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Interrelational Laboratory Information System for Data Storage and Retrieval
The necessity for a functional user friendly laboratory data management program has become evident as the quantity of information required for modern scientific research has increased to to titanic proportions. The required union of strong computer power, ease of operation, and adaptability have until recently been outside the realm of most research laboratories. Previous systems, in addition to their high cost, are necessarily complex and require software experts in order to effect any changes that the end user might deem necessary. This study examines the Apple Macintosh computer program Hypercard as an interactive laboratory information system that is user-friendly, cost effective, and adaptable to the changing demands within a modern molecular or microbiology.
The Interrelationship of Macro- and Microbenthos to Substrate Characteristics in Lake Ray Roberts Texas
The objective of this research was to determine if physical and microbial sediment characterizations could be used to explain benthic macroinvertebrate distribution in two branches of Lake Ray Roberts, Texas.
Interspecific Competition Between Hygrophila polysperma and Ludwigia repens, Two Species of Importance in the Comal River, Texas
Hygrophila polysperma is a plant native to Asia that has been introduced into the Comal River, TX and is thriving while Ludwigia repens, a species native to the river appears to be declining. Both plants have similar morphologies and occupy similar habitats in the river. Two plant competition experiments were conducted to examine the competitive interactions between the two species. First, an experimental design was developed in which established Ludwigia plants were 'invaded' by sprigs of Hygrophila to determine if established Ludwigia populations would be negatively impacted by invasion. The second experiment focused on establishment and growth of sprigs of each species under three competition scenarios. Results show that the continued growth of well-established Ludwigia plants was significantly depressed by the invasion of Hygrophila in comparison with those that had not been invaded. Furthermore, the growth of Hygrophila sprigs was uninhibited by the presence of Ludwigia, but the presence of Hygrophila negatively impacted the growth of Ludwigia sprigs. There was no difference in the growth of Hygrophila sprigs whether planted alone, with Ludwigia sprigs or even if planted into stands of established Ludwigia.
Investigating Human Gut Microbiome in Obesity with Machine Learning Methods
Obesity is a common disease among all ages that has threatened human health and has become a global concern. Gut microbiota can affect human metabolism and thus may modulate obesity. Certain mixes of gut microbiota can protect the host to be healthy or predispose the host to obesity. Modern next-generation sequencing technique allows accessing huge amount of genetic information underlying microbiota and thus provides new insights into the functionality of these micro-organisms and their interactions with the host. Multiple previous studies have demonstrated that the microbiome might contribute to obesity by increasing dietary energy harvest, promoting fat deposition and triggering systemic inflammation. However, these researches are either based on lab cultivation studies or basic statistical analysis. In order to further explore how gut microbiota affect obesity, this thesis utilize a series of machine learning methods to analyze large amount of metagenomics data from human gut microbiome. The publicly available HMP (Human Microbiome Project) metagenomic sequencing data, contain microbiome data for healthy adults, including overweight and obese individuals, were used for this study. HMP gut data were organized based on two different feature definitions: taxonomic information and metabolic reconstruction information. Several widely used classification algorithms: namely Naive Bayes, Random Forest, SVM and elastic net logistic regression were applied to predict healthy or obese status of the subjects based on the cross-validation accuracy. Furthermore, the corresponding feature selection algorithms were used to identify signature features in each dataset that lead to the differences between healthy and obese samples. The results showed that these algorithms perform poorly on taxonomic data than metabolic pathway data though lots of selected taxa are still supported by literature. Among all the combinations between different algorithms and data, elastic net logistic regression has the best cross-validation performance and thus becomes the best model. In this model, several important …
Investigating Novel Streptomyces Bacteriophage Endolysins as Potential Antimicrobial Agents
As antibiotic resistance has become a major global threat, the World Health Organization has urgently called scientists for alternative strategies for control of bacterial infections. Endolysin, a protein encoded by a phage gene, can degrade bacterial peptidoglycan (PG). Currently, there are three endolysin products in the clinical phase. We, thus, are interested in exploring novel endolysins from Streptomyces phages as only a few of them have been experimentally characterized. Using bioinformatics tools, we identified nine functional domain groups from 250 Streptomyces phages putative endolysins. NootNoot gp34 (transglycosylase; Nt34lys), Nabi gp26 (amidase; Nb26lys), Tribute gp42 (PGRP; Tb42lys), and LazerLemon gp35 (CHAP; LL35lys) were selected for experimental studies. We hypothesized that (1) the proteins of interest will have the ability to degrade PG, and (2) the proteins will be potential antimicrobial agents against ESKAPE safe relatives. The results showed that LL35lys, Nb26lys and Tb42lys exhibit PG-degrading activity on zymography and hydrolysis assay. The enzymes (400 µg/mL) can reduce PG turbidity to 32-40%. The killing assay suggested that Tb42lys possess a boarder range (Escherichia coli, Pseudomonas putida, Acinetobacter baylyi and Klebsiella aerogenes). While Nb26lys can attack Gram-negative bacteria, LL35lys can only reduce the growth of the Gram-positive strains with an MIC90 of 2 µg/mL. A higher concentration (≥300 µg/mL) of Nb26lys is needed to treat P. putida and K. aerogenes. Therefore, endolysins from Streptomyces phage have potential as possible antimicrobial agents against ESKAPE bacteria.
Investigating Realistic Scenarios of Biodiversity Loss on Ecosystem Functioning: Extirpation of Rare Species and Food Web Collapse in Tropical Floodplain Lagoons
This thesis investigates the influence of nonrandom species loss on the structure and functioning of trophic floodplain lagoons. Two experiments were conducted based on different realistic scenarios of biodiversity loss using multitrophic fish assemblages derived from long-term survey data. Loss of fish diversity influenced overall ecosystem multifunctionality of these lagoons through complex multitrophic interactions throughout the aquatic food web. These results indicate that biodiversity loss from diverse multitrophic ecosystems can influence ecosystem structure and function and likely deviate from simplified food chain dynamics or patterns that emerged from single trophic level studies.
