Dissertations / Theses on the topic 'Genotypic'
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Alghhamdi, Saad Saeed. "Genotypic analysis of 'mycobacterium tuberculosis'." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.536847.
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Edwards, Andrew M. "Genotypic and phenotypic diversity in Treponema." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392906.
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Marcar, Nico Emile. "Genotypic variation for manganese efficiency in cereals /." Title page, abstract and contents only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phm313.pdf.
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Natale, Alessandra Pia. "Genotypic and phenotypic flexibility of microbial communities." Thesis, University of Warwick, 2010. http://wrap.warwick.ac.uk/35530/.
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Paracoccus denitrificans is a facultative anaerobic Gram-negative α- proteobacterium able to shift to denitrification under anaerobic conditions (John & Whatley, 1978; Zumft, 1997). Because of its metabolic versatility, P. denitrificans has been used in this study as a model organism to investigate the role of environmental heterogeneity in maintaining metabolic flexibility in bacterial communities. The hypotheses underlying this study are: - Metabolic flexibility is maintained in situ by environmental heterogeneity and, specifically: - Under constant environmental conditions the metabolic flexibility of the generalist P. denitrificans will be lost by accumulation of mutations in unused genes. Chemostat cultures under constant aerobic conditions revealed how after ~150 generations genetic loci not in use under aerobic conditions (in particular nirS and nosZ) are subjected to a lower selective pressure that leads to a higher genetic polymorphism in the population. The phenotypic analysis of the population resulting from the same chemostat culture showed a lower specific growth rate and a higher yield compared to the ancestor population, suggesting a deactivation of concomitant denitrification and aerobic respiration (Robertson et al., 1988). Furthermore, the resulting population shows a down-regulation of expression of all three denitrification genes tested and a lower production of nitrous oxide (N2O). When cultured in batch cultures for a long period of time under aerobic conditions, P. denitrificans shows a similar adaptative response. Four parallel populations, originated from a common ancestor and propagated aerobically for more than 500 generations undertook some important communal genotypic and phenotypic changes that suggested that P. denitrificans repetitively adapts to constant environmental conditions by losing its characteristic metabolic flexibility. By following the first steps of loss of metabolic flexibility as an adaptative response to novel environmental conditions in a generalist model as P. denitrificans we could empirically witness the important role of the environment on bacterial evolution and speciation.
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Hoek, Kim Gilberte Pauline. "Investigation into genotypic diagnostics for mycobacterium tuberculosis." Thesis, Stellenbosch : Stellenbosch University, 2010. http://hdl.handle.net/10019.1/5479.
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Thesis (PhD )--University of Stellenbosch, 2010.ENGLISH ABSTRACT: Diagnostic delay is regarded as a major contributor to the continuous rise in tuberculosis (TB) cases and the emergence and transmission of multidrug-resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB). It is therefore essential that more rapid diagnostic methods are developed. Molecular-based assays have the potential for the rapid species-specific diagnosis of TB and associated drug-resistances directly from clinical specimens. We investigated whether high resolution melting analysis (HRM) could enable the rapid diagnosis of TB and associated drug resistance, since the HRM apparatus and reagents are relatively inexpensive and the methodology can easily be implemented in high incidence, low income regions. Application of this methodology allowed for the rapid identification of mycobacterial lymphadenitis from fine-needle aspiration biopsy (FNAB) samples in 2 studies. This was done by targeting the region of deletion 9 (RD9), present in M. tuberculosis and M. canettii, but absent from all other members of the complex. However, the sensitivity of the method was low (51.9% and 46.3%, respectively) when compared to the reference standard (positive cytology and/or positive culture). Despite this limitation our method was able to provide a rapid diagnosis in more than half of the infected patients with a relatively high specificity (94.0% and 83.3%, respectively). We therefore proposed a diagnostic algorithm allowing the early treatment of patients with both HRM and cytology results indicative of mycobacterial disease. We developed the Fluorometric Assay for Susceptibility Testing of Rifampicin (FAST-Rif) which allowed the rapid diagnosis of MDR-TB by detecting rifampicin (RIF) resistance mutations in the rpoB gene with a sensitivity and specificity of 98% and 100%, respectively. The FAST-Rif method was easily adapted to detect ethambutol (EMB) resistance due to mutations in the embB gene with a sensitivity and specificity of 94.4% and 98.4% respectively, as compared to DNA sequencing. The FAST-EMB method was a significant improvement over the inaccurate culture based method. We identified a strong association between EMB resistance (and pyrazinamide resistance) and MDR-TB and subsequently advised modifications to the current (2008) South African National TB Control Programme draft policy guidelines. Due to the potential for amplicon release, we adapted the FAST-Rif and FAST-EMB methods to a closed-tube one-step method using the detection of inhA promoter mutations conferring isoniazid (INH) resistance as a model. The method (FASTest-inhA) was able to identify inhA promoter mutations with a sensitivity and specificity of 100% and 83.3%. These mutations are of particular interest as they confer low level INH resistance and cross-resistance to ethionamide (Eto). Since inhA promoter mutations are strongly associated with XDR-TB in the Western and Eastern Cape Provinces of South Africa, data generated by the recently implemented GenoType® MDRTBPlus assay may allow individualised treatment regimens to be designed for a patient depending on their INH mutation profile. Our proposed treatment algorithm may be particularly useful in XDR-TB cases, for which only few active drugs remain available. Since current diagnostic methods all carry advantages and disadvantages, a combination of phenotypic and genotypic-based methodologies may be the best scenario while awaiting superior methods.
