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Pacheco, Fábio Luiz Camacho. "Identificação bacteriana por derivação de ácidos graxos extraídos de células íntegras." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/9/9139/tde-28092009-143513/.
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As salas limpas são amplamente empregadas em indústrias farmacêuticas destinadas a fabricar medicamentos e dispositivos estéreis. Nós empregamos coloração de Gram e cromatografia gasosa de ésteres metílicos de ácidos graxos extraídos de células íntegras de microrganismos ambientais para caracterizar e identificar bactérias isoladas em 50 salas limpas diferentes projetadas para a fabricação de medicamentos estéreis e para fornecer um perfil de ácidos graxos das espécies mais comuns de bactérias isoladas. Uma análise estatística nos permitiu corroborar estudos anteriores e confirmar que cocos Gram positivos é o grupo mais relevante de microrganismos presentes nas salas limpas avaliadas. A espécie predominante é Micrococcus luteus, isolada de salas classe B e de pessoal, seguida de Staphylococcus cohnii em classe C, Bacillus subtilis em classe A e Staphylococcus hominis em classe D. Os perfis de ácidos graxos destas bactérias são, na maioria, consistentes com as bibliotecas padrão. Nós também tentamos estabelecer uma correlação entre a estação do ano e o nível de contaminação, embora a análise de variância tenha mostrado que não há diferença significativa entre o nível de contaminação no decorrer das estações. Além do mais, análises repetidas com um aumento gradual de massa celular nos permitiram concluir que a quantidade ótima de material celular necessário para extração de ácidos graxos varia com a espécie de bactéria. Finalmente, um estudo comparativo de algumas bactérias incubadas em diferentes temperaturas confirmou que o perfil de ácidos graxos é altamente influenciado pela temperatura. Portanto, nós acreditamos que este trabalho possa contribuir para identificar e compreender a comunidade bacteriana de algumas salas limpas farmacêuticas.Clean rooms are largely employed in pharmaceutical companies whose purpose is to produce sterile drugs and devices. We employed Gram staining and gas chromatography of fatty acid methyl esters extracted from whole cells of environmental isolates to characterize and identify bacteria isolated in each of 50 different clean rooms designed for the manufacturing of sterile medicinal products and to provide a fatty acid profile of the most common species of isolated bacteria. Statistical analysis allowed us to corroborate previous studies and confirm that Gram-positive cocci are the most relevant group of microorganisms inside the studied clean rooms. The predominant species is Micrococcus luteus, isolated from Grade B zones and from personnel, followed by Staphylococcus cohnii in Grade C, Bacillus subtilis in Grade A and S. hominis in Grade D. Fatty acid profiles of these bacteria are, to a great extent, consistent with standard libraries. We also attempted to establish a correlation between season and level of contamination, although variance analysis showed that there is no significant difference on the level of contamination throughout seasons. Furthermore, repeated analysis with a gradual increase in cell mass allowed us to conclude that the optimal amount of cell material depends on the species of the bacteria studied. Finally, a comparative study with some bacteria incubated in different temperatures confirmed that fatty acid profile is highly influenced by temperature. Therefore, we believe that this work can contribute to identify and understand the bacterial community of some pharmaceutical clean rooms.
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O'Rourke, Michele Jane. "Identification and analysis of differentiation components in Bacillus subtilis 168." Thesis, University of Sheffield, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312365.
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Inal, Jameel. "Identification and analysis of plasmid-encoded antigenic proteins in Bacillus anthracis." Thesis, Open University, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314744.
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Jutras, Eileen Maura 1958. "Field-scale biofiltration: Performance evaluation and microbial analysis." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282533.
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Biofiltration has been shown to be an effective method for the remediation of volatile organic compounds (VOC's), particularly petroleum vapors extracted from the vadose zone. Many bacteria have the enzymatic pathways necessary for aerobic mineralization of VOC's to form cell biomass, carbon dioxide and water. Molecular methods such as nucleic acid hybridizations and the polymerase chain reaction (PCR), are methods that can be applied to environmental samples to characterize bacterial community structure and function. The research presented here reports the use of a field-scale biofilter for the remediation of unleaded gasoline vapors extracted from the vadose zone. An evaluation of contaminant removal efficiency over a five month period showed that the biofilter removed 90% of total petroleum hydrocarbons and greater than 90% of the EPA priority pollutants benzene, toluene, ethylbenzene, and xylene. The bacterial consortium in the biofilter medium readily adapted to increased loading rates, and variations in temperature and moisture. A combination of conventional cultural and molecular methods was used to track the bacterial populations over the course of the experiment. Polymerase chain reaction amplification of the small ribosomal subunit DNA sequence was used for identification of bacterial isolates and the design of DNA hybridization probes. Hybridization of these probes to community DNA samples taken from the biofilter over time revealed changes in specific bacterial populations as bioremediation occurred. Specifically, bacteria that could use gasoline, toluene, ethylbenzene or xylene were prevalent throughout the biofilter. Bacterial populations that could degrade xylene gradually increased over time, while overall total population size was the similar in the background sample and at the end of the study.
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Griffith, Rosemary Elaine. "Identification of mixtures of edible oils by the analysis of steryl esters." Thesis, University of Reading, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329564.
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Malecha, Michael Markus. "Identification of lubricant contaminants in beverage cans using spectroscopic analysis and chemometrics." Thesis, Cranfield University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269638.
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Yang, Zhan. "Conidia of Aspergillus fumigatus : functional analysis of surface components and identification of receptors for A549 epithelial cells." Thesis, Edinburgh Napier University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391004.
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Farnsworth, Jacob S. "Hot Spot Identification and Analysis Methodology." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3878.
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The Utah Department of Transportation (UDOT) Traffic and Safety Division continues to advance the safety of roadway sections throughout the state. To aid UDOT in meeting their goal the Department of Civil and Environmental Engineering at Brigham Young University (BYU) has worked with the Statistics Department in developing analysis tools for safety. The most recent of these tools has been the development of a hierarchical Bayesian Poisson Mixture Model (PMM) statistical model of traffic crashes and safety on UDOT roadways statewide and the integration of the results of this model in a Geographic Information System (GIS) framework. This research focuses on the enhancement of the framework for highway safety mitigation in Utah with its six primary steps: 1) network screening, 2) diagnosis, 3) countermeasure selection, 4) economic appraisal, 5) project prioritization, and 6) effectiveness evaluation. The framework was enhanced by developing a methodology for accomplishing the steps of network screening, diagnosis, and countermeasure selection. This methodology is titled, "Hot Spot Identification and Analysis." The hot spot identification and analysis methodology consists of the following seven steps: 1) identify problematic segments with safety concern, 2) identify problem spots within the segments, 3) micro analysis of problematic segments and spots, 4) defining the segment, 5) defining the problem, 6) evaluation of possible countermeasures, and 7) selection and recommendation of feasible countermeasures. The methodology is to help in the identification of hot spots with safety concerns so that they can be analyzed and countermeasures can be identified to mitigate the safety issues. Examples of how the methodology is to function are given with specific examples from Utah's state roadway network.
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Hoosain, Nisreen. "Phenotypic and molecular analysis of Helicobacter spp. and related micro-organisms identified in clinical & environmental specimens." Master's thesis, University of Cape Town, 2006. http://hdl.handle.net/11427/2709.
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Abruquah, Harry H. "Identification of host-pathogen interacting molecules of Campylobacter jejuni using phage display technology and in silico sequence analysis." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10813/.
