Dissertations / Theses on the topic 'Genetic methods for resistance detection'
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1
Thomas, Lee. "Genetic methods for Rapid Detection of Medically Important Nosocomial Bactera." Thesis, The University of Sydney, 2007. http://hdl.handle.net/2123/3575.
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The role of the microbiology laboratory is (1) to provide infection control information, so that highly transmissible isolates may be identified and appropriate control measures instigated as rapidly as possible and (2) to provide adequate information to the clinician enabling correct antibiotic choices to be made, particularly in the critically ill. Microbiological data is by definition slow as it is culture dependent: this study focused on the development of genetic, culture-independent methods for detection of resistance in nosocomial pathogens that could be introduced into the routine microbiology department and would fit into the routine workflow with a consequent reduction in time to result. Initially a duplex real-time polymerase chain reaction was developed for the rapid identification and detection of S. aureus and methicillin-resistance. This was optimised for immediate as-needs testing of positive blood cultures signalling with “Gram positive cocci, possibly staphylococcus” evident on Gram stain, on a random access real-time PCR platform. This technology, allowing early identification of S. aureus and its susceptibility to methicillin, by simple automated methodology, may soon become the standard for all microbiology laboratories servicing the critically ill. The second part of the study involved the development of a selective broth and multiplex PCR for detection of three important nosocomial isolates at this institution, methicillin-resistant S. aureus (MRSA), carbapenem-resistant Enterobacteriaceae, and multi-resistant Acinetobacter baumannii (MRAB). A multiplex PCR using four primer sets was designed to detect low colonisation levels of these isolates after overnight incubation in selective broth, significantly reducing the time to result and associated costs. This potentially useful epidemiological screening tool is practical, reproducible and sensitive with the potential of moving to an automated test (using real-time PCR, for example) in the future. The availability of early negative results judged by simple visual scanning (or by densitometry), means that the result is less operator-dependent, potentially reducing error rate. The last part of the study dealt with an important resistance phenotype, aminoglycoside resistance. There had been no recent comprehensive local surveys performed to determine the frequency of aminoglycoside resistance amongst the Enterobacteriaceae, or to identify the genetic determinants and their transmissibility. The isolates collected for the study were all resistant to at least one of gentamicin, tobramycin or amikacin. Identification of integron cassette arrays and use of specific internal primers identified at least one genetic determinant for gentamicin and tobramycin resistance in 22 of 23 isolates. Three isolates had two aminoglycoside resistance genes, and three isolates had three aminoglycoside resistance genes identified (Table 6.1). Transferable gentamicin-resistant plasmids were predominant amongst Klebsiella spp., but less so amongst Enterobacter spp. and E. coli. Gentamicin-resistant Klebsiella spp. were often ESBL positive, the genetic determinants of which were typically co-transferred on a conjugative plasmid. The importance of screening at a local level was demonstrated by the unexpected predominance of aac(6')-IIc amongst Enterobacter spp. and the detection of a new gene (aac(6')-LT). This part of the study has provided an understanding of the primary aminoglycoside resistance genes present in the local setting and their association with other resistances. This knowledge will allow development of assays for patient screening (clinical isolates and colonising flora), to better understand the epidemiology of aminoglycoside resistance and to allow better choice of antibiotic therapy related to presence or absence of these genes.
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Thomas, Lee. "Genetic methods for Rapid Detection of Medically Important Nosocomial Bactera." University of Sydney, 2007. http://hdl.handle.net/2123/3575.
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Master of ScienceThe role of the microbiology laboratory is (1) to provide infection control information, so that highly transmissible isolates may be identified and appropriate control measures instigated as rapidly as possible and (2) to provide adequate information to the clinician enabling correct antibiotic choices to be made, particularly in the critically ill. Microbiological data is by definition slow as it is culture dependent: this study focused on the development of genetic, culture-independent methods for detection of resistance in nosocomial pathogens that could be introduced into the routine microbiology department and would fit into the routine workflow with a consequent reduction in time to result. Initially a duplex real-time polymerase chain reaction was developed for the rapid identification and detection of S. aureus and methicillin-resistance. This was optimised for immediate as-needs testing of positive blood cultures signalling with “Gram positive cocci, possibly staphylococcus” evident on Gram stain, on a random access real-time PCR platform. This technology, allowing early identification of S. aureus and its susceptibility to methicillin, by simple automated methodology, may soon become the standard for all microbiology laboratories servicing the critically ill. The second part of the study involved the development of a selective broth and multiplex PCR for detection of three important nosocomial isolates at this institution, methicillin-resistant S. aureus (MRSA), carbapenem-resistant Enterobacteriaceae, and multi-resistant Acinetobacter baumannii (MRAB). A multiplex PCR using four primer sets was designed to detect low colonisation levels of these isolates after overnight incubation in selective broth, significantly reducing the time to result and associated costs. This potentially useful epidemiological screening tool is practical, reproducible and sensitive with the potential of moving to an automated test (using real-time PCR, for example) in the future. The availability of early negative results judged by simple visual scanning (or by densitometry), means that the result is less operator-dependent, potentially reducing error rate. The last part of the study dealt with an important resistance phenotype, aminoglycoside resistance. There had been no recent comprehensive local surveys performed to determine the frequency of aminoglycoside resistance amongst the Enterobacteriaceae, or to identify the genetic determinants and their transmissibility. The isolates collected for the study were all resistant to at least one of gentamicin, tobramycin or amikacin. Identification of integron cassette arrays and use of specific internal primers identified at least one genetic determinant for gentamicin and tobramycin resistance in 22 of 23 isolates. Three isolates had two aminoglycoside resistance genes, and three isolates had three aminoglycoside resistance genes identified (Table 6.1). Transferable gentamicin-resistant plasmids were predominant amongst Klebsiella spp., but less so amongst Enterobacter spp. and E. coli. Gentamicin-resistant Klebsiella spp. were often ESBL positive, the genetic determinants of which were typically co-transferred on a conjugative plasmid. The importance of screening at a local level was demonstrated by the unexpected predominance of aac(6')-IIc amongst Enterobacter spp. and the detection of a new gene (aac(6')-LT). This part of the study has provided an understanding of the primary aminoglycoside resistance genes present in the local setting and their association with other resistances. This knowledge will allow development of assays for patient screening (clinical isolates and colonising flora), to better understand the epidemiology of aminoglycoside resistance and to allow better choice of antibiotic therapy related to presence or absence of these genes.