Investigating the Effects of Inhaled Diesel Exhaust Particles on Gut Microbiome, Intestinal Integrity, Systemic Inflammation, and Biomarkers of Cardiovascular Disease in Wildtype Mice
We investigated the hypothesis that exposure to inhaled diesel exhaust PM can alter the gut microbiome and intestinal integrity, thereby promoting systemic inflammatory response and early CVD risk, which are exacerbated by HF diet. Furthermore, we investigated whether the observed exposure and diet-mediated outcomes could be mitigated through probiotic treatment. We performed an exposure study on C57Bl/6 male mice, placed on either a low fat (LF) diet or a high-fat (HF) diet, and exposed via oropharyngeal aspiration to 35 μg diesel exhaust particles (DEP) suspended in 35 μl of sterile saline or sterile saline controls (CON) twice a week for four weeks. A subset of mice on HF diet were dosed with 0.3 g/day (PRO, ~7.5x108 CFU/day) of probiotic Ecologic® Barrier 849 (Winclove Probiotics) in drinking water during the course of the study. For our first aim, we investigated the alterations in the gut microbiome, measured circulating cytokines and lipopolysaccharide (LPS), and measured CVD biomarkers in the heart. Our results revealed that exposure to inhaled DEP results in gut dysbiosis characterized by expansion of the phyla Verrucomicrobia and Proteobacteria and reduction in Actinobacteria, which was exacerbated by HF diet. Probiotics mitigated the DEP-mediated expansion of Proteobacteria and re-established Actinobacteria in the intestine of HF animals. Furthermore, we determined that exposure to inhaled DEP increases systemic LPS and inflammatory markers IL-1α, IL-3, G-CSF, and TNF-α. Furthermore, we found that inhaled DEP exposure results in increased CVD biomarkers sICAM-1, sP-selectin, and thrombomodulin in the heart. Probiotic treatment was effective in attenuating LPS, inflammatory responses, and CVD biomarkers in HF animals, validating the involvement of the microbiome in mediating inhaled DEP-mediated responses. Considering the effects we observed in the microbiota and systemically of the HF and probiotic treatment animals, we investigated the effects of inhaled DEP on intestinal integrity and inflammation in HF …
Investigating the Effects of Traffic-Generated Air-Pollution on the Microbiome and Immune Responses in Lungs of Wildtype Mice
There is increasing evidence indicating that exposure to air pollutants may be associated with the onset of several respiratory diseases such as allergic airway disease and chronic obstructive pulmonary disorder (COPD). Many lung diseases demonstrate an outgrowth of pathogenic bacteria belonging to the Proteobacteria phylum, and the incidence of occurrence of these diseases is higher in heavily polluted regions. Within the human body, the lungs are among the first to be exposed to the harmful effects of inhaled pollutants and microbes. Research in the past few decades have expounded on the air-pollution-induced local and systemic inflammatory responses, but the involvement of the lung microbial communities has not yet been well-characterized. Lungs were historically considered to be sterile, but recent advances have demonstrated that the lower respiratory tract is replete with a wide variety of microorganisms - both in health and disease. Recent studies show that these lung microbes may play a significant role in modulating the immune environment by inducing IgA and mucus production. Air pollutants have previously been shown to alter intestinal bacterial populations that increase susceptibility to inflammatory diseases; however, to date, the effects of traffic-generated air pollutants on the resident microbial communities on the lungs have not been explored. The microbiome is influenced by several factors, including diet and environmental exposures. A large percentage of the Western world population consumes a high-fat (HF) diet which has resulted in the epidemic of obesity. Consumption of an HF diet has been shown to alter the intestinal microflora and increase baseline inflammation. We aimed to understand whether diet might also contribute to the alteration of the commensal lung microbiome, either alone or related to exposure. Thus, we investigated the hypothesis that exposure to air pollutants can alter the commensal lung microbiota, thereby promoting alterations in the lung's immune and inflammatory …
Investigating the Mechanisms involved in Traffic-Generated Air Pollution: Mediated Disruption of the Blood-Brain Barrier in a Wild Type Mouse Model using a Pharmaceutical Intervention Approach
This study investigated whether oxLDL and/or angiotensin (Ang) II signaling pathways mediate traffic-generated air pollution- exposure induced alterations in blood-brain barrier (BBB) integrity and permeability in a healthy wild type (C57Bl/6) mouse model; additionally, whether these outcomes are exacerbated by a high fat-diet investigated. An environmentally relevant concentration of a mixture of vehicle engine exhaust (MVE) was used. To investigate the hypotheses, 12 wk old male C57Bl/6 mice on either a high fat (HF) or low fat (LF) diet were randomly assigned to inhalational exposure of either filtered-air (FA) or 30 µg PM/m3 diesel exhaust + 70 µg PM/m3 gasoline exhaust (MVE) for 6 hr/day for 30 days. Additionally, we examined mechanisms involved in MVE-mediated alterations BBB integrity using a novel BBB co-culture in vitro model, consisting of mouse primary cerebral vascular endothelial cells on an apical transwell and astrocytes in the basal compartment, which was treated with plasma from the mice on our exposure study. Our in vivo exposure study results showed that MVE inhalation resulted in increased circulating plasma oxLDL and Ang II, compared to FA controls. Additionally, we observed increased cerebral microvascular expression of oxLDL receptors, LOX-1 and CD-36, and Ang II receptor subtype 1 (AT1) in MVE-exposed C57Bl/6 mice, which was further exacerbated with consumption of an HF diet. Increased signaling of both Ang II and oxLDL was associated with decreased BBB integrity, as evidenced by the concurrent reduction in expression of tight junction (TJ) protein claudin-5 and increased permeability of sodium fluorescein (Na-F) from the blood into the cerebral parenchyma. Our results suggest that possible mechanisms involved in oxLDL and/or Ang II-mediated alterations in BBB integrity include oxidative stress and upregulated expression and activity of matrix metalloproteinase (MMP)-9, which is associated with degradation of TJ proteins in the BBB. Our in vitro BBB co-culture results …
Investigating the Molecular Framesworks of Phloem-Cap Fiber Development in Cotton (Gossypium hirsutum)
The current study focuses on the vascular cambium and the reiterative formation of phloem fiber bundles in cotton stems. The role of the TDIF-PXY-WOX pathway was examined in regulating cambial activity and the differentiation of phloem fibers. A study was conducted to identify and characterize the cotton WOX family genes, focusing on WOX4 and WOX14, aiming to identify and analyze their phylogenetic relationships, tissue-specific expression profiles, functional roles, and metabolic consequences. Through a sequence analysis of the Gossypium hirsutum genome, 42 cotton loci were identified as WOX family members. GhWOX4 exhibited a close homology to 7 loci, while GhWOX14 displayed homology with 8 loci. Tissue-specific expression analysis revealed prominent expression patterns of GhWOX4 and GhWOX14 in cotton internodes and roots, suggesting their involvement in vascular tissue development. Functional studies utilizing VIGS (virus-induced gene silencing) demonstrated that the knockdown of GhWOX4 and GhWOX14 resulted in a significant reduction in stem diameter and bast fiber production. This result suggests that secondary phloem fiber development is regulated by GhWOX4 and GhWOX14 genes in cotton. Additionally, the metabolic profiling of VIGS plants revealed significant alterations in amino acids, organic acids, and sugars, with implications for primary metabolic pathways. These findings suggest that GhWOX4 and GhWOX14 play pivotal roles in cotton plant development, including vascular tissue growth and phloem fiber production, and metabolic regulation.
Investigating the Spatial Relationship between Suicide and Race/Ethnicity: The Case for Alternate Rate Adjustment Techniques in Medical Geography
This work explores potential distortions created by race and ethnicity on the visualization, interpretation, and understanding of the spatial distribution of suicide in the United States. Due to radically different suicide rates among racial/ethnic groups, traditional crude or age-adjusted rates may introduce statistical confounding in both linear and spatial models. Using correlation, choropleth mapping, hot spot analysis, and location-allocation modeling, this work shows how traditional methods of health system planning may unintentionally overlook elevated risk in minority-dominated areas like inner cities, the Texas/Mexico border region, and the Deep South. The final chapter introduces a simulation protocol for examining potential distortions in datasets to identify spatial and non-spatial distortions created by the underlying population composition. Methodologically, this dissertation contributes to the discourse on place context versus population composition. More generally, this research points to potential hazards to creating a more inclusive and equitable healthcare system.
Investigation of cryopreservation methods for adherent nerve cell networks in vitro.
