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Molecular Modeling And Dynamics: Development Of A Model For The Glcosphingolipid Gt1b, Dustin Danowski, David Busath Aug 2013

Molecular Modeling And Dynamics: Development Of A Model For The Glcosphingolipid Gt1b, Dustin Danowski, David Busath

Journal of Undergraduate Research

Botulinum Neurotoxin (BoNT) is currently being widely researched a a possible treatment for many medical conditions, as well as for cosmetic purposes. However, the mechanism describing how this family of toxins interact with their receptors to cause endocytosis is not well understood. We have developed a model of the GT1b ganglioside receptor of BoNT that may be used for Molecular Modeling and Dynamics simulations. The development of such a model is necessary to understand the mechanism of BoNT endocytosis, which then helps us determine possible uses and dangers of the toxin as a medical treatment. We had planned to complete …

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Identification Of Insertion Points Of The Macrophage Fas-Induced Apoptosis (Mafia) Transgene, Robert E. Brown Iii, Dr. Sandra Burnett Aug 2013

Identification Of Insertion Points Of The Macrophage Fas-Induced Apoptosis (Mafia) Transgene, Robert E. Brown Iii, Dr. Sandra Burnett

Journal of Undergraduate Research

Without site direction, transgenes integrate randomly into the genome of target cells. The transgene used in macrophage fas-induced apoptosis (Mafia) mice was randomly incorporated and indications of multiple insertion sites were observed. Our goal in performing this study was to detect the exact insertion point of the transgene so as to ultimately develop a genetic test to verify expression of the transgene in Maifa mice. In Figure 1 the premise of our experimental design is explained. Polymerase Chain Reaction (PCR) is a scientific technique that is used to amplify a specific segment of DNA. To determine the insertion points of …

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Assessing The Effects Of Primer Specificity On Eliminating Numt Co-Amplification In Dna Barcoding, Matthew Moulton, Dr. Michael Whiting Aug 2013

Assessing The Effects Of Primer Specificity On Eliminating Numt Co-Amplification In Dna Barcoding, Matthew Moulton, Dr. Michael Whiting

Journal of Undergraduate Research

DNA barcoding is a method of species identification based on sequencing a short mitochondrial DNA fragment of Cytochrome Oxidase I (COI). A database of over 500,000 of these COI fragments, known as “barcodes,” has been established for nearly 38,000 species and is currently being used to help rapidly assign individuals to known species and highlight potential new species. However, the ability for DNA barcoding to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be co-amplified with the mitochondrial ortholog when using universal primers, which can lead to incorrect species identification and an overestimation …

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Orca Report, Tom Beckstead, Dr. Jack W. Sites Jr. Aug 2013

Orca Report, Tom Beckstead, Dr. Jack W. Sites Jr.

Journal of Undergraduate Research

Snakes of the Neotropical subfamily Dipsadinae are poorly known from both ecological and phylogenetic perspectives, despite unique feeding adaptations and bizarre diets. Some of these snakes specialize on snails and slugs (ecologists refer to them as “goo eaters”), and they have a unique dentition and jaw structure that permits them to extract gastropod snails from their shells. Others have enlarged rear fangs, are mildly venomous, and prey on ectothermal vertebrates such as frogs, frog eggs, and lizards (Fig. 1).

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Does Snap-25 Act As A V-Snare?, Nathan La Monica, Dr. Dixon Woodbury Aug 2013

Does Snap-25 Act As A V-Snare?, Nathan La Monica, Dr. Dixon Woodbury

Journal of Undergraduate Research

SNAP-25, a protein that is found abundantly in the brain, is a key player in the process of releasing neurotransmitters. Vesicles, or small spheres of lipid membranes, contain neurotransmitters and have numerous proteins that extend outward from the vesicle. To release the neurotransmitters proteins on the vesicle bind with proteins on the pre-synaptic membrane causing the fusion of the two membranes. SNAP-25 along with Syntaxin (membrane bound protein) and Synaptobrevin (vesicle bound protein) work together to form a complex called the SNARE complex (Bowen, 2004). The current theory on how this complex works is that SNAP-25 has to be bound …

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Detection Of Streptococcus Pyogenes On Applied Biosystems, Cepheid, And Rochereal-Time Pcr Platforms, Eldon Prince, Dr. Richard Robison Aug 2013

Detection Of Streptococcus Pyogenes On Applied Biosystems, Cepheid, And Rochereal-Time Pcr Platforms, Eldon Prince, Dr. Richard Robison

Journal of Undergraduate Research

Develop a real-time PCR assay to uniquely detect S. pyogenes on all three major real-time PCR platforms.

