of how difficult they are to gather data from. However, roots are a central part of the plant’s functions. Root associated genes are genes that are primarily used in the roots of the plants. The sequence of the promoter specifies and recruits transcription factors that regulate the expression of genes. The functional components of the promoter, called motifs, are the short, specific areas of the DNA sequence that specify protein binding. I am interested in understanding how root associated genes are activated more in the roots than in other parts of the plant. I researched which motifs are overrepresented in promoters found in Zea mays root associated genes. I conducted my research using 593 unique promoter sequences from the Root Gene and Promoter Database (RGPDB) and 572 unique plant transcription factor binding site motifs from the JASPAR 2020 motif database. I located positions in each promoter sequence where the motif is found using R code. I then counted the frequency of each motif in each promoter using Python code. The largest percentage of these genes were located in chromosomes 9 and 10. Secondly, I examined the predicted locations to identify promoters with a high number of motifs and motifs that are common. Currently, I am conducting motif enrichment analysis using the Clover software to find a subset of motifs that are overrepresented in the promoter sequences. These overrepresented motifs could be an important part of the promoter or a non-specific motif.
Author(s): Dani Schreiber
Presentation Title: VARIED CHANGES IN WATER LEVEL SIGNIFICANTLY AFFECT TRIOP LONGICAUDATUS EGG-LAYING BEHAVIOR
Faculty Sponsor: Brad Elder
Field of Study: Biology
Session Type: Poster
Abstract: Triop longicaudatus, also known as tadpole shrimp, are crustaceans that can be found across the globe in Asia, Africa, Australia, South America, and some parts of North America. (Week, 1990). These crustaceans have been dated back to over 300 million years ago through fossil records and have various uses for human health and entertainment as pets. Though how has such a small crustacean been able to survive over many changes in these environments? When the triops reach reproductive maturity around seven to nine days after hatching, they asexually produce fertilized eggs. The eggs then go through a specific dormant period, diapause, when dried out by environmental changes in water levels (Takahashi, 1977). To see if water level affects how many tadpole shrimp lay eggs during a seven-day period when the shrimp is at reproductive maturity, three different tanks were used to represent the change in water levels. Low water level tank, 1 cm, and high water level tank, 4 cm, had no significant difference in egg-laying behavior. Though when changing the water level every day in the ranges from 1 to 4 cm in the varied water level tank, there was a significant increase in the egg-laying behavior with a p-value of < 0.001. and an average of 5.7 shrimp laying eggs per day. Depending on the external environment that the triop shrimp are breeding in, this can be an indicator of why these crustaceans have been around so long and how they can adapt to external conditions to increase egg production.
Author(s): Haley Miller, Lilly Adams, Jared Bithell, and Erin Doyle
Presentation Title: IDENTIFYING PREDICTED TAL EFFECTOR BINDING SITES
Faculty Sponsor: Erin Doyle
Field of Study: Biology
Session Type: Poster
Abstract: Rice plants are crucial to agriculture and feeding the world population. An increasing issue with rice plants is that they are infected by Xanthomonas oryzae (Xoo) bacteria which leads to high rates of crop loss. Xoo uses transcription activator-like effector proteins (TALEs) to infect the plant. TALEs bind to effector binding elements (EBEs) in the genome of the plant in order to activate susceptibility genes. Although the target susceptibility genes of some TALEs have been identified, less is known about the EBEs and targets of “minor effect TALEs”, which cause small increases in susceptibility. To learn more about these TALEs and their target EBEs, TAL effector binding sites were identified in rice plants within known QTLs for disease susceptibility and resistance. Predicted EBEs and target genes were filtered based on proximity to gene start sites In the end, multiple lists were produced containing the potential TALE EBEs and target genes for XX TAL effectors. Predicted gene targets will be further characterized based on RNA seq data, gene functions, and information about variation.