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Campylobacter jejuni is the leading cause of human gastroenteritis world-wide, and the antecedent infection in Guillain-Barré syndrome. Although much progress has been made regarding its virulence determinants,our understanding of the molecular basis of C. jejuni pathogenesis still lags behind that of other enteric pathogens. Bacterial pathogenesis is often dependent on proteinaceous virulence factors transported to the bacterial cell surface or released into the external environment. Understanding the molecular basis of interactions between these proteins and host cells is necessary in understanding and controlling infections. Background: Previously identified adhesins of C. jejuni NCTC11168 have still not provided us with a total understanding of the pathogenesis of campylobacteriosis. It is hypothesized that as yet unidentified C. jejuni surface proteins interact with host proteins contributing to colonisation and pathogenesis. This study sought to screen the genome of C. jejuni NCTC11168 to identify additional genes that may code for other adhesins using phage display technology and in silico sequence analysis. Methods: A phage display library was constructed by the insertion of randomly fragmented chromosomal DNA of C. jejuni NCTC11168 into the phagemid vector pG8SAET. Following affinity panning of the library against holo- and apo-lactoferrin, enriched clones were screened with ELISA to identify affinity-binding clones. Several phage clones were randomly selected and their C. jejuni DNA inserts sequenced and analysed with bio-informatic tools. In order to identify novel autotransporter proteins of C. jejuni, the amino acid sequences of previously described adhesion-associated autotransporters were employed in BLAST searches of the predicted coding sequences of C. jejuni NCTC11168 genome database. Results: Screening of the phage display library resulted in the identification of C. jejuni NCTC11168 gene, Cj0609c, encoding a putative periplasmic protein, designated LimC, predicted to be a member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. Searching the genome of C. jejuni NCTC11168, Cj0628 was identified as coding a protein with characteristics of autotransporters, designated CapA. CapA was demonstrated to be surface-exposed, mutants of which had a lowered ability to associate with or invade Caco-2 cells and failed to colonize chicken guts, indicating that CapA plays a role in host association and colonization by Campylobacter. Conclusion: LimC may be involved in binding of C. jejuni to lactoferrin for iron acquisition in vivo, and/or play further role in adhesion, colonization and internalisation of C. jejuni into host cells. CapA also plays a role in adhesion. Further characterization of these proteins should contribute to our understanding of the pathogenesis of C. jejuni.
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Mukherjee, Maitreyee. "Identification, enumeration, and diversity of ammonia-oxidizing archaea in the Laurentian Great Lakes." Bowling Green State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1368022892.
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Zimmer, Sarah Kathryn. "Identification of the Hmu PSTUV operon and its’ role in Heme Utilization in Rhizobia Leguminosarum ATCC 14479." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/honors/501.
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Iron is an essential nutrient for the proper functioning of many bacterial physiological processes. A deficiency of iron in bacteria can cause inhibition of cell growth and changes in morphology. Under iron restricted environments, microorganisms seek out different methods of acquiring iron. Our lab reported that RhizobiumLeguminosarum ATCC 14479, a gram-negative soil bacterium, is capable of utilizing heme as the sole source of iron. This work focuses on identifying and sequencing the hmuPSTUVoperon to assess its’ possible role in heme utilization in R. leguminosarum biovar trifoliiATCC 14479. We have confirmed the presence of this operon and have completed the sequencing of each gene involved in the operon. We have used in-silico analysis to assess the possible function of each gene. In the future, gene knockout will be performed to confirm the function of the hmuPSTUVoperon.
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Southerland, L. S., Phillip R. Scheuerman, and N. S. Nicholas. "Analysis of Lead, Aluminum and Calcium in Southern Appalachian American Beach." Digital Commons @ East Tennessee State University, 2000. https://dc.etsu.edu/etsu-works/2926.
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Churchill, Robert. "Identification of environmental determinants of behavior disorders through functional analysis of precursor behaviors." Thesis, University of North Texas, 2001. https://digital.library.unt.edu/ark:/67531/metadc2814/.
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Methods for the determining the functional properties of problem behaviors are necessary for the design of successful treatments. Many of the currently utilized methodologies are chosen based on their speed, ease of application or for the perceived risk-reduction they afford. However, when thoroughly analyzed many of these methods fall short of their intended purpose. The current study attempted to assess dangerous problem behavior through a functional assessment of functionally related precursor behaviors during analog sessions. Results indicate that for three participants, placing the reinforcing contingencies on these related precursor behaviors produced differentiated outcomes during the assessment. These outcomes matched the outcomes of assessments of the more dangerous problem behaviors.
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Ko, Han Il. "Noncoliform enumeration and identification in potable water, and their senstivity to commonly used disinfectants." Virtual Press, 1997. http://liblink.bsu.edu/uhtbin/catkey/1041914.
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Tap water collected according to standard methods was examined for microbial presence. Epifluorescent diagnoses using redox probe 5-cyano-2,3ditolyl tetrazolium chloride (CTC), 4',6-diamidino-2-phenylindole (DAPI), and acridine orange (AO) were employed for direct evidence of microorganisms. Evidence of total (DAPI or AO), respiring (CTC) bacteria, and heterotrophic plate count (HPC) was determined on multiple occasions during the summer, fall, and winter 1996-1997. Pseudomonas aeruginosa, Acinetobacter sp., Bacillus licheniformis, and Methylobacterium rhodinum were isolated and identified by the API and Biolog system using GN and GP procedures. On the basis of comparisons presented in this study between the CTC method and the standard HPC procedure, it appeared that the number of CTC-reducing bacteria in the tap water samples was typically higher than that determined by HPC, indicating that many respiring bacteria detected by the CTC reduction technique fail to produce visible colonieson the agar media used. In the seasonal data obtained by the CTC method, no difference was shown among respiring bacterial counts obtained from June through January. In the examination of P. aeruginosa viability in presence of chlorine, the number of CTC-positive bacteria exceeded the number of CFU by more than 2 logs after exposure to chlorine, suggesting that reliance on HPC overestimate the efficacy of disinfection treatment. In inactivation assays using the Biolog MT plate, no sensitivity to chlorine or chloramine disinfectants was noted even at high concentration levels (5 mg/liter). Following initial drop, bacterial activities increased as contact time increased. Thus, it appears that the MT microplate provides too low a cell concentration, too great a contact time, and/or too low a concentration of tetrazolium dye within the well for successful analysis of disinfectant capability to selected bacterial strains isolated from distribution water.Department of Biology
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Gallagher, L. K., Brian G. Evanshen, Kurt J. Maier, and Phillip R. Scheuerman. "Bacterial Source Tracking in the Sinking Creek Watershed, using Antibiotic Resistance Analysis (ARA) and Ribotyping." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etsu-works/2946.
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Fisher, Suzanne, N. S. Nicholas, and Phillip R. Scheuerman. "Dendrochemical Analysis of Lead and Calcium in Southern Appalachian American Beech." Digital Commons @ East Tennessee State University, 2002. https://dc.etsu.edu/etsu-works/2872.
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The health of the northern hardwood forest in the southern Appalachian Mountains of Tennessee, North Carolina, and Virginia has gained attention from the media and environmental stakeholders due to a purported decline in forest health at higher elevations. This project examined lead (Pb) and calcium (Ca) concentrations in growth rings of an important northern hardwood species, American beech (Fagus grandifolia Ehrh.) at Mount Rogers and Whitetop Mountain, Virginia and attempted to examine concentration relationships with stem growth patterns. Dominant and codominant trees were sampled from 16 research plots at two elevations. Tree cores were crossdated, divided into sections of 10-yr periods, and analyzed using atomic absorption spectroscopy. Lead concentrations correlated negatively with ring width. Elevation and aspect were significantly associated with the Pb concentration, while Ca concentrations were only associated with aspect. Tree core samples taken from higher elevation plots contained higher Pb concentrations than samples collected from lower elevation plots, while the northwest and southwest aspects contained significantly higher amounts of Pb and Ca. Both Pb and Ca concentrations increased during the 1860s and again during the mid-1900s.