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Function Of Novel Nuclear Variant Bone Morphogenetic Protein (Nbmp2), Alina Schmidt, Dr. Laura C. Bridgewater Aug 2013

Function Of Novel Nuclear Variant Bone Morphogenetic Protein (Nbmp2), Alina Schmidt, Dr. Laura C. Bridgewater

Journal of Undergraduate Research

Bmp2 is an important growth factor that regulates many stages of development including the development of the heart, muscle, and bone. A novel nuclear variant of BMP2 was discovered before my addition to the lab and studies began to determine nBMP2’s function. Of main importance to my project was the creation of nBMP2 chimeric mice.

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Modifying The Apical Ectodermal Ridge In Embryological Development Of Vertebrates, Lauren Clough, Dr. Jeffery R. Barrow Aug 2013

Modifying The Apical Ectodermal Ridge In Embryological Development Of Vertebrates, Lauren Clough, Dr. Jeffery R. Barrow

Journal of Undergraduate Research

Vertebrate embryonic limb development is a complex process that involves many genes and processes. Patterning takes place along three axes, including the proximal-distal axis of the limb. The Apical Ectodermal Ridge (AER) helps to guide development along the proximal-distal axis, but the genetic and cellular mechanisms whereby it performs its roles are not well understood. This study attempted to discover whether the AER is able to recruit limb cells through oriented cell division through experiments with surgical manipulation of the AER in chicks and genetic manipulation in mice. By using cellular markers to determine apoptotic and mitotic indices, we have …

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Estimating Dispersal Of Spring Invertebrates Through Genetic Diversity, Keith Tanner, Dr. Dennis Shiozawa Aug 2013

Estimating Dispersal Of Spring Invertebrates Through Genetic Diversity, Keith Tanner, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The Great Basin contains many closed basins, separated by north-south lying mountain ranges and low east-west lying divides. The Sierra Nevada, on the western edge of the Great Basin, generates a rain shadow, making Nevada the driest state in the nation, with Utah as the second driest. The dryness of the Great Basin makes water a critical resource for life – for both humans and native organisms. As western urban areas have grown, water has become a limiting resource for both urban and rural development

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Life Histories Of Brook Trout (Salvelinus Fontinalis) And Their Replacement Of Cutthroat Trout (Oncorhynchus Clarki), Amy Burgess, Dr. Dennis Shiozawa Aug 2013

Life Histories Of Brook Trout (Salvelinus Fontinalis) And Their Replacement Of Cutthroat Trout (Oncorhynchus Clarki), Amy Burgess, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The cutthroat trout (Oncorhynchus clarki) is a member of the Salmonid family native to the western North America. Brook trout (Salvelinus fontinalis) is also a member of the salmonid family but a native to eastern North America, but has been introduced into many areas in western North America due to its popularity as a game fish. Observations of the invasion of nonnative brook trout (Salvelinus fontinalis) have often resulted in the replacement of cutthroat trout (Oncorhynchus clarki). While this is the case the underlying reasons for this replacement remain largely unknown (Peterson, 2004). Studies have been conducted looking at ecological …

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Whose Legs Are In The Water? Parsing Out Community Composition And Turnover Rates Of Plecoptera, Trichoptera, And Ephemeroptera, Sarah Walker, Dr. C. Riley Nelson Aug 2013

Whose Legs Are In The Water? Parsing Out Community Composition And Turnover Rates Of Plecoptera, Trichoptera, And Ephemeroptera, Sarah Walker, Dr. C. Riley Nelson

Journal of Undergraduate Research

Many beta diversity indicies, like most analytical tools in ecology, abstract the known relative abundances and species presence into outputs primarily useful for obtaining p-values and little else. Therefore, the purposes of this proposed beta diversity method were to simplify currently used similarity analyses for visualization and quantification of beta diversity, investigate its use in seasonal succession and other gradients in communities, and demonstrate an application of these methods in terms of both taxonomic and functional richness.

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Crandall Specimen Collection Database, Mark Valentine, Dr. Keith Crandall Aug 2013

Crandall Specimen Collection Database, Mark Valentine, Dr. Keith Crandall

Journal of Undergraduate Research

The goal of this project was to design and implement a database and web-based interface, to store information on the specimens collected for study in the Crandall lab. The creation of a user-friendly centralized database to warehouse the information on all of the specimens studied is anticipated to be of great use to the Crandall Lab.