AFRIKAANSE OPSOMMING: Die onvermoë om tuberkulose (TB), multi-weerstandige tuberkulose (MDR-TB) en uiters weerstandige tuberkulose (XDR-TB) vinnig te diagnoseer, is ‘n belangrike oorsaak vir die volgehoue toename en verspreiding daarvan. Dit is noodsaaklik dat diagnostiese toetse wat vinniger resultate oplewer, ontwikkel word. Molukulêre toetsing het die potensiaal om vinnig spesie-spesifieke diagnoses van TB en die weerstandigheid teen TB-medikasie te lewer. Hierdie studie wil vasstel of hoë-resolusie smeltingsanalise (HRS) ‘n vinnige diagnose van TB en die weerstandigheid teen TB-medikasie kan oplewer aangesien die relatiewe lae koste van reagense en apparaat, asook die minimale infrastruktuur en vaardighede wat vir dié toets benodig word, dit uiters geskik maak vir pasiënte in gebiede met ‘n hoë TB-insidensie en lae inkomste. Die toepassing van die HRS-metode op fynnaald-aspiraatbiopsies in twee afsonderlike studies, het gelei tot die vinnige identifisering van mikrobakteriële-limfadenitis. Dit is bemiddel deur die gebied van delesie 9 (RD9) teenwoordig in Mycobacterium tuberculosis en M. canettii, maar afwesig in al die ander lede van die kompleks, te teiken. Die sensitiwiteit van die metode was (51.9% en 46.3%, vir die twee studies onderskeidelik) in vergelyking met die verwysingstandaard (positiewe sitologie en/of positiewe kultuur). Ten spyte van dié beperking was ‘n vinnige diagnose in meer as die helfte van geïnfekteerde pasiënte met ‘n redelike hoë spesifisiteit (94.0% en 83.3%, onderskeidelik) moontlik. ‘n Diagnostiese algoritme wat gebaseer is op die resultate van die HRS en sitologie-toetse, is voorgestel om pasiënte vroeër te behandel. ‘n Fluorometriese toets (FAST-Rif) is ontwikkel vir die vinnige diagnose van MDR-TB deur mutasies in die rpoB-geen op te spoor met ‘n hoë sensitiwiteit en spesifisiteit (98% en 100%, onderskeidelik). Hierdie mutasies is verantwoordelik vir weerstandigheid teen die antibiotikum rifampicin (FAST-Rif) en word beskou as ‘n vinnige diagnose vir MDR-TB. Die FAST-Rif metode kon maklik aangepas word om mutasies in die embB-gene, verantwoordelik vir weerstandigheid teen die antibiotikum ethambutol (EMB), op te spoor. Die FAST-EMB-metode het ‘n sensitiwiteit en spesifisiteit van 94.4% en 98.4% onderskeidelik getoon in vergelyking met DNS volgordebepaling. Die FAST-EMB-metode was ‘n betekenisvolle verbetering op die onakkurate kultuurgebaseerde metodes. ‘n Sterk korrelasie tussen EMB-weerstandigheid (en weerstandigheid teen pyrazinamide) en MDR-TB is geïdentifiseer. Vervolgens is veranderinge aan die Suid-Afrikaanse Nasionale TB-beheerprogram se Konsepbeleidsgids (2008) voorgestel. Om die potensiële vrylating van amplikone te verhoed, is die FAST-Rif en FAST-EMB aangepas tot ‘n enkelstap geslote buissisteem deur gebruik te maak van die opsporing van inhA promotormutasies wat weerstandigheid teen isoniazid (INH) veroorsaak. Die metode het ‘n sensitiwiteit en spesifisiteit van 100% en 83.3% onderskeidelik, getoon. Hierdie mutasies veroorsaak laevlak weerstandigheid teen INH, maar ook kruisweerstandigheid teen ethionamide (Eto). Aangesien daar ‘n sterk verbintenis tussen inhA-promotormutasies en XDR-TB in die Oos en Wes-Kaapprovinsies van Suid-Afrika is, kan data van die GenoType® MDRTBPlus-toets moontlik gebruik word om ‘n meer geïndividualiseerde behandeling te ontwerp afhangende van die pasiënt se INH-mutasieprofiel. Ons behandelingsalgoritme is veral geskik vir XDR-TB pasiënte vir wie daar weinig aktiewe antibiotika beskikbaar is. Huidige diagnostiese metodes het almal voor- en nadele, dus bied ‘n kombinasie van fenotipiese en genotipiese metodes moontlik die beste oplossing totdat beter metodes ontwikkel word.
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Rayment, Sarah Jayne. "Phenotypic and genotypic analysis of intestinal spirochaetes." Thesis, Aston University, 1998. http://publications.aston.ac.uk/10969/.
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Pulsed field gel electrophoresis of 82 intestinal spirochaete isolates showed specific differentiation of Serpulina pilosicoli and Serpulina hyodysenteriae although considerable heterogeneity was observed, especially amongst S. pilosicoli isolates. In several cases genotypically similar isolates originated from different animals suggesting that cross-species transmission may have occurred. The Caco-2 and Caco-21HT29 cell models have been proposed as potentially realistic models of intestinal infection. Quantitation of adhesion to the cells showed isolate 3 82/91 (from a bacteraemia) to adhere at significantly greater numbers than any other isolate tested. This isolate produced a PFGE profile which differed from other S. pilosicoli isolates and so would be of interest for further study. Comparison of bacteraemic and other S. pilosicoli isolates suggested that bacteraemic isolates were not more specifically adapted for adhesion to, or invasion of the epithelial cell layer than other S. pilosicoli isolates. Genotypically similar isolates from differing animal origins adhered to the Caco-2 model at similar levels. Generation of a random genomic library of S. pilosicoli and screening with species specific monoclonal antibody has enabled the identification of a gene sequence encoding a protein which showed significant homology with an ancestral form of the enzyme pyruvate oxidoreductase. Immunoscreening with polyclonal serum identified the sequences of two gene clusters and a probable arylsulphatase. One gene cluster represented a ribosomal gene cluster which has a similar molecular arrangement to Borrelia burgdorjeri, Treponema pallidum and Thermatoga maritima. The other gene cluster contained an ABC transporter protein, sorbitol dehydrogenase and phosphomannose isomerase. An ELISA type assay was used to demonstrate that isolates of S. pilosicoli could adhere to components of the extracellular matrix such as collagen (type 1), fibronectin, laminin, and porcine gastric mucin.
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Green, Lauren M. "Phenotypic and genotypic characterisation of Clostrum Difficile." Thesis, Aston University, 2010. http://publications.aston.ac.uk/9584/.
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Clostridium difficile is at present one of the most common nosocomial infections in the developed world. Hypervirulent strains (PCR ribotype 027) of C. difficile which produce enhanced levels of toxins have also been associated with other characteristics such as a greater rate of sporulation and resistance to fluoroquinolones. Infection due to C. difficile PCR ribotype 027 has also been associated with greater rates of morbidity and mortality. The aim of this thesis was to investigate both the phenotypic and genotypic characteristics of two populations of toxigenic clinical isolates of C. difficile which were recovered from two separate hospital trusts within the UK. Phenotypic characterisation of the isolates was undertaken using analytical profile indexes (APIs), minimum inhibitory concentrations(MICs) and S-layer protein typing. In addition to this, isolates were also investigated for the production of a range of extracellular enzymes as potential virulence factors. Genotypic characterisation was performed using a random amplification of polymorphic DNA(RAPD) PCR protocol which was fully optimised in this study, and the gold standard method, PCR ribotyping. The discriminatory power of both methods was compared and the similarity between the different isolates also analysed. Associations between the phenotypic and genotypic characteristics and the recovery location of the isolate were then investigated. Extracellular enzyme production and API testing revealed little variation between the isolates; with S-layer typing demonstrating low discrimination. Minimum inhibitory concentrations did not identify any resistance towards either vancomycin or metronidazole; there were however significant differences in the distribution of antibiogram profiles of isolates recovered from the two different trusts. The RAPD PCR protocol was successfully optimised and alongside PCR ribotyping, effectively typed all of the clinical isolates and also identified differences in the number of types defined between the two locations. Both PCR ribotyping and RAPD demonstrated similar discriminatory power; however, the two genotyping methods did not generate amplicons that mapped directly onto each other and therefore clearly characterised isolates based on different genomic markers. The RAPD protocol also identified different subtypes within PCR ribotypes, therefore demonstrating that all isolates defined as a particular PCR ribotype were not the same strain. No associations could be demonstrated between the phenotypic and genotypic characteristics observed; however, the location from which an isolate was recovered did appear to influence antibiotic resistance and genotypic characteristics. The phenotypic and genotypic characteristics observed amongst the C. difficile isolates in this study, may provide a basis for the identification of further targets which may be potentially incorporated into future methods for the characterisation of C. difficile isolates.
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Gorman, Gráinne S. "Clinical and genotypic aspects of mitochondrial disease." Thesis, University of Newcastle upon Tyne, 2015. http://hdl.handle.net/10443/3034.
