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ItemAge and growth of the white crappie, Pomoxis Annularis Rafinesque, in Lake Waco, Texas.(1969) Chen, Terry Huei-Hsiung; Lind, Owen T., 1934-; Baylor University.The major collection of white crappie was from 17 July 1967, to 10 April 1968, by traps and gill nets. Other fish were taken by anglers and seines in June 1968. A total of 1142 fish were included in this study. Spawning season for Lake Waco crappie was from late February to early May and was at its peak in March and April. White crappie in Lake Waco may spawn after one year. Growth rate of Lake Waco white crappie was rapid. The average back-calculated total lengths(TL) for Lake Waco crappie for the last 4 years were as follows: 145mm for the first year’s growth, 216mm for the second age group, 271mm for the third age group, and 309mm for the fourth age group. In the white crappie scales started to develop on the caudal peduncle in fish 16mmTL. The first fully scaled fish observed was 31mmTL. The region between the dorsal fin and pectoral fin was the last place to develop scales. The mathematical expression of the length-weight relationship for the white crappie of Lake Waco is: log W = -5.6131 + 3.2954 log L where W= body weight in grams L=total length in millimeters. The body-scale relationship demonstrated a parabolar curve. The equation L=35.506219 + 1.215665 S + 0.000931 s2 fitted the body-scale relationship of Lake Waco white crappie well. Principal food items of white crappie were small fishes (mainly shads, Dorosoma cepedianum and D. petenense), aquatic insects, and small crustaceans. Lymphocystis was only found in the spring, and about 1.7 percent of the fish were infected. Infection by nematode parasites, Camallanus oxycephalus, was observed in the spring and summer, but infected fish showed no signs of weakness. ItemAlder cover drives nitrogen availability and decomposition of grass litter in salmon-rearing headwater streams, Kenai Peninsula, Alaska.(2010-10-08T16:26:59Z) Shaftel, Rebecca S.; King, Ryan Steven, 1972-; Biology.; Baylor University. Dept. of Biology.Terrestrial sources of nitrogen (N), such as N fixed by alder, may be important for sustaining production in headwater streams that typically lack subsidies of nutrients from spawning salmon. High nutrient concentrations in streams increase litter decomposition and can offset the low nutrient quality of grass litter. Alder cover was compared to watershed physiographic variables as predictors of stream N and contrasted over the growing season among 25 headwater streams. Leaf packs of bluejoint grass were deployed for two months across a nutrient gradient of 6 headwater streams. Alder cover explained over 75 – 96% of the variance in stream N. Bluejoint breakdown rates were related to dissolved stream nutrient concentrations and litter quality. A diversity of macroinvertebrate consumers utilized bluejoint for habitat and food. Alder drives stream N concentrations and the breakdown rate of bluejoint, which is an important consumer resource during the summer months when deciduous litter inputs are low. ItemAnalysis of Escherichia coli populations in a large watershed.(2008-06-10T20:44:35Z) Nemec, Michelle D.; Drummond Massengale, Andrea Rene.; Biology.; Baylor University. Dept. of Biology.Escherichia coli are one of the most common model organisms used today. This organism has played an integral role in our understanding of bacterial conjugation, phage genetics, and gene structure, and it is also responsible for many of the advances in the areas of proteomics and biotechnology. However, very little is known about the characteristics of E. coli populations in their natural habitats. In this study, three characteristics of E. coli populations isolated from nine different sources were investigated, including: 1) antibiotic resistance, 2) carbon–substrate usage, and 3) genetic diversity. Antibiotic resistance was examined using eight antibiotics. Overall, the incidence of amoxicillin resistance was high in all of the E. coli populations, and multi-drug resistance was common. Antibiotic resistance was prevalent across populations, and the highest level of resistance was found in isolates obtained from sewage and dairy cattle. The carbon–substrate utilization of the E. coli populations was examined using Biolog GN2 microplates. The fundamental metabolic capabilities of the E. coli isolates were relatively stable across populations; however, variation did occur in the extent to which some isolates in the populations could utilize the various carbon substrates. Metabolic similarities were greatest between E. coli isolates from the same population. Rep–PCR was implemented to assess the genetic diversity present in the various E. coli populations. Overall, the genetic diversity of the E. coli isolates appeared to be large. Unfortunately, there are very few other studies available with which to compare these data. The level of genetic diversity