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Stable Isotope Ratios In Leg Hairs A Better Diagnostic Tool For Eating Disorders, Stephanie Lindblad, Beverly Roeder Aug 2013

Stable Isotope Ratios In Leg Hairs A Better Diagnostic Tool For Eating Disorders, Stephanie Lindblad, Beverly Roeder

Journal of Undergraduate Research

Anorexia and bulimia are eating disorders that are extremely harmful and difficult to accurately diagnose. Currently the most frequent methods of diagnosis are subjective interviews and questionnaires. One example of these psychological diagnostic tools is the DSM-IV test, which has some serious problems associated with it. It relies heavily on self-report of patients, which subjects the results to dishonesty. The test is also unable to classify certain patients that do not meet specified characteristics. In addition, the DSM-IV has very limited physiological measures, such as BMI and menstrual status. Thus, the physiological consequences of anorexia and bulimia, including a feedback …

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The Influence Of Elevation On The Life History Of Mottled Sculpin, Aaron Fordham, Dr. Dennis Shiozawa Aug 2013

The Influence Of Elevation On The Life History Of Mottled Sculpin, Aaron Fordham, Dr. Dennis Shiozawa

Journal of Undergraduate Research

The Mottled Sculpin Cottus bairdii is found in cool to cold streams, creeks and rivers of northern North America (Page and Burr 1991). Sculpin are a benthic fish, living on the bottoms of the streams and rivers that they occupy. They reach 125 to 200 mm in total length when mature and can grow to 31mm-36mm by autumn of their first year of life (Ludwig and Normen 1969). Very little research has been conducted on the age and growth of C. bairdii and no comparative studies have been done examining the influence of elevation in their growth rates.

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Determining And Sharing Knowledge About Phylogenetic Relationships Of Collomia Species (Mountain-Trumpet Flowers), Lisa Busby, Dr. Leigh Johnson Aug 2013

Determining And Sharing Knowledge About Phylogenetic Relationships Of Collomia Species (Mountain-Trumpet Flowers), Lisa Busby, Dr. Leigh Johnson

Journal of Undergraduate Research

The plant genus Collomia shows great morphological and genetic diversity, however, its current classification is based on a morphological study done in 1940. This year I was able to assemble a great deal of DNA sequence information and compare the variation in these sequences with previous classifications to begin reevaluating the genus and further define relationships between Collomia species. I have also made a great deal of progress in sharing this data with the general public by helping to construct internet web pages for the Tree of Life Web Project.

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Altitudinal And Seasonal Comparison Of Insects In The Riparian Corridor Of The American Fork Canyon, Utah, Elizabeth J. Bankhead, Dr. C. Riley Nelson Aug 2013

Altitudinal And Seasonal Comparison Of Insects In The Riparian Corridor Of The American Fork Canyon, Utah, Elizabeth J. Bankhead, Dr. C. Riley Nelson

Journal of Undergraduate Research

A hot topic in ecology right now is the Mid-Domain Effect (MDE) as presented by Robert K. Colwell (2001). This null model states that the greatest species diversity along an elevation gradient will be found at the incline’s mid-point, if no other environmental gradients interfere. Another hypothesis involving elevation gradients is an abundance null-model created by John Terborgh (1971). The research set forth in this paper seeks to understand abundance and richness along an elevation gradient in a riparian system and help validate MDE.

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Prolactin’S Effect On Ccl28 Gene Expression, Susanne Linderman, Dr. Eric Wilson Aug 2013

Prolactin’S Effect On Ccl28 Gene Expression, Susanne Linderman, Dr. Eric Wilson

Journal of Undergraduate Research

The purpose of my project was to determine whether or not the hormone prolactin had an effect on CCL28 gene expression. CCL28 is a chemotactic protein (chemokine) that attracts IgA antibody secreting cells (ASC) to the lactating mammary gland. Receptor proteins on the surface of IgA antibody secreting cells recognize the surrounding CCL28 concentrations, and cause these cells to migrate towards the source of CCL28.

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Genetic Investigation Of The Protein Phou, Christopher D. Rice, Dr. William Mccleary Aug 2013

Genetic Investigation Of The Protein Phou, Christopher D. Rice, Dr. William Mccleary

Journal of Undergraduate Research

Phosphate is a necessary chemical compound for life at any level. Organisms have developed different means of obtaining phosphate from their environments and maintaining an intracellular phosphate homeostasis. The creation and maintenance of such a homeostasis at the very least requires mechanisms for sensing phosphate levels within and without the cell and phosphate transporters which can be regulated accordingly. The protein PhoU is involved in this phosphate response regulation. While PhoU is found in Escherichia coli, a very broad range of bacteria contain homologues with several closely conserved regions suggesting not only that PhoU-like proteins are important for many microorganisms …

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Twinkle Primase/Helicase Protein In Arabidopsis Thaliana, Travis Hunt, Dr. Brent Nielsen Aug 2013

Twinkle Primase/Helicase Protein In Arabidopsis Thaliana, Travis Hunt, Dr. Brent Nielsen

Journal of Undergraduate Research

The overall goal of the project was to study the role of DNA recombination in maintenance of plant mitochondrial DNA (mtDNA). Recombination is the process by which a molecule of DNA is nicked or broken and then the end is joined to a different but homologous DNA molecule.