3
Robberts, Frans Jacob Lourens. "Genetic investigations of pneumocystis jirovecii : detection, cotrimoxazole resistance and population structure." Thesis, Link to the online version, 2005. http://hdl.handle.net/10019.1/1304.
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Thomas, Lee Carolyn. "Genetic methods for rapid detection of medically important nosocomial bacteria." Connect to full text, 2007. http://hdl.handle.net/2123/3575.
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Thesis (M. Sc. Med.)--University of Sydney, 2007.Title from title screen (viewed 15 October 2008). Submitted in fulfilment of the requirements for the degree of Master of Science in Medicine to the Discipline of Medicine, Faculty of Medicine. Includes bibliographical references. Also available in print form.
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Cohen, Joseph Paul. "Crater detection via genetic search methods to reduce image features." Thesis, University of Massachusetts Boston, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1550596.
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Recent approaches to crater detection have been inspired by face detection's use of gray-scale texture features. Using gray-scale texture features for supervised machine learning crater detection algorithms provides better classification of craters in planetary images than previous methods. When using Haar features it is typical to generate thousands of numerical values from each candidate crater image. This magnitude of image features to extract and consider can spell disaster when the application is an entire planetary surface. One solution is to reduce the number of features extracted and considered in order to increase accuracy as well as speed. Feature subset selection provides the operational classifiers with a concise and denoised set of features by reducing irrelevant and redundant features. Feature subset selection is known to be NP-hard. To provide an efficient suboptimal solution, four genetic algorithms are proposed to use greedy selection, weighted random selection, and simulated annealing to distinguish discriminate features from indiscriminate features. Inspired by analysis regarding the relationship between subset size and accuracy, a squeezing algorithm is presented to shrink the genetic algorithm's chromosome cardinality during the genetic iterations. A significant increase in the classification performance of a Bayesian classifier in crater detection using image texture features is observed.
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Konstantinidis, Michalis. "Preimplantation genetic diagnosis : new methods for the detection of genetic abnormalities in human preimplantation embryos." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:28611f65-7729-4293-9c3f-4fc3f0cc39d7.
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Preimplantation genetic diagnosis (PGD) refers to the testing of embryos produced through in vitro fertilization (IVF) in order to identify those unaffected by a specific genetic disorder or chromosomal abnormality. In this study, different methodologies were examined and developed for performance of PGD. Investigation of various whole genome amplification (WGA) methods identified multiple displacement amplification as a reliable method for genotyping single cells. Furthermore, this technology was shown to be compatible with subsequent analysis using single nucleotide polymorphism (SNP) microarrays. Compared to conventional methods used in this study to perform single cell diagnosis (e.g. multiplex PCR), WGA techniques were found to be advantageous since they streamline the development of PGD protocols for couples at high risk of transmitting an inherited disorder and simultaneously offer the possibility of comprehensive chromosome screening (CCS). This study also aimed to develop a widely applicable protocol for accurate typing of the human leukocyte antigen (HLA) region with the purpose of identifying embryos that will be HLA-identical to an existing sibling affected by a disorder that requires haematopoietic stem cell transplantation. Additionally, a novel microarray platform was developed that, apart from accurate CCS, was capable of reliably determining the relative quantity of mitochondrial DNA in polar bodies removed from oocytes and single cells biopsied from embryos. Mitochondria are known to play an important role in oogenesis and preimplantation embryogenesis and their measurement may therefore be of clinical relevance. Moreover, real-time PCR was used for development of protocols for CCS, DNA fingerprinting of sperm samples and embryos and the relative quantitation of telomere length in embryos (since shortened telomeres might be associated with reduced viability). As well as considering the role of genetics in terms of oocyte and embryo viability assessment and the diagnosis of inherited genetic disorders, attention was given to a specific gene (Phospholipase C zeta) of relevance to male infertility. A novel mutation affecting the function of the resulting protein was discovered highlighting the growing importance of DNA sequence variants in the diagnosis and treatment of infertility.
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Uygun, Sahra. "Development Of Analysis Methods For Cry1ac And Sam-k Gene Lines In Tomato Using Pcr And Real-time Pcr." Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/3/12611991/index.pdf.
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Genetically modified organisms are entering the human diet in all over the world. In order to have transparency in the foods that are being consumed, there is a need to trace the genetically modified organisms (GMOs) in the market and consequently this need brings the necessity of analytical methods that are capable of detecting, identifying and quantifying the transgenic events. These analytical methods also form the basis of the labeling regulations that are tried to be formed regarding GMOs. The main aim of this study is to develop and apply the detection methods for the two of the tomato events, delayed ripening and insect resistant. Currently the only validated detection methods are mainly for the corn, soybean, and cotton. There is no validated detection method for tomato. Tomato is one of the most consumed food products in Turkey and it is also among the controversial organisms in terms of genetic modifications and labeling, therefore the analysis of the genetic modifications in tomato is crucial. In this study, DNA-based detection is performed, with PCR being the chosen method of study. In order to detect the GMO-derived DNA, the method of analysis includes the following studies: species-specific, screening, gene-specific, construct-specific and inverse PCR. In addition, the quantification method is developed using the real-time PCR. In order to develop the procedure of identification method, the reference samples are used and the unknown varieties that are to be analyzed using this method are expected to have similarities with the authorized transgenic events.
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Pecetti, Luciano. "Genetic resources and selection methods for drought and salinity resistance in durum wheat." Thesis, Bangor University, 1994. https://research.bangor.ac.uk/portal/en/theses/genetic-resources-and-selection-methods-for-drought-and-salinity-resistance-in-durum-wheat(119af68a-9751-4451-a54e-6c16fdb941ed).html.