varied between each population of isolates; although, isolates from the same population tended to be more genetically similar than isolates from different populations. Finally, Jackknife analysis demonstrated that the various E. coli populations were more distinct from each other genetically than they were based on antibiotic resistance or carbon–utilization. When all three characteristics were combined, relatively clear distinctions could be made between most populations. When the characteristics of E. coli isolated from water were compared with the characteristics of the isolates from the other sources, the majority of the water isolates were most similar to E. coli obtained from cattle. ItemAnalysis of the microfilariae-specific transcriptome of Brugia pahangi during mosquito infection.(2016-04-05) Cotten, Michael A., 1992-; Sim, Cheolho.Development of a transmission-blocking vaccination may provide cost-effective means of preventing the spread of lymphatic filariasis. Here, vaccine candidates were derived from the transcriptomic profiles of two separate developmental life stages of B. pahangi: microfilariae and third-stage larval. Analysis of these differential transcripts provided a detailed overview of expression profiles unique to each developmental stage. Differentially expressed transcripts were scored before the 14 highest ranked transcripts were validated via qRT-PCR. Seven candidate genes were identified as potential targets for transmission-blocking vaccines; two types of Serpins, two types of Cathepsin, Hsp70, Ubiquitin, and Chitinase. Genes selection was limited to secretory or transmembrane proteins in order to increase the proficiency of transmission-blocking vaccine candidates. Finally, we discussed the potential role of each candidate gene in B. pahangi during the midgut infection stage in the mosquito Culex pipiens. ItemAnti-tumor properties of CD40 ligand when delivered as a transgene by the conditional replicative oncolytic adenovirus AdEH to breast cancer cells.(2007-02-14T21:54:39Z) Gomes, Erica Manuela.; Tong, Alex W.; Biomedical Studies.; Baylor University. Institute of Biomedical Studies.Cancer-selective biotherapy and gene therapy have been considered to be the next horizon towards developing a cure for breast cancer. CD40 ligand (CD40L), a member of the tumor necrosis factor superfamily, relays critical growth signals in various hematological malignancies and carcinomas. We previously demonstrated that recombinant CD40L can directly inhibit breast cancer cell growth. However a potential limitation of CD40L therapy is systemic toxicity. To improve efficacy of gene delivery and limit CD40L expression to the tumor micro-environment, we have generated a conditionally replicative virus (AdEHCD40L) that delivers CD40L selectively to breast carcinomas. Tumor/tissue-specific promoters (hypoxic/HIF-1α response and estrogen response elements) were incorporated to limit CD40L expression to the tumor microenvironment. Viral E1A and CD40L transgene expression was examined in breast cancer lines with low constitutive (T47D) or no (BT-20) HIF-1α expression. Both cell lines displayed significantly increased CD40L expression under viral- permissive conditions (T47D: 65.5 ± 3.9% with increased HIF-1α vs. 38.5 ± 2.8% under uninduced condition, p = 0.01; BT20: 43.2 ± 14.9% vs. 10.6 ± 0.2%, p = 0.03). AdEHCD40L produced markedly stronger inhibition compared to the parental construct (T47D: 53.7 ± 15.2% vs. 32.1 ± 11.7%, p = 0.02; BT20: 25.8 ± 10.2% vs. 15.2 ± 6.8%, p = 0.03), suggesting that growth inhibition encompassed CD40L-mediated and viral oncolytic events. Replicative activity of AdEHCD40L was comparable to the wild type adenovirus in breast cancer cells and attenuated in normal lung fibroblast cells, with reduced growth inhibitory impact. Preliminary findings on mechanisms of AdEHCD40L cytotoxicity indicated increased apoptotic (Annexin V+) and necrotic (propidium iodide incorporation) activities that were accompanied by reduced IBα, phosphorylation, G2M/S cell cycle arrest, culminating in an increased sub-G0 fraction, and altered chemokine/cytokine expression. AdEHCD40L biodistribution and its maximum tolerated dose (2x108 pfu) evaluated in mice were comparable to that of other conditional-replicative adenoviruses. Anti-tumor efficacy of AdEHCD40L showed a reduction in mean tumor diameter of MDA-MB-231 (44-58%) and T47D (49%) human breast cancer xenografts in SCID mice. These findings illustrate the applicability of CD40L gene transfer approach for experimental treatment of human breast cancer. ItemAre aquatic food webs vulnerable to copper and gold engineered nanoparticles?