Cryopreservation in suspension is commonplace for a variety of cell types. However, cryopreservation of adherent cells has achieved limited success. This research aimed to cryopreserve adherent nerve cell networks in vitro in a manner that preserved network morphology and physiology. Successful implementation would enable long term storage of adherent neuronal networks on microelectrode arrays and on-demand access for use in pharmacological and toxicological testing. Based upon morphological assessments, excellent post-thaw preservation was obtained and post-thaw cultures survived in a transitional medium for up to 3.5 hours. However, transitions to native culture medium post-thaw presented difficulties, ultimately resulting in necrosis. A discussion of methods to supplement the current research and increase post-thaw viability is included in the thesis.
Investigation of Gene Functions in the Cyanotrophic Bacterium Pseudomonas fluorescens NCIMB 11764
Pseudomonas fluorescens NCIMB 11764 (Pf11764) is one of a group of bacteria known as cyanotrophs that exhibit the unique ability to grow on toxic cyanide as the sole nitrogen source. This ability has previously been genetically linked to a conserved cluster of seven genes (Nit1C), the signature gene (nitC) coding for a nitrilase enzyme. Nitrilases convert nitriles to ammonia and a carboxylic acid. Still, for the Pf11764 NitC enzyme (Nit11764), no in vivo substrate has been identified, and the basis of the enzyme's requirement for cyanide growth has remained unclear. Therefore, the gene was cloned and the enzyme was characterized with respect to its structure and function. These efforts resulted in the unique discovery that, aside from its nitrilase activity, Nit11764 exhibits nuclease activity towards both DNA and RNA. This ability is consistent with computer analysis of the protein providing evidence of a preponderance of amino acids with a high probability for RNA binding. A Nit11764 knock-out mutant was shown to exhibit a higher sensitivity to both cyanide (KCN) and mitomycin C, both known to induce chromosomal damage. Thus, the overall conclusion is that Nit11764, and likely the entire Nit1C gene cluster, functions as a possible repair mechanism for overcoming the damage inflicted on Pf11764 nucleic acids by toxic cyanide. Towards a further investigation of the Nit1C gene cluster in Pf11764, a second gene (nitH) annotated as a monooxygenase was also investigated. Interestingly, computer-based analysis shows that NitH also harbors a preponderance of RNA-binding amino acids. The nitH gene was cloned into an expression vector with the long-range goal of defining its role in CN utilization.
Investigation of Inhibitory Influences in Neuronal Monolayer Networks Cultured from Mouse Spinal Cord
The effects of the inhibitory neurotransmitters gammaamino butyric acid (GABA) and glycine were characterized on spontaneous activity recorded from mouse spinal cord cultures. The GABA concentration which completely inhibited burst activity was chosen as a quantifiable measure of culture drug response and was used to 1) assess interculture and intraculture variability, 2) determine the influence of culture age and initial activity on GABA responses, and 3) compare the GABA responses between networks obtained from whole spinal cord and ventral half spinal cord. Results showed that 1) no significant variability existed either within or among cultures, 2) the initial culture activity directly affected GABA responses, 3) the culture age had no effect on GABA responses, and 4) there was no significant difference in GABA responses between the two spinal cord tissues.
Investigation of Lead Hydrolytic Polymerization and Interactions with Organic Ligands in the Soil/Sediment-Water Environment
The objective of this research was to investigate lead speciation in the soil/sediment-water environment and to better understand how the species affect lead mobility under different environmental conditions. The research involved both field soil and sediment samples as well as standard lead solutions. Field samples were fully characterized and extracted by aqueous and organic solvents. The results were compared and evaluated with the metal speciation model, MINTEQA2. Hydrolytic polymerization and organic complexation studies were conducted with standard lead solutions under controlled experimental conditions. Results of the field samples showed that pH, dissolved cations, ionic strength, dissolved organic matter, and nature of the soil/sediment matrix play major roles in the distribution and mobility of lead (Pb) from contaminated sites. In the aqueous equilibration experiment, the magnitude of Pb2+ solubilization was in the order of pH4>pH7>pH9. The results were in good agreement with MINTEQA2 predictions. An important finding of the research is the detection of Pb polymerization species under controlled experimental conditions. At pH 5.22, Pb polymeric species were formed at rate of 0.03 per day. The role of Pb complexation with organic matter was evaluated in both field and standard samples. Different methodologies showed three types of organically bound Pb. A very small fraction of Pb, in the ppb range, was extractable from the contaminated soil by polar organic solvents. Sequential extractions show that 16.6±1.4 % of the Pb is organically complexed. Complexation of Pb with fulvic acid provided new information on the extent of Pb association with soluble organic matter. The overall results of this research have provided new and useful information regarding Pb speciation in environmental samples. The results, in several instances, have provided verification of MINTEQA2 model's prediction. They also revealed areas of disagreement between the models prediction and the experimental results. A positive note regarding the experimental …
Investigation of Strategies for Improving STR Typing of Degraded and Low Copy DNA from Human Skeletal Remains and Bloodstains
Forensic STR analysis is limited by the quality and quantity of DNA. Significant damage or alteration to the molecular structure of DNA by depurination, crosslinking, base modification, and strand breakage can impact typing success. Two methods that could potentially improve STR typing of challenged samples were explored: an in vitro DNA repair assay (PreCR™ Repair Mix) and whole genome amplification. Results with the repair assay showed trends of improved performance of STR profiling of bleach-damaged DNA. However, the repair assay did not improve DNA profiles from environmentally-damaged bloodstains or bone, and in some cases resulted in lower RFU values for STR alleles. The extensive spectrum of DNA damage and myriad combinations of lesions that can be present in forensic samples appears to pose a challenge for the in vitro PreCR™ assay. The data suggest that the use of PreCR™ in casework should be considered with caution due to the assay’s varied results. As an alternative to repair, whole genome amplification (WGA) was pursued. The DOP-PCR method was selected for WGA because of initial primer design and greater efficacy for amplifying degraded samples. Several modifications of the original DOP-PCR primer were evaluated. These modifications allowed for an overall more robust amplification of damaged DNA from both contemporary and historical skeletal remains compared with that obtained by standard DNA typing and a previously described DOP-PCR method. These new DOP-PCR primers show promise for WGA of degraded DNA.
Investigation of the Pharmacokinetics of Diazepam in Juvenile Channel Catfish (Ictalurus Punctatus)
The presence of pharmaceuticals in the environment is becoming an increasing regulatory and scientific concern. Thus, the metabolic profile and bioconcentration potential of diazepam, a model benzodiazepine, were examined, as well as effects on the endocrine system in channel catfish. Through the use of specific and non-specific cytochrome P450 (CYP450) inhibitors, it was determined that CYP3A-like enzymes may play a role in the biotransformation of diazepam into temazepam; however, the isoform(s) required for the formation of other metabolites is still unknown. Overall, only around 7-8% of diazepam is biotransformed into two known metabolites. Due to the lack of inherent metabolism of diazepam in channel catfish, further analysis was conducted to determine the tissue-specific bioconcentration potential of diazepam in catfish. Various tissues were analyzed for the presence of diazepam as well as metabolites and bioconcentration factors (BCF) were calculated, which were all well below regulatory threshold values (> 2000). Additionally, modulation of the endocrine system by diazepam was examined by measuring steroid hormone concentrations and analyzing mRNA expression of selected steroidogenic enzymes and receptors. Two steroidogenic enzymes were modulated following diazepam exposure, indicating potential endocrine disrupting properties of diazepam. Together, these data suggest that diazepam exhibits low metabolic transformation rates in channel catfish, which may lead to accumulation of benzodiazepine compounds that may negatively affect the endocrine system. However, further studies should be aimed at identifying other steroidogenic enzymes and/or receptors that may be modulated following diazepam exposure.