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LeCoultre, T. D., and Phillip R. Scheuerman. "A Metal-Analysis and Risk Assessment of Heavy Metal Uptake in Common Garden Vegetables." Digital Commons @ East Tennessee State University, 2001. https://dc.etsu.edu/etsu-works/2927.
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Bassett, David R. "Use of Roadway Attributes in Hot Spot Identification and Analysis." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5642.
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The Utah Department of Transportation (UDOT) Traffic and Safety Division continues to advance the safety of roadway sections throughout the state. In an effort to aid UDOT in meeting their goal, the Department of Civil and Environmental Engineering at Brigham Young University (BYU) has worked with the Statistics Department in developing analysis tools for safety. The most recent of these tools has been the development of a hierarchical Bayesian Poisson Mixture Model (PMM) of traffic crashes known as the Utah Crash Prediction Model (UCPM), a hierarchical Bayesian Binomial statistical model known as the Utah Crash Severity Model (UCSM), and a Bayesian Horseshoe selection method. The UCPM and UCSM models helped with the analysis of safety on UDOT roadways statewide and the integration of the results of these models was applied to Geographic Information System (GIS) framework. This research focuses on the addition of roadway attributes in the selection and analysis of “hot spots.” This is in conjunction with the framework for highway safety mitigation migration in Utah with its six primary steps: network screening, diagnosis, countermeasure selection, economic appraisal, project prioritization, and effectiveness evaluation. The addition of roadway attributes was included as part of the network screening, diagnosis, and countermeasure selection, which are included in the methodology titled “Hot Spot Identification and Analysis.” Included in this research was the documentation of the steps and process for data preparation and model use for the step of network screening and the creation of one of the report forms for the steps of diagnosis and countermeasure selection. The addition of roadway attributes is required at numerous points in the process. Methods were developed to locate and evaluate the usefulness of available data. Procedures and systemization were created to convert raw data into new roadway attributes, such as grade and sag/crest curve location. For the roadway attributes to be useful in selection and analysis, methods were developed to combine and associate the attributes to crashes on problem segments and problem spots. The methodology for “Hot Spot Identification and Analysis” was enhanced to include steps for the inclusion and defining of the roadway attributes. These methods and procedures were used to help in the identification of safety hot spots so that they can be analyzed and countermeasures selected. Examples of how the methods are to function are given with sites from Utah’s state roadway network.
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Tau, Kimberly R. "Molecular and Cellular Analysis of Chlamydia Trachomatis: Persistence and Reactivation." Digital Commons @ East Tennessee State University, 1992. https://dc.etsu.edu/etd/2804.
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Chlamydia trachomatis (CT) is the most prevalent sexually-transmitted infection in the United States. It has been suggested that CT infections can become latent. This has not been substantiated. CT persistence was examined at the molecular and cellular level in vitro and in vivo. Penicillin treatment of CT in vitro results in abnormal inclusions and reduced recovery of infectious CT. Penicillin did not inhibit initial stages of infection, but did downregulate CT rRNA levels after 25 hours post-inoculation (p.i.). DNA amplification was employed to differentiate between a resolved infection and a persistent one. Utilizing a primer pair that amplified a 144 bp fragment in the CT MOMP gene, CT-persistently-infected McCoy cells maintained in penicillin medium were examined. Though undetectable by other assay methods, these cells harbored the CT genome for 18 passages. Removal of penicillin 1, 3 or 6 passages p.i. and subsequent cultivation in permissive medium resulted in "recovery" to productive infection. Removal of penicillin at later passages resulted in low level inclusion formation but no infectious progeny. Penicillin treatment in vitro resulted in a persistent infection undetectable by most methods. Female C$\sb3$H/HeNCRL mice were inoculated with CT intrauterinely and intravaginally in two separate experiments. In one, CT infection was established in untreated and Depo-Provera (DP)-pretreated mice. DP pretreatment enhanced vaginal shedding of infectious CT. A negative vaginal culture did not correlate with elimination of CT from the upper tract. In the second, penicillin therapy did not halt vaginal CT shedding, however, it reduced frequency of recurrent vaginal CT shedding. To examine reactivation, culture-negative mice ($\geq$2 successive vaginal cultures) were injected with cortisone-acetate (CA) or DP; mice from same subpopulation injected with saline served as controls. Transient vaginal CT shedding was reactivated in penicillin-treated mice (14% CA-injected), and in unmedicated mice (28% CA-injected, 33% DP-injected). Saline injection did not reactivate vaginal CT shedding. At time of sacrifice (16 or 22 weeks p.i.) no infectious CT was detected in upper tract tissues, although tissue damage was observed in most mice (70-71%). It is unknown if these mice harbored a persistent infection undetectable by culture. Further work utilizing molecular techniques is needed to resolve this question.
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Bester, Linka. "Detection and identification of wine spoilage microbes using PCR-based DGGE analysis." Thesis, Stellenbosch : University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/1558.
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Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2009.Grape juice is transformed into wine through the complex processes of alcoholic and malolactic fermentation that is performed by yeasts, lactic acid bacteria and acetic acid bacteria. However, the microbes involved in these processes do not only take part in ensuring the successful production of wine, but also cause spoilage of the wine if their growth is not controlled. Conventional, culture-dependent methods of microbiology have been used as the main technique in detecting and identifying these spoilage microbes. Cultureindependent techniques of molecular biology have recently become more popular in detecting possible spoilage microbes present in must and wine, since it allows the detection and identification of viable, but non-culturable microbes and are not as timeconsuming as conventional microbiological methods. The aim of this study was to investigate the sustainability of polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) analysis in detecting wine spoilage microbes inoculated into sterile saline solution (SSS) (0.85% (m/v) NaCl) and sterile white wine and red wine as single microbial species and as part of mixed microbial populations. Three methods of DNA isolation from SSS, sterile white wine and sterile red wine inoculated with reference microbial strains were compared in terms of DNA concentration and purity, as well as simplicity of the technique. These three DNA isolation methods were the TZ-method, the proteinase K-method and the phenol extraction method. DNA could not successfully be isolated from red wine using any of the three DNA isolation methods. The TZ-method was the method of choice for the isolation of DNA from inoculated SSS and sterile white wine as this technique gave the best results in terms of simplicity, DNA concentration and purity. PCR and DGGE conditions were optimised for the universal primer pair, HDA1-GC and HDA2, the wine-bacteria specific primer pair, WBAC1-GC and WBAC2, and the yeast specific primer pair, NL1-GC and LS2. DNA from Acetobacter pasteurianus, Lactobacillus plantarum, Pediococcus pentosaceus, Oenococcus oeni, Brettanomyces bruxellensis and Saccharomyces cerevisiae were amplified with the appropriate primers and successfully resolved with DGGE analysis. PCR and DGGE detection limits were successfully determined when 106 cfu.ml-1 of the reference microbes, A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis were separately inoculated into SSS and sterile white wine. It was possible to detect low concentrations (101 cfu.ml-1) with PCR for A. pasteurianus, Lb. plantarum, Grape juice is transformed into wine through the complex processes of alcoholic and malolactic fermentation that is performed by yeasts, lactic acid bacteria and acetic acid bacteria. However, the microbes involved in these processes do not only take part in ensuring the successful production of wine, but also cause spoilage of the wine if their growth is not controlled. Conventional, culture-dependent methods of microbiology have been used as the main technique in detecting and identifying these spoilage microbes. Cultureindependent techniques of molecular biology have recently become more popular in detecting possible spoilage microbes present in must and wine, since it allows the detection and identification of viable, but non-culturable microbes and are not as timeconsuming as conventional microbiological methods. The aim of this study was to investigate the sustainability of polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) analysis in detecting wine spoilage microbes inoculated into sterile saline solution (SSS) (0.85% (m/v) NaCl) and sterile white wine and red wine as single microbial species and as part of mixed microbial populations. Three methods of DNA isolation from SSS, sterile white wine and sterile red wine inoculated with reference microbial strains were compared in terms of DNA concentration and purity, as well as simplicity of the technique. These three DNA isolation methods were the TZ-method, the proteinase K-method and the phenol extraction method. DNA could not successfully be isolated from red wine using any of the three DNA isolation methods. The TZ-method was the method of choice for the isolation of DNA from inoculated SSS and sterile white wine as this technique gave the best results in terms of simplicity, DNA concentration and purity. PCR and DGGE conditions were optimised for the universal primer pair, HDA1-GC and HDA2, the wine-bacteria specific primer pair, WBAC1-GC and WBAC2, and the yeast specific primer pair, NL1-GC and LS2. DNA from Acetobacter pasteurianus, Lactobacillus plantarum, Pediococcus pentosaceus, Oenococcus oeni, Brettanomyces bruxellensis and Saccharomyces cerevisiae were amplified with the appropriate primers and successfully resolved with DGGE analysis. PCR and DGGE detection limits were successfully determined when 106 cfu.ml-1 of the reference microbes, A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis were separately inoculated into SSS and sterile white wine. It was possible to detect low concentrations (101 cfu.ml-1) with PCR for A. pasteurianus, Lb. plantarum, iv Pd. pentosaceus, and B. bruxellensis in SSS when amplified with the HDA1-GC and HDA2 primer pair. A PCR detection limit of 102 cfu.ml-1 was determined in sterile white wine for Pd. pentosaceus and 103 cfu.ml-1 for B. bruxellensis using this primer pair. The results obtained from the PCR amplification with the WBAC1-GC and WBAC2 primer pair compared well with the results of the HDA1-GC and HDA2 primer pair. The results from the DGGE detection limits indicated that it was possible to detect lower concentrations (101 – 102 cfu.ml-1) of A. pasteurianus, Lb. plantarum and Pd. pentosaceus with the HDA1-GC and HDA2 primer pair than the WBAC-GC and WBAC2 primer pair (102 – 104 cfu.ml-1). Lower detection limits were also determined for B. bruxellensis amplified with the HDA1-GC and HDA2 primer pair (103 – 104 cfu.ml-1) than with the NL1-GC and LS2 primer pair (105 cfu.ml-1). PCR and DGGE detection limits for the inoculation of A. pasteurianus, Lb. plantarum and B. bruxellensis at an inoculum of 108 cfu.ml-1 as part of mixed populations in SSS and sterile white wine compared well with the results obtained from the reference microbes inoculated as single microbial species. PCR detection limits of 101 cfu.ml-1 were determined for all three reference microbes inoculated as part of mixed populations when amplified with the HDA1-GC and HDA2 and the WBAC1-GC and WBAC2 primer pairs. It was observed that similar or higher DGGE detection limits were obtained for the reference microbes inoculated in sterile white wine (101 – 107 cfu.ml-1) than when inoculated into SSS (101 – 105 cfu.ml-1). PCR-based DGGE analysis proved to be a technique that could be used successfully with the universal, wine-bacteria and yeast specific primer pairs for the detection of A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis. The culture-independent technique makes the early detection of possible spoilage microbes at low concentrations in wine possible.
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Patent, Keisha Marie. "National Animal Identification System: An Analysis of Willingness to Comply Among Ohio and Kentucky Beef Show Participants." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1392980060.
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Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.
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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host.
The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population.
With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.
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Samols, Mark Atienza. "Identification and Functional Analysis of Micro-RNAs Encoded by Kaposi’s Sarcoma-Associated Herpesvirus." Case Western Reserve University School of Graduate Studies / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1181143062.
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Romas, Lisa. "Functional identification of microorganisms that transform mercury in marine sediments." Wright State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=wright1278616625.
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Trexler, Ryan Vincent. "Lipid Analysis and Microbial Community Characterization of Subsurface Shale." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480679153855158.
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Lang, Cassandra C., and University of Lethbridge Faculty of Arts and Science. "Identification and metabolic characterization of host-specific enterococci for use in source-tracking faecal contamination." Thesis, Lethbridge, Alta. : University of Lethbridge, Faculty of Arts and Science, 2005, 2005. http://hdl.handle.net/10133/265.
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Metabolic were used to evaluate Enterococcus as an indicator of faecal pollution. Enterococci were isolated using m-Enterococcus agar and speciated using conventional biochemical tests. Forty percent of the isolates were identified and metabolically characterized by the automated Biolog system. The biochemical test scheme recognized 16 enterococcal species, while Biolog recognized nine. Both methods identified E. faecalis at the greatest frequency. Overall species frequencies varied between the two methods. Biolog was unable to identify 31% of the isolates; 7% of the isolates were unidentified by the biochemical test scheme. Of the identified isolates, metabolic profiling with Biolog achieved speciation with 60 substrates. Unique profiles were obtained for 89% of the isolates. Isolates also demonstrated inter-trial differntial metabolism of substrates. This and the large number of unidentified isolates suggest great diversity among enterococci. Diversity and inter-trial metabolic inconsistencies will complicate use of enterococcal metabolic profiles as a source-tracking tool.xxiii, 264 leaves ; 29 cm.
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Marinelli, Zachary A. "Identification of a putative metK selenite resistance gene in Stenotrophomonas maltophilia OR02." Youngstown State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1516345597337997.
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Beligala, Dilshan Harshajith. "Identification of Rhizobial Symbionts Associated with Lupinus SPP." Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1435855654.
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Ray, Anirban. "Identification, Enumeration and Diversity of Nitrifying Bacteria in the Laurentian Great Lakes." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1351276518.
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Boling, Bryan Kenneth. "A framework and quantitative methodology for the identification of cost-effective environmental policy for civil aviation." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53459.
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Compared to the relative wealth of information surrounding design in the context of system-of-systems there has been little research surrounding policy making in system-of-systems. While the adoption of a formal approach and lexicon for system-of-systems problems has been proposed by researchers, the specific inclusion of regulatory policies in system-of-systems is still largely absent or underdeveloped. Typically, there is no distinction between internal policies of an organization and exogenous policies coming through regulatory channels. Further, researchers have yet to formally employ a standardized framework to regulatory policy problems in the context of a system-of-systems. As international regulatory bodies are calling on world States to identify and select “baskets of measures” to address CO2 emissions from civil aviation, there is a growing recognition that doing so will require a framework for policy identification and selection. Despite this recognition, such a framework has yet to be established.
This research develops a formal lexicon for public policy as a part of system-of-systems, and employs a formalized process to explore multiple established, planned, and potential policies in the context of the global civil aviation system. Existing architectures and lexicons will be expanded to include regulatory policies that have often been treated as exogenous forcing functions in system-of-systems problems. Ultimately, a process for informed quantitative decision making to support concurrent CO2 regulatory policy analysis and design in the civil aviation system-of-systems is established. The developed methodology will allow policy makers to systematically identify effective policy space, while maintaining the objectivity of the analyst.
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Idrus, Amwazi. "Identification of physical-environmental characteristics of Ciliwung Watershed, West Java, Indonesia, using a geographic information system." Virtual Press, 1992. http://liblink.bsu.edu/uhtbin/catkey/834631.