(2020-11-04) Perrotta, Brittany G., 1991-; King, Ryan Steven, 1972-Freshwater ecosystems are exposed to engineered nanoparticles through municipal and industrial wastewater-effluent discharges and agricultural non-point source runoff. These same anthropogenic waste streams which contain high concentrations and diversity of nanoparticles also contain excess nitrogen and phosphorus. The interaction between nanoparticles (NPs) and nutrients remains poorly understood within the context of aquatic food webs. To address this interaction, I examined the impacts of a citrate-coated gold nanoparticle (AuNPs) and a commercial pesticide containing Cu(OH)2 nanoparticles (CuNPs) on aquatic food webs under both ambient and enriched nutrient conditions. In the 2016 CEINT Wetland Mesocosm study, mesocosms were exposed repeatedly with low, environmentally realistic concentrations of nanoparticles and nutrients over the course of a 9-month experiment. My work during this study determined decreased insect emergence in nanoparticle treatments, aquatic to riparian metal export via aquatic insect emergence, and subsequent metal accumulation in riparian spiders. In that same study, I demonstrated that consumers exposed to nanoparticles doubled excretion rates of nitrogen and phosphorus and likely contributed to the increased persistence of algal blooms as observed in our mesocosm experiment. To address these findings, I designed and executed a stream microcosm experiment to validate and mechanistically understand ecological responses observed in our mesocosm study, increased consumer nutrient excretion rates and persistence of algal blooms. The microcosm study demonstrated a high impact of dissolved gold to algal biomass, nutrient uptake, and bacterial community composition of both periphyton and snail gut. Engineered NPs and nutrients have significant and quantifiable effects on aquatic ecosystems, though responses may not be easily measured or are sub-lethal, in many cases and require monitoring over long time periods. Overall, my results suggest that 1) NPs decrease insect emergence and exhibit trophic transfer from aquatic insects to riparian spiders and 2) double consumer mediated nutrient recycling rates resulting in a higher availability of nutrients available for plant uptake and 3) increase the algal biomass and alter microbial communities in periphyton and snail gut microbiome. Thus, the long-term effects of NPs and nutrients in aquatic ecosystems could significantly alter aquatic ecosystem function. Aquatic food webs are indeed vulnerable to engineered nanoparticles. ItemBacterial dynamics at the sediment-water interface of a stratified, eutrophic reservoir.(2007-03-08T15:35:55Z) Christian, Bradley W.; Lind, Owen T., 1934-; Biology.; Baylor University. Dept. of Biology.Sediment-water interfaces (SWIs) are loci of dynamic physical, chemical, and biological interactions in stratified, eutrophic reservoirs. Seasonal reservoir mixing and stratification affects SWI physicochemical processes as well as bacterial abundance, diversity, biomass, and metabolism. Because SWI bacteria transform chemicals and release nutrients that affect water quality and eutrophication, seasonal changes in these bacterial dynamics help define reservoir carbon and nutrient cycles and trophic interactions. Four studies were conducted to assess SWI bacterial dynamics in Belton Reservoir, a eutrophic, monomictic impoundment. The first utilized [3H]-L-serine to measure SWI bacterial activity and biomass production. Highest activity and production occurred during summer stratification under anoxic conditions. Lowest activity and production occurred under oxic conditions during autumnal overturn and winter mixing. The second study consisted of two parts, both utilizing Biolog EcoPlates to measure SWI carbon substrate utilization rates (CSURs). The first part tested the effectiveness and interpretability of EcoPlates. Optimal use was dependent upon inoculum density, incubation temperature, and aerobic/anaerobic incubation techniques. The second part concluded that CSURs for carbohydrates were highest during onset of stratification and winter mixing, CSURs for amino acids were highest during winter mixing, and CSURs for carboxylic acids were highest during late season stratification. The third study analyzed quantities and sources of SWI carbon, nitrogen, and bulk organic matter (OM). OM concentration did not differ among seasons. Inorganic carbon and nitrogen differed seasonally. OM C/N ratios and stable isotopes (13C and 15N) were significantly different at the SWI of the shallowest depths, indicating that OM at this site was of allochthonous origin. The last study utilized automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) to elucidate total and sulfate-reducing (SRB) SWI bacterial diversity and similarity. Total SWI bacterial diversity did not significantly differ. During stratification, high similarity occurred among sites on individual dates. During mixing, high similarity occurred through time. Although SRB are functionally strict anaerobes, they exhibited higher richness during oxic rather than anoxic conditions. ItemBacterial growth on UV-B photolytically produced dissolved organic matter.