Irrigation Methods and Their Effects on Irrigation Water Efficiency in High Tunnels
Improving water efficiency is and will continue to be a top concern to meet the world food production demands for a growing population. By having a clear understanding of water efficiencies, communities will be able to address these concerns from an economic standpoint and use more productive methods to grow food and limit water consumption. This study examines the water efficiencies of three irrigation methods over a single growing season in southeastern Oklahoma. Two crops, tomatoes and cucumbers, were grown using drip irrigation, a self-wicking container, and a non-circulating hydroponics barrel. Results at the end of the season showed the drip irrigation method had the highest water efficiency in terms of yield of product over water applied for both crops. The drip irrigation method also had the lowest associated set up costs and second lowest time requirements after the hydroponics method. These results were found to be consistent with other studies that compared drip irrigation to other irrigation methods and showed drip to have the highest water efficiencies.
Isolation and analysis of cotton genomic clones encompassing a fatty acid desaturase (FAD2) gene
Polyunsaturated fatty acids are major structural components of plant chloroplast and endoplasmic reticulum membranes. Two fatty acid desaturases (designated FAD2 and FAD3) desaturate 75% of the fatty acids in the endoplasmic reticulum. The w -6 fatty acid desaturase (FAD2) may be responsible for cold acclimation response, since polyunsaturated phospholipids are important in helping maintain plant viability at lowered temperatures. To study regulation of FAD2 gene expression in cotton, a FAD2 gene was isolated from two genomic libraries using an Arabidopsis FAD2 hybridization probe and a cotton FAD2 5¢ -flanking region gene-specific probe, respectively. A cotton FAD2 gene was found to be in two overlapping genomic clones by physical mapping and DNA sequencing. The cloned DNA fragments are identical in size to cotton FAD2 genomic DNA fragments shown by genomic blot hybridization. The cotton FAD2 coding region has 1,155 bp with no introns and would encode a putative polypeptide of 384 amino acids. The cotton FAD2 enzyme has a high identity of 75% with other plant FAD2 enzymes. The enzyme has three histidine-rich motifs that are conserved in all plant membrane desaturases. These histidine boxes may be the iron-binding domains for reduction of oxygen during desaturation. To confirm that this FAD2 enzyme is functional, a plasmid construct containing the cotton FAD2 coding region was transformed into Saccharomyces cerevisiae. The transformed yeast cells were able to catalyze the conversion of oleic acid (C18:1) into linoleic acid (C18:2). The FAD2 gene contains an intron of 2,967 bp in its 5¢ -flanking region, 11 bp upstream from the initiation codon. The intron could be essential for transcriptional regulation of FAD2 gene expression. Several putative promoter elements occur in the 5¢ -flanking region of this gene. A potential TATA basal promoter element occurs at 41 bp upstream from the cap site. Two presumptive helix-loop-helix (bHLH) …
Isolation and Bioinformatic Characterization of Four Novel Bacteriophages from Streptomyces toxytricini
Six initial phage isolates with high titer lysates were obtained using Streptomyces toxytricini B-5426 as the host bacterium. These isolates were named Goby, Toma, Yosif, Yara, Deema, and Hsoos. However, upon completion of the sequencing, it was found that the Yara and Hsoos isolates were identical, as were Goby and Deema. As a result, final analysis was completed on only the four unique isolates. All of the phages mentioned above were isolated from soil samples from different locations. Also, they had different sizes of plaques, ranging from 0.3 – 0.9mm. Yosif had the largest plaque size. Yara's head diameter was 79nm with tail diameter of 94nm.
Isolation and Characterization of a New Capsule-Forming Bacterium
A unique, previously undescribed Gram-negative bacterium was isolated from several soils in Texas and extensively characterized in this study. The cells measured 1-2 by 4-6 μm. The distinguishing characteristic of the bacterium is the extraordinary capsular material which surrounds the cells. The new isolates are aerobic, mesophilic, non motile and have the ability to utilize a variety of organic compounds as the sole source of carbon and energy. The organism grows optimally at 30° C and the optimal pH lies between 7.0-8.0. The isolates produce catalase but oxidase is not produced. They do not produce indole or hydrogen sulfide. The organism can hydrolyze gelatin and Tween 80 but not starch, esculin and casein. The major cellular fatty acid is anteiso 15:0. The guanine and cytosine content is 58-62 mole%. The organism's taxonomic position was further established by specific gene probes, 16S rRNA homology, DNA homology and "ribotyping." These data showed that it was most closely related to members of the genus Paenibacillus, although somewhat divergent from other species classified in this genus. After careful evaluation of the results obtained during this study, it is proposed that this unique bacterium be named Paenibacillus velasolus sp. nov.
Isolation and Characterization of Malic Enzyme from Ascaris suum
A procedure for the isolation of malic enzyme from muscle tissue of the roundworm Ascaris suum is described. The fractionation method yields relatively large quantities of the enzyme,with a specific activity of fifteen moles of malate converted to pyruvate and carbon dioxide per min per mg at 25º. Homogeneity was established with analytical ultracentrifugation, zone electrophoresis, isoelectric focusing, and rechromatography. The molecular weight of the enzyme was 250,000, and it is dissociated under several conditions into four identical monomers of 64,000 daltons. The enzyme exists as a single electrophoretic form and prefers manganous and NAD over other cations and NADP. Ammonium sulfate competes with manganous for the active site and titration with DTNB yields eight thiol groups per mole. Titration of the first four thiol groups is accompanied by a complete loss in enzyme activity. Equilibrium dialysis, product inhibition, and initial velocity studies suggest a rapid-equilibrium random sequential mechanism for the Ascaris suum malic enzyme. The presence of 1.3 binding sites per subunits was determined for L-ma late. Antisera prepared against A. suum malic enzyme reacted to a small extent with the NAD malic enzymes from two free-living nematodes, Panarellus redivivus and Turbatrix aceti. A correlation coefficient of 0.911 was obtained upon comparing the amino acid composition of A. suum and E. coli malic enzymes. Some sequence homology is predicted between these malic enzymes. The physiological interpretation favors the binding of malate initially, with the subsequent addition of NAD to the enzyme.
Isolation and Characterization of Phages Infecting Streptomyces azureus
Isolating novel phages using Streptomyces azureus, which produces antibiotic thiostrepton, as a host, and characterizing the genomes may help us to find new tools that could be used to develop antibiotics in addition to contribute to the databases of phages and specifically, Streptomyces phages. Streptomyces phages Alsaber, Omar, Attoomi, Rowa, and ZamZam were isolated using during this study. They were isolated from enriched soil and sequenced by Illumina sequencing method. They were isolated from three different geographical regions. They are siphoviridae phages that create small clear plaques with a diameter of approximately 0.5-1 mm, except for Rowa which has cloudy plaques, and they have varied sizes of their heads and tails. ZamZam was not characterized at this time. The sequencing shows that they are circular genome with 3' sticky overhang and various genomes' sizes with high percentage of GC content with the average of 66%. Alsaber was classified under sub-cluster BD3, while Omar was categorized under sub-cluster BD2. They share the same cluster of Cluster BD. Rowa was placed in Cluster BL and Attoomi is currently a singleton that does not fit into an established cluster. Alsaber yields 76 putative genes with no tRNA, Omar 81 putative genes with 1 tRNA. Attoomi 53 putative genes with no tRNA, and Rowa with 61 orfs and 7 tRNA. Rowa also was a putative temperate phage due to its lysogenic activity, and Row was not able to reinfect the lysogenic strain, S. azureus (Rowa). All of the isolated phages infected S. indigocolor, while only Attoomi and Rowa were able to infect S. tricolor. Upon completion of this project, we acquired more data and understanding of S. azureus phages and Actinobacteriophage in general, which will expand the scale of future research of Streptomyces bacteriophages.