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Ciliwung Watershed is the most developed area in Indonesia. However, development needs have caused overexploitation of the available resources, which have eventually caused deterioration of the environment of this watershed, and caused several areas to be more prone to natural hazards. This study develops certain Geographic Information System models to identify the physical-environmental characteristics of the watershed, in an attempt to avoid further improper resources utilization. These models yield the soil erosion critical areas, landslide potential areas, the spread of sea water intrusion, land subsidence potential areas, surface runoff characteristic, natural hazards prone areas, and groundwater recharge area.Based on these yielded characteristics, the general physical capability of this watershed can be delineated, which consists of five capability zones : Zone I, the flood prone area that also occupies by seawater intrusion and potential land subsidence areas; Zone II, the area that is affected by excessive groundwater withdrawal, which has sea water intrusion areas and prone to land subsidence; Zone III, the groundwater recharge area for Jakarta Plain; Zone IV, the most capable area for physical development; and Zone V, upper part of the watershed which has landslide potential areas, soil erosion critical areas, and volcanic eruption prone areas.Department of Natural Resources
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Rutherford, Alexander Fenner. "Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents." PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/1555.
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Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood.
The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota.
Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields.
There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source.
Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale.
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Vigren, David. "Identification of Environmental Plastic Samples from a Caribbean Beach Survey by Near-Infrared Spectroscopy with the MicroNIR and Chemometric Analysis." Thesis, Örebro universitet, Institutionen för naturvetenskap och teknik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-45772.
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MicroNIR is a portable near-infrared diffuse reflection spectroscope. Its suitability for identifying environmental plastic polymers was evaluated through a series of performance tests. The plastic samples were collected during a beach survey in the Caribbean. First a reference database was built by analysing a series of reference plastic polymers. Prediction models were constructed by using principal component analysis (PCA) and cluster analysis on 2D- and 3D-scatterplots. Measurements of samples with a surface area down to 1 mm2 were successfully identified with the prediction models. Blend spectra were created by measuring two polymers simultaneously, from which each polymer NIR-fingerprint were able to be individually extracted from the blend spectra by subtracting the NIR-fingerprint of the opposite polymer. Prediction models were used to identify the samples in the tests with household plastics and the environmental plastic samples, collected in the Caribbean. Out of the forty-eight samples collected forty (83%) were identified. Twenty-seven were identified as polyethylene (56%), eleven as polypropylene (23%), one as polystyrene (2%), and one as polyamide (2%).
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Hudson, Kyle D. "Vibration-based damage detection with new operational response and waveform analysis methodology." Thesis, University of Iowa, 2010. https://ir.uiowa.edu/etd/820.
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Vibration-based damage identification (VBDI) techniques have been developed in part to address the problems associated with an aging civil infrastructure. To assess the potential of VBDI as it applies to highway bridges in Iowa, three applications of VBDI techniques were considered in this study: numerical simulation, laboratory structures, and field structures. VBDI techniques were found to be highly capable of locating and quantifying damage in numerical simulations. These same techniques were found to be accurate in locating various types of damage in a laboratory setting with actual structures. Although there is the potential for these techniques to quantify damage in a laboratory setting, the ability of the methods to quantify low-level damage in the laboratory is not robust. When applying these techniques to an actual bridge, it was found that some traditional applications of VBDI methods are capable of describing the global behavior of the structure but are most likely not suited for the identification of typical damage scenarios found in civil infrastructure. Measurement noise, boundary conditions, complications due to substructures and multiple material types, and transducer sensitivity make it very difficult for present VBDI techniques to identify, much less quantify, highly localized damage (such as small cracks and minor changes in thickness). However, while investigating VBDI techniques in the field, a novel methodology, operational response and waveform analysis (ORWA), was developed to extend the focus of traditional VBDI techniques by correlating bridge damage to operational structural motion. It was found that if the frequency-domain response of the structure can be generated from operating traffic load, the structural response can be animated and used to develop a holistic view of the bridge's response to various automobile loadings. By animating the response of a field bridge, concrete cracking (in the abutment and deck) was correlated with structural motion and problem frequencies (i.e., those that cause significant torsion or tension-compression at beam ends) were identified. Furthermore, a frequency-domain study of operational traffic was used to identify both common and extreme frequencies for a given structure and loading. Finally, a finite element analysis of a structure similar to the field bridge was carried out to supplement and partially verify experimental results. Further work should (1) perfect the process of collecting high-quality operational frequency response data; (2) expand and simplify the process of correlating frequency response animations with damage; and (3) develop efficient, economical, pre-emptive solutions to common damage types identified by ORWA.
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Lang, Ruby A. "ANALYSIS AND OPTIMIZATION OF COLORIMETRIC NANOSENSORS FOR RAPID DETECTION OF MICROBES IN WATER." DigitalCommons@CalPoly, 2020. https://digitalcommons.calpoly.edu/theses/2186.
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Access to safe water is a basic human right recognized by the United Nations General Assembly in 2010 (WHO, 2020). However, a least 2.2 billion people globally still are without safely managed water services meaning they use a drinking water source that can be contaminated with faeces (WHO, 2020). With such a pressing global health issue, it is clear that improvement to water systems is important and required in the Agenda 2030 Sustainable Development Goals (SDGs). However, to improve water systems and prove they are safe water sources, water quality testing must occur. A solution to this issue is the development of rapid detection sensors for pathogens in water. The first chapter of this thesis aims to create an informed list of rapid detection sensors that should be focused on for future development. This is achieved by using multicriteria decision analysis techniques based on using two consecutive processes. The first is the Analytic Hierarchy Process (AHP), which was used to develop weightings for criteria being measured for different sensor alternatives. The second process is the Technique of Order Preference Similarity to the Ideal Solution (TOPSIS), which was used to perform the ranking of the sensors being reviewed based on the weighted criteria. The outcome of the multicriteria decision analysis was identifying the top 5 rapid detection nanosensors for future development. They can be further improved to include field scale applications while also achieving lower detection limits and shorter detection times. The cost for these sensors could possibly be reduced by changing the nanoparticles that the sensor is composed of. Through improved methods, the goal of creating a cost effective, rapid-detection nanosensor for bacteria (e.g., Shiga-toxin producing E. coli) in drinking water can be achieved by prioritization of research on these promising nanosensors. The second chapter of the thesis focuses on optimizing a gold nanosensor developed in 2015 by Raweewab T. and Rawiwan L, hereafter called the “Original Method.” The goal was to reduce the cost and improve the reusability of their indirect colorimetric gold nanosensor without compromising the simplicity of the detection platform. With a reusable and more cost-effective sensor, field applications for water quality testing in water system projects in impoverished areas can be more obtainable. The nanoparticle itself was the target of optimization in this study. The hypothesis was that the polyethylenimine (PEI) coating on the gold nanoparticle surface is the governing factor of how the sensor functions, meaning the core nanomaterial does not affect the function of the sensor. In this study, the results showed that sensor still maintained its function after replacing the PEI coated gold nanoparticle used in the Original Method with PEI coated silver nanoparticles. These findings indicated that with further development and future research, it will be possible to use less expensive nanoparticles for making the nanosensor. It will also be possible to make this sensor reusable through the development of PEI coated magnetite nanoparticles. Their magnetic quality could allow for recovering the nanosensors from the test media, then re-conditioned and used again.
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Unger, Maria. "Identification of brominated organic compounds in aquatic biota and exploration of bromine isotope analysis for source apportionment." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-38871.
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Brominated organic compounds (BOCs) of both natural and anthropogenic origin are abundant in the environment. Most compounds are either clearly natural or clearly anthropogenic but some are of either mixed or uncertain origin. This thesis aims to identify some naturally produced BOCs and to develop a method for analysis of the bromine isotopic composition in BOCs found in the environment. Polybrominated dibenzo-p-dioxins (PBDDs) in the Baltic Sea are believed to be of natural origin although their source is unknown. Since marine sponges are major producers of brominated natural products in tropical waters, BOCs were quantified in a sponge (Ephydatia fluviatilis) from the Baltic Sea (Paper I). The results showed that the sponge does not seem to be a major producer of PBDDs in the Baltic Sea. In this study, mixed brominated/chlorinated dibenzo-p-dioxins were however discovered for the first time in a background environment without an apparent anthropogenic source. The use of nuclear magnetic resonance spectroscopy (NMR) is unusual in analytical environmental chemistry due to its sample requirements. Preparative capillary gas chromatography was used to isolate a sufficient amount of an unidentified BOC from northern bottlenose whale (Hyperoodon ampullatus) blubber (Paper II) to enable NMR analysis for identification of the compound. The bromine isotopic composition of BOCs may give information on the origin and environmental fate of these compounds. The first steps in this process are the development of a method to determine the bromine isotope ratio in environmentally relevant BOCs (Paper III) and measuring the bromine isotope ratio of several standard substances to establish an anthropogenic endpoint (Paper IV).At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.