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Mitochondrial myopathies are a clinically multifarious group of genetic disorders that affect the central nervous system and skeletal muscles and other organs heavily dependent on aerobic metabolism. They are typically characterised by multi-system involvement and have extensive phenotypic and disease burden variability. These diseases are often relentlessly progressive with high morbidity and mortality. The biochemical and molecular basis of many of the common mitochondrial myopathies has been elucidated over the last decade, yet the association between mitochondrial gene mutations and clinical symptoms, requires further elucidation. I propose to clearly define the clinico-pathological and molecular features of adults with mitochondrial disease and evaluate if there is a clear correlation between clinical phenotype and the underlying genetic defect. Identifying clear clinical features should help guide genetic diagnosis and enable tailored counselling regarding potential disease progression. Unfortunately, to date, there are few effective treatments and no known cure for patients with mitochondrial myopathies. Exercise has been shown to hold significant positive effects upon skeletal muscle function and perceived health- related quality of life in patients with mitochondrial myopathies. The molecular basis of many of the common mitochondrial disorders has been elucidated over the last decade and although there is a vast spectrum of phenotypic expression throughout different genotypes, common symptoms are reported. Perceived fatigue is often a prominent symptom in patients with mitochondrial disease but to date, its prevalence, severity and aetiology is poorly understood. I wish to determine the prevalence and nature of perceived fatigue in a large, genetically heterogeneous group of patients with mitochondrial disease and systematically assess potential covariates of fatigue compared to healthy controls and patients with Myalgic Encephalopathy /Chronic Fatigue Syndrome. Health-related quality of life is important for understanding the impact and progression of chronic disease and is increasingly recognised as a fundamental patient-based outcome measure in both clinical intervention and research. Generic outcome measures have been extensively validated to assess health-related quality of life across populations and different disease states. However, due to their inclusive construct, it is acknowledged that not all relevant aspects of a specific illness may be captured. Hence there is a need to develop a disease-specific health-related quality of life measures that centre on symptoms characteristic of a specific disease or condition and their impact. SF-36 and its abbreviated version SF-12 are currently the only tools used routinely for measuring patient-reported outcomes in our patients with mitochondrial myopathies. I wish to explore the conceptualisation, development and preliminary psychometric evaluation (validity and reliability) of a mitochondrial disease -specific health-related quality of life measure, which may be used both in research and clinical settings. Indeed, in a condition where the natural history of the disease is poorly understood and therapeutic options are limited, long-term preservation of health-related quality of life in patients with mitochondrial disease poses a real challenge.
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Gilchrist, Tamara Louise. "Genotypic and phenotypic characterisation of Streptococcus uberis." Thesis, University of Glasgow, 2011. http://theses.gla.ac.uk/2938/.
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Streptococcus uberis is an important bovine mastitis pathogen, which places a significant financial burden upon the dairy industry. Determining the genetic diversity of a collection of field isolates and the mechanisms by which S. uberis colonises the host were the general aims of this project, in particular the determination of the basis for bacterial persistence despite antibacterial therapy. Multi-locus sequence typing identified high levels of recombination within the population, but also a single dominant clonal complex which comprised nearly all sequence types which were isolated from more than one animal. The dominant clonal complex also comprised isolates, derived, however, from both persistent and non-persistent infections, but RAPD typing demonstrated that these isolates can differ in genetic composition elsewhere in the genome. Whole genome sequencing of additional S. uberis isolates confirmed that despite significant homology between much of these genomes, novel genetic material was commonly obtained by phage insertion and horizontal gene transfer. Isolates with identical housekeeping sequences are thus highly likely to differ in their virulence gene repertoires. In this study, the potential for differentiating S. uberis isolates based instead upon protein profiles derived from mass spectrometry of disrupted whole cells was therefore also explored. Differentiation between small numbers of isolates was achieved after optimisation of this protocol, however, discriminatory ability and reproducibility were somewhat compromised when the technique was scaled up to analyse 50 Italian isolates. During the period of study, profile differences between persistent and non-persistent isolates could not be explored. Basic methods were thus also utilised in an attempt to identify factors which promoted bacterial survival in vitro; and a defined medium, representative of the udder environment, was optimised for this purpose. The use of this medium permitted the demonstration that S. uberis was reliant upon magnesium and manganese for proliferation and that, interestingly, the absence of iron did not inhibit bacterial growth. It was also shown that S. uberis had the ability to directly utilise casein, identifying a potential alternative pathway for the acquisition of essential nutrients from nutritionally-limited environments. It was also observed that to a limited extent S. uberis seemed to produce a siderophore. Although this remains to be confirmed, it may correlate with the observation that iron, although not essential for proliferation, improved the growth rate of the bacterium. It was also notable that most novel genes, identified from S. uberis genome sequences, exhibited functions for nutrient metabolism, demonstrating that flexibility in nutrient acquisition is central to the ability of the bacteria to adapt, permitting survival in vastly different environments. The use of the defined medium also demonstrated that S. uberis was able to form biofilms; this ability being variable depending on the growth conditions used and the isolate studied. Most significantly, under conditions representative of the mammary gland, there was an apparent trend for high levels of biofilm formation to correlate with isolates from persistent infections. Biofilm formation by Staphylococcus aureus is considered to be pivotal to the development of chronic mastitis, thus, biofilms may similarly play a role in S. uberis persistence. In an attempt to identify the molecular basis for S. uberis biofilm formation, genes with homology to those of the intercellular adhesion (ica) operon, well described for their involvement in Staphylococcus epidermidis and S. aureus biofilm formation, were identified in the genome sequence of S. uberis 0140J. A targeted mutagenesis protocol was optimised to ‘knock out’ these genes and observe the subsequent effects of these mutations on biofilm formation. During the course of this study, two of these potential biofilm genes (hasA and SUB 0809) were deleted from the S. uberis 0140J chromosome. Surprisingly, deletion of these genes did not retard subsequent biofilm formation, but instead biofilm formation was dramatically improved in the mutant strains. Characterisation of mastitis-causing S. uberis strains and a detailed understanding of the pathogenicity of the organism are required to further the development of a successful vaccine. The research presented in this thesis has increased the knowledge of these important research objectives and optimised techniques which will allow further advancement of knowledge in this field.
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Bhatnagar, Sandeep. "Phenotypic and genotypic characterization of high lysine maize." Texas A&M University, 2004. http://hdl.handle.net/1969.1/3154.
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Quality Protein Maize (QPM) with the mutant gene opaque-2 (o2), has higher
lysine and tryptophan content and hard endosperm which is less susceptible to
mechanical and biological damage. Three experiments were conducted to characterize the
phenotypic and genotypic characteristics of high lysine maize. In the first experiment two
separate diallels including 7 white and 9 yellow QPM inbreds were evaluated in five
southern USA environments to estimate the general (GCA) and specific combining
abilities (SCA) for grain yield and to identify potential heterotic relationships among
them. QPM hybrids yielded less than commercial checks. GCA effects across
environments were non-significant for grain yield but highly significant for secondary
traits. Best yielding hybrids resulted from crosses among inbreds from different programs
(CIMMYT, Mexico; University of Natal, South Africa and TAMU, USA). In the second
experiment testcrosses between QPM inbreds and Tx804, were evaluated for agronomic
performance, aflatoxin resistance and quality. QPM inbreds in testcrosses have similar
flowering dates, plant height, ear height and test weights but lower grain yield than
normal checks. Population 69 inbreds and their testcrosses were least susceptible to
aflatoxin. Aflatoxin in testcrosses was positively correlated with endosperm texture
(0.67) and kernel integrity (0.60) but negatively correlated with grain yield (-0.30) and
silking date (-0.50). Tryptophan content was negatively correlated with endosperm
modification. Amino acid levels of inbred lines were significantly correlated with those
of hybrids, but with low predictive value. In the third experiment 92 high lysine maize
inbreds with different origins [Stiff Stalk, Non Stiff Stalk, Pop 69, temperate (Tx802,
Tx804, Tx806, B97, B104) and exotic subtropical lines (CML161, Do940y and Ko326y)]
were haplotyped on a cM scale utilizing 43 mapped SSR markers to characterize genetic
diversity on chromosome 7, estimate linkage disequilibrium around opaque-2 locus and
determine the parental contribution in some inbreds. Dendrograms of genetic similarity
showed clusters in agreement with the different origin of inbreds. A total of 200 alleles
were detected with an average of 4.7 alleles/locus. Significant linkage disequilibrium was
detected around opaque-2 locus. Parental contributions of haplotypes showed segments
of chromosome 7 exclusively contributed by one or the other parent.