Isolation and Characterization of Polymorphic Loci from the Caribbean Flamingo (Phoenicopterus ruber ruber): New Tools for Wildlife Management
Methods to determine genetic diversity and relatedness within populations are essential tools for proper wildlife management. Today the approach of choice is polymerase chain reaction-based microsatellite analysis. Seven new polymorphic loci were isolated from a microsatellite-enriched Caribbean flamingo genomic library and used to characterize survey populations of Caribbean and African greater flamingos. In addition, four of these loci were used to verify parentage relationships within a captive-breeding population of African greater flamingos. Parentage predictions based upon gamekeeper observations of breeding and nesting did not always agree with genetic-based parentage analyses of the nine suggested family groups. Four family groups were supported (groups I, II, III and VI) by there results. However, an analysis of the remaining five suggested groups, with a total of eight offspring/dam and eight offspring/sire suggested relationships, yielded seven exclusions of the suggested dam and six exclusions of the suggested sire. This put the overall suggested dam exclusion rate at 35% and exclusion rate for suggested sires at 29%. Although the keeper observation data for our family groups must be considered a variable of concern at this time, these findings are certainly suggestive that more carefully controlled studies may reveal that flamingos are not monogamous as long accepted, but rather socially monogamous or even promiscuous. Thus we have now been able to both characterize and demonstrate the utility of our polymorphic microsatellite loci. We hope these results will interest additional wildlife facilities in further parentage and behavioral studies that will collectively aid to improve monitoring and maintenance of genetic diversity, and as provide better insight into breeding habits of both wild and captive populations.
Isolation and Characterization of the Operon Containing Aspartate Transcarbamoylase and Dihydroorotase from Pseudomonas aeruginosa
The Pseudomonas aeruginosa ATCase was cloned and sequenced to determine the correct size, subunit composition and architecture of this pivotal enzyme in pyrimidine biosynthesis. During the course of this work, it was determined that the ATCase of Pseudomonas was not 360,000 Da but rather present in a complex of 484,000 Da consisting of two different polypeptides (36,000 Da and 44,000 Da) with an architecture similar to that of E. coli ATCase, 2(C3):3(r2). However, there was no regulatory polypeptide found in the Pseudomonas ATCase.
Isolation and Genomic Characterization of 45 Novel Bacteriophages Infecting the Soil Bacterium Streptomyces griseus
Bacteriophages, or simply "phages," are the most abundant biological entities on the planet and are thought to be the largest untapped reservoir of available genetic information. They are also important contributors to both soil health and nutrient recycling and have significantly influenced our current understanding of molecular biology. Bacteria in the genus Streptomyces are also known to be important contributors to soil health, as well as producing a number of useful antibiotics. The genetic diversity of large (> 30) groups of other actinobacteriophages, i.e. phages infecting a few close relatives of the Streptomycetes, has been explored, but this is the first formal effort for Streptomyces-infecting phages. Described here are a group of 45 phages, isolated from soil using a single Streptomycete host, Streptomyces griseus ATCC 10137. All 45 phages are tailed phages with double-stranded DNA. Siphoviruses predominate, six of the phages are podoviruses, and no myoviruses were observed. Notably present are seven phages with prolate icosahedral capsids. Genome lengths and genome termini vary considerably, and the distributions of each are in line with findings among other groups of studied actinobacteriophages. Interestingly, the average G+C among the 45 phages is around 11% lower than that of the isolation host, a larger disparity than reported for other groups of actinobacteriophages. Eighteen of the phages carry between 17 and 45 tRNAs and 12 of those carry a single tmRNA. Forty-three phages were grouped into seven clusters and two subclusters based on dot plot analysis, average nucleotide identities, and gene content similarities. Two phages were not clustered with other phages in this dataset. A total of 5250 predicted genes were sorted into 1300 gene "phamilies," with about 8% of the total phamilies having only a single member. Analysis of gene content among the 45 phages indicates first that most clusters presented here appear to …
Isolation, Characterization and Physiological Studies of Cyanide-Utilizing Bacteria
Ten bacteria capable of growth on the metal-cyano complex, tetracyanonickelate (II) {K2 [Ni(CN)J } (TCN), supplied as the sole nitrogen source, were isolated. Seven isolates were identified as pseudomonads while the remaining three were classified as Klebsiella species. In addition to TCN, all isolates were able to utilize KCN although it was significantly more toxic. The degradation of TCN was most complete when supplied at growth-limiting concentrations, did not occur when ammonia was present, and resulted in the formation of nickel cyanide [Ni(CN)2] as a degradation product.
Isolation of a Pseudomonas aeruginosa Aspartate Transcarbamoylase Mutant and the Investigation of Its Growth Characteristics, Pyrimidine Biosynthetic Enzyme Activities, and Virulence Factor Production
The pyrimidine biosynthetic pathway is an essential pathway for most organisms. Previous research on the pyrimidine pathway in Pseudomonas aeruginosa (PAO1) has shown that a block in the third step of the pathway resulted in both a requirement for exogenous pyrimidines and decreased ability to produce virulence factors. In this work an organism with a mutation in the second step of the pathway, aspartate transcarbamoylase (ATCase), was created. Assays for pyrimidine intermediates, and virulence factors were performed. Results showed that the production of pigments, haemolysin, and rhamnolipids were significantly decreased from PAO1. Elastase and casein protease production were also moderately decreased. In the Caenorhabditis elegans infection model the nematodes fed the ATCase mutant had increased mortality, as compared to nematodes fed wild type bacteria. These findings lend support to the hypothesis that changes in the pyrimidine biosynthetic pathway contribute to the organism's ability to effect pathogenicity.
Key Factors Influencing Retention Rates among Historically Underrepresented Student Groups in STEM Fields
The aim of the study was to identify the factors that have an influence on the completion rates of undergraduate students in the fields of science, technology, engineering and mathematics (STEM). Using Tinto's retention rate theory as the theoretical foundation, data were collected from freshman who were enrolled in the years 2005 to 2008. Results showed gender and first-generation status were significant predictors of STEM completion and time taken to complete the degree. Institutional bias played a role in race/ethnicity not being a factor affecting completion rates, as this study was conducted at a Predominantly White Institution. SAT scores and first and second-year college GPA showed to have the most prominent influence on both STEM completion rate and time taken to complete the degree. Females with higher first-year college GPA and higher high school rank finished faster. Similar results were found with first-generation students as well. Students belonging to ethnic minority groups with higher SAT scores and college GPA had greater success in STEM fields as well. The study results can be used to increase completion rates of underrepresented students in the STEM fields, given what we know about the interactions between underrepresented student groups and the most important predictors.
