STRATA
STRATA, the STudent Research, Academic, and Talent Archive, is a collection of selected Fort Lewis College student work, including undergraduate research, senior seminar papers, published works, conference presentations, and other creative and artistic projects. Search by name, subject, title, or academic department.
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- Characterization of Acidobacterium Capsulatum Growth in Minimal Media Containing Glucose as a Single Carbon Source
- Acidobacterium capsulatum is an acidophilic organism first isolated in 1991 from an acid mine drainage in Japan. The bacterium has been shown to be very prevalent in the soil and is thought to play a vital role in the ecosystem. The metabolic pathways of this bacterium are not well known making it an ideal subject for conducting metabolic research. Genomic information suggests in glycolysis the enzyme aldolase is not present. These studies are being done in an attempt to understand how A. capsulatum is metabolizing glucose. Research was conducted on A. capsulatum in a minimal medium using glucose as a single carbon source to try and better understand glucose metabolism. We were able to characterize the growth of the A. capsulatum by measuring changes in glucose concentration, protein concentration, and cell density as measured by absorbance at 600 nm and pH level. These experiments were perfomed by inoculating one liter of media with a one percent of a liquid inoculum of actively growing cells. We grew the Acidobacterium capsulatum in one liter of minimal media containing 10 mM glucose as a single carbon source, a standard E. coli mineral mix, and Bryant's vitamin mixture and various salts. The medium was brought to a pH of 3.1. Lowry Protein assays and hexokinase-based glucose assays were performed daily and correlated to cell growth. Using these methods we were able to correlate glucose consumption with bacteria growth, protein production and changes in pH. From the growth curve information, we found that the optimal time for harvesting cells is about 90 hours from the time of inoculation. We found that A. capsulatum used all measurable amounts of glucose under these minimal media conditions in three primary ways. The glucose was used to create biomass, it was used to expend energy creating biomass, and it was used to create an extracellular polysaccharide. By correlating glucose consumption to protein concentration, we can estimate the percentages of glucose present as biomass and as extracellular polysaccharides and the percentage of glucose utilized as fuel to create the biomass.
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- Characterization of Aldolase and Transaldolase Activities in Acidobacterium Capsulatum
- Acidobacterium capsulatum, a mildly acidophilic, chemotrophic, aerobe with the ability to grow on glucose, is found in diverse soil and aquatic conditions worldwide, suggesting a significant role in carbon and nutrient cycling in the environment. A. capsulatum has successfully been cultured and its genome has been completed, allowing for genome-directed studies of the organism's glucose metabolizing capabilities. Based on the genomic information, this organism was thought to lack aldolase, but contained two putative transaldolase genes (TA), one of which contains an EF-hand domain (TAEF). However, recent results show there are aldolase and transaldolase activities in cell-free lysate. We are continuing to characterize the aldolase and transaldolase activities in cell-free lysates to better understand how these enzymes play a role in partitioning of carbon from glucose between energy production and biomass formation. The pH dependence of the aldolase and transaldolase activities found to have a narrow optimal activity around pH 7.4 in the crude cell lysate. The two putative transaldolase genes have been PCR amplified, cloned into a pET151 directional TOPO expression vector, and transformed into E. coli. Sequencing of the TAEF and TA genes showed proper insertion into the expression vector. Current work is focusing on expression and purification of the TA and TAEF proteins. Genomic and structural features of the transaldolase genes and proteins are being characterized through bioinformatics tools such as Pymol, NCBI gene searches, and Cn3D. Structural homologs are being used to identify structurally similar features in the A. capsulatum transaldolase enzymes. Conserved active site residues have been identified using these same homologs as model transaldolases. These bioinformatics studies support the hypothesis that the A. capsulatum transaldolases are capable of catalyzing the accepted transaldolase mechanism. Future work will focus on identifying an aldolase gene and characterizing key regulatory points of glucose metabolism. The identification of aldolase will be done through bioinformatics tools as described above, comparing it to hypothetical proteins in the A. capsulatum genome.