Author(s): Tate Nech, Erin Doyle
Presentation Title: C. ACNES BACTERIOPHAGES ISOLATED FROM A PORE STRIP IS USEFUL FOR INFECTING AND LYSING C. ACNES BACTERIA
Faculty Sponsor: Erin Doyle
Field of Study: Biology
Session Type: Poster
Abstract: Acne vulgaris is a skin condition that affects 3 out of 4 people between the ages of 12 and 24. Cutibacterium acnes is an anaerobic bacteria that resides in clogged pores on the skin and causes acne vulgaris. The majority of antibiotic treatments used against acne-causing bacteria have lost their efficacy. Bacteriophages are viruses that infect and kill specific host bacteria. C. acnes bacteriophages can potentially be used as an alternative treatment option for antibiotic-resistant C. acnes infections. Microcomedones are formed when the sebaceous duct and pore openings on the skin become clogged with dirt or other particles and may contain acne-causing bacteria and phages that infect them. This study is an attempt to isolate C. acnes bacteriophage(s) from pore strips and use those bacteriophages singularly or in a combination to infect and lyse C. acnes bacteria. To investigate this, study participants will use pore strips to collect microcomedones from their faces. The participants in this study are from individuals who work at or attend Doane University. We will isolate C. acnes bacteriophages from the pore strips samples. Afterwards, the phage will be enriched and plated with C. acnes bacteria for amplification and characterization. Once the plaques have formed, they will be examined and categorized based on plaque morphology. Unique plaques will be used to grow lysates for storage and further study. This study should provide the groundwork for future research to be conducted to find a possible alternative treatment utilizing bacteriophage for acne vulgaris.
Author(s): Hannah Dunse
Presentation Title: THE EFFECTS OF SAMHD1 OVER EXPRESSION ON SRLV INFECTION RATE IN SHEEP CELLS
Faculty Sponsor: Dane Bowder
Field of Study: Biology
Session Type: Poster
Abstract: SRLV is a virus genetically similar to HIV-1 that infects sheep and goats. This virus easily spreads within a herd and can be very damaging to countries that rely on these animals for daily life. In order to reduce loss to farmers, research has begun to look at restrict factors’ roles in stopping the spread of viruses. Restriction factors are proteins that work to disrupt the viral replication cycle. SAMHD1 is a restriction factor that prevents translation and transcription from occurring by limiting dNTP pools within the cell. It is a known restriction factor for similar viruses. Over expression of SAMHD1 will decrease the rate of SRLV infection in sheep cells, because SAMHD1 is a known powerful restriction factor of genetically similar viruses. SAMHD1 will be isolated and inserted into a plasmid. Sheep cells will then be transfected with the SAMHD1 plasmid and infected with SRLV. Cells that contain the SAMHD1 plasmid should have a decreased infection rate compared to cells that did not receive the plasmid.
Author(s): Jason Iltz, Tyler Cunningham, Dane Bowder
Presentation Title: INVESTIGATION OF APOBEC3C AS A RESTRICTION FACTOR FOR THE KOI HERPESVIRUS (KHV)
Faculty Sponsor: Dane Bowder
Field of Study: Biology
Session Type: Poster
Abstract: Koi herpesvirus (KHV) is a highly contagious virus, from the herpesviridae family, that causes significant mortality in the cyprinid family of fish, which includes koi fish, common carp,. KHV is not curable, and the only treatment that has been shown to slightly improve mortality rates is increasing the temperature of the water. APOBEC3C is a gene that encodes for the APOBEC-3C viral restriction factor. APOBEC3C is a cytidine deaminase that adds lethal mutations to viral genomes, rendering progeny virions unable to infect. KHV shows significant mortality rates in infected populations, largely because clinical signs of this virus show only 24-48 hours before the fish begin to die. KHV has caused significant economic losses in the commercial fishing industry as well as the ornamental fish industry due to its mortality rates and highly contagious nature. The goal of this study is to determine if APOBEC3C is a viable restriction factor of KHV. To achieve this goal we will generate an expression plasmid containing APOBEC3C and EGFP, transfecting the plasmid into koi fin cells, then infecting the transfected cells, and measuring viral yield to determine the effects of APOBEC3C.
Author(s): Makayla Rice, Tessa Durham Brooks, Marissa Foster
Presentation Title: DEVELOPING A FASTER METHOD FOR MEASURING CHEMOTAXIS USING IMAGE ANALYSIS
Faculty Sponsor: Tessa Durham Brooks
Field of Study: Biology
Session Type: Poster
Abstract: Chemotaxis is the movement of a motile organism towards a certain substance due to a chemical gradient. It’s necessary for the development of beneficial and pathogenic microbes. Unfortunately, previous methods are too time intensive and utilize low-throughput processes, making larger screening studies difficult. This study aimed to create a new, faster method of analyzing chemotaxis towards amino acids. A method was developed in which agarose plugs containing chemoattractant were placed in the center of a well in a six-well plate containing a small volume of stained bacteria. Images were taken over time and the intensity of the stain around the plug, also visualized as the ‘cloudiness’ around the plug was measured. An increase in cloudiness is being interpreted as positive chemotaxis. In order to validate this measurement, each component of the system was examined individually and in combination with the other components in a series of negative controls to determine if any configuration of the components could contribute to an increase in cloudiness around the plug could not be attributable to chemotaxis. The potentially confounding variables that were tested include: serine, glutamate, and blank plugs in the presence of serine, safranin dye, sodium chloride, ninhydrin, M. luteus, NO chloramphenicol, and combinations of those previously listed. The results of this experiment will inform future method improvements, enabling the measurement of chemotaxis at a faster rate.