A laboratory course in experimental genetics for the biology major.
This manual has been designed for a class of twenty- four students concurrently enrolled in the lecture course. The laboratory aids in the learning process and fosters an interest in the science of genetics. This manual and the experiments contained within are both informative and fun. The manual correlates with and expands upon the genetics course. Each investigation, with the exception of the Drosophila melanogaster project, can be completed in a 3-4 hour timeframe. This manual provides a “hands on” experience of theories simply discussed in the lecture course. This manual is intended to be a one-source manual where each investigation is designed to include an adequate introduction. Special attention has been given for each investigation with both the student and instructor in mind.
Landscape forest modeling of the Luquillo Experimental Forest, Puerto Rico.
This thesis contributes to modeling the dynamics of forest community response to environmental gradients and disturbances over a mountain landscape. A gap model (FACET) was parameterized for species of various forest types (Tabonuco, Colorado, Dwarf and Palm), for many terrain conditions and was modified and extended to include species response to excess soil moisture and hurricanes. Landscape cover types were defined by dominance of species of each forest type and canopy height. Parameters of the landscape model (MOSAIC) were calculated from multiple runs of FACET. These runs were determined by combining terrain variables (elevation and soil) and hurricane risk. MOSAIC runs were analyzed for distribution patterns. Geographic Information Systems software was used to process terrain variables, hurricane risk and MOSAIC model output.
The Larval Lipids of the Chironomid Midge Glyptotendipes Barbipes (Staeger)
This problem was concerned with determining the total lipid content and individual lipid composition of the larvae of a local chironomid, Glyptotendipes barbipes (Staeger).
The Last Laugh: Selected Edwardian Punch Cartoons of Edward Linley Sambourne
The illustrative work of Edward Linley Sambourne for Punch magazine during the period 1901-1910 addresses a myriad of political topics prevalent during the Edwardian period in British history. This thesis examines two of those topics - Women's Suffrage and Socialism - through their artistic treatment by one of Britain's most influential periodicals. Through a study of the historical context and iconography of selected cartoons-of-the-week, one is better equipped to understand and appreciate the meaning, message, and humor in the cartoons. Chapter 1 introduces the Sambourne, Punch magazine, and the Edwardian period in general. Chapters 2 and 3 discuss four Women's Suffrage cartoons and four Socialism cartoons respectively. Chapter 4 draws conclusions regarding Sambourne's techniques as a cartoonist as well as the relationship between the text and image in his illustrations.
Leaf elemental analysis and growth characteristics of mycorrhizal treated post oak seedlings via particle induced X-ray emission spectroscopy.
Growth and element assimilation was investigated in post oak seedlings exposed to four different treatment combinations of fertilization and ectomycorrhizal inoculation. Element concentration in excised leaves was analyzed via particle induced X-ray emission spectrometry with a 1.8 MeV proton macrobeam. Mean growth was significantly different across the treatment groups as well as mean concentration of Mg, Al, S, K, Ca, Fe, Cu, and Zn. The data suggest that fertilization rather than mycorrhizal inoculation had a stronger influence on plant growth and nutrient uptake. A follow up study was conducted with a 3 MeV microbeam. A 850 μm2 scanned area of a post oak leaf produced topographical maps of 11 elements.
Lethal and Sublethal Effects of Hemoxidants, Particularly Nitrite, on Selected Aquatic Animals
A research program was developed to investigate basic and applied aspects of toxicity, both lethal and sublethal, of hemoxidants, particularly nitrite, on fish, non-fish aquatic vertebrates, and crayfish. The major objectives of this research were to determine A) acute and sublethal toxicity of nitrite to selected aquatic organisms: 1. aquatic salamander larvae, Ambystoma texanum, 2. swamp crayfish, Procambarus simulans, 3. bluegill, Lepomis macrochirus, 4. bullfrog, tadpoles, Rana catesbiana, 5. channel catfish, Ictalurus punctatus, B) the influence of environmental chloride on acute and sublethal exposures to hemoxidants: 1. on acute nitrite toxicity to salamander larvae, crayfish, and bluegill, 2. on nitrite-induced methemoglobinemia in bullfrog tadpoles, Rana catesbian, C) the effect of environmental hydrogen ion concentrations (pH) on acute nitrite toxicity 1. to the crayfish, Procambarus simulans, 2. to the bluegill, Lepomis macrochirus, D) the effect of temperature in sublethal exposures to nitrite 1. methemoglobin formation in channel catfish exposed at different acclimation temperatures, 2. recovery from methemoglobinemia at different acclimation temperatures, E) the effect of the fish anesthetic TMS-222 on nitrite-induced methemoglobinemia in channel catfish 1. supression of nitrite-induced methemoglobinemia, 2. dose-response curve for TMS-222 induced methemoglobinemia, and F) if a methemoglobin reductase system is present in channel catfish.
Life Histories Behavior and Space Partitioning in Selected Species of Western North American Plecoptera
Five species of stoneflies (Zapada haysi, Plumiperla diversa, Taenionema pacificum, Isoperla petersoni, Arcynopteryx compacta) from the North Slope and Interior of Alaska were examined for seasonal patterns of emergence of adults and growth of nymphs. Generally growth was retarded during the winter in this region, and all species except I. petersoni completed growth prior to January. The life cycles of six stonefly species (Prostoia besametsa, Triznaka signata, Sweltsa coloradensis. Isoperla fulva, Skwala parallela, Claassenia sabulosa) are described from northern New Mexico. In this region growth was generally less retarded during the winter than in Alaska; P. besametsa completed all nymphal growth during late fall and winter. Drumming behavior of a Colorado population of Pteronarcella badia was described using an evolutionary framework to explain the maintenance of signal variation in this species. Laboratory experiments were used to explore the effect of intraspecific and interspecific interactions on spatial partitioning in P. badia and Claassenia sabulosa. P. badia exhibited clumping and distributed itself as the surface area of substrate in low densities; however, in the presence of C. sabulosa its distribution was random and different from available surface area. A field study was used to examine spatial partitioning by three New Mexico stonefly species (I_. fulva, P. besametsa, T. signata) and to ascertain patterns of microdistribution relating to several abiotic and biotic factors. Generally, there was an interaction of the measured abiotic parameters (current, water temperature, time) with nymphal size. Additionally, void space and sample volume were successfully used to compare biotic densities among leaf and mineral substrates, which were higher in leaf packs than in mineral substrates.
Life History and Case Building Behaviors of Phylloicus ornatus (Banks) (Trichoptera: Calamoceratidae) In Two Spring Fed Tributaries in the Central Edwards Plateau Bioregion of Texas
The life history and case-making behaviors of Phylloicus ornatus from two springfed first order streams in the Edwards Plateau Bioregion of Texas were studied from January 1998 to November 1999. Field larval, pupal and adult samples and laboratory rearings indicated a multivoltine cycle. First instars differ from late instars in number of labral setae and in having a unique spur-like claw on each lateral hump. Larval development was asynchronous with second through fifth instars and pupae present most months. First instars were present April through July, October and November. Case making of first instar and case reconstruction of later instars extracted from their cases was documented by videophotography.