(1995) Velarde, Gabriela; Lind, Owen T., 1934-; Baylor University.The effect of ultraviolet radiation into the Lake Chapala trophic processes was investigated in this study. Responses of bacterial populations to changes in UV radiation exposed water were significantly greater (bacterial biomass increased 57% and cell concentration increased 92%) compared to those populations that were grown in water covered by glass as UV blocker. Measurements for penetration of ultraviolet radiation in the water column of Lake Chapala were made at midday and to a depth of 0.45 m in one of the clearest parts ofthe lake (Station 11). Ten per cent of the UV radiation that reached the surface ofthe lake was still present at 0.2 m of depth. The extinction coefficient was 10.1 m. For a lake with low phytoplankton productivity, the supply of organic carbon via photolysis ofrefractory material may be an important supplement to bacteria in the water column. ItemBacteroides fragilis outer membrane vesicles are used for secretion of a discrete subset of bacterial RNAs that stimulate an immune response in colonic epithelial cells.(May 2023) Sheikh, Aadil, 1996-; Greathouse, K. Leigh.Alterations in the diversity and function of the gut microbiome are associated with changes in the host physiology, including inflammation. A critical component of the inflammatory response system are receptors capable of sensing foreign nucleic acids (e.g. small RNAs) that are carried as cargo in bacterial outer membrane vesicles (OMVs). The mechanisms by which human extracellular RNAs elicit immune responses have been well established, while the contribution of bacterial sRNA to host physiology remain unclear. We hypothesize that pathogenic and commensal microbes use OMV-associated small RNA species to differentially affect host inflammatory responses. First, we profiled the small RNA contents of purified OMVs from a commensal strain (NTBF) and a pathogenic strain (ETBF) of Bacteroides fragilis. To distinguish the differences in the sRNA profiles of both strains and their OMVs, we conducted small RNA-seq and identified enrichment of discrete sRNA species in OMVs that were also differentially expressed between the two strains. This evidence led us to investigate the differential effects of these OMVs upon intestinal epithelial cells. To understand the effects of OMVs on pattern recognition receptors, we treated Toll-like receptor (TLR) reporter cells with NTBF and ETBF vesicles. We observed activation of TLR2 in a dose-dependent manner, and activation of TLRs 3 and 7 at high doses of OMVs. Using Caco-2 and HT29 cells exposed to OMVs from each strain, we ran qPCR to test several pro- and anti-inflammatory cytokines. We observed that both strains upregulate the expression of IL-1β and TGFβ, but NTBF stimulates a greater IL-8 response compared to ETBF. These results indicate that bacteria may preferentially load small RNAs into vesicles that target host cells, which differentially affect host immune responses through RNA-sensing pathways. Overall, our data suggest a key function of bacterial small RNAs and their OMV vehicles in controlling host immune system. ItemBasking dynamics among sympatric turtle species (Trachemys scripta elegans, Pseudemys texana, and Graptemys pseudogeographica kohnii) in Waco Creek, Texas.(2013-09-24) Bardwell, Jeff H.; Duhrkopf, Richard.; Biology.; Baylor University. Dept. of Biology.The premise of this manuscript condenses into three words: turtles on logs. Turtles splaying their limbs and sunning themselves on emergent deadwood is commonly known as basking. Basking involves ectotherms taking advantage of solar radiation to boost their core temperature and fuel metabolic processes. This study examines a community assemblage of three turtle species within the Family Emydidae—Trachemys scripta elegans: Red-eared Slider, Pseudemys texana: Texas River Cooter, and Graptemys pseudogeographica kohnii: False Map Turtle—in Waco Creek, Texas, a tributary of the Brazos River, from 2010-2012. Turtles were collected daily via specialized traps which take advantage of repetitive basking habits, individually marked, measured, identified, and then released from June to October 2010, April to October 2011, and April to October 2012. Multiple recaptures allowed for observation of individual, population, and community progression over time. This manuscript asks three fundamental questions about the role of basking behavior in the Waco Creek emydid turtles: 1) What is the significance of the basking community assemblage composition in Waco Creek, 2) How do basking trap modifications and population demographic selection affect group trap response, and 3) How do polynomial and k-growth mixed models describe juvenile turtle logistic growth? Trachemys scripta elegans comprise 46%, Pseudemys texana 32%, and Graptemys pseudogeographica kohnii 23% sample composition within the Waco Creek basking turtle assemblage. All mature populations were significantly male skewed and turtle demographics exhibited several expected