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The relevance of drought and salinity stress under Mediterranean conditions is reviewed and prospects for crop improvement against these constraints are discussed. Field trials under severe drought in Syria highlighted the importance of earliness to ensure satisfactory yields. Peduncle length and frost tolerance were also important attributes. Under more favourable conditions in Sicily, the yield components per se (number of spikes, number of kernels and kernel weight) had greater influence on genotype performance. At both locations of evaluation high yields were attained through different architectures of traits. Durum wheat genetic resources proved very variable. Genotypes were identified which could be used as donors of adaptive characters in breeding programmes. The CERES-Wheat growth model was used for the two locations, using historical weather data and two genotypes of known adaptation to the region. Early heading was a positive attribute, particularly in Syria. At both sites, lengthening of the grain filling period resulted in higher yields. Three sowing dates were simulated. "Early" sowing (1 November) had the highest simulated yield in both environments, suggesting a possible agronomic means to improve yields under stress. Simulated yields were in most cases within 15% of measured values when a comparison was possible. The ability to adjust osmotically was sought in seedlings artificially exposed to drought stress during early development. One entry appeared to possess this feature. However, another genotype, of known tolerance under real conditions, did not show this ability. Therefore, osmotic adjustment during early stages of ontogeny does not seem unequivocally able to identify the best genotypes under drought. Salt tolerance of durum wheat genetic resources was assessed measuring early growth under controlled environment. The data indicated that the results may be somewhat experiment-specific when using different growing techniques such as hydroponics and sand-culture. Finding tolerant tetraploid entries in terms of plant survival and ion uptake seemed difficult. However, variability existed and some entries, less susceptible than others, were noted. They could be used for breeding. For instance, they could be valuable recipient for the introgression of identified resistance mechanisms from other taxa.
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Jurstrand, Margaretha. "Detection of Chlamydia trachomatis and Mycoplasma genitalium by genetic and serological methods." Doctoral thesis, Örebro : Universitetsbiblioteket : Örebro University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-793.
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Treuerne, Balazs Krisztina Eszter. "Methods for the surveillance of urgent drug-resistant bacterial threats." Thesis, University of Sydney, 2020. https://hdl.handle.net/2123/24498.
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Despite being a natural phenomenon, antibacterial resistance has been accelerated and the increasing rates of antibiotic therapy failure is now having a significant impact upon public health and the economy in every country of the world. As a result of declining investment and innovation in the development of novel antimicrobial agents, it is vitally important to preserve the currently effective agents through more regulated and tailored therapeutic interventions. In order to do so, rapid, robust, sensitive and specific diagnostic tests should be available to end-users. The incorporation of fluorogenic substrates into solid or liquid media could allow for the development of such tests, and the aim of this study was to investigate this relatively unexploited area of microbiology.
Fluorogenic media for bacterial detection employ a non-fluorescent (fluorogenic) enzyme substrate, which is only converted to its fluorescent form when acted upon by a specific enzyme expressed by a bacterium of interest. In this research project, prolyl and pyroglutamyl aminopeptidase substrates were synthesized using coumarin fluorophores, which were linked to the enzyme targeting portions (proline or pyroglutamic acid) via self-immolative linkers. The fluorescence properties of the substrates were evaluated and compared with those of the respective fluorophores. The fluorescence intensity of the substrates was generally lower than that of the fluorophores, even at a 10-fold higher concentration, which is a key advantage for their use as diagnostic tools. A significant difference was observed between the fluorescence intensity of the different fluorophores, depending on their substituents. An ester linkage between the fluorophore and linker corresponded with a greater difference in fluorescence intensity from their corresponding fluorophore than for ether-linked substrates. However, ether-linked substrates generally showed greater differences in their emission wavelength maxima from the fluorophores, making them more suitable substrates for use in the detection of enzymatic activity.
These enzyme substrates were then evaluated against a range of clinically relevant pathogenic bacteria in order to determine the sensitivity and specificity of these probes and their potential use in clinical diagnostics. Ester-linked substrates underwent spontaneous hydrolysis in aqueous media, while those with ether links remained stable and only produced fluorescence signals when acted upon by bacterial enzymes. Prolyl aminopeptidase substrates showed specificity to S. typhimurium and no enzyme activity was observed in clinically relevant species, including C. freundii, E. cloacae, Shigella spp., and S. typhi, however, their sensitivity for S. typhimurium remained low. Pyroglutamyl aminopeptidase substrates showed promising results against Enterobacteriaceae, and, exploiting the difference between their lactose fermentation rate, incorporating the substrate in MacConkey solid media proved to be a successful approach to distinguishing K. pneumoniae from other 3 clinically relevant enterobacter species, C. freundii, E. cloacae and S. marcescens with 91.7 % positive predictive and 95.2% negative predictive values based upon a 48-hour detection time. When combined with meropenem, and introducing the substrate in solution to overnight cultures, this method allowed the distinction of carbapenem-resistant K. pneumoniae from resistant E. coli, P. aeruginosa and A. baumannii in as little as 1 hour.
In addition, a potential chromogenic ribosidase substrate was prepared and evaluated in growth media, however, this substrate showed poor stability in aqueous solution.
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Dufresne, Philippe J. "Development and validation of molecular markers for the detection of disease resistance alleles in Lactuca sativa." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=78352.
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In this study, RAPD (Randomly Amplified Polymorphic DNA) and SCAR (Sequence Amplified Characterized Region) markers found within 5 centiMorgans of known disease resistance loci in L. sativa were tested for their potential use in MAS. Out of thirty RAPD and SCAR markers evaluated, ten were found to be reliable predictors of disease resistance or susceptibility across a wide range of commercial and reference cultivars. Direct sequencing of seven selected markers did not reveal any significant similarity with known sequences. Three SNPs (Single Nucleotide Polymorphism) associated with two markers found in close proximity to corky root (cor) and Lettuce mosaic virus resistance (mo12) genes were identified. This information was used in the development of a non-electrophoresis PCR-based assay called FRET (Fluorescence Resonance Energy Transfer) hybridization probes assay.
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Herrera-Foessel, Sybil A. "Enhancing the genetic diversity and durability of leaf rust resistance in durum wheat /." Uppsala : Dept. of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200701.pdf.
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Wong, Kam Cheung. "Intelligent methods of power system components monitoring by artificial neural networks and optimisation using evolutionary computing techniques." Thesis, University of Sunderland, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285580.
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Holmans, Peter Alan. "Maximum likelihood methods for the detection of genetic linkage and association using affected sibling pairs." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320004.
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Kokozidou, Maria. "Evaluation of PCR methods for detection, species identification and determination of genetic variation in L. infantum." [S.l.] : [s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968411525.
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Östholm, Balkhed Åse. "Extended-Spectrum ß-Lactamase-Producing Enterobacteriaceae : Antibiotic consumption, Detection and Resistance Epidemiology." Doctoral thesis, Linköpings universitet, Avdelningen för mikrobiologi och molekylär medicin, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-104216.
