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Advanced Molecular and Microbial Techniques: a Complete Laboratory Notebook

Description: The purpose of this project is to produce a complete and thorough notebook that may be used to supplement laboratory coursework. Its intent is to be used primarily by the students to aid them in understanding background information and the proper laboratory procedures involved in various types of experiments. The laboratory notebook is a summation of all the experiments and procedures used in the six-credit hour Advanced Microbial and Molecular Biology (BIOL 5160) course offered during the summer semester at the University of North Texas. This class is a team taught effort by Professors O'Donovan and Kunz. The course is constructed as an intensive practice exercise to teach the student about gene mutations, biosynthetic pathways, preparation and analysis of plasmid DNA, and many other topics included in the notebook.
Date: May 1998
Creator: Brito-Rodriquez, Carmen Lydia

Alterations in Human Baroreceptor Reflex Regulation of Blood Pressure Following 15 Days of Simulated Microgravity Exposure

Description: Prolonged exposure to microgravity is known to invoke physiological changes which predispose individuals to orthostatic intolerance upon readaptation to the earth's gravitational field. Attenuated baroreflex responsiveness has been implicated in contributing to this inability to withstand orthostatic stress. To test this hypothesis, eight individuals were exposed to 15 days of simulated microgravity exposure using the 6° head-down bed rest model. Prior to, and after the simulated microgravity exposure, the following were assessed: a) aortic baroreflex function; b) carotid baroreflex function; c) cardiopulmonary baroreflex function; and d) the degree of interaction between the cardiopulmonary and carotid baroreflexes.
Date: August 1993
Creator: Crandall, Craig G. (Craig Gerald)

Analysis of the Trypanosoma brucei Genome and Identification and Characterization of a Gene Family Encoding Putative EF-Hand Calcium-Binding Proteins

Description: The flagellum of Trypanosoma brucei contains a family of antigenically related EF-hand calcium-binding proteins which are called the calflagins. Genomic Southern blots indicated that multiple copies of calflagin genes occur in T brucei. All of the copies were contained in a single 23 kb Xhol-Xhol fragment. Genomic fragments of 2.5 and 1.7 kb were cloned that encoded calflagin sequences. Two new members of the calflagin family were found from genomic clone sequences. The deduced amino acid sequences of the genomic clones showed the calflagin genes were arranged tandemly along the genomic fragments and were similar to previously described calflagins. The calflagin genes were related by two unrelated 3' flanking sequences. An open reading frame that was unrelated to any calflagin was found at the 5' end of the 2.5 kb genomic fragment. Each encoded protein (~24,000u) contained three EF-hand calcium-binding motifs and one degenerate EF-hand motif. In general, variability among the T. brucei calflagins is greater than related proteins in T. lewisii and T. cruzi. This variability results from amino acid substitutions at the amino and carboxy termini, and duplication of internal segments.
Date: May 1998
Creator: DeFord, James H. (James Henry), 1956-

Assembly of Pseudomonas putida Aspartate Transcarbamoylase and Possible Roles of the PyrC' Polypeptide in the Folding of the Dodecameric Enzyme

Description: Aspartate transcarbamoylase (ATCase) of Pseudomonas putida consists of two different polypeptides, PyrB and PyrC' (Schurr et al, 1995). The role of the PyrC' and the assembly of PyrB and PyrC' have been studied. The ATCase made in vitro of P.putida PyrB with P.putida PyrC', and of E.coli PyrB with P.putida PyrC ' were generated under two different conditions, denaturation and renaturation, and untreated. It was found that PyrC' plays a role in the enzymatic regulation by ATP, CTP and UTP. In addition to playing a role in substrate binding, the PyrB polypeptide is also involved in effector binding (Kumar et al., manuscript in preparation). The most energetically preferred form of the P.putida WT is a dodecamer with a molecular mass of 480 kDa. The ratio between the PyrB and the PyrC' is 1:1. In studies of nucleotide binding, it was discovered that the P.putida PyrB was phosphorylated by a protein kinase in the cell extract. In the presence of 20 mM EDTA, this phosphorylation was inhibited and the inhibition could be overcome by the addition of divalent cations such as Zn2+ and Mg2+. This result suggested that the phosphorylation reaction required divalent cations. In the CAD complex of eukaryotes, phosphorylations of the CPSase and the linker region between ATCase and DHOase did not occur in the presence of UTP and it was hypothesized (Carrey, 1993) that UTP and phosphorylation(s) regulated the conformational change in the enzyme complex. Therefore, the same idea was approached with P.putida ATCase, where it was found that 1.0 mM UTP inhibited the phosphorylation of PyrB by more than 50%. These results suggested that the regulation of the conformational change of the P.putida ATCase might be similar to that of CAD. Furthermore, peptide mapping for phosphorylation sites was performed on P.putida ATCase WT, WT --11 amino acids ...
Date: May 1999
Creator: Hongsthong, Apiradee, 1970-