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Braun-Reichhart, Christina Franziska Maria. "Genotypic and phenotypic characterization of INSC94Y transgenic pigs." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-162894.
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James, Andrew Thomas. "Genotypic variation in soybean for drought stress response /." St. Lucia, Qld, 2003. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17408.pdf.
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Ho, Siu-leuk, and 何笑略. "Development of genotypic resistance testing for integrase inhibitor." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B45446386.
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Tsui, Sze-pui, and 崔詩珮. "Genotypic characterisation of type 2 von Willebrand disease." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193528.
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von Willebrand disease (VWD) is the most common autosomal bleeding disorder. It is divided into type 1, 2 and 3. Type 2 VWD shows qualitative defects in VWF and is further sub-classified into type 2A, 2B, 2M and 2N, each having different functional defects in VWF. Most of the associated mutations are located at the exons in VWF which encode for the affected functional domains. Diagnosis of VWD is currently based on history and phenotypic tests, which can be difficult often times. Therefore, molecular diagnosis of type 2 VWD is an attractive alternative. There are only a few genotypic characterisation studies of type 2 VWD in Chinese. This study aims to provide genetic data of type 2 VWD in Hong Kong.
Archive DNA samples of 21non-type 2N type 2 VWD patients (Group 1), 15 type 2N/mild haemophilia A (HA) patients (Group2) and 35 control subjects were recruited. VWF exon 27, 28 and exon 18, 19, 20, 23, 24 were Sanger sequenced in Group 1 and Group 2 subjects, respectively. All seven exons were sequenced in the control subjects.
Seven of 21 Group 1 subjects were found to have pathogenic mutation sin exon 28, with 2being novel. Only 1 Group 2 subject was found to be heterozygous for a novel non-synonymous variation at exon 23, the significance of which could not be ascertained. Sixteen benign polymorphisms were detected from exons sequenced in patients and controls.
The low pathogenic mutation detection rate may suggest that the pattern of mutation in Chinese is different from other populations. The possibility of misdiagnosis in a proportion of these patients cannot be excluded in view of the known difficulty in patient ascertainment in VWD and the limited phenotypic diagnostic tools available in Hong Kong. Further studies of other exons are indicated to document the mutation spectrum of type 2 VWD in our Chinese population. RNA work and functional studies are required to fully characterise novel sequence variations found. High throughput mutation detection platforms and better phenotypic characterisation will facilitate the introduction of VWD genotyping into routine clinical diagnostics.published_or_final_version
Pathology
Master
Master of Medical Sciences
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Webb, T. E. F. "Genotypic and phenotypic studies of inherited prion disease." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/669507/.
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Background: Inherited prion diseases (IPD) show remarkable clinical heterogeneity, posing problems for clinicians in making an early diagnosis and raising questions about genetic or environmental modifiers. The P102L prion protein gene (PRNP) mutation, one of the most frequently identified causes of IPD, has been linked to a large English kindred for three decades. A series of further smaller kindreds did not share apparent ancestry with this large kindred, raising the possibility of distant common ancestry of a rare mutation or no ancestry and relatively common novel mutations occurring. Identification of the genetic modifiers of phenotype may have implications for sporadic and variant Creutzfeldt-Jakob disease (sCJD), and neurodegeneration more widely, while novel mutation rates in PRNP inform study of the unknown aetiology of sCJD. IPD, although rare, has unique advantages in terms of looking for genetic modifiers of prion disease. Methods: Genealogical work and microsatellite haplotyping was carried out on cases of IPD P102L. Clinical information on affected patients was collected retrospectively as well as prospectively. Heritability estimates of IPD were produced by comparing parental and offspring phenotypes. The expanded collection of IPD cases with reliable clinical information (composing P102L and other IPD associated mutations), allowed for the testing of candidate genetic modifiers of phenotype. Polymorphisms previously reported to have an impact on prion disease susceptibility or phenotype were tested, along with a panel of candidate polymorphisms selected from a genome-wide association study (GWAS) in vCJD. Findings: Common ancestry between the known large P102L kindred and a number of previously unlinked P102L kindreds was identified. However, a number of apparently unrelated IPD P102L kindreds remain, suggesting that multiple separate mutational events are responsible: PRNP codon 102 may be a mutation ‘hot- spot’. Microsatellite work on other IPD subtypes in the UK and from elsewhere in Europe also finds evidence of the existence of multiple unrelated kindreds. The genotype-phenotype analysis discovered that codon 129 is a modifier of IPD P102L; in that codon 129 homozygosity is associated with an earlier age at clinical onset. Also identified was a possible effect of APOE genotype on IPD. APOE-E4 is associated with a significantly later age at onset in IPD, which has recently been identified in other categories of neurodegenerative disease. Interpretation: Overall, this work provides indirect support for the plausibility of the ‘somatic mutation hypothesis’ of sporadic CJD (sCJD), by suggesting a relatively frequent novel mutation rate in PRNP. The genetic contribution to phenotypic heterogeneity in IPD was estimated. This contribution is significant and may inform the search for genetic modifiers of susceptibility to acquired prion disease. The models established to analyse IPD as a quantitative trait will be used in future prion disease GWAS.
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Rakha, Emad Abd El-A. "Phenotypic and genotypic characteristics of human breast carcinoma." Thesis, University of Nottingham, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417122.
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Hoffman, Kristin Elizabeth. "Genotypic confirmation of transimmunization-induced dendritic cell maturation." [New Haven, Conn. : s.n.], 2008. http://ymtdl.med.yale.edu/theses/available/etd-12022008-132841/.
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Neal, Shona Elaine. "Genotypic diversity and epidemiological typing of Bordetella pertussis." Thesis, University of Glasgow, 2004. http://theses.gla.ac.uk/30856/.
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The resurgence of pertussis in several highly vaccinated countries has stimulated this study of the genotypic diversity and epidemiological typing of Bordetella pertussis. The genotypic variation of B. pertussis was investigated in 318 UK clinical isolates from 1920-2002, vising pertactin (prnA) and pertussis toxin SI subunit (ptxA) gene typing. To date, the evaluation of typing methods used for B. pertussis has not been performed extensively. Therefore, in this thesis, the recognised methods, namely serotyping, pulsed-field gel electrophoresis (PFGE) using Xbal, and IS1002-RFLP analysis, were evaluated. It was found that, PFGE typing gave a good discrimination index value, but gave a low score for reproducibility, and further work is required to optimise this method. Furthermore, if prnA and ptxA gene typing were included in the evaluation, combined with serotyping, this combination would equal the discrimination of PFGE. Other typing methods attempted for B. pertussis included direct sequencing of adenylate kinase (adk) and filamentous haemagglutinin genes (fhaB), and single-enzyme amplified fragment length polymorphism (AFLP) analysis with a selection of enzymes and selective primers. The type strain and a clinical strain, generated one and six single nucleotide polymorphisms (SNPs) in adk and fhoB, respectively. The discriminatory ability of the single-enzyme AFLP analysis was not satisfactory, as only a few different profiles were seen in the nine isolates tested. However, at least four AFLP profiles were generated using PstI enzyme, and the selective primer Pst-C. The direct detection and epidemiological typing of B. pertussis in 20 previously untypable clinical samples was attempted using prnA, ptxA as targets. Six clinical extracts generated prnA and ptxA (5/6) sequence data, therefore confirming that these typing procedures on B. pertussis PCR-positive clinical specimens is worthwhile in order to generate the prnA and ptxA distributions from babies or adults presenting atypical symptoms. This strategy should also be encouraged in other country that have studied prnA and ptxA allele distributions, in order to update the representation of the genetic diversity of B. pertussis.