The Life History and Contributions to the Ecology of Camelobaetidius variabilis Wiersema 1998 (Ephemeroptera: Baetidae) in Honey Creek, Oklahoma
A study of the life history and ecology of Camelobaetidius variabilis was conducted in Honey Creek, OK from February 2003-April 2004. Nymph development was assessed using changes in external morphology. Laboratory reared nymphs were used to calculate number of degree days to complete development (772 degree days at 20.8° C ±.38° C), which was used to determine voltinism. Field collected nymph microhabitat distribution was used in assessing microhabitat distribution. Nymphal thermoregulation was assessed during the winter and spring by comparing nymphal numbers present in shaded and un-shaded habitats. Camelobaetidius variabilis nymphs showed preference for algal microhabitats during the spring and leaf packs in the winter. Nymphs inhabited leaf packs to increase metabolic rate during the winter. Increased temperatures aid in development of nymphs. Camelobaetidius variabilis exhibited a multivoltine life cycle with six overlapping generations.
Life History and Secondary Production of Caenis latipennis Banks (Ephemeroptera: Caenidae) in Honey Creek, Oklahoma
A study of the life history and secondary production of Caenis latipennis, a caenid mayfly, was conducted on Honey Creek, OK. from August 1999 through September 2000. The first instar nymph was described. Nymphs were separated into five development classes. Laboratory egg and nymph development rates, emergence, fecundity, voltinism, and secondary production were analyzed. C. latipennis eggs and nymphs take 132 and 1709 degree days to develop. C. latipennis had an extended emergence with five peaks. Females emerged, molted, mated, and oviposited in an estimated 37 minutes. Mean fecundity was 888.4 ± 291.9 eggs per individual (range 239 -1576). C. latipennis exhibited a multivoltine life cycle with four overlapping generations. Secondary production was 6,052.57 mg/m2/yr.
Life History And Secondary Production Of Cheumatopsyche Lasia Ross (Trichoptera: Hydropsychidae) With Respect To A Wastewater Treatment Facility In A North Texas Urban Stream
This study represents the first shift in multivoltine life history of Cheumatopsyche species from a wastewater treatment plant (WWTP) in North America. Populations of C. lasia were examined upstream and downstream of the Denton’s Pecan Creek WWTP August 2009 through November 2010. C. lasia is multivoltine in Pecan Creek with three cohorts observed upstream of the WWTP and four possible cohorts downstream. A fourth generation was possible downstream as thermal inputs from WWTP effluent resulted in elevated water temperatures that allowed larval development to progress through the winter producing a cohort ready to emerge in spring. Production of C. lasia was 5 times greater downstream of the WWTP with secondary production estimates of 1.3 g m-2 yr-1 and 4.88- 6.51 g m-2 yr-1, respectively. Differences in abundance were due to increased habitat availability downstream of the WWTP in addition to continuous stream flow from inputs of wastewater effluent. Results also suggest that C. lasia is important for energy transfer in semiarid urban prairie streams and may serve as a potential conduit for the transfer of energy along with emergent contaminants to terrestrial ecosystems. These finding highlight the need for more quantitative accounts of population dynamics (voltinism, development rates, secondary production, and P/B) of aquatic insect species to fully understand the ecology and energy dynamics of urban systems.
Life History Biology of the Desert Nesting Seagull Larus modestus
Gray gulls Larus modestus are unique among birds of northern Chile as the only species nesting in the interior Atacama Desert, and the only seagull nesting far (30 - 100 km) from surface water. During breeding-nesting (August - February) gray gulls congregate on the coast of northern Chile where they feed and initiate courtship. As early as August, breeding pairs commute daily to the inner desert to establish nesting territories, round-trip distances of 60-200 Km. During incubation (30 days) and brooding (7 days) adults alternate daily foraging flights to the coast. Afterwards, both adults forage daily for their chick(s) until fledging (ca. 60 days). Foraging flights and thermoregulatory costs during the period of maximal solar radiation, when ground temperatures may reach 61 C in the day and drop to 2 C at night, have selected for adaptations which minimize those costs: tolerance of hypothermia and hyperthermia; dark plumage; low egg-shell water vapor conductance; low standard metabolic rate; elaborate repertory of thermoregulatory behavior which allow adults to take advantage of microclimatic variations in the desert and minimize costs relative to a sympatric congenor, Larus belcheri scheduling foraging flights to take advantage of optimal atmospheric conditions and presence of forage fish (anchovies) close to the surface; scheduling migration to coincide with anchovy production and levels of interspecific competition; and reduced clutch size ( ≤ 2) relative to most seagulls. Periodic El Nino-Southern Oscillations (ENSO), which reduce principal food items of gray gulls, have selected for 'bet hedging" tactic by which L. modestus either ceases reproduction or varies clutch size between one and two, as observed during and after the 1982-83 ENSO. During a typical reproductive season, breeding pairs allocate a minimum of 39 percent of their net metabolized energy (NME) to foraging flights. Including energy content of eggs, females have an overall …
Life History Energetics of The Red-Eared Turtle, Pseudemys scripta in North Central Texas
A population of the red-eared slider, Pseudemys scripta, in north central Texas was studied from 1975 to 1980. A life history energy budget was developed for a typical individual in the population and the population dynamics were estimated. A growth model relating growth rate to mean plastron length (PL) was developed from recapture data and used to 1) establish age classes and 2) age individuals. Growth rate was highly variable in both sexes. Females grew more rapidly than males and attained a larger maximum size (230 mm and 195 mm PL in females and males respectively). Females reached sexual maturity in their ninth year at a PL of 185-190 mm. Males matured in their sixth year at a PL of 90-100 mm. Females produced three clutches annually; clutch size ranged from 7 to 14 (X=10.3; N=20). Ova were enlarged in the early spring and ovulation began in late April and early May. Egg laying occurred from mid- May through June. Both egg size and clutch size increased with female body size. Lipid levels were variable within and among seasons. No annual lipid cycling pattern was evident in females. The proportion of assimilated energy devoted to reproduction, a measure of reproductive effort (RE), by females, was 13 per cent the first year of maturity (9 y) and increased to 20 per cent by their twentieth year. Lifetime RE was 16 per cent. Population density was estimated as 51 males and 50 females per ha in a 8.2-ha area of the lake. Young juveniles (less than 2 y) were not present although other subadult age classes were about equally represented. Fewer adults were encountered. An annual total production of 4000 eggs was estimated for the population present in 1977. A survival rate of from 2 to 18 per cent was estimated for …
Life History of Mayatrichia ponta Ross (Trichoptera: Hydroptilidae) in Honey Creek, Turner Falls Park, Oklahoma
The life history and ontogenetic microhabitat change of Mayatrichia ponta Ross were investigated in Honey Creek, Turner Falls Park, Murray Co., Oklahoma, U.S.A. from August 1994 to August 1995. The shape of larval cases changed from a small cone to a cylinder. M. ponta had an asynchronous multivoltine life history with considerable cohort and generation overlap; five generations were estimated. The development rate was reduced in winter. The winter generations of M. ponta had wider head capsule widths (136-165 μm) than summer generations (121-145 μm). The sex ratio of adults was 1.43 ♂ : 1 ♀. Fecundity ranged from 46 to 150 eggs/female. Fifth instar larvae and pupae aggregated on the bottom side of substrates. Early instars were distributed evenly on all sides of substrates. General patterns of ontogenetic microhabitat shift in aquatic insects are categorized as flow mediated, flow independent, and population interactions and other resources mediated.