Assessing Effects of an Environmental Education Field Science Program Fostering Responsibility at an Urban Middle School

Description: The study investigated the ability of an extracurricular program to influence environmental responsibility of sixth and seventh graders. The Children's Environmental Attitude and Knowledge Survey (CHEAKS) was evaluated for appropriateness in assessing the worth of this particular environmental education strategy emphasizing water quality fieldwork and technology. CHEAKS is designed with psychometric reliability and validity that may be used in comparing disparate programs. Wilcoxon two sample tests were used to analyze data gathered from two student groups; one participated in an "Enviro-Mentals Club"; the other received no treatment. Analysis showed no significant change in environmental attitudes between groups, but did show significance (p <= 0.05) in environmental knowledge growth. Therefore, the investigated program had marginal success in influencing environmental responsibility.
Date: May 1999
Creator: Sills, Blake

Attenuation of Escherichia Coli Aspartate Transcarbamoylase Expressed in Pseudomonas Aeruginosa Mutant and Wild Type Strains

Description: No apparent repression of pyr gene expression in Pseudomonas aeruginosa is observed upon addition of exogenous pyrimidines to the growth medium. Upon introduction of the subcloned Escherichia coli pyrBI genes for aspartate transcarbamoylase (ATCase) into a P. aeruginosa pyrB mutant strain, repression was observed in response to exogenously fed pyrimidine compounds. The results proved that it is possible to bring about changes in pyrimidine nucleotide pool levels and changes in transcriptional regulation of gene expression as a result. Thus, the lack of regulatory control in P. aeruginosa pyr gene expression is not due to an inability to take up and incorporate pyrimidine compounds into metabolic pools, or to an inability of the RNA polymerase to respond to regulatory sequences in the DNA but is probably due to a lack of specific regulatory signals in the promoter of the genes themselves.
Date: December 1994
Creator: Liu, Haiyan, 1966-

Biochemical Identification of Molecular Components Required for Cyanide Assimilation in Pseudomonas fluorescens NCIMB 11764

Description: Utilization of cyanide as a nutritional nitrogen source in P. fluorescens NCIMB 11764 was shown to involve a novel metabolic mechanism involving nonenzymatic neutralization outside of cells prior to further enzymatic oxidation within. Several cyanide degrading enzymes were produced by NCIMB 11764 in response to growth or exposure to cyanide, but only one of these cyanide, oxygenase (CNO), was shown to be physiologically required for assimilation of cyanide as a growth substrate.
Date: May 1998
Creator: Chen, Jui-Lin

Biodiversity of Caddisflies (Trichoptera) of the Interior Highlands of North America

Description: Caddisflies (Trichoptera) were collected from over 500 different locations throughout the Interior Highlands (Ozark, Ouachita, Arbuckle, and Wichita Mountains) between March 1990 and March 1994. I systematically sampled representative lotic and lentic habitats in 131 natural watersheds that comprise the 17 different physiographic subregions of this area. From my examination of approximately 60,000 specimens, surveys of regional museum collections, and review of literature records, I document 229 species distributed in 16 families and 58 genera. Included in this total are 27 endemic species and 15 new regional records. Descriptions are provided for a species new to science (Cheumatopsyche robisoni), four larvae (Helicopsyche limnella, H. piroa, Marilia species A, Polycentropus crassicornis) and a female (Helicopsyche piroa). Hydropsyche reiseni Denning, previously known only from the Arbuckle Mountains, is reduced in synonymy with H. arinale Ross. Further, I provide illustrated family, generic, and selected species-level keys that reflect this regional biodiversity.
Date: August 1994
Creator: Moulton, Stephen R. (Stephen Richard)

Biodiversity of Dragonflies and Damselflies (Odonata) of the South-Central Nearctic and Adjacent Neotropical Biotic Provinces