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Tarus, Anita, and Elea Juell-Skielse. "Identification of Key Activities Contributing to Macro Plastic Waste Flows on the Shoreline of Koh Chang, Thailand : A Quantification of Macroplastic Waste Items." Thesis, KTH, Hållbar utveckling, miljövetenskap och teknik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-254208.
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Sustainable development is vital in order for Thailand to continue to develop as in previous years. However, sustainable development cannot be achieved if the amount of macroplastic littering into the oceans does not decrease. In order to facilitate future decision making regarding this issue, this report aims to identify which human activities that contribute the most to the present macroplastic waste items on Thai shorelines. This identification was performed through a simplified material flow analysis based on observations and simple calculations on the island Koh Chang in Ranong. A comparative study was performed on the dissimilar island Koh Larn in Pattaya in order to eliminate any error factors caused by the specific environment on Koh Chang. It was deduced that Grocery Consumption, Fishing and Dining were the Key Activities on the two islands that contributed to the present macroplastic waste. Tourism was also shown to be a great contributor. The study did not find any signs of a current Rate of Accumulation on Koh Chang. However, there were always macroplastic waste items present in the sampling areas which implies that they might pose a threat to the ecosystems. Further research is needed in order to find a suitable solution for this problem.En hållbar utveckling är central för att Thailand ska kunna fortsätta utvecklas på samma sätt som skett de senaste åren. Hållbar utveckling kan dock inte uppnås om mängden makroplaster som hamnar i haven inte minskar. För att underlätta framtida beslutsfattande ämnar denna rapport att identifiera de mänskliga aktiviteter som i störst utsträckning bidrar till de makroplastföremål som går att finna på thailändska kuststräckor. Denna identifiering utfördes genom en simplifierad materialflödesanalys som baserades på observationer och simpla beräkningar på ön Koh Chang i Ranong. En jämförande studie utfördes på den annorlunda ön Koh Larn i Pattaya för att eliminera felfaktorer som kan ha uppstått på grund av Koh Changs specifika förutsättningar. Studien visade att Livsmedelskonsumption, Fiske, och Restaurangbesök var de Nyckelaktiviteter som bidrog till det befintliga makroplastavfallet. Turism visade sig också vara en stor bidragare till makroplastavfall. Studien kunde inte visa på någon Ackumuleringsgrad på Koh Chang. Trots detta fanns alltid makroplastföremål närvarande i provtagningsområdena på Koh Chang, vilket antyder att dessa föremål skulle kunna innebära ett hot mot ekosystemen. Vidare efterforskningar krävs för att hitta en passande lösning på problemet.
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Borglin, Matthew R. "Analysis of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (OSA), A Bioactive Food Starch Modifier Compound." DigitalCommons@CalPoly, 2020. https://digitalcommons.calpoly.edu/theses/2168.
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Matthew R. Borglin
This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection Agency (EPA) to create a new category of sanitizer specifically designed for treatment of mature biofilms. The efficacy of sanitizers in this new regulatory category is determined by the EPA protocols MB-19 and MB-20. The EPA’s protocols outline methods for cultivating, treating, and measuring effects on Pseudomonas aeruginosa biofilms in a continuous flow stir bar bioreactor. Biofilm modification by OSA was verified by the presence of octenyl esters on OSA treated biofilms with single point Raman spectrophotometry. OSA modified biofilm’s antimicrobial properties were first investigated with crystal violet staining in 96-well microtiter plates with inconclusive results. However, effective antimicrobial properties where apparent when using the CDC Biofilm Reactor. OSA treatments consistently returned a 6-log CFU/coupon reduction in biomass compared to controls. Inhibition of planktonic and/or biofilm regrowth was demonstrated using the 96-well plate methodology. This thesis demonstrated the effectiveness of OSA chemical esterification reaction as a biofilm treatment. In doing so, this work suggests a new approach for biofilm remediation by chemically modifying the structural components of biofilm.
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Couto, Manuela Soares. "Molecular identification of clinical and strains environmental Burkholderia pseudomallei, from the State of CearÃ: based on analysis regions 16S and 16S-23S ribosomal DNA nuclear." Universidade Federal do CearÃ, 2009. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=10501.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel SuperiorMelioidosis is a potentially fatal disease caused by the bacterium Burkholderia pseudomallei, considered emerging in Brazil since the first cases were reported in 2003, on State of CearÃ. This study aimed to perform the molecular identification of 31 isolates of B. pseudomallei (26 clinical and 5 environmental) maintained in the culture collection of CEMM (Specialized Center for Medical Mycology), based on sequences 16S and 16S-23S rRNA. The DNA of these samples was extracted with the kit Wizard  Genomic DNA Purification (Promega), quantified by spectrophotometry and stored at 4ÂC. The amplification of a fragment of 302 bp of 16S-23S rRNA specific to B. pseudomallei was performed by PCR reaction with primers Bp1 and Bp4. The sequencing of 16S and 16S-23S rRNA was performed by using of the kit DYEnamicTM ET terminators cycle sequencing (GE Healthcare). The phylogenetic tree of 16S rRNA and the sequence identity matrix and sequence difference count matrix based on the 16S-23S rRNA were generated by the program MEGA4, version 4.1. The results confirmed the identification of 15 strains of B. pseudomallei (5 clinical and 10 environmental), which represents 48.4% of the isolates analyzed in this study. The phylogenetic tree based on 16S rRNA shows that the clinical and environmental isolates of B. pseudomallei of State of Cearà are evolutionarily clustered with the strains B. pseudomallei MSHR346 (Australia), B. pseudomallei 1106a (Thailand), B. pseudomallei K96243 (Thailand), B. pseudomallei 1710b (Thailand) and B. pseudomallei 668 (Australia). Using the same extraction kit was possible to extract DNA from B. pseudomallei directly from clinical specimen (bronchoalveolar lavage), confirming a new case of melioidosis in Ubajara/CE. In this study, the use of PCR for amplification of a fragment of 302 bp of 16S-23S rRNA identified correctly B. pseudomallei, and to confirm the discrimination between B. pseudomallei and B. mallei, the sequencing of the 16S and 16S-23S rRNA genes was performed. The technique of PCR coupled with sequencing of 16S and 16S-23S rRNA resulted in a high sensitivity and specificity of detection of B. pseudomallei in this study.