seasonal behavior patterns. The community has a large abundance of juveniles, young males, and immature females regardless of species. In addition, juvenile T. scripta appear to be the most actively basking demographic. Between individual demographic behavior and trap design as predictors for trap response, demographic behavior was significant across most response variables whereas trap design variables were not. This study pioneered a new technique for comparing turtle logistic growth models using a polynomial mixed model as a control. With an adequate sample size and consistent seasonal dispersal, results from this technique agree with reports from the literature and look promising. ItemBat activity in forest margins : canopies, edges, seasonality, and competition.(2011-12-19) Pettit, Thomas W.; Wilkins, Kenneth T., 1953-; Biology.; Baylor University. Dept. of Biology.Forest edges provide open space that bats often use to travel and forage. As another type of margin, forest canopies provide similar structural space for bat activities. Such margins may supply bats in forests with the structural resources they require, such that some species could compete over edge space as a preferred habitat type. This project examined the role of forest canopies and edges as an important habitat type for bats through the observation and examination of bat activity levels. Bat communities in the Rocky Mountains of northern Utah (summers 2008-2009) and the pineywoods of eastern Texas (fall 2009 and spring 2010) were observed through the use of Anabat SD1 bat detectors. Activity levels of bats in Utah were much higher in forest edges than in canopies. This phenomenon appears to have a strong seasonal component, during which period competition over edge resources intensifies between high and low frequency guild bats. In the pineywoods of eastern Texas, bat activity levels also differ between canopies and edges, but bats in this habitat seem to shift seasonally between margin types. These shifts may coincide with seasonal migrations of some bat species. Future research would further investigate seasonality in bat activity, and better define the role of clutter in bat activity in forest margins. ItemBiological nitrogen fixation in a nitrogen limited tropical lake, Lake Chapala, Mexico.(1987) Glass, Joan Ann; Lind, Owen T., 1934-; Baylor University.The objective of my study was to quantify the rate of biological nitrogen fixation in Lake Chapala, Mexico. Lake Chapala is the largest lake in Mexico. It is an ancient, tropical lake which is shaped in an east-west culde-sac with the inflow and outflow at the eastern end. Previous work showed low available nitrogen leading to nitrogen limitation of primary production. These measurements of available nitrogen ranged from undetectable to 1.8 _ - | mg 1 on an east-west gradient of sampling stations throughout the year. Nitrogen levels were lowest at the western end of the lake. Biological nitrogen fixation rates were expected to increase as the ambient nitrogen decreased. However, biological nitrogen fixation, measured by the acetylene reduction technique, was negligible at all stations. A reverse from the expected gradient of nitrogen fixation was found in the water from Lake Chapala when mixed with known nitrogen-fixing cyanobacteria. Greater nitrogen fixation by the added cyanobacteria was found with greater available nitrogen in the water. Also, the rate of nitrogen fixation by the introduced cyanobacteria increased when the water from Lake Chapala was filtered. This increased rate i i i of nitrogen fixation by the introduced cyanobacteria was attributed to the removal of an inhibitor within the water of Lake Chapala, Mexico. The lack of nitrogen fixation in Lake Chapala was attributed to the lack of filamentous cyanobacteria. There are three factors which may have inhibited the growth or functioning of cyanobacteria: 1) The high winds mixing this shallow lake inhibited growth of chains and mat formation of cyanobacteria. 2) Wind-induced turbidity contributed to light inhibition of cyanobacteria in the water column and sediments. 3) Organism on the suspended particulates or chemical compounds adsorbed to the suspended particulates may have been an inhibiting factor. ItemBiological trait responses of river macroinvertebrate assemblages to a phosphorus gradient.(2016-11-28) Housley, Lauren M., 1984-; King, Ryan Steven, 1972-Phosphorus is the most important nutrient driving anthropogenic eutrophication of inland fresh waters. Several river basins in the Ozark Highlands and Boston Mountains ecoregions of central North America have elevated concentrations of total phosphorus, due to both point-source discharges and nonpoint source runoff in their catchments. Benthic macroinvertebrate responses, expressed as density and biomass of biological trait groups (functional feeding group, voltinism), were modeled across a steep phosphorus gradient spanning 35 river locations. Biomass and density increased across the gradient, and communities shifted from diverse, insect-dominated communities to communities dominated by small, multivoltine taxa (such as Chironomidae) and benthic algal grazers, particularly pleurocerid snails. These shifts are likely related to increased benthic primary production and supply of phosphorus to small-bodied consumers with high phosphorus demand (under the growth rate hypothesis). These results imply that phosphorus enrichment can have significant effects at multiple trophic levels in river ecosystems. ItemBlubber fatty acid signature analysis of harbor seals in Alaska, 1997-2010.