Author(s): Sadie Finnegan
Presentation Title: IMPACTS OF HEMP-CONDITIONED SOIL ON CORN GROWTH AND NUTRITION
Faculty Sponsor: Tessa Durham Brooks
Field of Study: Biology
Session Type: Poster
Abstract: Hemp is a recently legalized crop grown for its fiber, seed, and chemical extracts, but also contributes to carbon deposition in the soil. There are many benefits that come with growing hemp as a crop, such as preventing soil erosion, detoxifying the soil, suppressing weeds and reducing herbicide use, and a useful source for converting CO2 to biomass. In Nebraska, corn is rotated with soybeans to enhance soil health, help reduce soil erosion, improve the physical and chemical properties of the soil, and improve crop yield. This study was conducted to determine potential beneficial effects of hemp as a rotational crop in Nebraska. Seeds of B73, a sequenced inbred line of maize, were sterilized and germinated. Soil was taken from a field that was conditioned by hemp growth. Unconditioned soil from the same area was collected as a control. B73 seeds were planted in pots containing hemp-conditioned soil or control soil. Pots of soil from each condition without B73 were also prepared. Pots were placed in a greenhouse under natural light conditions. Corn height and internodal length were measured weekly. The number of weeds in each pot were counted. Dry weight was taken at the end of the experiment. Elemental analysis was conducted of the soil and bulk tissue. Results from this study will show the potential of hemp as a rotational crop to increase the yield of corn, to reduce herbicide usage, and to store more carbon into the soil.
Author(s): Caden Ross
Presentation Title: IDENTIFYING MAMMALIAN INSULATOR PROTEINS IN A YEAST ASSAY
Faculty Sponsor: Brett Schofield
Field of Study: Biology
Session Type: Poster
Abstract: Tightly compacted regions of DNA called heterochromatin consist largely of repeated DNA sequences and silenced genes. It is caused by specific histone modifications such as H3K9me3 which have the propensity to spread to adjacent regions of DNA. This causes genes to become silenced by the position effect when they are moved close to a region of heterochromatin. Insulator elements and proteins serve to limit the spread of these repressive chemical markers. While the identity of insulator proteins in simple eukaryotic cells are well understood, only one mammalian protein - CTCF - has been shown to possess insulator activity. Here we test the feasibility of using a yeast-based assay to screen candidate mammalian proteins for insulator activity. The assay directs chimeric proteins to a region between a telomere and a sub-telomeric gene that is usually silenced by the position effect. Candidate proteins with insulator activity will shelter the downstream gene from the heterochromatin, causing it to activate. However, it is unclear whether mammalian proteins will retain insulator properties in a yeast cell. We have tested four orthologs of CTCF using this assay, none of which show insulator activity. These results suggest that this yeast assay may not be an efficient way to screen mammalian proteins for insulator activity.
Author(s): Andrew Theiler
Presentation Title: ANALYSIS OF THE CONVERSION OF DEOXYMYOGLOBIN TO CARBOXYMYOGLOBIN VIA THE CO RELEASE FROM A CARBON MONOXIDE RELEASING MOLECULE
Faculty Sponsor: Chris Huber
Field of Study: Biology
Session type: Poster
Abstract: Carbon monoxide is a colorless, odorless, nonirritant gas that can cause detrimental health effects in humans with prolonged acute exposure. This research aims to discover a way to detect these trace amounts of carbon monoxide in blood to be able to warn individuals of the side effects to such exposure such as neurological and cardiorespiratory problems. There is currently no technology available to detect these small doses of carbon monoxide in blood in a timely and inexpensive manner. Before any such technology can be developed, this research first aims to draw a connection between the release of carbon monoxide from a carbon monoxide releasing molecule (CORM) and carbon monoxide’s attachment to myoglobin, which can be found in human blood. Prior to any CO exposure, the myoglobin was deoxygenated via the addition of sodium dithionite. Carbon monoxide was then released by the CORM solution, Mn2(CO)10 , through the excitation from a cold light source. Once released from the CORM solution, CO could then attach itself to the deoxymyoglobin. The myoglobin’s molecular composition was analyzed through UV/Vis Spectroscopy to determine if CO had indeed bound itself to the hemoglobin’s iron center. Through this process, the deoxygenation of myoglobin has been achieved. However, further investigation needs to be conducted to investigate whether attachment of CO to myoglobin has occurred.