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Goh, Shan. "Phenotypic and genotypic characterisation of bacteriophages of Clostridium difficile." University of Western Australia. Microbiology Discipline Group, 2003. http://theses.library.uwa.edu.au/adt-WU2004.0018.
Full textAbstract:
Clostridium difficile is an important hospital-acquired pathogen causing C. difficile-associated diarrhoea (CDAD) in patients exposed to antibiotics. The lack of information on bacteriophages of C. difficile, and the potential of phages as therapeutic agents for the treatment of CDAD, prompted the isolation and characterisation of phages active against clinical isolates of C. difficile in order to determine the prevalence and significance of phages of this anaerobe. Three (5.4 %) of 56 clinical C. difficile isolates induced by mitomycin C yielded dsDNA phages C2, C5, C6 and C8. The four phages differed from previously described C. difficile phages in particle morphology, burst size and host range. C2, C5 and C8 particles were members of the family Myoviridae, while C6 belonged to Siphoviridae. The burst sizes were 5 for C2, 7 for C5, 19 for C6 and 33 for C8. C8 had the broadest host range, lysing 27 out of 56 (48 %) C. difficile isolates, followed by C6 (43 %), C5 (20 %) and C2 (20 %). Superinfection experiments, restriction enzyme analysis and Southern hybridisation showed C2 and C5 to be closely related with C8 somewhat related to them, however, C6 was distantly related to the other three phages. C2 was further characterised as a representative phage. Its genome did not possess cohesive ends, and was shown to integrate chromosomally via an attP site identified within a 1.9 kb HindIII fragment. However, an integrase gene, which is typically close to the attP region, was not located. Nine of 16 HindIII fragments of C2, including the 1.9 kb fragment, were cloned into pUC18. Approximately 9 kb of the estimated 43 kb genome of C2 was sequenced and analysed. Seven of the nine translated sequences were homologous to phage structural proteins, two sequences were not homologous to any relevant protein in the Genbank and EMBL databases, and one was homologous to proteins of Clostridium species. Nucleotide homology between the C2 sequences and the recently sequenced C. difficile strain CD630 was found in three regions within CD630 genome. Seven of the nine sequences, including the 1.9 kb fragment, were clustered in one region. These data suggest that the genes constitute a phage structural gene module. The presence of C2-like sequences in CD630, and Southern hybridisation of C. difficile strains using phage probes, suggested related prophage sequences may be commonly present in this bacterial species. An investigation was carried out to determine the presence of toxin genes tcdA and tcdB, and PaLoc-associated gene tcdE, in phage DNA. In addition, the effect of phage infection on toxin production of toxigenic C. difficile strains was studied. Of the three genes, tcdE only was detected in phages C2, C5 and C8, but not in C6. Strains that maintained phages in a stable manner (lysogens) were isolated and used in toxin studies. The amount of toxin B produced was measured by cytotoxic assays using Vero cells, and toxin A production was measured by ELISA. Although phages did not encode toxin A or B genes, there was a significant increase in toxin B production in some lysogens. There was no increase in toxin A production. Transcriptional analyses of tcdA and tcdB in lysogens and parental strains was performed by real-time RT-PCR and Northern hybridisation to determine whether phage was affecting regulation of toxin transcription. Phage did not appear to affect toxin gene transcription, although results from real-time RT-PCR and Northern hybridisation were conflicting. A phage induced from the highly toxigenic reference strain VPI 10463 was also briefly characterised and investigated for its effect on toxin production in VPI 10463. The phage, ΦCV, had similar particle morphology to C2, C5 and C8, and had some HindIII bands in common with C2 and C5. Two cured variant strains produced significantly less toxin B compared to VPI 10463. In conclusion, several important properties of C. difficile phages were characterised. It appears these temperate phages may play a role in toxin production making them unsuitable as therapeutic agents for the treatment of CDAD. However, C2 phage may have potential as the basis for an integrative vector that will add to the genetic tools available for clostridia.
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Troell, Karin. "Genotypic and phenotypic characterization of Haemonchus contortus in Sweden /." Uppsala : Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200636.pdf.
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Gale, Catherine Victoria. "Genotypic and phenotypic variation in the human immunodeficiency viruses." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1444689/.
Full textAbstract:
Despite the involvement of multiple genetic variants of HIV in the causation of disease worldwide, most research has focussed on subtype B, the prevalent subtype in the western world. As a consequence, it is currently not clear whether genetically distinct HIV strains have different biological properties that cause differences in in vivo transmission, disease progression, replication capacity or sensitivity to antiretroviral drugs. In order to increase the ease of classification of viral diversity and thus aid studies into its importance, a novel genotyping tool for classifying HIV-1 subtype based on pol sequence, produced routinely during drug resistance monitoring, has been developed in this thesis. A dataset of 187 full-length HIV-1 sequences was used to generate Gag, Pol, Protease-Reverse Transcriptase (PR-RT) and Env protein sequence alignments. Phylogenetic analyses enabled generation of subtype specific alignments and, whilst sequence variation in the PR-RT dataset was low, this variation was adequate for PR-RT subtype assignment. The subtyping tool, named STAR, utilises position specific scoring matrices (PSSMs) derived from these subtype specific multiple sequence alignments and results in highly accurate reclassification of the subtype alignment sequences, with 98.6% of sequences being accurately assigned a subtype. Subsequent to the development of STAR the importance of HIV genetic variation classified as subtype, was addressed. A comparison of the relative growth capacity of HIV-1 primary isolates of subtypes A, B, C, D, F, group O and HIV-2 was performed in two T-cell environments. A novel reporter cell line was developed specifically to facilitate this work. Clear and consistent differences in in vitro growth phenotype in terms of rate and cytopathogenicity were detected, indicative of intrinsic differences between the HIV-1 types and subtypes. This work was extended by the utilisation of microarray technology which offers the possibility to analyse, at any given time point, the transcriptome of a virus-infected cell. A comparison of the transcriptional responses within T-cells to infection with HIV-1 subtype B, Group O and HIV-2 enabled identification of both core and diverging transcriptional response programs. Whilst the core response program provides insight into the most essential interactions between virus and host during HIV infection of T-cells, analysis of the diverging responses provide evidence that genetically divergent strains of HIV may interact differently with the host. It is proposed that these differences may have the potential to influence disease outcome.
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Logan, J. F. J. "Vascular mechanisms in glaucoma - a phenotype and genotypic analysis." Thesis, Queen's University Belfast, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246424.
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Bullock, James Michael. "The maintenance of genotypic diversity in a clonal plant." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279711.
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Erkuş, Oylum Harsa Şebnem. "Isolation, Phenotypic And Genotypic Charecterization of Yoghurt Starter Bacteris/." [s.l.]: [s.n.], 2007. http://library.iyte.edu.tr/tezler/master/gidamuh/T000641.pdf.
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Abebe, Almaz. "HIV-1 subtype C in Ethiopia genotypic and phenotypic variation /." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2000. http://dare.uva.nl/document/82577.
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Raorane, Manish. "Genotypic and phenotypic relationships in Jatropha : Genome and Gene analysis." Thesis, University of Newcastle Upon Tyne, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.519579.