Description: The south-central United States serves as an important biogeographical link and dispersal corridor between Nearctic and Neotropical elements of western hemisphere odonate faunas. Its species are reasonably well known because of substantial collections, but there has been no concerted effort to document the extent of biodiversity and possible geographic affinities of dragonflies and damselflies of this region. The recent discoveries of Argia leonorae Garrison, Gomphus gonzalezi Dunkle and Erpetogomphus heterodon Garrison from southern and western Texas and northern Mexico suggest that Odonata species remain to be discovered in this area, particularly from far south Texas and northern Mexico. I have documented a total of 12,515 records of Odonata found in 408 counties within the south-central U.S. A total of 73 species of damselflies and 160 species of dragonflies was revealed in the region. The 233 (197 in Texas) Odonata species are distributed among 10 families and 66 genera. Illustrated family, generic, and species-level keys are provided. Since the beginning of this work in the Fall of 1993, one species has been added each to the Louisiana and Oklahoma faunas, and 12 species have been added, previously unreported from Texas, including four new to the U.S. The area of highest Odonata biodiversity overall (161 spp.) is in the Austroriparian biotic province. The greatest degree of faunal similarity between the south-central U.S. and other intra-continental regions was observed for the eastern (64%) United States. Diversity is a function of area, and as expected, the numbers of breeding birds and Odonata, in each contiguous U.S. state are positively correlated (r=0.376, n=33, p=0.031). There is, however, no strong correlation between land area and species diversity within the region, but those natural biotic provinces (Austroriparian, Texan, Balconian) where aquatic systems and topographic heterogeneity are the greatest provide a broader spectrum of potential Odonata habitats and ...
Date: May 1999
Creator: Abbott, John C.

Biogeographic Relationships of Pocket Gophers (Geomys breviceps and Geomys bursarius) in the Southeastern Portion of Their Ranges

Description: This research utilized population genetic analyses (protein starch-gel electrophoresis and DNA sequencing of the cytochrome b mtDNA gene), host-parasite specificity (lice coevolution), remote sensing of satellite data, and geographic information systems (GIS) to characterize newly discovered populations of pocket gophers (genus: Geomys) in Arkansas. These populations are isolated and occur in seemingly unsuitable habitat in the Ozark Mountains of Arkansas. Analyses of electrophoretic and ectoparasite data suggested the populations in the Ozark Mountains represented isolates allied to Geomys bursarius, a species not known to occur in Arkansas. Comparison of mitochondrial DNA sequence data of the cytochrome b gene with that of other taxa and morphometric analyses confirmed that these populations are most closely allied to G. bursarius occurring to the north in Missouri. Moreover, these mtDNA sequence analyses indicated a degree of differentiation typical of that between other subspecies of pocket gophers. Therefore, these populations represent a distinct genetic entity in an intermediate stage of speciation and should be designated as a new subspecies, Geomys bursarius ozarkensis. Molecular clock analysis revealed a time of lineage divergence for this new subspecies as approximately 511,000 YBP. Due to the isolated nature and limited distribution of this subspecies, an evaluation of critical habitat needs was initiated. Remote sensing and GIS technologies were used to identify and describe suitable habitat Computerized classification of satellite imagery of suitable vegetation, integrated with ancillary digital information on soil associations, roads, and water systems, revealed that human activity had played a positive role in the establishment and dispersal of pocket gophers in this area. This research represents an initial combination of classical systematic tools with remote sensing and GIS to investigate biogeographic patterns and evolution. This project establishes a framework for using an interdisciplinary approach to studying organisms with limited distributions, determining evolutionary status, and providing recommendations for ...
Date: August 1998
Creator: Elrod, Douglas Allen

Biological and Toxicological Responses Resulting from Dechlorination of a Major Municipal Wastewater Treatment Plant Discharge to the Trinity River

Description: Federal regulations such as the Clean Water Act (P.L. 92-500), and its amendments, direct the Environment Protection Agency (EPA) to implement programs to control the releases of conventional pollutants and toxics into the waterways of the United States. The EPA began requiring treatment plants to conduct toxicity tests (biomonitoring) of their effluent discharges. To control toxicity caused by chlorination of wastewater discharges, the EPA also began requiring some treatment facilities to dechlorinate their wastewater before discharging. This research was funded by the EPA to document the changes that occurred in the Trinity River from the dechlorination of the effluent from Ft. Worth's Village Creek municipal wastewater treatment plant. The study occurred over a two year period beginning in August 1990. A wide variety of biological field assessments and toxicological assays were used to measure various responses. Seven river stations, covering approximately twenty river miles, and the treatment plant effluent were assessed. Two of the river stations were upstream from the treatment plant and used as reference sites. The remaining five river stations were downstream from the treatment plant, spread out over seventeen river miles. The study evaluated the impact of chlorination prior to dechlorination, which served as a baseline. Responses determined during dechlorination were compared to the baseline data. An overall improvement in species richness and diversity was seen at those river stations which had previously been adversely impacted by chlorine. Aquatic toxicity tests, such as those required to be used by dischargers, were conducted during this study. Periodic toxicity was observed with these tests in the effluent and river samples after dechlorination was initiated. Those tests, along with in situ toxicity assays, proved to be good predictors of biological community responses.
Date: August 1995
Creator: Guinn, Richard J. (Richard Joe)