Chemistry
Author(s): Matthew Jamison
Presentation Title: GOLD MICROTOXIN SENSOR
Faculty Sponsor: Dr. Huber
Field of Study: Chemistry
Session Type: Oral
Abstract: Carbon monoxide concentration is difficult to precisely measure in small concentrations, potentially resulting in late detection of relatively exposure in individuals. One potential method for precisely detecting low concentrations of carbon monoxide in blood is to utilize Raman Spectroscopy. Some molecules, such as heme, will undergo increased Raman enhancement when bound to a metal substructure. Heme undergoes this phenomenon when bound to a gold nanoparticle resulting in a potential platform to accurately and precisely measure low concentrations of carbon monoxide. A platform is developed utilizing Heme capped gold nanoparticles which is tested through exposure to cyanide inorder to develop a method for further studies with carbon monoxide.
Author(s): Alexis Burke, Professor Chris Huber
Presentation Title: USING RAMAN SPECTROSCOPY TO VIEW CYANIDE BONDED TO HEME ON GOLD NANOPARTICLE PLATFORMS
Faculty Sponsor: Professor Chris Huber
Field of Study: Chemistry
Session Type: Poster
Abstract: Heme is the iron complex in the blood, a specific part of hemoglobin that bonds to both oxygen and carbon dioxide and is crucial to the respiratory system’s function. Using Raman spectroscopy, a type of spectroscopy utilizing vibrations to record and visualize bonds within molecules, the iron of heme bonding with oxygen and cyanide can be examined. While heme, by itself, has a too weak Raman signature, so we would be recording reliable data, it can be mixed with gold nanoparticles (AuNPs), acting as an amplifier that enables the Raman spectra to pick it up; this technique is called surface-enhancing Raman spectroscopy (SERS). A home-built Raman spectrometer was used to collect the SERS spectra at an excitation of 785 nm. The SERS spectra demonstrates the successful binding of AuNPs to the heme compound. We are beginning to collect data on different cyanide solutions in an aqueous solution. Cyanide bonds very quickly with the heme, so using a deoxygenating agent can break the iron’s bond with the oxygen and bond the iron with cyanide. By recording and storing data on both the oxygen sample and the cyanide sample, we will collect data on carbon monoxide bonding to heme using our SERS technique. Additionally, we will be working with bigger molecules that contain heme, such as myoglobin and hemoglobin.
Engineering
Author(s): Paul Sandoz, Richard Dover, Sam Vanderslice
Presentation Title: TUBE BENDING DIE DEVELOPMENT USING FINITE ELEMENT ANALYSIS AND 3-D PRINTING
Faculty Sponsor: Joel TerMaat
Field of Study: Engineering
Session Type: Poster
Abstract: Dies are created from alloy steel or aluminum depending on the type of pipe or tube that is being bent. The use of 3D print material like kevlar, plastics, or polymers is not extensively researched for the use in tooling for mass part production. The development and testing of different mounts, geometries, and materials that incorporate 3D printing into Tube Bending Dies would greatly benefit companies by giving them the ability to create abnormal pipe bends. This project brushes the surface of the abilities of a basic Stratasys 3D printer to create tooling capable of bending ¾ inch tubes on a manual tube bender. The bender die designs were tested using different prototype models and a final model was idealized, but not built once the testing was done. The manual tube bender and SolidWorks FEA analysis was used to identify the weakest areas of the design. The final design was not completed, but the hypothesis of different materials and more precise 3D printing capabilities make the development of Tube Bending Dies possible.
Author(s): Hayden Fry, Orlando Quiroz, Tyler Sherrill, Levi Houlton, Kolin Whisler
Presentation Title: DEVELOPMENT OF OMAHA CHILDREN’S MUSEUM ANIMATRONICS CONTROL BOX UTILIZING A RASPBERRY PI
Faculty Sponsor: Cale Stolle
Field of Study: Engineering
Session Type: Poster
Abstract: The animatronics control box for the Omaha Children’s Museum (OCM) will be replacing their current obsolete system. The control box will offer more and versatile controls for the 4-6 motors in any given animatronic OCM utilizes. Two programs have been created for the project, one that runs the motor and the other gives the user an interface to program the timing for the motors. These animatronics are being used for plays and OCM wanted them to behave more realistically to give children the best experience possible.