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Agostinelli, Andres Mateo. "PHENOTYPIC AND GENOTYPIC SELECTION FOR HEAD SCAB RESISTANCE IN WHEAT." UKnowledge, 2009. http://uknowledge.uky.edu/gradschool_theses/582.
Full textAbstract:
Fusarium Head Blight (FHB) is a destructive disease caused by Fusarium graminearum that affects wheat (Triticum aestivum L.) worldwide. Breeding for resistance to FHB is arguably the best way to combat this disease. However, FHB resistance is highly complex and phenotypic screening is difficult. Molecular markers are a promising tool but breeding programs face the challenge of allocating resources in such a way that the optimum balance between phenotypic and genotypic selection is reached.
An F2:3 population derived from a resistant x susceptible cross was subjected to phenotypic and genotypic selection. For phenotyping, a novel air separation method was used to measure percentage of damaged kernels (FDK). Heritability estimates were remarkably high, which was attributed to the type of cross and the quality of phenotyping. Genotypic selection was done by selecting resistance alleles at quantitative trait loci (QTL) on the 3BS (Fhb1) and the 2DL chromosomes. Fhb1 conferred a moderate but stable FHB resistance while the 2DL QTL conferred a surprisingly high level of resistance but with significant interaction with the environment. Phenotypic selection conferred higher or lower genetic gains than genotypic selection, depending on the selection intensity. Based on these results, different selection strategies are discussed.
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Mlamla, Zandile Cleopatra. "Improving methods for genotypic drug resistance testing in Mycobacterium tuberculosis." Thesis, Stellenbosch : University of Stellenbosch, 2011. http://hdl.handle.net/10019.1/6756.
Full textAbstract:
Thesis (MScMedSc)--University of Stellenbosch, 2011.ENGLISH ABSTRACT: An important next step to Tuberculosis control relies on the translation of basic science and modern diagnostic techniques into primary health care clinics. These assays must be rapid, inexpensive, interpretation of results must be easy and they must be simple so that a healthcare worker with limited training can perform the tests under safe conditions. This study consists of four aims. The first aim was to develop a methodology to sterilize sputum specimens for rapid TB diagnosis and drug resistance testing. Candidate bactericides were identified from the literature, and tested for their bactericidal activity in Mycobacterium tuberculosis. We identified ultraseptin®aktiv as a powerful bactericidal agent which sterilizes sputum specimens for subsequent safe handling prior to light emitting diode microscopy and it also provides a DNA template for PCR-based tests. An algorithm has been proposed for the processing of specimens and rapid diagnosis of TB and drug resistant TB while patients wait for results. Recently, the World Health Organization has endorsed the MTBDRplus test for diagnosis of TB and drug resistant TB. However genotypic tests may have more problems than anticipated. With the HIV pandemic, an increase of non-tuberculous mycobacteria has been reported. The sensitivity of genotypic tests in specimens with underlying non-tuberculous mycobacterial species therefore requires further evaluation. This study therefore also aimed at determining the reliability of the MTBDRplus assay for detection of drug resistant TB where non-tuberculous bacterial load is high. Clinically relevant non-tuberculous mycobacterium DNA and DNA from a multi-drug resistant TB isolate were obtained. Ratios of the different NTM with the MDR-TB DNA were made and subjected to the MTBDRplus assay. Known mix NTM and TB infected clinical isolates and sputum sediments were also evaluated for TB and drug resistance detection on the MTBDRplus assay. Under these conditions, this study provides evidence that the MTBDRplus test cannot reliably detect TB and drug resistance TB in specimens with underlying non-tuberculous mycobacteria. Thirdly, to evaluate the sensitivity of the MTBDRplus assay for detecting drug resistance in hetero-resistant isolates, ratios were made using purified DNA from an MDR and pan-susceptible TB isolate. The MTBDRplus assay was then performed on the different ratios. We report that the MTBDRplus assay can efficiently detect wild type DNA in genes associated with resistance during the early evolution of drug resistance. However, in the later stage during treatment when both the wild type and mutants are present, the detection limit for the mutant DNA was 1:55. Due to these results, the MTBDRplus assay should still be further improved or other tests should be developed to address these limitations. And finally to combat cross amplicon contamination during the final steps of genotypic detection with the MTBDRplus assay, a proof of concept for a patentable closed tube line probe device was proposed on the 4th aim. This device can be improved to enable automated drug resistance genotyping of multiple specimens. The results of this study highlight the need for a sensitive inexpensive point of care drug resistance test that does not require intensive training.
AFRIKAANSE OPSOMMING: 'n Belangrike volgende stap om Tuberkulose te beheer is om basiese wetenskap resultate te gebruik sodat moderne diagnose tegnieke ontwikkel kan word wat in primêre gesondheidsorg klinieke toegepas kan word. Hierdie toetse moet vinnig, goedkoop, en die interpretasie van resultate moet maklik wees. Die toetse moet eenvoudig wees sodat 'n gesondheidswerker met beperkte opleiding die toetse onder veilige omstandighede kan uitvoer. Hierdie studie bestaan uit vier doelwitte, waarvan die eerste was om 'n metode te ontwikkel vir die sterilisasie van sputum monsters vir vinnige TB diagnose en die toesting van middelweerstandigheid. Kandidaat kiemdodende middels was geïdentifiseer vanaf die literatuur en die middels se kiekdodende aktiviteit was getoets op Mycobacterium tuberculosis. Ons het ultraseptin®aktiv geïdentifiseer as 'n kragtige kiemdodende middel wat bakteria in sputum monsters steriliseer vir veilige hantering voordat diagnose met 'n lig uitstralende diode mikroskopie gedoen kan word. Hierdie behandeling met ultraseptin®aktiv bied ook 'n DNA templaat vir PCR-gebaseerde toetse. 'n Algoritme is voorgestel vir die hantering van monsters en die vinnige diagnose van sensitiewe- en middel weerstandige Tuberkulose terwyl die pasiënte by die kliniek wag vir die resultate. Onlangs het die Wêreld Gesondheid Organisasie die genotipiese MTBDRplus toets vir die diagnose van Tuberkulose en middel-weerstandige Tuberkulose onderskryf. Hierdie toets word tans op groot skaal in Suid Afrika gebruik. Dit kan egter wees dat genotipiese toetse baie meer probleme kan he as wat aanvanklik verwag is. Die HIV pandemie gaan toenemend gepaard met n toename van nie-tuberkulose mycobacteria. Die sensitiwiteit van genotipiese toetse op monsters met onderliggende nie-tuberkulose mikobakteriese spesies vereis dus verdere evaluasie. Die doel van hierdie studie was ook om die betroubaarheid van die MTBDRplus-toets te bepaal vir die opsporing van middelweerstandige TB waar die nie-tuberkulose bakteriële lading hoog is. DNA van kliniese relevante nie-tuberkulose mikobakteria en multi-middelweerstige TB isolate was bekom. Verskillende verdunnigs van die spesifieke NTM DNA te same met die van MDR-TB DNA is gemaak en onderwerp aan die MTBDRplus toets. Bekende gemengde NTM- en TB geïnfekteerde kliniese isolate en sputum sedimente was ook geevalueer vir die opsporing van TB en middel weerstandigheid met die MTBDRplus toets. Hierdie studie verskaf bewyse dat die MTBDRplus toets nie betroubaar is met die diagnose van sensitiewe- en middel weerstandige Tuberkulose in monsters met onderliggende nie-tuberkulose mycobacteria nie. Verskillende verdunnings van gesuiwerde DNA van MDR en pan-sensitiewe TB isolate is gemaak om die sensitiwiteit van die MTBDRplus toets vir die opsporing van middelweerstandigheid te bepaal. Die MDRDRplus toets is gebruik met hierdie verdunnings. Resultate in hierdie studie toon dat die MTBDRplus toets effektief is met die identifisering van wilde-tipe DNA (dit beteken middel sensitief) in gene wat geassosieer word met middel weerstandigheid gedurende die vroeë ontwikkeling van weerstandigheid. Hier teenoor toon die resultate dat in die later stadium tydens behandeling, wanneer beide die wilde-tipe (sensitief) en mutante DNA (weerstandig) teenwoordig is, is die opsporingslimiet vir die mutante DNA maar 1:55. As gevolg van hierdie resultate raai ons aan dat die MTBDRplus toets nog verder verbeter moet word of dat ander toetse ontwikkel moet word om hierdie beperkinge aan te spreek. Amplikon kruiskontaminasie kan n groot impak hê op die betroubaarheid van enige genotipiese diagnostiese toets. Die finale stappe van MTBDRplus toets behels die gebruik van 'n oop sisteem sodat kontaminasie maklik kan plaasvind. In die 4de doewit 'n konsep vir 'n patenteerbare geslotebuis toestel ontwikkel en die resultate het getoon dat kontaminasie suksesvol uitgeskakel kan word. Hierdie toestel kan verbeter na 'n outomatiese apparaat verbeter word sodat die module genotipering van verskeie monsters moontlik kan maak. Die resultate van hierdie studie beklemtoon die noodsaaklikheid van 'n sensitiewe goedkoop “point of care” diagnostiese toets wat nie intensiewe opleiding benodig nie.