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Effect Of Selenium On The Expression Of The Androgen Receptor And Nuclear Factor Kappa-B In Human Prostate Cancer Cells, Daniel Tandberg, Dr. Merrill J. Christensen Aug 2013

Effect Of Selenium On The Expression Of The Androgen Receptor And Nuclear Factor Kappa-B In Human Prostate Cancer Cells, Daniel Tandberg, Dr. Merrill J. Christensen

Journal of Undergraduate Research

Selenium has been established as a promising chemopreventive element for prostate cancer. Several different mechanisms have been studied to delineate selenium’s anti-cancer effect, but the exact target and mechanism has yet to be clearly defined. Previous studies have established an inhibitory relationship between the nuclear factor kappa B (NF-κB) and selenium, as well as the Androgen Receptor (AR) and selenium in human LNCap cells. Both NF-κB and AR are constituently active during prostate cancer development, and their deactivation by selenium might be one of the mechanisms by which selenium acts as a chemopreventative agent. The purpose of our research is …

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The Derivatives Of Resveratrol And Prostate Cancer, Dallin Snow, Dr. Merrill Christensen Aug 2013

The Derivatives Of Resveratrol And Prostate Cancer, Dallin Snow, Dr. Merrill Christensen

Journal of Undergraduate Research

Resveratrol has been shown to be a very effective anticarcinogenic compound, in addition to its anti-viral, anti-aging, anti-inflammatory, and life prolonging effects. Resveratrol binds the estrogen receptor beta which in turn down regulates the androgen receptor, which is active in prostate cancer. Past studies of the effects of resveratrol on human prostate cancer cells have shown that it increases the rate of apoptosis and decreases proliferation in a dose and time dependent manner (Benitez, 2007). Also, a 2004 study exploring the absorption and metabolism of resveratrol in humans indicated that it is metabolized at a rapid rate by humans. It …

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An In Vitro Examination Of The Effect Of Cholesterol On Vesicle Exocytosis, Brandon Forbes Aug 2013

An In Vitro Examination Of The Effect Of Cholesterol On Vesicle Exocytosis, Brandon Forbes

Journal of Undergraduate Research

Neurons communicate to other cells by releasing neurotransmitter through a process called exocytosis. Exocytosis of neurotransmitter containing vesicles to their plasma membranes is via the SNARE protein complex. Studies that have examined the SNARE protein complex, using an in vitro lipid bilayer model, have thus far not examined the effects of cholesterol on the SNARE driven fusion. As a research hypothesis, I expect that cholesterol will have a positive effect on the rate of SNARE driven fusion events.

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Correlation Between Mc540 Fluorescence And Ps Exposure In Apoptotic Cells, Liz Gibbons, Dr. John Bell Aug 2013

Correlation Between Mc540 Fluorescence And Ps Exposure In Apoptotic Cells, Liz Gibbons, Dr. John Bell

Journal of Undergraduate Research

The purpose of my project was to further study cell membrane changes during apoptosis, or programmed cell death. This was an extension of the research being done by Dr. Bell and my fellow students on the susceptibility of cells to the enzyme secretory phospholipase A2 (sPLA2). This enzyme hydrolyzes cell membranes, but only those with certain lipid properties. In general, only cells that are dead, injured, or dying display significant susceptibility to sPLA2 while healthy cells resist hydrolysis (Nielson, 2000). We use fluorescent probes to study these membrane lipid properties and how they change as the cells undergo apoptosis. These …

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The Relationship Between High-Salt And Estrogen On Blood Pressure Under Basal And Stressed Conditions In The Female Offspring Of Sprague Dawley Rats That Were Subjected To High Or Normal Salt Diets During Pregnancy, Brandon G. Wilkinson, Dr. James Porter Aug 2013

The Relationship Between High-Salt And Estrogen On Blood Pressure Under Basal And Stressed Conditions In The Female Offspring Of Sprague Dawley Rats That Were Subjected To High Or Normal Salt Diets During Pregnancy, Brandon G. Wilkinson, Dr. James Porter