Author(s): Tyler Sheldon, Brandon Crom
Presentation Title: LOCATING BLOOD CLOTS THROUGH THE INTEGUMENTARY SYSTEM USING AN INFRARED-BASED OPTICAL SCANNER
Faculty Sponsor: Chris Wentworth
Field of Study: Engineering
Session Type: Poster
Abstract: Blood clots are very dangerous, and are not easily found. The modern way to locate one of these clots is by using ultrasound or magnetic resonance imaging (MRI). Near infrared waves can be used to see through the skin layers and help locate these clots easier. A camera is used to record the refraction of light off of an object, and is then run through an image processor on a Raspberry Pi. This project will be able to show the optics of the behavior of light on the veins as well as the density in that area of the vein. It would be able to distinguish the darker area of the clot from the rest of the flowing blood in a vein. Producing a faster and more portable way of detecting blood clots.
Author(s): Kaitlyn Andreessen, Noah Symonsbergen, Anthony Laravie
Presentation Title: CONCRETE CANOE
Faculty Sponsor: Emmeline Watson
Field of Study: Engineering
Session Type: Poster
Abstract: The National Concrete Canoe Competition has been and remains a staple in the University level engineering scene. Every year hundreds of schools apply for the chance to compete. This year will mark Doane University’s first nationally recognized project. This project will be completed in three main phases. The first phase is dedicated to ideation and designing. A general shape for the canoe will be designed with CAD and simulations will be run on it. The concrete formulation will also take place during the first phase. Then miniature canoes will be constructed to test. The phase will end with ordering supplies to create the final product. The second phase will start with refining the design and then constructing the prototype. Once the Alpha prototype has been cured, it will be tested to ensure that the canoe meets all the design requirements outlined in this proposal. After testing, either a Beta prototype will be created to improve the design or duplicates of the Alpha prototype.
Environmental Science
Author(s): Bailey Gasseling, Christine Rost
Presentation Title: AN EXPLORATORY STUDY EXAMINING NEBRASKA'S INNOVATORS OF HEMP CULTIVATION
Faculty Sponsor: Blake Colclasure
Field of Study: Environmental Science
Session Type: Poster
Abstract: Agriculture is an industry that contributes to a safe and affordable food supply for an interconnected global population. Row crops, such as corn and soybean rotations, have raised environmental concerns. Soil degradation, soil loss, water depletion, and excessive pesticide use have been documented. Threats from a changing climate and a low commodity market encourage research on crop alternatives. The 2018 Farm Bill removed hemp as a controlled substance, making the crop federally legal in the U.S. Hemp can be incorporated into crop rotations, increasing crop diversity, and improving soil quality. Hemp’s root system reduces soil erosion, removes soil toxins, and adds organic matter. Hemp is fairly resilient to pests and drought and has the capacity to serve as a carbon sink. The products of hemp range from cannabinoids and consumable grain to eco-friendly, fiber-based items. Despite the potential for hemp to become a sustainable crop, barriers may exist to its wide-spread adoption. In this qualitative research, we examined first-year hemp farmers in Nebraska and documented their perceived challenges and success. Diffusion of Innovations Theory guided the development of a semi-structured interview script. Fourteen hemp farmers were interviewed. Each interview lasted between 30 and 45 minutes. Interviews were transcribed and coded, and themes emerged pertaining to the five stages of the adoption process: 1) knowledge, 2) persuasion, 3) decision, 4) implementation, and 5) confirmation. Findings indicate a lack of infrastructure, agronomic knowledge, and grower support. Government regulations, unexpected growing challenges, and negative public stigma may further impede wide-spread adoption.
Author(s): Nicholas Aus
Presentation Title: SODIUM CHLORIDE POLLUTION AND ITS EFFECTS ON TRIOPS
Faculty Sponsor: Russ Souchek
Field of Study: Environmental Science
Session Type: Poster
Abstract: Salt pollution is a non point source pollution that is from De-icing agents used during the winter months to prevent ice on roads. This brine is used in most states that have colder winters. Once the snow and ice melt this salty water can enter many different water sources. On animal that can be effect by this salt water runoff is Triops, which usally reside in temporal ponds. I studied the effects this salt pollution had on triops.