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ESBL-producing Enterobacteriaceae are emerging worldwide and they are frequently multi-drug resistant, thus limiting treatment options for infections caused by these pathogens. The overall aim of the thesis was to investigate ESBL-producing Enterobacteriaceae in a Swedish county. First, we developed a molecular method, a multiplex PCR assay for identification of SHV, TEM and CTX-M genes in clinical isolates of Enterobacteriaceae with an ESBL phenotype. From 2002 until the end of 2007 all isolates of ESBL-producing Enterobacteriaceae in Östergötland, Sweden were further investigated. The prevalence of ESBL-producing Enterobacteriaceae was low, <1%, but increasing,while the antibiotic consumption remained unchanged. CTX-M enzymes, particularly CTX-M group 1, dominate in our region as well as in the rest of Europe. Furthermore, we have investigated antimicrobial susceptibility by performing MIC-testing in a large, well-characterized population of CTX-M-producing E. coli. Only three oral antimicrobial agents (fosfomycin, nitrofurantoin and mecillinam) demonstrated susceptibility above 90%. High susceptibility, >90%, was also demonstrated for carbapenems, colistin, tigecycline and amikacin. Sixty-eight per cent of ESBL-producing E. coli was multi-resistant, and the most common multi-resistance pattern was the ESBL phenotype with decreased susceptibility to trimethoprim, trimethoprim-sulfamethoxazole, ciprofloxacin, gentamicin and tobramycin. Isolates belonging to CTX-M group 9 are generally more susceptible to antibiotics than the CTX-M group 1-producing E. coli. Finally, a prospective multicentre case-control study examined the prevalence of ESBL-producing Enterobacteriaceae in faecal samples before and after travel abroad and the risk factors of acquisition. Sixty-eight of 226 travellers (30%) had ESBL-producing Enterobacteriaceae in the faecal flora. The geographical area visited had the highest impact on acquisition, with highest the risk for travellers visiting the Indian subcontinent, followed by Asia and Africa north of the equator. Also, acquisition of ESBL-producing Enterobacteriaceae during travel is associated with abdominal symptoms such as diarrhoea. Age also seemed to affect the risk of acquiring ESBL-producing Enterobacteriaceae, the highest risks were found among travellers ≥ 65 years. This thesis has contributed to increased understanding of the epidemiology of ESBL-producing Enterobacteriaceae and their susceptibility to both beta-lactam and non-beta-lactam agents.
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Ciampa, Julia Grant. "Multilocus approaches to the detection of disease susceptibility regions : methods and applications." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:8f82a624-7d80-438c-af3e-68ce983ff45f.
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This thesis focuses on multilocus methods designed to detect single nucleotide polymorphisms (SNPs) that are associated with disease using case-control data. I study multilocus methods that allow for interaction in the regression model because epistasis is thought to be pervasive in the etiology of common human diseases. In contrast, the single-SNP models widely used in genome wide association studies (GWAS) are thought to oversimplify the underlying biology. I consider both pairwise interactions between individual SNPs and modular interactions between sets of biologically similar SNPs. Modular epistasis may be more representative of disease processes and its incorporation into regression analyses yields more parsimonious models. My methodological work focuses on strategies to increase power to detect susceptibility SNPs in the presence of genetic interaction. I emphasize the effect of gene-gene independence constraints and explore methods to relax them. I review several existing methods for interaction analyses and present their first empirical evaluation in a GWAS setting. I introduce the innovative retrospective Tukey score test (RTS) that investigates modular epistasis. Simulation studies suggest it offers a more powerful alternative to existing methods. I present diverse applications of these methods, using data from a multi-stage GWAS on prostate cancer (PRCA). My applied work is designed to generate hypotheses about the functionality of established susceptibility regions for PRCA by identifying SNPs that affect disease risk through interactions with them. Comparison of results across methods illustrates the impact of incorporating different forms of epistasis on inference about disease association. The top findings from these analyses are well supported by molecular studies. The results unite several susceptibility regions through overlapping biological pathways known to be disrupted in PRCA, motivating replication study.
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Tom, Bryan Matthew. "A COMPARISON OF NONINVASIVE SURVEY METHODS FOR MONITORING MESOCARNIVORE POPULATIONS IN KENTUCKY." UKnowledge, 2012. http://uknowledge.uky.edu/forestry_etds/10.
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Harvest data are typically used to evaluate mesocarnivore population dynamics in many states, including Kentucky. While relatively easy to collect, these data are subject to reporting biases, and inferences about population trends can often only be made at coarse spatial scales. Gray fox (Urocyon cinereoargenteus), bobcat (Lynx rufus), and coyote (Canis latrans) populations in Kentucky are managed primarily through harvest data used to establish future harvest quotas. Increasingly, noninvasive survey methods have been used to characterize a number of population parameters for a variety of species; however, successful use of these methods is often site-specific. We assessed the efficacy and cost-effectiveness of two noninvasive survey methods, scat detection dogs and rub-pad hair snares, for surveying mesocarnivore species at two sites in the mixed-mesophytic forest of northeastern Kentucky. We sampled 100 hair snares covering approximately 100km2 and 27 transects covering approximately 27km2 from which 7 hair samples and 261 scat samples were collected respectively. Hair snares cost $397/sample at 6.4 hours/day, while scat detection dogs cost $47/sample at 4.9 hours/day. Genetic methods were used to identify biological samples to species and individual. Our findings should prove useful to state wildlife managers in comparatively evaluating methods for future mesocarnivore monitoring.
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Sargison, Neil Donald. "Development of genetic crossing methods to identify genes associated with macrocyclic lactone resistance in the sheep nematode parasite, Haemonchus contortus." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4395.