Journal of Undergraduate Research

Cardiovascular disease (CVD) is the number one leading cause of death in the United States. High blood pressure (hypertension) is a form of CVD and affects nearly 1 in 3 American adults. Men are more likely than women to develop hypertension until 45 years of age. However, percentages of women diagnosed with hypertension rise to exceed that of men around 45-54 years of age.1 This trend in hypertension is a clear age-related sex dimorphism. The trend suggests that following the onset of menopause, women have a higher risk of hypertension, a risk that continues to rise with age.2-3 Current research …

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The Relationship Between Zyxin And Rac1 In Cell Junction Formation, Dan Brereton, Ryan Vellinga, Craig Barnette, Dr. Marc Hansen Aug 2013

The Relationship Between Zyxin And Rac1 In Cell Junction Formation, Dan Brereton, Ryan Vellinga, Craig Barnette, Dr. Marc Hansen

Journal of Undergraduate Research

In order to better understand how cancer metastasizes we must discover how cancer cells are able to break down their cell-cell junctions.

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Characterization Of Osteoarthritic Degeneration In Sedc Mutant Mice, David Holt, Dr. Robert Seegmiller Aug 2013

Characterization Of Osteoarthritic Degeneration In Sedc Mutant Mice, David Holt, Dr. Robert Seegmiller

Journal of Undergraduate Research

Spondyloepiphyseal dysplasia congenita (SEDC) is a recessive human genetic disorder characterized by skeletal abnormalities and early onset osteoarthritis (OA).1 Type II and the alpha 3 chain of type XI collagen together are integral in the development of normal articular cartilage (AC) and are both encoded by the Col2a1 gene.2 Spondyloepiphyseal dysplasia congenita (sedc) mice have a missense mutation of the Col2a1 gene within the triple helical region of type II collagen, affecting its production, leading to development of abnormal AC.

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Genetic Diversity Of Native Utah Flora, Benjamin Brulotte, Dr. Mikel Stevens Aug 2013

Genetic Diversity Of Native Utah Flora, Benjamin Brulotte, Dr. Mikel Stevens

Journal of Undergraduate Research

Amplified fragment length polymorphisms are a reliable, straightforward method of determining the genetic diversity of species. Frequently this method of determining genetic diversity has been used in conservation efforts because of its cost effectiveness, and efficiency. We set out to characterize the genetic diversity of three native species of wildflower common in the Intermountain West, and frequently used in Forest Service revegetation projects.

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Does Predator Environment Predict Life History Traits In The Livebearing Fish Poecillia Gillii?, K. Nicole Schoonmaker, Dr. Jerald B. Johnson Aug 2013

Does Predator Environment Predict Life History Traits In The Livebearing Fish Poecillia Gillii?, K. Nicole Schoonmaker, Dr. Jerald B. Johnson

Journal of Undergraduate Research

The process of natural selection drives the evolution of species which results in the survival of individuals whose traits are most adaptable to a specific environment and the death of individuals whose traits are less fit. Thus, populations of a single species that reside in habitats with differing environmental pressures can have different physical (phenotypic) or genetic (genotypic) traits. An understanding of the environmental pressures that create variation in traits and observation of that variation is important to understanding the adaptability and evolution of living organisms.

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Are Morphology And Performance Predation-Related? Swimming Speed And Ontological Shape Comparisons Between Populations Of A Live-Bearing Fish, Elizabeth Hassell, Dr. Mark Belk Aug 2013

Are Morphology And Performance Predation-Related? Swimming Speed And Ontological Shape Comparisons Between Populations Of A Live-Bearing Fish, Elizabeth Hassell, Dr. Mark Belk

Journal of Undergraduate Research

I used my ORCA grant for my honors thesis in biology, which has been a great success. The results are not yet complete because the depth of this project goes beyond the one-year time frame of a typical ORCA project; however, our planned schedule is still in place and the final results of this study will be submitted for publication in the coming months.

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An Objective Diagnosis Of Eating Disorders Stable Isotope Analysis Of Hair, Brooke Allen, Beverly Roeder Aug 2013

An Objective Diagnosis Of Eating Disorders Stable Isotope Analysis Of Hair, Brooke Allen, Beverly Roeder

Journal of Undergraduate Research

Eating disorders (EDs) are a group of mental illnesses that afflict up to two percent of the population . The group of illnesses consists of anorexia, bulimia, and EDNOS (Eating Disorders Not Otherwise Specified). The diagnostic methods for eating disorders that are currently accepted by the American Psychiatric Association are problematic, because they rely mainly upon patient responses to self-report or physician-administered examinations. These assessments do not always return accurate diagnoses, because they are primarily subjective in nature . Thus, a more objective method for diagnosis, one which is more focused on physiological measures than on subjective questions, is needed …

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