(2022-03-21) Neises, Victoria M., 1985-; Trumble, Stephen John.The projected course and rate of global climate change presents major challenges to the wellbeing and survival of Arctic and subarctic marine mammals. In Alaska, the harbor seals (Phoca vitulina richardii) broad range and severe population decline within certain regions led to increased research efforts to investigate the potential influence of diet changes on their lack of recovery. While these studies provide the foundation of knowledge regarding Alaskan harbor seal foraging ecology, detailed temporal and spatial changes in the harbor seals diet and possible impacts of diet overlap with other Alaskan pinnipeds has yet to be investigated. To date, the majority of harbor seal diet studies have used traditional diet determination methods. Due to the inherent limitations and sampling biases associated with these traditional techniques, blubber fatty acid (FA) analysis has emerged as one of the best methods of investigating diet in marine mammals. The goal of this dissertation was to characterize blubber FAs of Alaskan harbor seals through the evaluation of 15-years of blubber FA signatures. To gain an understanding of spatial and temporal differences, harbor seal blubber FA profiles were qualitatively investigated for regional, seasonal, and age class differences. In addition, to examine possible prey resource partitioning between different species populations, we compared regional and seasonal FA profiles of harbor seals and Steller sea lions within Prince William Sound and Southeast, Alaska. Lastly, differences between harbor seal reproductive state (pregnant, lactating, non-lactating-non-pregnant females), mother-pup pairs, and pinniped families were investigated to explore harbor seal blubber FA distribution during lactation. Key findings demonstrate the large degree of diet variability among harbor seal stocks within Alaska and shed light on how diet differences among Alaskan pinniped populations, and the physiological and behavioral limitations of the harbor seal lactation strategy, may be impairing population recovery in certain areas. As a sentinel species in Alaska, the ability to survey blubber FAs of harbor seals provides a way to not only monitor diet changes that could lead to population level impacts, but also provides a means to oversee prey community changes and ecosystem health within the regions they inhabit. ItemCharacterization of a nonsense-mediated mRNA decay (NMD) copper regulon.(2015-07-17) Peccarelli, Megan C., 1988-; Kebaara, Bessie W.The nonsense-mediated mRNA decay (NMD) pathway was originally identified as a pathway that degrades mRNAs harboring premature termination codons. NMD is now also recognized as a pathway that degrades natural mRNAs. In Saccharomyces cerevisiae, five features are known to target natural mRNAs to NMD. The extent to which natural mRNAs from the same functional group are regulated by this pathway is not widely known. Here, we invested eight mRNAs involved in copper homeostasis that are predicted to be sensitive to NMD. We found that majority of these mRNAs have atypically long 3'-Untranslated Regions (UTRs) that could potentially target them for NMD-mediated degradation. We investigated the sequence elements that target a subset of these mRNAs to NMD and found that the long CTR2 3'-UTR and the COX23 3'-UTR are sufficient to target an NMD-insensitive mRNA to NMD. We also found that the COX19 and FRE2 3'-UTRs contribute to the degradation of the transcripts by the pathway. Additional studies involving sequence elements demonstrated that lengthening the open reading frame of CTR2 abrogates NMD, preventing degradation of the mRNA. Moreover, we found that transcription of CTR2 mRNAs driven by the GPD promoter causes altered NMD sensitivity when compared to CTR2 driven by the CTR2 promoter. Lastly, we found that low copper growth conditions affect NMD sensitivity of the MAC1 mRNA; demonstrating that NMD can be influenced by environmental conditions. The studies presented here are novel in that they investigate the regulation of functionally related, natural mRNAs by NMD. We show that the regulation of these mRNAs is transcript specific, and that regulation can be influenced by sequence elements as well as the environmental conditions. ItemCharacterization of Hemicentin in