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There is a pressing need to develop strategies to reduce the emergence of macrocyclic lactone anthelmintic resistance in sheep flocks. Management practices aimed at maintaining anthelmintic susceptible nematodes in refugia while achieving a satisfactory level of production may prove to be useful. However, sensitive molecular tests are required to monitor the subtle effects of these practices on the frequency of resistance alleles within nematode populations. To-date, conventional studies of candidate genes coding for the known methods of action of macrocyclic lactone anthelmintics have produced a complex picture, highlighting the relevance of different approaches to the identification of resistance markers. This thesis describes the development of a single nematode parent genetic crossing method and discusses its application to identify molecular markers for anthelmintic resistance. Parasitological and molecular verification of successful inbreeding of the MHco3 strain of H. contortus derived from the progeny of a genetic cross between single nematode parents is described. The single parent genetic crossing method has enabled the production of diverse inbred lines of the MHco3 H. contortus and may prove useful for genome assembly, or for the development of a genetic map. The study has afforded insights to the biology of H. contortus and effects of host immunity on nematode parasites. New information is presented concerning the period during which adult female nematodes continue to shed fertilised eggs after removal of males, the development of unfertilised H. contortus eggs, and the population genetics of mixed infections of two different strains of H. contortus. Novel backcrossing experiments initially between a macrocyclic lactone resistant (MHco4 or MHco10) and a susceptible (MHco3) strain of H. contortus and then between ivermectin treated backcross generations and the parental susceptible strain are described. The resources provided by these experiments should enable comparative genomic analysis and conventional molecular biology to identify resistance genes derived from the parental resistant strains in fourth backcross generations that are the same as a parent ivermectin susceptible population, apart from the presence of alleles linked to anthelmintic resistance, derived from parent resistant strains.
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Preston, Jessica. "Overcoming the Current Limitations of Next-Generation Sequencing with New Methods for Local Assembly of Genomes and High-Specificity Rare Mutation Detection." Thesis, University of Oregon, 2016. http://hdl.handle.net/1794/19700.
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The relatively low cost of Next-Generation Sequencing (NGS) has enabled researchers to generate large amounts of sequencing data in order to identify disease-causing mutations and to assemble simple genomes. However, NGS has inherent limitations due to the short DNA read lengths and high error rate associated with the technique. The short read lengths of NGS prevent the assembly of genomes with long stretches of repetitive DNA, and the high error rate prevents the accurate detection of rare mutations in heterogeneous populations such as tumors and microbiomes.
I have co-developed new NGS methods to overcome these challenges. In order to increase the effective read length of NGS reads, local de novo assembly of short reads into long contigs can be achieved through the use of Paired-End Restriction-site Associated DNA Sequencing (RAD-PE-Seq). With the RAD-PE method, I sequenced a stickleback fosmid and generated contigs with an N50 length of 480 nucleotides. In order to eliminate false-positive mutations caused by the high error rate of NGS, the Paired-End Low Error Sequencing (PELE-Seq) method was developed, which uses numerous quality control measures during the sequencing library preparation and data analysis steps in order to effectively eliminate sequencing errors. Control testing of the PELE-Seq demonstrates that the method completely eliminates false-positive mutations at sequencing read depths below 20,000X coverage, compared to a ~20% false-positive rate obtained with previous methods. The high accuracy of the PELE-Seq method allows for the detection of ultra-rare mutations in a genome, which was previously impossible with NGS.
This dissertation includes previously published and unpublished co-authored material.
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Montanari, Sara. "Identification and mapping of genomic regions controlling fire blight and psylla resistance and hybrid necrosis in pear." Thesis, Angers, 2015. http://www.theses.fr/2015ANGE0063/document.
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Le feu bactérien et le psylle causent d’importantes pertes économiques dans les zones de production du poirier dans le monde entier. Le développement de nouvelles variétés de poirier résistantes à ces bio-agresseurs constitue un enjeu majeur dans le cadre d’un programme de lutte intégrée. L’objectif de ce projet de thèse est l'étude du déterminisme génétique de la résistance vis-à-vis de ces deux bio-agresseurs. La thèse a été réalisée dans le cadre d’une collaboration internationale entre Fondazione Edmund Mach (Italie), Institut de Recherches en Horticulture et Semences (France) et Plant & Food Research (Nouvelle-Zélande). Une descendance interspécifique de poirier T003 x ‘Moonglow’ a été développée avec pour objectif de cumuler les résistances au feu bactérien et au psylle provenant de variétés asiatiques et européennes de Pyrus. Deux cartes génétiques ont été élaborées pour T003 et ‘Moonglow’ sur la base de marqueurs SNP (Single Nucleotide Polymorphism) et SSR (microsatellite), et la cartographie de QTLs (Quantitative Trait Loci) a permis de démontrer le déterminisme polygénique de la résistance à ces bio-agresseurs. Une sélection assistée par marqueurs (MAS) peut donc être engagée pour ces deux caractères. Des incompatibilités génétiques ont aussi été observées dans une partie de la descendance, ce qui a permis de cartographier pour la première fois chez le poirier les zones du génome liées au phénomène de « nécrose hybride ». Le développement de marqueurs liés aux gènes létaux devrait permettre aux sélectionneurs d’éviter les combinaisons incompatibles en croisement qui peuvent impacter certains caractères agronomiques co-ségrégant avec ces gènes létauxThe goal of this PhD project was to study the genetic architecture of pear resistance to two of its most significant diseases and pests, fire blight and psylla, which cause severe yield losses in all the main pear production regions worldwide. The development of new pear varieties with resistance against these two biotic stresses is of major interest for Integrated Pest Management. This project was designed in a joint collaboration among Fondazione Edmund Mach (Italy), Institut de Recherches en Horticulture et Semences (France) and Plant & Food Research (New-Zealand). The interspecific pear F1 progeny T003 x ‘Moonglow’ was developed with the purpose of cumulating resistances to fire blight and psylla deriving from Asian and European pear cultivars. Single nucleotide polymorphism (SNP) and simple sequence repeat (SSR)-based genetic maps were built for T003 and ‘Moonglow’. Quantitative Trait Loci (QTLs) were detected for the resistances, demonstrating their polygenic nature. Marker-assisted selection (MAS) can now be applied for these two traits. Furthermore, the segregating population exhibited genetic incompatibilities, and the genomic regions associated with hybrid necrosis were mapped for the first time in pear. Development of molecular markers linked to the lethal genes should allow breeders to avoid crosses leading to incompatible combinations that could affect the expression of important agronomic traits co-segregating with these genes
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Sahin, Fikrettin. "Detection, identification and characterization of strains of Xanthomonas campestris pv. vesicatoria by traditional and molecular methods, and resistance in Capsicum species to Xanthomonas campestris pv. vesicatoria pepper race 6 /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487945320758679.
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Tibbo, Markos. "Productivity and health of indigenous sheep breeds and crossbreds in the central Ethiopian highlands /." Uppsala : Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200651.pdf.
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SANTOS, Silas Garrido Teixeira de Carvalho. "Avaliação criteriosa dos algoritmos de detecção de concept drifts." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/17310.