A melioidose à uma doenÃa potencialmente fatal causada pela bactÃria Burkholderia pseudomallei, sendo considerada emergente no Brasil desde que os primeiros casos foram reportados em 2003, no Estado do CearÃ. Este estudo pretendeu realizar a identificaÃÃo molecular de 31 isolados de B. pseudomallei (cinco clÃnicos e 26 ambientais) mantidos na coleÃÃo de culturas do CEMM (Centro Especializado em Micologia MÃdica), com base nas sequÃncias 16S e 16S-23S DNAr. O DNA destas amostras foi extraÃdo com o kit Wizard Genomic DNA Purification (Promega), quantificado por espectrofotometria e armazenado a 4ÂC. A amplificaÃÃo de um fragmento de 302 pb da regiÃo espaÃadora 16S-23S DNAr especÃfico para B. pseudomallei foi realizada por meio de reaÃÃo de PCR com os primers Bp1 e Bp4. O sequenciamento das regiÃes 16S e 16S-23S DNAr foi realizado pelo mÃtodo da terminaÃÃo da cadeia pelo didesoxinucleotÃdeo, usando-se o kit DYEnamicTM ET terminators cycle sequencing (GE Healthcare). A Ãrvore filogenÃtica da regiÃo 16S DNAr e as matrizes sequÃncia identidade e contagem de diferenÃas baseadas na regiÃo 16S-23S DNAr foram geradas pelo programa MEGA4, versÃo 4.1. Os resultados confirmaram a identificaÃÃo de 15 cepas de B. pseudomallei (cinco clÃnicas e dez ambientais), o que corresponde a 48.4% dos isolados em estudo. A Ãrvore filogenÃtica baseada na regiÃo 16S DNAr demonstra que os isolados clÃnicos e ambientais de B. pseudomallei do Estado do Cearà sÃo evolutivamente agrupados com as cepas B. pseudomallei MSHR346 (AustrÃlia), B. pseudomallei 1106a (TailÃndia), B. pseudomallei K96243 (TailÃndia), B. pseudomallei 1710b (TailÃndia) e B. pseudomallei 668 (AustrÃlia). Com a utilizaÃÃo do mesmo kit de extraÃÃo tambÃm foi possÃvel extrair DNA de B. pseudomallei diretamente de espÃcime clÃnico (lavado brÃnquico), confirmando um novo caso de melioidose no MunicÃpio de Ubajara/CE. Em nosso estudo, o uso da PCR para a amplificaÃÃo de um fragmento de 302 pb da regiÃo 16S-23S DNAr identificou corretamente B. pseudomallei, sendo que para confirmar a discriminaÃÃo entre B. pseudomallei e B. mallei, o sequenciamento das regiÃes 16S e 16S-23S DNAr foi realizado. A tÃcnica de PCR aliada ao sequenciamento das regiÃes 16S e 16S-23S do DNA ribossÃmico nuclear resultaram em uma elevada sensibilidade e especificidade de detecÃÃo de B. pseudomallei neste estudo.
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Chendra, Edwin. "Examination of regression modeling for estimating airbone [sic] fungal infiltration loss factor." Oklahoma City : [s.n.], 2005.
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Maris, Elisabeth. "Éco-conception par une Approche Multicritère d’un Système Polymère/Traceurs/Détecteur pour le tri automatisé par spectrométrie de fluorescence UV-VIS en vue d’augmenter la recyclabilité des produits." Thesis, Paris, ENSAM, 2014. http://www.theses.fr/2014ENAM0022/document.
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Le recyclage des matériaux issus de produits en fin de vie est un enjeu important pour préserver nos ressources de matières premières qui sont de plus en plus rares et dont l'extraction est de plus en plus impactante pour l'environnement. Pourtant certains matériaux sont peu recyclés. C'est le cas des polymères de couleur sombre.L'originalité de ce travail est d'avoir intégré dans le processus de conception deux stratégies de l'écoconception : les limites des procédés de tri actuel et les limites sur les ressources. Cette démarche a abouti à concevoir un matériau et son procédé de recyclage. Ce système apporte potentiellement un bonus écologique en permettant de produire plus de matières recyclées sur le marché en satisfaisant les consommateurs en apportant une traçabilité de ces matières et une technologie nouvelle validée par la mise au point d'un démonstrateur couplé à un convoyeur industrielThe recycling of materials from end of life products is a important issue to preserve our resources of raw materials which are more and more rare and the extraction of which is more and more impactant for the environment. Nevertheless certain materials are little recycled. It is the case of dark colored polymers.The originality of this work is to have integrated into the process of design two strategies of ecodesign: the limits of current sorting processes and the limits on the resources. This approach succeeded to design a material and its process of recycling. This system brings potentially an environmental bonus by allowing producing more recycled materials on the market, satisfying the consumers by bringing a traceability of these materials and a new technology validated by the development of a demonstrator coupled with an industrial conveyor
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Janjua, Safia. "Genetic Analysis of Snow Leopard Population Employing Next Generation Sequencing For Its Improved Conservation And Management." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1598870693394148.
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Ax, Erika. "Dietary Patterns : Identification and Health Implications in the Swedish Population." Doctoral thesis, Uppsala universitet, Klinisk nutrition och metabolism, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-250280.
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We eat foods not nutrients. What is more, we eat them in combinations. Consequently, capturing our complex food habits is likely an advantage in nutrition research. The overall aim of this doctoral thesis was therefore to investigate dietary patterns in the Swedish population –nutrient intakes, nutritional biomarkers and health aspects. Prostate cancer is the most common cancer among men in the developed world. However, the impact of dietary factors on disease risk is largely unknown. In Study I we investigated the association between a Mediterranean- and a Low-carbohydrate-high-protein dietary pattern and prostate cancer risk, in a cohort of elderly Swedish men. The latter (but not the former) was associated, inversely, with prostate cancer risk when taking validity in food records into account. Diet is one of our main exposure routes to environmental contaminants. Hence, such exposure could act as a mediating factor in the relation between diet and health. In Study II we investigated the association between; a Mediterranean- and a Low-carbohydrate-high-protein dietary pattern, as well as the official dietary recommendations, and circulating levels of environmental contaminants, in an elderly Swedish population. The first two patterns were positively related to levels of both persistent organic pollutants and heavy metals, whilst the dietary recommendations were inversely associated to dioxin and lead. Finally, although dietary patterns are likely to influence health, little is known about current dietary patterns in Sweden. In Study III we used a data-reduction method to identify dietary patterns in a nationwide sample of the Swedish population. Two major patterns were derived; a Healthy pattern of foods generally considered healthy (e.g. vegetables, fruits, fish and vegetable-oils) and a Swedish traditional pattern (with e.g. meats, potatoes, sauces, non-Keyhole milk-products, sweet-bakery products and margarine). Derived patterns were associated to population characteristics and the Healthy dietary pattern was inversely associated to anthropometric variables in Study IV. Dietary characteristics of the patterns were well reflected in correlations to nutrient intake and (to a lesser extent) in nutritional biomarkers. In conclusion dietary patterns for overall health should be considered, as well as other lifestyle-factors, when interpreting results in nutrition epidemiology and establishing dietary recommendations.
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Meinert, Cornelia [Verfasser], W. G. [Akademischer Betreuer] Lorenz, and U. J. [Akademischer Betreuer] Meierhenrich. "Isolation and identification of environmental pollutants from complex mixtures using effect-directed analysis and preparative capillary gas chromatography / Cornelia Meinert. Betreuer: W. G. Lorenz ; U. J. Meierhenrich." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2011. http://d-nb.info/1025134710/34.
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Ibáñez-Peral, Raquel. "Analysis of microbial diversity in an extreme environment: White Island, New Zealand." Australia : Macquarie University, 2009. http://hdl.handle.net/1959.14/44764.
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"June, 2008".Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences, 2009.
Bibliography: p. 227-259.
Literature review -- Materials and methods -- Sampling sites and sampling material -- Enrichment cultures and molecular analyses -- Optical and binding characterisation of the QDs -- Applications of the QDs -- Concluding remarks.