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- Characterization of CD9 as an Alternative Receptor for IL-16 Signaling in Cerebellar Granule Neurons
- Interleukin-16 (IL-16) was initially described as a pro-inflammatory cytokine. IL-16 has diverse immunoregulatory effects in various tissues and has recently been shown to induce neurite outgrowth in cerebellar granule neurons. In neurons IL-16 binds to the CD4 receptor, which triggers a signaling pathway that upregulates the expression of c-Fos. c-Fos transcriptionally regulates genes that promote proliferation, growth, and survival of neurons (Fenster et al., 2010). In previous studies, cerebellar granule neurons isolated from CD4 knockout mice still exhibited c-Fos expression and increased neurite outgrowth when treated with IL-16 (Fenster et al., 2010). This indicates that in cerebellar granule neurons, IL-16 could be binding to an alternative receptor in order to elicit this response. We hypothesize that the tetraspannin receptor CD9 may be the alternative to CD4 in cerebellar granule neurons. In other cells throughout the body, CD9 has been identified as an alternative receptor for IL-16 signaling. For instance, human mast cells respond to IL-16 treatment in a CD9-mediated pathway (Qi et al., 2005). Using several cellular and molecular biology techniques, we characterized the CD9 receptor in cerebral granule neurons. In this study we demonstrated that CD9 is present in high concentrations in cerebellar granule neurons as well as the whole brain. In addition, CD9 is highly dispersed throughout neurons and co-localization occurs with the synaptic protein PSD-95. Also CD9 is expressed in higher concentrations in neurons in comparison to CD4. Our data provides evidence to the support the hypothesis that CD9 acts as an alternative receptor of CD4 in cerebellar granule neurons. Our analysis will lay the foundation for further studies of IL-16-mediated signaling through CD9 in neurons.
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- Characterization of a Novel Fungal Species Found on Resident Bats in Colorado: Is Pseudogymnoascus Destructans Here?
- White nose syndrome has caused the death of millions of bats throughout the eastern United States. Since the 2006 discovery of Psuedogymnoascus destructans (P. destructans) in New York, the psychrophilic fungus has been observed as far west as Oklahoma. With bat populations seeing 70% decrease in numbers after being infected with P. destructans, we sampled bats from around Crestone, Colorado in order to determine if P. destructans was affecting local bat populations. Fungal spore samples were inoculated onto agar plates and incubated at 8 °C and 20 °C. Out of 144 fungal samples ten came back as potential matches for P. destructans, identified through ITS sequence analysis, and were then sequenced for the IGS and LSU regions for further analysis. All of the sequences for the IGS region yielded an unknown species of the Psuedogymnoascus genus and the LSU sequences matched to P. pullulans and P. pannorum. Morphologically, our unknown sample shared some characteristics with P. destructans but differed enough for us to believe our fungus may be a novel species.
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- Characterization of a Yeast Histone G13a Mutant Strain That "Escapes" Gene Silencing
- Histones and chromatin structure are vital for regulating gene transcription. Through previous work, a glycine to alanine mutation at position 13 (G13A) of the histone H4 tail was found to increase silencing of the yeast ADE2 gene, resulting in a red phenotype. Interestingly, this mutant was found to be able to "escape" this repression and become phenotypically white. The red and white phenotypes of the G13A mutant are being characterized in an attempt to understand how the "escaping" process occurs. Characterization methods included analysis of growth—to determine global transcription levels—and histone purification for acetylation level determination by tandem mass spectrometry.
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- Characterizing Hybridization Between Canis Familiaris and Canis Lupus Through Genetic Analysis Using Microsatellite DNA Data
- Hybridization between the grey wolf (Canis lupus) and the domestic dog (Canis familiaris) is an arising problem for wolf conservation. This phenomenon is caused by the displacement of natural ecological niches, causing these two species to share territory. This sharing of territory can lead to successful reproduction resulting in a hybrid species called the wolf-dog. Long-term direct hybridization between wolfs and dogs has the potential to introduce novel dog genes into the wolf gene pool and subsequent back-crossing of hybrid-derived wolf-dogs to wolfs could spread these dog genes widely through wolf populations leading to a loss of genetic purity with the eventual genetic extinction of the species. Wolfwood Refuge takes part in caring for wolves, dogs and wolf-dogs as an effort to provide adequate homes for these animals. It is important to know the presence of wolf and dog genes in these individuals to better understand conservation and management issues of the grey wolf. Using microsatellite DNA markers we genotyped 20 animals from Wolfwood Refuge and compared them to control full dogs and full wolves. This provided an unbiased assessment of proportional parentage independent from the exhibited phenotype. We expected to see that designations of parentage supplied by the curator based on observed phenotypes would be greatly different from what we found genetically. We found that seven of the 20 animals were different than what the curator hypothesized. Most animals had a combination of both dog and wolf genes present in their DNA. Our results show that gene movement between wolfs and dogs is extensive and that phenotypic characterization is likely not accurate. More vigilance to controlling dog-wolf hybridization will be necessary if the gene pool of the grey wolf is to be maintained.