Biology and Energetics of Tropisternus Lateralis Nimbatus (SAY) (Coleoptera: Hydrophilidae) in a Playa on the Southern High Plains of Texas and Aquatic Coleoptera Diversity from Seven Playas on the Southern High Plains of Texas

Description: A study of the biology of Tropisternus lateralis, a hydrophilid beetle, was conducted during the flood period of a single playa on the Southern High Plains of Texas from early June 1995 through early September 1995. Mechanism of colonization, tolerance/avoidance to drought, larval density, and secondary production were analyzed. T. lateralis colonized playas from surrounding aquatic habitats and avoided drought through aerial dispersion. Once in the playa, larval density increased over time. Secondary production was 1.31 g/m2/.25 yr. In addition, aquatic Coleoptera diversity was studied in seven playas on the Southern High Plains of Texas. A total of twenty three species were identified from the study region. Nine species not reported in playa literature were identified.
Date: December 1997
Creator: Cook, Robert E. (Robert Edward), 1969-

Blood Pressure Regulation During Simulated Orthostatism Prior to and Following Endurance Exercise Training

Description: Cardiovascular responses and tolerance to an orthostatic stress were examined in eight men before and after eight months of endurance exercise training. Following training, maximal oxygen consumption and blood volume were increased, and resting heart rate reduced. Orthostatic tolerance was reduced following training in all eight subjects. It was concluded that prolonged endurance training decreased orthostatic tolerance and this decrease in tolerance appeared associated with attenuated baroreflex sensitivity and alterations in autonomic balance secondary to an increased parasympathetic tone noted with training.
Date: May 1992
Creator: Stevens, Glen Harold John

Changes in Heterozygosity Through Time in American Standardbred and American Saddlebred Horses (1960-1990)

Description: Observed and expected heterozygosity (H) levels for ten electrophoretic blood marker loci and expected H for seven red blood cell (RBC) anitgen/antibody loci were examined for 20 years in American Standardbred and 30 years in American Saddlebred horses. Standardbreds were classed by gait, Trotter and Pacer, and evaluated separately in most analyses. 4,404 Trotters and 12,271 Pacers were found to have statistically highly significant losses of mean total observed H through time for the ten electrophoretic loci (P<0.005), although in Trotters the loss was more extreme (P<<0.001). Loss of H in 5984 Saddlebreds was not significant (P=0.259). Correlations of RBC expected H through time showed decreases in all three groups.
Date: May 1992
Creator: King, Judith A. (Judith Ann), 1955-

Characterizing Spontaneous Neurophysiological Activity with Measures of Statistical Serial Dependence: a Summary Statistic and an Extension of the Joint Interval Histogram

Description: Two measures which indicate statistical serial dependence were evaluated. The n-dimensional Average Stored Information index (ndASI) is a measure of conditional information, which compares the entropies of higher order conditional distributions to estimate average statistical serial dependence. The generalized ranked joint interval histogram (RJIH-o) is a new nonparametric graphical analysis method. It extends the joint interval histogram by depicting longer interval sequences and can be interpereted precisely analagously to the joint interval histogram. The generalized ranked joint interval histogram correctly represents independence in a Poisson process model and statistical serial dependence in a directionally reinforced Markov model. The generalized ranked joint interval histogram correctly depicts the underlying periodic and strange attractors in a standard map model. Both measures can be used to effectively analyze interspike interval sequences from spontaneous neurophsyiological activity effectively.
Date: August 1994
Creator: Weil, Jon C. (Jon Christopher)

Chemotactic Response of Lumbricus terrestris Coelomocytes to Larval and Adult Stages of Rhabditis pellio

Description: Experiments were performed to assess the suitability of Rhabditis pellio, a nematode found in earthworms, as a challenge organism for use in development of a biomarker assay to determine the potential of chemicals to suppress the immunocompetence of the non-specific immune system. To accomplish this goal, information on the life cycle of R. pellio was determined; including effects of incubation time and temperature on growth rates; along with information on the immune response elicited in the earthworm, Lumbricus terrestris. Immune parameters measured were coelomocyte migration toward and attachment to R. pellio larvae and adults. Preliminary background information showed that R. pellio has potential as a challenge organism for development of a biomarker assay.
Access: This item is restricted to the UNT Community Members at a UNT Libraries Location.
Date: December 1999
Creator: Medrano, Jennifer Centurion