White island, the most active volcano in New Zealand, is a poorly studied environment that represents an ideal site for the investigation of acidophilic thermophiles. The microorganisms present on here are continually exposed to extreme environmental conditions as they are surrounded by steamy sulphurous fumaroles and acidic streams. The sediment temperature ranges from 38°C to 104°C whilst maintaining pH values below 3. A survey of the volcanic hydrothermal system of White Island was undertaken in order to gain insights onto the microbial diversity using culture-dependant techniques and molecular and phylogenetic analyses. A novel liquid medium based on "soil-extract" was designed which supported growth of bacterial and archaeal mixed cultures. Molecular analyses revealed that the dominant culturable bacterial species belong to the Bacteroidetes, Firmicutes and α-Proteobacteria groups. Several previously uncultured archaeal species were also present in the mixed cultures. The knowledge gained from these studies was intended to help in the development of a novel microbial detection technique suitable for community analysis. -- Conventional molecular techniques used to study microbial biodiversity in environmental samples are both time-consuming and expensive. A novel bead-based assay employing Quantum dots (QDs) was considered to have many advantages over standard molecular techniques. These include high detection speeds, sensitivity, specificity, flexibility and the capability for multiplexed analysis. QDs are inorganic semiconductor nanoparticles made up of crystals about the size of proteins. It has been claimed that the physical and chemical properties of the QDs have significant advantages compared to organic dyes, including brighter fluorescence and resistance to photo-bleaching. Their optical properties facilitate the simultaneous imaging of multiple colours due to their flexible excitation and narrow band emission. Functionalised QDs are able to bind to different biological targets such as DNA, allowing high-throughput analysis for rapid detection and quantification of genes and cells. -- The optical and physical characteristics of the QDs as well their interaction with biomolecules are shown to be suitable for the development of a novel bead-based technique able to target the key microbial species and identify them by flow cytometric measurements (FCM). The broad absorption and narrow emission spectra of the QDs, as well as their fluorescence intensity and specify to target biomolecules, was compared to other organic fluorophores. The potential advantages and limitations of QDs as a fluorophores for biological applications are discussed. -- The data acquired during this study provides a broad overview of the microbial diversity and ecology of the volcanically-active hydrothermal systems of White Island and constitutes the baseline for the development of a novel bead-based technique based on QDs.
Mode of access: World Wide Web.
xvii, 259 p. ill. (some col.)
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Karolski, Bruno. "Metagenômica comparativa e perfil metabólico in silico de solos no município de Cubatão, SP." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-05112013-111556/.
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Cubatão, o maior pólo industrial da américa latina também já foi uma das cidades mais poluídas do mundo. Os 30 anos de intensa atividade industrial vêm pressionando o meio ambiente com substâncias tóxicas e afetando gravemente a saúde da população. Dentre as substâncias contaminantes mais importantes da região estão os derivados de petróleo como o benzeno, tolueno, etilbenzeno e xilenos. Conhecidos como BTEX, eles são produzidos e utilizados em larga escala e a contaminação ocorre frequentemente através de vazamentos. Nos solos, devido à sua solubilidade em água, essas substâncias podem se espalhar por longas distâncias a partir do ponto afetado contaminando locais distantes. Já foi comprovada a capacidade de micro-organismos de sobreviver e até utilizar BTEX como fonte de carbono. Os micro-organismos adaptados catabolizam os contaminantes transformando-os em substâncias menos tóxicas e até mesmo eliminando-os do ambiente, capacidade de grande interesse econômico e ambiental. Nessa linha, nossa proposta visa o estudo das comunidades microbianas de solos afetados e não afetados por BTEX. Para isso foi utilizada a metagenômica como abordagem de estudo identificando-se diferenças qualitativas e quantitativas nas estruturas microbianas de três diferentes locais do município de Cubatão, sendo um deles afetado diretamente por BTEX. Pelo método utilizado e aqui desenvolvido, foi possível identificar um panorama metabólico geral identificando-se genes relevantes e o potencial de degradação de hidrocarbonetos aromáticos de micro-organismos conhecidos e desconhecidos, revelando melhor o potencial metabólico dos solos identificados. Os resultados apresentados podem contribuir para um melhor entendimento da dinâmica in situ de uma comunidade microbiana afetada por BTEX assim como melhorar o conhecimento sobre a comunidade microbiana de um local altamente impactado como Cubatão.Cubatão is the largest industrial site in Latin America and was in the past one of the most polluted cities in the world. 30 years of intense industrial activity has pushed environmental limits with toxic substances and has severely affected the inhabitants\' health. Among the contaminants found in the region, the petroleum derivatives benzene, toluene, ethylbenzene and xylenes are the most important. Known collectively as BTEX, they are produced and used at a large scale and contamination frequently occurs. Because it is highly soluble in water, when in soil BTEX can spread long distances from the original contamination site, thus affecting large areas. Some microorganisms are known to live in contaminated environments and use contaminants such as BTEX as a unique carbon source for energy production. They catabolize contaminants into less dangerous products or even eliminate them from environment, a feature which has great commercial and environmental interest. We therefore compared the microbial communities in soils which were affected and un-affected by BTEX contamination. To this end, we used a metagenomics approach and developed a comparison method to identify microorganisms and degradation potential of soils studied. We found qualitative and quantitative differences in microbial structures from three different sites in Cubatão County, one of which is contaminated with BTEX. We constructed a metabolic overview identifying important genes, degradation potential and microorganisms related to BTEX degradation. The results presented here could contribute to understanding the in situ dynamics of a BTEX affected microbial community as well as improving our knowledge of the microbial community of Cubatão, a highly environmentally impacted place.
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Pisarczyk, Elizabeth W. "The effect of garlic mustard (Alliaria petiolata) density on soil nutrient availability and microbial enzyme activity in Northwest Ohio : a gradient analysis /." Connect to full text in OhioLINK ETD Center, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=toledo1260236506.
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Thesis (M.S.)--University of Toledo, 2009.Typescript. "Submitted as partial fulfillment of the requirements for The Master of Science Degree in Biology (Ecology-track)." "A thesis entitled"--at head of title. Bibliography: leaves 28-32.
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Damaso, Natalie. "Biogeographical Patterns of Soil Microbial Communities: Ecological, Structural, and Functional Diversity and their Application to Soil Provenance." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/3006.
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The current ecological hypothesis states that the soil type (e.g., chemical and physical properties) determines which microbes occupy a particular soil and provides the foundation for soil provenance studies. As human profiles are used to determine a match between evidence from a crime scene and a suspect, a soil microbial profile can be used to determine a match between soil found on the suspect’s shoes or clothing to the soil at a crime scene. However, for a robust tool to be applied in forensic application, an understanding of the uncertainty associated with any comparisons and the parameters that can significantly influence variability in profiles needs to be determined. This study attempted to address some of the most obvious uncertainties of soil provenance applications such as spatial variability, temporal variability, and marker selection (i.e., taxa discrimination). Pattern analysis was used to validate the ecological theories driving the soil microbial biogeography. Elucidating soil microbial communities’ spatial and temporal variability is critical to improve our understanding of the factors regulating their structure and function. Microbial profiling and bioinformatics analyses of the soil community provided a rapid method for soil provenance that can be informative, easier to perform, and more cost effective than approaches using traditional physico-chemical data. This study also showed that stable profiles may allow comparison between evidence and a possible crime scene despite the time lapse (4 years) between sample collections, however, this is dependent on the analysis method, site, vegetation, and level of disturbance. Marker selection was also an important consideration for profiling. Even though Fungi look promising for single taxon soil discrimination, the additional markers can help discriminate between a wide variety of soil types. As in human identification, the more DNA markers queried the greater the discrimination power. Lastly, this study illustrated a novel method to query the iron relating genes and ability to design a novel marker that can easily be used to profile the functional diversity of a soil community to enhance soil classification. Overall this research demonstrated the potential and effectiveness of using microbial DNA from soil, not just for comparison, but also for intelligence gathering to pinpoint the geographic origin of the soil.
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Hendricks, Luanne R. "Soil Bioavailability of Aminomethylphosphonic Acid: A Metabolite of Glyphosate." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1592583268434087.
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