C. elegans(2020-04-21) Ahumada, Abraham; Haworth, Emma; Ross, Kylie; Sowinski, Halee; Antony, Keerthi; Myeongwoo, Lee; Baylor University. Dept. of Biology; Baylor University.; Baylor University. Dept. of BiologyCharacterization of Hemicentin in C. elegans Emma Haworth, Kylie Ross, Halee Sowinski, Keerthi Antony, Abraham Ahumada Department of Biology, Baylor University, One Bear Place 97388, Waco, TX 76798, U.S.A In the nematode, Caenorhabditis elegans, the him-4 gene linked to the X chromosome encodes hemicentin protein, a component of the extracellular matrix (ECM), which is characterized by 45 immunoglobulin repeats, and fibulin-like domains. The ECM is a three-dimensional network composed of proteins and sugars deposited outside of the cell. ECM proteins are typically large, glycosylated, and contain repeats and motifs for cell binding. Hemicentin is specifically present in the basement membrane (BM), a special sheet-like ECM, that plays an important role in cell migration and tissue attachment, and stability of mitotic germ cells. HIM-4 contains six RGD motifs, a protein sequence specific to the integrin binding receptor. In the following study, CRISPR gene editing was used to create mutations in him-4 at two of the six RGD sequences. These sequences were targeted to replace the D amino acid (Aspartic Acid) with the E amino acid (Glutamic Acid). This mutation in him-4 causes defective phenotypes related to cell binding. We have isolated several targeted animals with tissue fragility, suggesting that the RGD sequence is vital for the function of the protein; the gene editing may interfere with hemicentin binding to the integrin receptor. The disruption of the ECM causes improper attachment of the gonad BM to epithelial BM leading to the hemorrhaging of the gonads and the intestines in C. elegans. The observation of the hemorrhaging phenotype and the single-worm PCR will be used to detect CRISPR-induced homozygous alleles. This research may allow for further studies on gonad development and human orthologs of the hemicentin protein. The connection between the hemicentin protein and the ECM deformities may offer insight into diseases associated with tissue fragility. ItemChemical toxicity distributions in aquatic toxicology : relative sensitivities of estrogenicity assays and ecotoxicity of parabens in model freshwater organisms.(2008-12) Dobbins, Laura L.; Brooks, Bryan W.; Biology.; Baylor University. Dept. of Biology.A probabilistic ecological hazard assessment technique, chemical toxicity distributions, was used to examine the relative sensitivities of in vitro and in vivo assays for detecting estrogenicity, and to assess the hazards associated with parabens to model aquatic organisms, Pimephales promelas and Daphnia magna. Parabens represent a class of understudied personal care products with estrogenic activity that have been detected in surface waters. MCF-7 and rainbow trout vitellogenin induction were found to be the most sensitive in vitro and in vivo assays of estrogenicity, respectively. Parabens were determined to not pose a hazard to aquatic organisms at levels that are environmentally relevant, based on the bioassay endpoints evaluated. A screening level assessment further identified estrogenic activity of select parabens to adult male P. promelas. This thesis demonstrated the utility of chemical toxicity distributions for determining sensitivities among toxicological models and for assessing those compounds for which environmental exposure data are limited. ItemComparing the genetic diversity of late Pleistocene Bison with Modern Bison bison using ancient DNA techniques and the mitochondrial DNA control region.(2007-01-22T18:45:33Z) Douglas, Kory C.; Baker, Lori; Adams, Robert P.; Biology.; Baylor University. Dept. of Biology.The transition between the Pleistocene and Holocene Epochs brought about a mass extinction of many large mammals. The genetic consequences of such widespread extinctions have not been well studied. Using ancient DNA and phylogenetic techniques, we compared the genetic diversity and phylogenetic relatedness of extinct Pleistocene Bison ranging from Siberia to mid-latitude North America (10,000 ybp to 50,000 ybp) to extant Bison bison. The mitochondrial DNA control region was sequenced from 10 Bison priscus skulls obtained from the Kolyma Region of Siberia, Russia. Control region sequences from other Pleistocene Bison and Bison bison were obtained from Genbank. Our analysis indicates a measurable loss of genetic diversity in Bison bison compared to Pleistocene Bison. Furthermore, the Pleistocene Bison population was strongest in North America from a time period of 30,000 ybp to 10,000 ybp, and the genetic diversity present in this population is not represented in the Bison bison population. ItemConstructing a nectar delivery system for mosquito control using Impatiens walleriana.