Author(s): Trystan Brandt
Presentation Title: AGONISTIC RESPONSE OF CRAYFISH TO AGRICULTURAL CHEMICAL RUNOFF
Faculty Sponsor: Russ Souchek
Field of Study: Environmental Science
Session Type: Poster
Abstract: Chemical runoff into waterways is a very common occurrence across the globe. This research looks at how some of this chemical runoff particularly from agricultural fields affects the agonistic behavior between Procambarus clarkii (Crayfish). The crayfish used in this study were placed in a tub of water and observed before and after being subjected to real recorded levels of Atrazine and 2,4-D. The trials included 4 separate chemical groups. There was a control group, an Atrazine group, a 2,4-D group, and a group that had both Atrazine and 2,4-D. By looking at and comparing the interactions between the same pairs of crayfish both before and after the chemical treatment it can be determined what kind of effect chemical runoff can have on the agonistic behavior of crayfish. The trials have so far shown no indication that chemical runoff has a significant effect on the agonistic behavior of crayfish.
Author(s): Rebecca Hervert
Presentation Title: GENOMIC DATA CONFIRMS BACTERIOPHAGE KRPA IS A LYSOGENIC A3 BACTERIOPHAGE.
Faculty Sponsor: Erin Doyle
Field of Study: Environmental Science
Session Type: Poster
Abstract: A bacteriophage is a virus that infects a host bacteria cell and replicates. There are two forms of infection, and these include lysogenic and lytic. Mycobacteriophage KRPa appears to be a lysogenic phage when plated with host bacteria Mycobacterium smegmatis. We were interested in if KRPa has the specific genes which indicate it has a lysogenic life cycle. KRPa’s genome was assembled using Newbler, assessed for quality in Consed, and auto-annotated and BLASTed using DNAMaster to determine location and function of genes. A BLAST of the genome determined the known closest relatives of KRPa and assigned a cluster and subcluster. The morphology and genomic structure are similar to known A3 bacteriophages. The presence of an integrase categorizes KRPa as a lysogenic bacteriophage. Further analysis of the genome found defined ends, the presence of structural genes in the left arm, and a 3’ sticky overhang; which is an overhang of the leading strand, where it would connect with other portions of a continued sequence. These features are possessed by bacteriophages of an A cluster, specifically an A3 subcluster. The lysogenic A3 and lytic bacteriophages vary significantly in genome length, structure, and morphology, which was determined by comparing the genome of KRPa to known lytic bacteriophages. Now that we have determined that KRPa is a lysogenic bacteriophage and assigned it to a cluster, it can be used as a model for future bacteriophage research.
Author(s): Christine Rost
Presentation Title: FACTORS INFLUENCING NEBRASKA 3-5TH GRADE TEACHERS' USE OF OUTDOOR LEARNING ENVIRONMENTS
Faculty Sponsor: Dr. Blake Colclasure
Field of Study: Environmental Science
Session Type: Poster
Abstract: A growing body of literature suggests that there is an increasing disconnect between children and the outdoors. This phenomenon, coined “nature deficit disorder”, has had negative impacts on the development of children, including declines in mental, physical, and spiritual health. One strategy to increase all children’s exposure to the outdoors is through the formal school system. The use of outdoor learning environments in educational settings has not only been linked to improvements in children's health, but also has educational advantages, such as increasing students’ cognitive development, attention, and creativity. Despite clear advantages for the use of outdoor learning environments, they are often not highly used. This research investigated factors that influenced 3-5th grade teachers’ use of outdoor learning environments during normal teaching responsibilities. The Theory of Planned Behavior guided the development of a survey instrument used to assess teachers’ attitude, perceived subjective norm, and perceived behavior control of using outdoor learning environments. Additionally, teachers’ environmental attitude and personal demographic variables were added to a linear regression model that was used to predict significant variables influencing teachers’ use of outdoor learning environments. Lastly, teachers ranked barriers to using these environments. Based on the results of this research, we provide specific strategies to increase teachers’ use of outdoor learning environments, and therefore exposing more children to the outdoors and yielding the many advantages of outdoor learning environments.
Honors
Author(s): Olivia DeFord, Ryleigh Gebers, Matthew Jamison, Jordan Klein, Madison Lambley, Breanna Patterson, Tanner Sand, Lexis Stuchlik
Presentation Title: SOCIETAL REACTIONS TO SHARED TRAUMATIC EVENTS: FOUR CASE STUDIES
Faculty Sponsor: Timothy Hill
Field of Study: Honors
Session Type: Oral
Abstract: The coronavirus pandemic has killed over 500,000 Americans, placing questions about the reaction to society-spanning traumatic events at top of mind. Through an examination of four cases studies--the 1906 San Francisco Earthquake, the Great Depression, the AIDS epidemic of the 1980s, and 9/11--we search for commonalities that may help us understand how our current society will react to our present, tragic circumstances.