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FACEPE
A extração de conhecimento em ambientes com fluxo contínuo de dados é uma atividade que vem crescendo progressivamente. Diversas são as situações que necessitam desse mecanismo, como o monitoramento do histórico de compras de clientes; a detecção de presença por meio de sensores; ou o monitoramento da temperatura da água. Desta maneira, os algoritmos utilizados para esse fim devem ser atualizados constantemente, buscando adaptar-se às novas instâncias e levando em consideração as restrições computacionais. Quando se trabalha em ambientes com fluxo contínuo de dados, em geral não é recomendável supor que sua distribuição permanecerá estacionária. Diversas mudanças podem ocorrer ao longo do tempo, desencadeando uma situação geralmente conhecida como mudança de conceito (concept drift). Neste trabalho foi realizado um estudo comparativo entre alguns dos principais métodos de detecção de mudanças: ADWIN, DDM, DOF, ECDD, EDDM, PL e STEPD. Para execução dos experimentos foram utilizadas bases artificiais – simulando mudanças abruptas, graduais rápidas, e graduais lentas – e também bases com problemas reais. Os resultados foram analisados baseando-se na precisão, tempo de execução, uso de memória, tempo médio de detecção das mudanças, e quantidade de falsos positivos e negativos. Já os parâmetros dos métodos foram definidos utilizando uma versão adaptada de um algoritmo genético. De acordo com os resultados do teste de Friedman juntamente com Nemenyi, em termos de precisão, DDM se mostrou o método mais eficiente com as bases utilizadas, sendo estatisticamente superior ao DOF e ECDD. Já EDDM foi o método mais rápido e também o mais econômico no uso da memória, sendo superior ao DOF, ECDD, PL e STEPD, em ambos os casos. Conclui-se então que métodos mais sensíveis às detecções de mudanças, e consequentemente mais propensos a alarmes falsos, obtêm melhores resultados quando comparados a métodos menos sensíveis e menos suscetíveis a alarmes falsos.
Knowledge extraction from data streams is an activity that has been progressively receiving an increased demand. Examples of such applications include monitoring purchase history of customers, movement data from sensors, or water temperatures. Thus, algorithms used for this purpose must be constantly updated, trying to adapt to new instances and taking into account computational constraints. When working in environments with a continuous flow of data, there is no guarantee that the distribution of the data will remain stationary. On the contrary, several changes may occur over time, triggering situations commonly known as concept drift. In this work we present a comparative study of some of the main drift detection methods: ADWIN, DDM, DOF, ECDD, EDDM, PL and STEPD. For the execution of the experiments, artificial datasets were used – simulating abrupt, fast gradual, and slow gradual changes – and also datasets with real problems. The results were analyzed based on the accuracy, runtime, memory usage, average time to change detection, and number of false positives and negatives. The parameters of methods were defined using an adapted version of a genetic algorithm. According to the Friedman test with Nemenyi results, in terms of accuracy, DDM was the most efficient method with the datasets used, and statistically superior to DOF and ECDD. EDDM was the fastest method and also the most economical in memory usage, being statistically superior to DOF, ECDD, PL and STEPD, in both cases. It was concluded that more sensitive change detection methods, and therefore more prone to false alarms, achieve better results when compared to less sensitive and less susceptible to false alarms methods.
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Ferro, Isabelle Dangui. "Avaliação de diferentes métodos para a detecção e contagem de Campylobcter spp. isolado de carcaças de frango e determinação da prevalência e resistência antimicrobiana dos isolados = Evaluation of different methods for the detection and counting Campylobcter spp. isolated from chicken carcass in the state of Paraná and determination of the prevalence and antimicrobial resistance of isolated / Isabelle Dangui Ferro ; orientadora, Renata Ernlund Freitas de Macedo ; co-orientador Wanda Moscalewsli Abraão." reponame:Biblioteca Digital de Teses e Dissertações da PUC_PR, 2012. http://www.biblioteca.pucpr.br/tede/tde_busca/arquivo.php?codArquivo=2286.
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Dissertação (mestrado) - Pontifícia Universidade Católica do Paraná, São José dos Pinhais, 2012Bibliografia: f. 102-107
Os produtos de origem animal são reconhecidos como fontes primárias de contaminação por vários enteropatógenos. Entre eles, nas últimas décadas, o gênero Campylobacter vem se destacando como o maior causador de surtos de gastrenterites humanas nos países
] The products of animal origin are recognized as primary sources of contamination by various pathogens. Among them the genus Campylobacter has emerged as the major cause of human gastroenteritis outbreaks in developed countries. Due to its importance in
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Harrysson, Mattias. "Fault Location Algorithms in Transmission Grids." Thesis, Högskolan i Halmstad, Sektionen för ekonomi och teknik (SET), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:hh:diva-26314.
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The rapid growth of the electric power system has in recent decades resulted in an increase of the number of transmission lines and total power outage in Norway. The challenge of a fast growing electrical grid has also resulted in huge increases of overhead lines and their total length. These lines are experiencing faults due to various reasons that cause major disruptions and operating costs of the transmission system operator (TSO). Thus, it’s important that the location of faults is either known or can be estimated with reasonably high accuracy. This allows the grid owner to save money and time for inspection and repair, as well as to provide a better service due to the possibility of faster restoration of power supply and avoiding blackouts. Fault detection and classification on transmission lines are important tasks in order to protect the electrical power system. In recent years, the power system has become more complicated under competitive and deregulated environments and a fast fault location technique is needed to maintain security and supply in the grid. This thesis compares and evaluates different methods for classification of fault type and calculation of conventional one-side and two-side based fault location algorithms for distance to fault estimation. Different algorithm has been implemented, tested and verified to create a greater understanding of determinants facts that affect distance to faults algorithm’s accuracy. Implemented algorithm has been tested on the data generated from a number of simulations in Simulink for a verification process in implemented algorithms accuracy. Two types of fault cases have also been simulated and compared for known distance to fault estimation.
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Weinstein, Zohar. "Substandard antimicrobial drugs: detection methods and their contributions to antibiotic resistance." Thesis, 2018. https://hdl.handle.net/2144/32951.