(2020-11-18) Pruett, Grace E., 1991-; Kearney, Christopher Michel, 1958-Mosquitoes are vectors of numerous human pathogens. These pathogens are spread when female mosquitoes blood feed to lay eggs. Since males do not feed on blood and females mostly need blood to produce eggs, both consume plant nectar as a primary source of energy. Previously, a study of mosquito nectar preference showed that extrafloral nectar from Impatiens walleriana is an attractive food source for mosquitoes and has potential to become a platform for delivering targeted peptides to mosquitoes. However, since this study was conducted indoors, the assumption that impatiens nectar will attract mosquito feeding outdoors needs to be tested. This dissertation tests three components necessary for the development of mosquitocidal nectar technology: (1) the assumption that mosquitoes will feed on impatiens nectar outdoors; (2) the development of mosquito-specific peptides; and (3) the development of a nectar expression model in Impatiens walleriana. The first component of outdoor nectar feeding was tested by measuring the nectar feeding of 3 mosquito species in outdoor, simulated gardens. This work demonstrated that the nectar of Impatiens walleriana is highly attractive to mosquitoes in an outdoor setting despite the presence of potentially compounding factors. To develop mosquito-targeted peptides for the second component, an external loop of Domain III from the Dengue virus type 2 envelope glycoprotein was attached to the fluorescent protein EGFP and spider toxin Hv1a and fed to Aedes aegypti and Culex quinquefasciatus mosquitoes. The midgut binding of the targeted EGFP and specific oral toxicity of the targeted Hv1a in Ae. aegypti but not Cx. quinquefasciatus indicates that the addition of the targeting domain conferred species-specific targeting to these proteins. For the third technology component, to develop a nectar expression model in Impatiens walleriana, nectary promoters and a nectar-specific signal peptide were identified from Impatiens walleriana using RNA, DNA and protein sequencing. These methods identified promoters for phylloplanin and SWEET14 homologs and a nectar-specific signal peptide from the phylloplanin homolog. These elements will be used alongside other non-native promoters and signal peptides to see which promoter/signal peptide combination achieves the highest level of foreign protein expression in transgenic impatiens nectar. The first component of outdoor nectar feeding was tested by measuring the nectar feeding of 3 mosquitoes species in outdoor, simulated gardens. This work demonstrated that the nectar of Impatiens walleriana is highly attractive to mosquitoes in an outdoor setting despite the presence of potentially compounding factors. To develop mosquito-guided peptides for the second component, an external loop of Domain III from the Dengue virus type 2 envelope glycoprotein was attached to the fluorescent protein EGFP and spider toxin Hv1a and fed to Aedes aegypti and Culex quinquefasciatus mosquitoes. The midgut binding of the guided EGFP and specific oral toxicity of the guided Hv1a in Ae. aegypti but not Cx. quinquefasciatus indicates that the addition of the guiding domain conferred species-specific targeting to these proteins. For the third technology component, to develop a nectar expression model in Impatiens walleriana, nectary promoters and a nectar-specific signal peptide were identified from Impatiens walleriana using RNA, DNA and protein sequencing. These methods identified promoters for phylloplanin and SWEET14 homologs and a nectar-specific signal peptide from the phylloplanin homolog. These elements will be used alongside other non-native promoters and signal peptides to see which promoter/signal peptide combination achieves the highest level of foreign protein expression in transgenic impatiens nectar. ItemCTR2 and the nonsense-mediated mRNA decay pathway in Saccharomyces cerevisiae.(2012-11-29) Wang, Xuya.; Kebaara, Bessie W.; Biology.; Baylor University. Dept. of Biology.The nonsense-mediated mRNA decay (NMD) pathway recognizes and degrades mRNA with premature termination codon and some natural mRNA as well. CTR2 is a natural mRNA degraded by NMD in Saccharomyces cerevisiae. The goals of this research were to identify the sequence features that target the CTR2 mRNA for NMD and the physiological consequences resulting from this degradation. These goals were addressed by making fusion constructs and determining total cellular, cytoplasmic and vacuolar copper levels in wild-type and nmd mutant yeast cells. Features contribute to the NMD-mediated degradation of CTR2 were identified. When cultured in medium with excess copper, nmd mutants accumulated significantly higher vacuolar copper levels than wild-type yeast cells, however nmd mutants accumulated significantly less cytoplasmic copper levels than that in wild-type yeast cells. These results are consistent with the inference that nmd mutants tolerate excess copper as a result of ctr2p transporting excessive copper from cytoplasm into vacuole.