Information Science & Technology
Author(s): Noah Shoemaker
Presentation Title: AN APP FOR A VIRTUAL NEIGHBORHOOD TOUR
Faculty Sponsor: Alec Engebretson
Field of Study: Information Science & Technology
Session Type: Oral
Abstract: The Near South Neighborhood Association in Lincoln puts on an annual tour of their historic homes. This year, because of COVID-19, people are not allowed inside the homes due to health concerns. As a result, the neighborhood association asked for a mobile application that could help supplement the cut-back tour. This app contains data on the homes, with their description and their location. This info is used to create an archive of the homes, as well as an interactive map of the locations. The app also contains a QR code scanner, which can be used to scan QR codes on signs around the neighborhood, letting the visitors learn more about that particular feature. My presentation will highlight the requirements of the application, the design of the application to meet those requirements, and the steps taken to implement the design. A demonstration of the application and the tools used to create it will also be provided.
Author(s): Ivan Ortega-Nguyen, Devan Standley
Presentation Title: ROMHACK POKEMON PROJECT
Faculty Sponsor: Alec Engebretson/Mark Meysenburg
Field of Study: Information Science & Technology
Session Type: Oral
Abstract: The objective of our project was to reuse some of the existing assets of Pokémon Fire Red originally created in 1998 but due to it having limited memory capacity we used the remastered version of the game created in 2004 with a memory capacity that is six times the amount of the original copy. Using a GUI modifier known as Advanced Map we were able to create as well as edit the pathing, logic, and sprites in order to make a scaled version of Doane as well as some of the key historical features of Doane with natural elements. To run the game we used an emulator known as Visual Boy Advance which allows us to see what the game would be like to play as the user and to find bugs that the user may come across. The final bit of software that was required for the build of our project was a script editor which was used to make influences on the GUI and interactions for the user in game. The editor we used is called Pksvuii which is an assembly-like language that requires allocation of memory using hexadecimals with portions of language resembling C++ in order to be more developer friendly. The end product is a software program that enables us to create a custom demo with unique storytelling and AI. The purpose of our senior project is to showcase our finds and ultimately a version of campus with a custom Pokémon campaign.
Author(s): Cameron Swanson
Presentation Title: DOANE HELP DESK DUSC APP
Faculty Sponsor: Alec Engebretson
Field of Study: Information Science & Technology
Session Type: Oral
Abstract: For my senior show, I collaborated with Tiger Tech, the help desk at Doane University, to create a mobile application to gamify the work of their support personnel. Currently, Tiger Tech has a website to track points for completing support tasks which incentives the student workers to do more. I talked with the administrators of Tiger Tech about the need to make a mobile application similar to the website. My project involved the analysis, design and implementation of a mobile application to make it easier for the students and administrators to view and change points using a native application on a mobile device. This project required learning and applying technologies throughout the full stack of the application. In particular, the front-end involved the application of React Native to create a native mobile app for both the iOS and Android platforms. The back-end involved understanding the preexisting database of WordPress and using an application programming interface (API) that allows the mobile application’s front-end to access the database. My presentation will overview the project requirements, and discuss select technologies and how they were used in the design and implementation of the application. I will also demonstrate the application which currently is a partially functional prototype.
Author(s): Justin Matthews, Ian White, Kira Reisdorph, Monte McNeil
Presentation Title: CROWDFARE - TICKETING WEB APPLICATION
Faculty Sponsor: Alec Engebretson
Field of Study: Information Science & Technology
Session Type: Oral
Abstract: For this project, our main goal is to create a full stack web-application that provides tickets for high school events. This site will allow high schools to post events online and sell tickets virtually to spectators. When people show up they will scan their ticket to get into the event hands-free with a QR code. This project is built with a various assortment of technologies that make up a full-stack web application. Amongst our team of four individuals, we divided the application into four separate parts: UX/UI design, frontend, backend, and server development. Our UX/UI design was created in Axure, frontend is composed using React and Javascript, the backend using Typescript, NextJS, and ExpressJS and lastly, the server infrastructure is hosted on Amazon Web Services. For our presentation we will first discuss the overview of our application along with the design and planning. We will also provide an in depth look at each part of the application and a demo showing all of the parts working together.