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Substandard and counterfeit medicines are major obstacles to the treatment of infectious diseases. Substandard medicines vary from standard drugs in terms of dose, bioavailability, or the presence of impurities. Current methods to identify substandard and counterfeit antimicrobial drugs are either resource intensive or have poor specificity. This dissertation examined two issues related to poor quality antimicrobial medicines: 1) Methods to detect and prevent the consumption of substandard drugs. 2) The relationship between substandard medicines and the evolution of rifampicin resistance. This dissertation advanced two technologies that may aid in the detection of substandard medicines: aptamers and biosensors. Oligonucleotide aptamers may be adapted for drug detection by coupling binding events to changes in fluorescence, luminescence or colorimetric signals. A computational model was developed to discover experimental factors that increase the probability of selecting a high affinity aptamer. Among them are: micromolar drug target concentration, high affinity substrate to partition aptamers, and high aptamer library affinity distribution. Random losses of aptamers due to experimental noise greatly decreased the probability of selecting an aptamer. Experimental parameters to optimize the process of aptamer discovery for small molecules are discussed. Bacterial biosensors are an alternative strategy for the detection of active pharmaceutical ingredients. Here, luciferase-expressing Escherichia coli were used to create profiles of drug interactions for anti-mycobacterial drugs. Drug interactions were tested by the Loewe additivity model. A novel method to differentiate rifamycin drugs from the drug degradation product rifampicin quinone was developed by analyzing each drug’s unique interactions.
While subinhibitory drug doses are known to select for antimicrobial resistance in vitro, the role of substandard anti-mycobacterial medicines in the development of rifampicin resistance remains poorly understood. The role of the drug degradation product rifampicin quinone on rifamycin resistance was assessed through in vitro studies of bacteria. Wild type Escherichia coli and Mycobacterium smegmatis cultured in the presence of rifampicin quinone acquired high levels of resistance to rifamycin drugs. Resistance was associated with genetic mutations in the rifampicin resistance cluster of the rpoB gene. The studies presented here demonstrate that substandard medicines can contribute towards rifamycin resistance, and offer methodologies to identify substandard medicines.2020-10-24T00:00:00Z
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Hsiao, Hsiangyu, and 蕭翔宇. "Development of molecular serotyping, detection methods and analysis of antibiotic resistance of Salmonella spp. in environmental water." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/91370292514198624448.
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碩士國立中正大學
應用地球物理研究所
99
Salmonella spp. are widely distributed in the environment, which are found in livestock, wild animals and water. It can cause serious diseases in both human beings and animals, and infections with non-typhoidal Salmonella are a significant cause of illness and death worldwide.Furthermore, resistance to various classes of antimicrobial agents has been encountered in many bacteria of medical relevance. Particularly, attention has been paid to zoonotic bacteria such as Salmonella. In our study, we combined traditional culture method and molecular method to detect Salmonella in environmental water and to analyze its antimicrobial resistance. The aim of this study is to detect the occurrence of Salmonella from environmental water of Puzih stream and Kaupin River in Taiwan by polymerase chain reaction (PCR), then identify the serovar of Salmonella by PFGE and Multiplex PCR. At last, we use PCR and Disk Difussion Method to evaluate the antibiotic resistance of Salmonella. The occurrence frequency of Salmonella from Puzih stream was 21% (21/100) and Kaupin River was 40.35 % (23/57). The 44 positive water samples by culture method were further identified as S. Typhimurium (1/44), S. Bareilly (13/44), S. Isangi (3/44), S. Choleraesuis (2/44), S. Potsdam (1/44), S. Albany (10/44), S. Derby (4/44), S. Kedougou(3/44), S. Potsdam(1/44), S. Mbandaka(1/44), S. Oranienburg(1/44), S. Weltevreden(1/44), S. Agona(1/44) 以及 S. Newport (3/44)by biochemical testing, serological identification and PFGE. On the other hand, antibiotic resistance bacteria do exist in environmental water, and Salmonella spp. in environmental water also have the same trend of antibiotic resistance with clinical samples, including multidrug resistance Salmonella. Studies are needed to determine the sources of different multidrug-resistant Salmonella serotypes. Continued surveillance is needed to monitor changes in resistance trends and to detect further emergence of resistant Salmonella serotypes in Taiwan.
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Sousa, Ana Catarina da Silva e. "Development of rapid methods for the detection of pathogenic microorganisms, based on NAM-FISH technology." Master's thesis, 2018. http://hdl.handle.net/10773/25528.
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The access of pathogenic microorganisms to the human body can compromise
the health of the individual, causing several clinical manifestations. Helicobacter
pylori and Campylobacter are two important gastrointestinal pathogens. H.
pylori infection is one of the most common human infections, whose treatment
includes the administration of antibiotics, namely fluoroquinolones (FQ).
However, there has been an increasing resistance of H. pylori to FQ, which can
lead to treatment failures, making it important not only to detect the bacterium
but also to define its resistance profile. Campylobacter is currently considered
the leading cause of bacterial foodborne illnesses, usually associated with the
consumption of raw meat. The detection of pathogenic microorganisms can be
achieved by conventional culture techniques or by molecular methods, namely
immunological tests or nucleic acid detection. Biomode is an innovative
company that develops and commercializes rapid diagnostic methods based on
Nucleic Acid Mimic (NAM) – fluorescence in situ hybridization (FISH)
technology, which enables the rapid detection of microorganisms, through the
hybridization of complementary fluorescent probes with specific sequences
present in the target microorganism. In this context, the present work focused
on two applications of NAM-FISH. In the clinical area, the main objective was
the development of a method for the detection of H. pylori and its resistance to
FQ. For this purpose, Peptide Nucleic Acid (PNA) and Locked Nucleic Acid
(LNA)/2'OMe probes were designed for the detection of mutations that cause
resistance. In order to cover the most prevalent mutations, as well as the wildtype
phenotype, 5 LNA/2'OMe probes were selected. In the area of food safety,
the objective was the optimization of a PNA-FISH method for Campylobacter
detection in food samples. A preliminary testing of the inclusivity/exclusivity of
the Campylobacter probe resulted in the detection of two non-target
microorganisms, H. cinaedi and H. pamatensis. To optimize the procedure,
samples of raw broiler meat inoculated artificially with C. jejuni were used. Prior
to PNA -FISH, a new step was introduced in which the enriched samples are
subjected to a centrifugation (10 000 g), followed by resuspension in 0.1% Triton
X-100, in order to reduce the strong autofluorescence shown in samples without
any treatment. The possibility of a two-step sample enrichment was also tested,
however, this approach did not show advantages compared to the one-step
procedure. Additionally, a robustness test, required by the AOAC International
to obtain product certification, was performed, which showed that the variation
of the parameters of the time and temperature of hybridization influence the
performance of the method, showing that the PNA-FISH conditions must be
strictly controlled. The results obtained in this study showed that the PNA-FISH
method is suitable for the rapid detection of Campylobacter in food samples.