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- Chasing Fossils: The Timing and Extent of an Upright Calamites/Lycopod Forest, Pennsylvanian Hermosa Group, SW Colorado
- This study investigates a unique Calamites-bearing layer exposed in the Pennsylvanian Hermosa Group, north of Durango, Colorado. In these strata, three previously undocumented localities containing over 65 Calamites and one 4m x 50cm lycopod fossil were identified. These plant fossils are found encased by braided river deposits, composed of trough crossbedded, felspathic-arenites. At the locality providing the best exposure of the three new locations, a 72 meter thick stratigraphic section was measured. Using a combination of biostratigraphic marker-beds and measured sections, the strata were correlated to Sequence Two of the Hermosa Cliffs (Gianniny and Miskell-Gerhardt, 2009). This correlation helps delineate the lateral extent, and the early Desmoinesian age of the Calamites-bearing layer (Eastep and Gianniny, 2013) along a 4.5 kilometer section of the Hermosa Group. These new data update the depositional model for Sequence Two, of Gianniny and Miskell-Gerhardt (2009). In addition to this, these fossils provide evidence for repeated pulses of fluvial deposition and rapid subsidence on thistectonically active eastern margin of the Paradox Basin.
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- Chemical Signatures of Perovskite in Katungite Dikes of the Navajo Volcanic Field: Implications for Magma Sources and Conditions
- A series of west-trending ultramafic and ultrapotassic dikes (katungite) are exposed in the west-central part of the Navajo volcanic field. These katungite dikes contain high concentrations (up to 5% volume) of perovskite along with associated olivine, phlogopite, mellilite, and apatite. Perovksite in these rocks occurs as euhedral to subhedral crystals with complex growth and chemical-zonation patterns. The perovksite forms either as isolated rounded to pyramid-shaped crystals, "flower" aggregates, and "necklaces" around earlier formed phenocrysts of olivine. A study of the chemical signatures of perovskite in the NVF katungite samples reveals that they mostly consist of the end member perovksite CaTiO3(96-98 mol. %). The perovskite crystals have extremely elevated abundances of rare-earth elements with LREE enriched 10,000 to 30,000 times chondrite with 0.1 to 0.7 weight percent of Nb2O3, La2O3, Ce2O3, Pr2O3, Nd2O3, and SrO. Overall, however, the perovskite in the katungite samples tends to be more ceroan, and exhibit elevated concentrations of U (40 to 100 ppm) and Th (300-2000 ppm). Prominent zonation in perovskite indicates a complex history of crystallization during magma explacement in which LREE oxides tend to show a decrease in concentration from core to rim whereas SrO show an increase. According to the oxygen barometer of Bellis & Canil (2007), the NVF katungite samples span a wide range of oxygen fugacities relative to the Ni-NiO buffer, ranging from -4 to 0 with DNNO increasing with increasing Fe2O3. The DNNO values tend to become more negative from the cores to rims of individual crystals. This suggests that the magmas associated with these rocks were in a moderately to slightly reduced state during emplacement and were buffered by a C-H-O volatile phase that increased with crystallization. Most elements show an increase in concentration with higher Fe2O3 and higher DNNO. This hints that the distribution of most elements in the perovksite is closely allied to the oxidation state of the magma. We interpret the DNNO data as evidence the magmas for the NVF katungite dikes were generated by melting of a deeper mantle source than NVF minettes. A variety of geochemical trends indicate that the minettes were generated by partial melting of metasomatized lithospheric mantle.
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- Cherry Blossom
- Artwork by Kristina Orlovsky published in Fall 2012 - Winter 2013 issue of Images.
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- Chimney Rock: A Cultural Ecological Model of Adaptation
- This research demonstrates that people were present in the Chimney Rock Archaeological Area (CRAA) before the "Chaco System" expanded north into the region. This paper incorporates the results of a re-evaluation of site 5AA256, which was conducted during the summer of 2008. Julian Steward's model of cultural ecology is used to reconstruct the agricultural subsistence system of the resident population. The astronomical significance of Chimney Rock combined with the presence of naturally formed sediment traps provide a possible explanation for the incorporation of the eight existing communities at Chimney Rock into the Chaco system. Finally, it is suggested that the astronomical knowledge regarding the spires was present among the inhabitants of the region before the expansion of the Chaco system into the area.
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- China's One Child Policy: Effects on Women and Girls
- China's One Child Policy was put in place in attempts to slow down their growing population. Although the Policy has helped control the population size, unseen consequences and unintended cultural change has occurred. There were rewards given to families who abided by the policy, such as education for children and wage bonuses. Families who did not follow the One Child Policy were often punished with forced sterilizations and economic sanctions. As sons are valued over daughters in Chinese culture, the rewards and punishments caused a phenomenon called "missing girls." The term "missing girls" refers to aborted female fetuses, neglected and abused daughters, as well as undocumented girls and adoptions. This has caused a skewed sex ratio in China of 115 males at birth to only 100 females at birth. Not all of the effects of the Policy are negative though. In some areas, mainly urban ones, women and girls are afforded with more opportunities than before, including higher education and better career options. It remains to be seen how the change of the One Child Policy to a Two Child Policy will affect the sex ratio and the positive aspects that the original policy created.
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- Ciluffo - Consent Form
- Consent form for "‘Old Pueblo Ska’: Ska Music in the Southwest, 1992-1999" by Danial Ciluffo