The Life History of the Mayfly Isonychia sicca (Walsh) (Ephemeroptera--Siphlonuridae) in an Intermittent Stream in North Central Texas
The life history of Isonychia sicca (Walsh) was elucidated from samples collected at Clear Creek from Oct. 1976-Jun. 1978, and Elm Fork of the Trinity River from Sept. 1977-Jun. 1978, Denton County, Texas. Adaptations for existence in an intermittent stream were of primary concern. Eggs are capable of diapausing through hot, dry summers and cold, wet or dry winters. Diapause is broken in the fall after rehydration and/or in the spring. I. sicca is usually bivoltine during a Sept.-Jul. wet period. Observations from Elm Fork indicate that emergence continues to Oct. if the stream remains permanent. Considerable overlap occurs between overwintering, spring, and summer populations.
Linkage of a nitrilase-containing Nit1C gene cluster to cyanide utilization in Pseudomonas fluorescens NCIMB 11764.
Pseudomonas fluorescens NCIMB 11764 (Pf11764) is uniquely able to grow on the poison cyanide as its sole nitrogen source. It does so by converting cyanide oxidatively to carbon dioxide and ammonia, the latter being assimilated into cellular molecules. This requires a complex enzymatic machinery that includes nitrilase and oxygenase enzymes the nature of which are not well understood. In the course of a proteomics analysis aimed at achieving a better understanding of the proteins that may be required for cyanide degradation by Pf11764, an unknown protein of 17.8 kDa was detected in cells exposed to cyanide. Analysis of this protein by ESI-coupled mass spectrometry and bioinformatics searches gave evidence of strong homology with a protein (Hyp1) of unknown function (hypothetical) present in the bacterium Photorhabdus luminescens subsp. laumondii TTO1 (locus plu_1232). A search of available microbial genomes revealed a number of Hyp1 orthologs the genes of which are found in a conserved gene cluster known as Nit1C. Independent studies revealed that in addition to Hyp1, Pf11764 possesses a gene (nit) specifying a nitrilase enzyme whose closest homologue is a nitrilase found in Nit1C gene clusters (77% amino acid identity). DNA sequence analysis has further revealed that indeed, hyp1Pf11764 and nitPf11764 are contained in a cluster that includes also a gene specifying an oxygenase. Given the possible connection of Nit1C-endoded nitrilase and oxygenase enzymes to enzymatic cyanide degradation, there is strong reason for thinking that the genes specifying these enzymes contribute to bacterial growth on cyanide in those bacteria containing the Nit1C cluster. Because the biological function of the Hyp1 protein is currently unknown, it was cloned and the protein expressed in E. coli so that its properties could further be explored. Unfortunately, the expression of the protein in an insoluble form complicated these analyses. However, at least two lines of …
Linkage of the Nitrilase-Encoding Nit1C Gene Cluster to Cyanotrophy in Acinetobacter haemolyticus
The Nit1C cluster is a conserved gene cluster of seven genes that confers bacterial growth on cyanide as the sole nitrogen source. Bacteria with this ability are referred to as cyanotrophs. To date, the linkage between Nit1C and cyanotrophy has only been demonstrated for environmental isolates but the cluster also exists in certain medically related bacteria. In this study, a nosocomial isolate, Acinetobacter haemolyticus ATCC 19194, carrying Nit1C also displayed the ability to grow on cyanide. Growth on cyanide was accompanied by the induction of the cluster as was the mere exposure of cells to cyanide. Expression of the cluster was determined by measuring the activity of the nitrilase (NitC) coded for by the cluster and by transcriptional analysis (qRT-PCR). However, a disconnect between nitC message and NitC protein was observed depending on the phase of the growth cycle, the disconnect being related to proteolytic digestion of the NitC protein. Ironically, the cluster was also discovered to be upregulated in the absence of cyanide under nitrogen starvation conditions paralleling biofilm formation. The basis of the genetic linkage to cyanotrophy is not understood but taken together with results showing that nitrogen starvation and biofilm formation are also physiologically associated with Nit1C expression, points to a critical role for the cluster in stress-induced adaptation.
Linkage Relationships of Greenbug Resistance in Barley, Hordeum Vulgare L.
The linkage relationship and arm location of the gene for greenbug resistance in the variety Will was determined by using primary trisonomics and tertiary trisomic homozygous translocations. The gene for greenbug resistance was found to be on linkage group 1 by using primary trisonomics. The gene was located on the cetromere segment of the Tl-6a translocation by using a tertiary trismoic homozygous for greenbug resistance. The data further substantiates the feasibility of using trisomics in placing genes on proper linkage groups.
Lipids and Phospholipase Activity of Vibrio Cholerae
One purpose of this investigation is to determine the fatty acid and lipid content of typical Vibrio cholerae cells. The comparison of cholera lipid constituents with those of closely-related bacteria might be of taxonomic value. Furthermore, chemical characterization of the cholera vibrio could provide useful criteria for identification of these disease-producing microorganisms.
Lipogenic Proteins in Plants: Functional Homologues and Applications
Although cytoplasmic lipid droplets (LDs) are the major reserves for energy-dense neutral lipids in plants, the cellular mechanisms for packaging neutral lipids into LDs remain poorly understood. To gain insights into the cellular processes of neutral lipid accumulation and compartmentalization, a necessary step forward would be to characterize functional roles of lipogenic proteins that participate in the compartmentalization of neutral lipids in plant cells. In this study, the lipogenic proteins, Arabidopsis thaliana SEIPIN homologues and mouse (Mus Musculus) fat storage-inducing transmembrane protein 2 (FIT2), were characterized for their functional roles in the biogenesis of cytoplasmic LDs in various plant tissues. Both Arabidopsis SEIPINs and mouse FIT2 supported the accumulation of neutral lipids and cytoplasmic LDs in plants. The three Arabidopsis SEIPIN isoforms play distinct roles in compartmentalizing neutral lipids by enhancing the numbers and sizes of LDs in various plant tissues and developmental stages. Further, the potential applications of Arabidopsis SEIPINs and mouse FIT2 in engineering neutral lipids and terpenes in plant vegetative tissues were evaluated by co-expressing these and other lipogenic proteins in Nicotiana benthamiana leaves. Arabidopsis SEIPINs and mouse FIT2 represent effective tools that may complement ongoing strategies to enhance the accumulation of desired neutral lipids and terpenes in plant vegetative tissues. Collectively, our findings in this study expand our knowledge of the broader cellular mechanisms of LD biogenesis that are partially conserved in eukaryotes and distinct in plants and suggest novel targets that can be introduced into plants to collaborate with other factors in lipid metabolism and elevate oil content in plant tissues.
Lizard Tail Autotomy: Some Aspects of its Ecology and Energetics
Autotomy (self-induced loss) of body parts has evolved independently as a predator defense mechanism in several major animal phyla. The mechanism among vertebrates, including 13 of the 20 recognized lizard families, is tail autotomy. Its occurrence among the majority of lizard families offers an excellent opportunity to examine the effects of a major selective force on the ecology and evolution of a group of organisms. The research of this study was designed to examine experimentally (i) the function of tail autotomy, (ii) the function of autotomized tail movement, (iii) the energetics of autotomized tail movement, and (iv) the energetic costs of autotomy of an energy-rich tail to reproduction.
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