With this work, it is concluded that although the two NAM-FISH based methods
are a promising alternative for the detection of H. pylori and Campylobacter,
they both require optimization.O acesso de microrganismos patogénicos ao corpo humano pode comprometer a saúde do indivíduo, provocando variadas manifestações clínicas. Helicobacter pylori e Campylobacter são dois importantes patógenos gastrointestinais. A infeção por H. pylori é uma das infeções humanas mais comuns, cujo tratamento inclui a administração de antibióticos, nomeadamente fluoroquinolonas (FQ). Contudo, tem-se verificado um aumento da resistência de H. pylori a FQ, o que pode resultar em falhas no tratamento, tornando-se importante não só a deteção da bactéria, mas também a definição do seu perfil de resistência. Campylobacter é atualmente considerada a principal causa de doenças transmitidas por alimentos, encontrando-se normalmente associada ao consumo de carne crua. A deteção de microrganismos patogénicos pode ser alcançada por técnicas de cultura convencionais ou por métodos moleculares, nomeadamente testes imunológicos ou de deteção de ácidos nucleicos. A Biomode é uma empresa inovadora que desenvolve e comercializa métodos de diagnóstico rápidos baseados na tecnologia de hibridação fluorescente in situ (FISH) de ácidos nucleicos mímicos (NAM), NAM-FISH, que possibilita a deteção rápida de microrganismos, através da hibridação de sondas fluorescentes complementares com sequências específicas presentes no microrganismo alvo. Neste contexto, o presente trabalho teve como foco duas aplicações do NAM-FISH. Na área clínica, o objetivo principal foi o desenvolvimento de um método para a deteção de H. pylori e da resistência a FQ. Para tal, procedeu-se ao desenho de sondas de Peptide Nucleic Acid (PNA) e Locked Nucleic Acid (LNA)/2’OMe para a deteção de mutações causadoras da resistência. De forma a cobrir as mutações mais prevalentes, bem como o fenótipo wild-type, foram selecionadas 5 sondas de LNA/2’OMe. Na área da segurança alimentar, foi objetivo a otimização de um método de PNA-FISH para a deteção de Campylobacter em amostras alimentares. Um ensaio preliminar da inclusividade/exclusividade da sonda Campylobacter resultou na deteção de dois microrganismos não-alvo, H. cinaedi e H. pamatensis. Para a otimização do procedimento, foram utilizadas amostras de carne de frango crua, inoculadas artificialmente com C. jejuni. Antes do PNAFISH, foi introduzido um novo passo, no qual as amostras enriquecidas são sujeitas a uma centrifugação (10 000 g), seguida de ressuspensão em 0.1% Triton X-100, com o objetivo de reduzir a autofluorescência forte visualizada em amostras sem qualquer tratamento. Testou-se também a possibilidade de um enriquecimento das amostras em dois passos, no entanto, esta abordagem não demonstrou vantagens comparativamente ao procedimento em um passo. Efetuou-se ainda um teste de robustez, requerido pela AOAC International para a obtenção de certificação de produto, que revelou que a variação dos parâmetros do tempo e temperatura de hibridação influenciam a performance do método, pelo que as condições do PNA-FISH devem ser rigorosamente controladas. Os resultados obtidos neste estudo mostraram que o método PNAFISH é adequado para a rápida deteção de Campylobacter em amostras alimentares. Com este trabalho conclui-se que, embora os dois métodos baseados em NAM-FISH sejam uma opção promissora para a deteção de H. pylori e Campylobacter, ambos necessitam de otimização futura.
Mestrado em Biotecnologia
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Kokozidou, Maria [Verfasser]. "Evaluation of PCR methods for detection, species identification and determination of genetic variation in L. infantum / submitted by Maria Kokozidou." 2003. http://d-nb.info/968411525/34.
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Yang, Man-Hsia, and 楊滿霞. "Statistical Methods for Genome-wide Detection of QTL Hotspots toward Understanding the Complex Genetic Architecture of Quantitative Traits Using Public Databases with Application to Rice." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/7782ff.
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博士國立臺灣大學
農藝學研究所
107
Genome-wide detection of quantitative trait loci (QTL) hotspots underlying variation in many molecular and phenotypic traits has been a key step in various biological studies since the QTL hotspots are highly informative and can be linked to the genes for the quantitative traits. Several statistical methods have been proposed to detect QTL hotspots. These hotspot detection methods rely heavily on permutation tests performed on summarized QTL data or individual-level data (with genotypes and phenotypes) from the genetical genomics experiments. In this article, I proposed a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases. First, a simple statistical method based on the uniform distribution is derived to convert the QTL interval data into the expected QTL frequency (EQF) matrix. And then, to account for the correlation structure among traits, the QTLs for correlated traits are grouped together into the same categories to form a reduced EQF matrix. Furthermore, a permutation algorithm on the EQF elements or on the QTL intervals is developed to compute a sliding scale of EQF thresholds, ranging from strict to liberal, for assessing the significance of QTL hotspots. With grouping, much stricter thresholds can be obtained to avoid the detection of spurious hotspots. Real example analysis and simulation study were carried out to illustrate our procedure, evaluate the performances and compare with other methods. It showed that our procedure can control the genome-wide error rates at the target levels, provide appropriate thresholds for correlated data and be comparable to the methods using individual-level data in hotspot detection. Depending on the thresholds used, more than 100 hotspots are detected in GRAMENE rice database. I also performed a genome-wide comparative analysis of the detected hotspots and the known genes collected in the Rice Q-TARO database. The comparative analysis revealed that the hotspots and genes were conformable in the sense that they co-localize closely and were functionally related to relevant traits. Our statistical procedure can provide a framework for exploring the networks among QTL hotspots, genes and quantitative traits in biological studies. The R package QHOT that produce both numerical and graphical outputs of QTL hotspot detection in the genome are available on the worldwide web http://www.stat.sinica.edu.tw/chkao/ and has been submitted to Comprehensive R Archive Network (CRAN).
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"Optimising aspects of a soybean breeding programme." Thesis, 2008. http://hdl.handle.net/10413/738.
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