Medical Research Council of South Africa
University of Stellenbosch, Dept. of Molecular Biology and Human Genetics
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Silver, Karlee Linnea. "Genotypic and phenotypic approaches to pathways involved in humoral autoimmunity." Thesis, University of Oxford, 2006. http://ora.ox.ac.uk/objects/uuid:1a18398f-942a-49a4-bd2e-a8ec4b4f647f.
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Ghadiali, Alifiya H. "Studies on Mycobacterium avium subsp. paratuberculosis genotypic and phenotypic variations /." Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1110229469.
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Thesis (Ph. D.)--Ohio State University, 2005.Document formatted into pages; contains xxi, 216 p. Includes bibliographical references. Abstract available online via OhioLINK's ETD Center; full text release delayed at author's request until 2006 March 9.
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Singh, Navdeep. "The genotypic characterisation of human herpesvirus 8 in different groups." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1446698/.
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The prevalence of human herpesvirus 8 (HHV-8) in patients with Kaposi's sarconna (KS) or people at risk of developing KS is high, while that in low-risk populations remains unclear. Use of disparate serological assays for anti HHV-8 detection contributes to this uncertainty. Hypothesising that in populations at low risk of HHV-8, the detection of HHV-8 genome enhances the specificity of and lends sensitivity to estimations of HHV-8 prevalence, studies were conducted to compare the genoprevalence and molecular epidemiology of HHV-8 in UK subpopulations at varying risk of HIV infection or KS: blood donors, human immunodeficiency virus (HIV)-infected individuals, bone marrow transplant (BMT) recipients, and patients with chronic fatigue syndrome (CFS). A protocol for amplifying sub-genomic HHV-8 DNA was first developed using blood originating from HIV-seropositive patients, from which CD45+ cells were immunomagnetically separated and their extracted DNA submitted to nested PCR. It was determined that such an approach afforded greater sensitivity to HHV-8 DNA detection than approaches based on PCR applied to separated peripheral blood mononuclear cells. Using the improved protocol, DNA from open reading frame (ORF) 26 of the HHV-8 genome could be amplified from 24% of blood donor samples. In a subsequent donor group, DNA from ORFs 26 and K1 was detectable in 8% and 9%, respectively. ORF K1 sequences could be classified as belonging to genotypes A1, A4 and C3. HHV-8 seropositivity in the second group was 12% and 24%, as determined by two antibody assays, and The Genotypic characterisation of Human Herpes Virus 8 in Different Groups. herpes simplex virus-2 seropositivity was 0%. No associations were found between HHV-8 genome and anti HHV-8 detection. The findings in the BMT and CFS groups further substantiate the hypothesis that HHV-8 infection is more widespread than previously thought, carriers may not mount antibody responses detectable by current serological assays, and the principal HHV-8 transmission route is not sexual.
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Nardozza, Simona <1980>. "Genotypic variation in Actinidia deliciosa fruit size and carbohydrate content." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/722/.
Full textAbstract:
In a global and increasingly competitive fresh produce market, more attention is being
given to fruit quality traits and consumer satisfaction. Kiwifruit occupies a niche
position in the worldwide market, when compared to apples, oranges or bananas. It is a
fruit with extraordinarily good nutritional traits, and its benefits to human health have
been widely described.
Until recently, international trade in kiwifruit was restricted to a single cultivar, but
different types of kiwifruit are now becoming available in the market. Effective
programmes of kiwifruit improvement start by considering the requirements of
consumers, and recent surveys indicate that sweeter fruit with better flavour are
generally preferred. There is a strong correlation between at-harvest dry matter and
starch content, and soluble solid concentration and flavour when fruit are eating ripe.
This suggests that carbon accumulation strongly influences the development of kiwifruit
taste.
The overall aim of the present study was to determine what factors affect carbon
accumulation during Actinidia deliciosa berry development. One way of doing this is by
comparing kiwifruit genotypes that differ greatly in their ability to accumulate dry
matter in their fruit. Starch is the major component of dry matter content. It was
hypothesized that genotypes were different in sink strength. Sink strength, by definition,
is the effect of sink size and sink activity.
Chapter 1 reviews fruit growth, kiwifruit growth and development and carbon
metabolism.
Chapter 2 describes the materials and methods used.
Chapter 3, 4, 5 and 6 describes different types of experimental work.
Chapter 7 contains the final discussions and the conclusions
Three Actinidia deliciosa breeding populations were analysed in detail to confirm that
observed differences in dry matter content were genetically determined. Fruit of the
different genotypes differed in dry matter content mainly because of differences in
starch concentrations and dry weight accumulation rates, irrespective of fruit size. More
detailed experiments were therefore carried out on genotypes which varied most in fruit
starch concentrations to determine why sink strengths were so different.
The kiwifruit berry comprises three tissues which differ in dry matter content. It was
initially hypothesised that observed differences in starch content could be due to a larger
proportion of one or other of these tissues, for example, of the central core which is
highest in dry matter content. The study results showed that this was not the case.
Sink size, intended as cell number or cell size, was then investigated. The outer pericarp
makes up about 60% of berry weight in ‘Hayward’ kiwifruit. The outer pericarp
contains two types of parenchyma cells: large cells with low starch concentration, and
small cells with high starch concentration. Large cell, small cell and total cell densities
in the outer pericarp were shown to be not correlated with either dry matter content or
fruit size but further investigation of volume proportion among cell types seemed
justified. It was then shown that genotypes with fruit having higher dry matter contents
also had a higher proportion of small cells. However, the higher proportion of small cell
volume could only explain half of the observed differences in starch content. So, sink
activity, intended as sucrose to starch metabolism, was investigated.