Classification of Toolmark Surfaces on Zipper Teeth

Description: This study proposes the classification of the toolmark under the heads of zipper teeth as a subclass characteristic as outlined by the Association of Firearm and Toolmark Examiners (AFTE). Two separate cases in which zipper teeth were found at crime scenes prompted this study. Brass zipper teeth manufactured by YKK were taken from 20 pairs of jeans and studied using a Reichert comparison microscope at 4X power. Photographs were taken and over 750 comparisons made. It was found that the toolmarks on each side on the 20 zippers were unique and independent of all other sides. The observations made in this study indicate that classifying zipper teeth toolmarks as a subclass characteristic is valid.
Date: December 1999
Creator: Jacobsen, Dawn

Comparison of Aspartate Transcarbamoylase and Pyrimidine Salvage in Sporosarcina urea, Sprolactobacillus inulinus, Lactobacillus fermentum, and Micrococcus luteus

Description: The enzyme that catalyzes the committed step in pyrimidine biosynthesis, aspartate transcarbamoylase, has been compared in selected endospore-forming organisms and in morphologically similar control organisms. The ATCases and pyrimidine salvage from Sporosarcina ureae, Sporolactobacillus inulinus, Lactobacillus fermentum, and Micrococcus luteus were compared to those of Bacillus subtilis. While the ATCases from Sporosarcina ureae, Sporolactobacillus inulinus, and L. fermentum were found to exhibit characteristics to that of Bacillus with respect to molecular weight and kinetics, M. luteus ATCase was larger at approximately 480 kDa. Furthermore, pyrimidine salvage in Sporosarcina ureae and M. luteus was identical to those of B. subtilis, while pyrimidine salvage of Sporolactobacillus inulinus and L. fermentum resembled that of the pseudomonads.
Date: August 1994
Creator: Barron, Vincent N. (Vincent Neal)

A Comparison of Predicted and Actual Trophic Status of Lake Ray Roberts, Texas Based on Chlorophyll A

Description: Two years before impoundment, the trophic status of Lake Ray Roberts was predicted by applying the total phosphorus input into the Organization for Economic Cooperation and Development (OECD) eutrophication model. Predicted mean summer epilimnetic (MSE) chlorophyll a of Elm Fork arm, Isle duBois arm and Main Body were in the eutrophic category of the OECD model. Observed MSE chlorophyll a two years after impoundment of Elm Fork arm, Isle duBois and Main Body had not reached their predicted means and were at the mesotrophic-eutrophic boundary of the OECD model. Six years after impoundment, observed MSE chlorophyll a for Main Body, was closer to its predicted mean and in the eutrophic category of the OECD model. Six years after impoundment, Elm Fork arm was the most productive area of Lake Ray Roberts. Observed means of chlorophyll a, total phosphates, suspended solids and turbidity were often highest in the Elm Fork arm. Wastewater effluent from Gainesville and Valley View, TX, had an impact on productivity in Elm Fork arm.
Date: May 1999
Creator: Lytle, Lili Lisa

Comparison of Remediation Methods in Different Hydrogeologic Settings Using Bioplume II

Description: A contaminant fate and transport computer model, Bioplume II, which allows simulation of bioremediation in ground water systems, was used to compare the effects of 11 remediation scenarios on a benzene plume. The plume was created in three different hydrogeologic settings from the simulation of an underground gasoline storage tank leak.
Date: May 1996
Creator: White, Sherry A. (Sherry Anne)

Construction of a Physical Map of Moraxella (Branhamella) catarrhalis Strain ATCC25238

Description: In order to gain a better understanding of this microorganismand its role in human pathogenesis, a physical map of Moraxella catarrhalis type strain ATCC25238 was constructed using pulsed field gel electrophoresis (PFGE) in combination with Southern hybridization techniques. Restriction endonucleases Not I, Rsr II, and Sma I were used to digest the chromosomal DNA. An overlapping circular map was generated by cross-hybridization of isolated radiolabeled fragments of Moraxella catarrhalis genomic DNA to dried PFGE gels. The number and location of the 16S and 23S ribosomal RNA genes were determined by digestion with l-Ceul enzyme and by Southern hybridization. Virulence-associated genes, the gene for β-lactamase, and housekeeping genes were also placed onto the physical map.
Date: May 1999
Creator: Nguyen, Kim Thuy