Physics
Author(s): Quin Bullerdiek, C.D. Wentworth
Presentation Title: CREATING A COMPUTATIONAL FLUID DYNAMICS PLATFORM FOR STUDYING SHEAR STRESS EFFECTS ON BIOFILM MORPHOLOGY
Faculty Sponsor: C.D. Wentworth
Field of Study: Physics
Session Type: Oral
Abstract: The morphology of a biofilm depends on both biological and physical effects. The mechanical effects of fluid flow across the biofilm is an important physical effect. Performing theoretical studies on the physical effects of fluid flow on a complex biofilm structure requires using a computational fluid dynamics (CDF) method. In this project, we created a functional CFD platform based on the FEniCS Project open-source finite element package and the ParaView open-source scientific visualization application. Our computing platform ran on an Ubuntu Linux Virtual Machine running on a Windows 10-based computer. We obtained some preliminary simulation data for fluid flow in a 2-dimensional channel with one irregular boundary.
Author(s): Ashlyn Ewen, C. D Wentworth
Presentation Title: BIOFILM MORPHOLOGICAL ANALYSIS USING THE GRAY-LEVEL CO-OCCURRENCE MATRIX
Faculty Sponsor: C.D Wentworth
Field of Study: Physics
Session Type: Poster
Abstract: Biofilms can form complex three-dimensional structures depending on physical and biological factors in the environment and the microbial cell genome. Developing methods of describing the morphology is challenging due to the variety of structures that these communities display. This project was concerned with developing morphological measurements made on microscope stack images of biofilms based on the Gray-Level Co-occurrence Matrix (GLCM). The data set consisted of 24-hour growth experiments for the bacteria species Pseudomonas aeruginosa grown at 37 [℃] and different values of shear stress provided by media flowing across the growth surface. Code was developed to calculate the GLCM texture characteristics contrast, dissimilarity, energy, and homogeneity, along with generating a GLCM texture image. We investigated how these textural characteristics changed as the pixel neighborhood included in the GLCM increased, both in single frames and during the 24-hour time interval. We also investigated how these characteristics change with increasing shear stress.
Sociology
Author(s): Jordan Klein
Presentation Title: RELIGIOUS AND SPIRITUAL INFLUENCES ON ATTITUDES OF CAPITAL PUNISHMENT
Faculty Sponsor: Kari Gentzler
Field of Study: Sociology
Session Type: Oral
Abstract: This presentation examines the influence of religion and spirituality on punitive public policy. Using the 2018 GSS, data from 2,348 American respondents were collected from a questionnaire involving information on religious and spiritual attitudes and behaviors. A cross-tabulation analysis was used to analyze any association between support of capital punishment and certain religious and spiritual variables. This study confirms findings of previous research confirming that a strong belief in Hell is associated with a higher support capital punishment, confirming prior research that beliefs of religious evil are associated with general punitive attitudes. Other divergent findings highlight the diverse combinations of religious beliefs among Americans adults, the multidimensional nature of religious research, the high level of religious salience in the U.S., and the need more research on the subject.
Spanish
Author(s): Aztryd Lima
Presentation Title: BELIEFS ABOUT INDIGENOUS LANGUAGES IN RURAL NEBRASKA
Faculty Sponsor: Joshua Pope
Field of Study: Spanish
Session Type: Oral
Abstract: When people come from Latin American regions of either bilingualism or sole use of indigenous languages and they immigrate to a place like Crete, Nebraska, one can wonder what occurs. The goal of this project was to collect empirical data to support or revise the observations that local speakers use an indigenous language as a social tool and how these languages referred to as dialecto ‘dialect'’ instead of lengua ‘language,’ can portray linguistic and/or cultural inferiority towards the indigenous language. Three research questions framed the research a) what are the extralinguistic factors that are associated with the use of indigenous languages in Crete, b)what are the beliefs about indigenous languages that members of Crete’s Hispanic community hold specifically in rural Nebraska, c) what are some factors that, at least partially, explain those beliefs. We conducted five interviews and administered questionnaires to the members of the speakers of a dialect in Crete. The data collected includes responses to hypothetical situations, questions related to personal and parental beliefs, multilingualism, language choice, etc. In addition, personal data about generation of immigration, length of time in the United States, regional and national origin, linguistic experiences, neighborhood residency in Crete ,and social lives was collected. Through the research conducted we were able to gather that there are extralinguistic factors associated with the use of language like how long they lived in their native country and we were able to understand the perspective of five individuals of the Crete community on indigenous languages.