In transiently starch storing sinks, such as tomato fruit and potato tubers, a pivotal role
in carbon metabolism has been attributed to sucrose cleaving enzymes (mainly sucrose
synthase and cell wall invertase) and to ADP-glucose pyrophosphorylase (the
committed step in starch synthesis). Studies on tomato and potato genotypes differing in
starch content or in final fruit soluble solid concentrations have demonstrated a strong
link with either sucrose synthase or ADP-glucose pyrophosphorylase, at both enzyme
activity and gene expression levels, depending on the case. Little is known about
sucrose cleaving enzyme and ADP-glucose pyrophosphorylase isoforms. The
HortResearch Actinidia EST database was then screened to identify sequences
putatively encoding for sucrose synthase, invertase and ADP-glucose
pyrophosphorylase isoforms and specific primers were designed. Sucrose synthase,
invertase and ADP-glucose pyrophosphorylase isoform transcript levels were anlayzed
throughout fruit development of a selection of four genotypes (two high dry matter and
two low dry matter). High dry matter genotypes showed higher amounts of sucrose
synthase transcripts (SUS1, SUS2 or both) and higher ADP-glucose pyrophosphorylase
(AGPL4, large subunit 4) gene expression, mainly early in fruit development. SUS1-
like gene expression has been linked with starch biosynthesis in several crop (tomato,
potato and maize). An enhancement of its transcript level early in fruit development of
high dry matter genotypes means that more activated glucose (UDP-glucose) is
available for starch synthesis. This can be then correlated to the higher starch observed
since soon after the onset of net starch accumulation. The higher expression level of
AGPL4 observed in high dry matter genotypes suggests an involvement of this subunit
in drive carbon flux into starch. Changes in both enzymes (SUSY and AGPse) are then
responsible of higher starch concentrations. Low dry matter genotypes showed
generally higher vacuolar invertase gene expression (and also enzyme activity), early in
fruit development. This alternative cleavage strategy can possibly contribute to energy
loss, in that invertases’ products are not adenylated, and further reactions and transport
are needed to convert carbon into starch. Although these elements match well with
observed differences in starch contents, other factors could be involved in carbon
metabolism control. From the microarray experiment, in fact, several kinases and
transcription factors have been found to be differentially expressed.
Sink strength is known to be modified by application of regulators. In ‘Hayward’
kiwifruit, the synthetic cytokinin CPPU (N-(2-Chloro-4-Pyridyl)-N-Phenylurea)
promotes a dramatic increase in fruit size, whereas dry matter content decreases. The
behaviour of CPPU-treated ‘Hayward’ kiwifruit was similar to that of fruit from low dry
matter genotypes: dry matter and starch concentrations were lower. However, the CPPU
effect was strongly source limited, whereas in genotype variation it was not. Moreover,
CPPU-treated fruit gene expression (at sucrose cleavage and AGPase levels) was
similar to that in high dry matter genotypes. It was therefore concluded that CPPU
promotes both sink size and sink activity, but at different “speeds” and this ends in the
observed decrease in dry matter content and starch concentration. The lower “speed” in
sink activity is probably due to a differential partitioning of activated glucose between
starch storage and cell wall synthesis to sustain cell expansion.
Starch is the main carbohydrate accumulated in growing Actinidia deliciosa fruit.
Results obtained in the present study suggest that sucrose synthase and AGPase
enzymes contribute to sucrose to starch conversion, and differences in their gene
expression levels, mainly early in fruit development, strongly affect the rate at which
starch is therefore accumulated. This results are interesting in that starch and Actinidia
deliciosa fruit quality are tightly connected.
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Richards, Rebecca. "Phenotypic and genotypic investigation of persistent Staphylococcus aureus bacteraemia isolates." Thesis, University of Leicester, 2015. http://hdl.handle.net/2381/39405.
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Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) remain a serious clinical threat and a leading cause of healthcare- and community-associated infections. Blood stream infections or bacteraemia caused by S. aureus are further complicated by the phenomenon of bacterial persistence and treatment failure despite confirmed in vitro susceptibility of the infecting strain to the administered antibiotics. Moreover, it is unclear how S. aureus evades the host immune system for the prolonged duration of a persistent infection. This study aimed to answer these two clinically relevant, biological questions by characterising multiple persistent and resolved MRSA bacteraemia isolates with the view to identifying persistent isolate associated phenotypic and genotypic traits, and novel mechanism(s) for persistence development. From this work, two distinctly novel S. aureus persistence mechanisms are presented. The first involved in vivo strain evolution induced by antibiotic exposure (daptomycin) during two independent incidences of persistence (PB1 and PB3), resulting in mprF gain-of-function mutations in the persisting bacterial population. This led to daptomycin non-susceptibility and the emergence of novel persistence associated virulence phenotypes, which included a nutrient deprived growth adaption, increased immune evasion, adhesion and stress response associated surface proteins, and attenuated virulence. The second mechanism presented (PB2 and PB5) did not display any defining persistence associated traits; however these bacteraemia were not treated with daptomycin, which further supports the daptomycin induced, MprF mediated persistence mechanism presented for the PB1 and PB3 cases. This study is the first of its kind to investigate multiple persistent MRSA bacteraemia inclusive of numerous temporally spaced infective isolates, in parallel with contemporaneous resolved bacteraemia isolates of the same genetic background. The subsequent findings of this study have massive implications for the current clinical regimes implemented during complex S. aureus bacteraemia, particularly antibiotic treatment choices, and potentially for other cases of bacterial infection where persistence is frequently observed.
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Kanaga, Megan K. "Ecological Effects of Genotypic Diversity on Community and Ecosystem Function." DigitalCommons@USU, 2009. https://digitalcommons.usu.edu/etd/517.
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Genotypic diversity within populations can have important evolutionary consequences, but the ecological effects of intraspecific genetic variation on community and ecosystem function have only been studied in a few systems. I present the results of a three-year study designed to address the ecological impacts of genotypic diversity in quaking aspen (Populus tremuloides Michx.), using aspen genotypes planted across genotypic diversity levels (monoculture and mixture) and watering treatment levels (well-watered and water-limited). First, I demonstrated that significant variation exists among genotypes for a wide range of growth, morphological and physiological traits, and quantified high heritability and coefficient of genetic variation values for those traits. This demonstrates that heritable phenotypic variation exists within an aspen population, which could potentially have community and ecosystem implications. Secondly, I collected ground-dwelling arthropods across experimental treatment levels to determine if there are any community-level implications of genotypic diversity and watering treatment. Ground-dwelling arthropods were significantly affected by the genotypic diversity × watering treatment interaction, such that arthropod taxonomic diversity was lowest in water-limited genotypic mixtures. This result runs counter to the bulk of the plant diversity-arthropod diversity literature, which predicts that plant and arthropod diversity should be positively correlated, and highlights the importance of environmental conditions in mediating the plant-arthropod diversity relationship. Lastly, I show that there are no overall effects of genotypic diversity or watering treatment on tree growth patterns. Instead, there are high levels of variation among genotypes in their responses to treatments (significant genotype × diversity × watering treatment interactions), which are often opposing in direction. I also show that there are significant collection site × diversity × watering treatment interactions, demonstrating that genotypes vary in their response to experimental treatments based in part on their original collection site conditions in the field. This study demonstrates that aspen populations contain high levels of genotypic diversity, but that the ecological effects of genotypic diversity are mediated by the environment (in this case, watering treatment) and can be considerably more complicated than found in most previous studies.
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Booth, Kevin T. "Unraveling the genotypic and phenotypic complexities of genetic hearing loss." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6549.
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Hereditary hearing loss is the most common sensory disorder, affecting 1 in 500 newborns. There are more than 538 million individuals with genetic hearing loss worldwide and this number is expected to grow to 1 billion over the next three decades. Currently, the only option for individuals with hearing loss is mechanical intervention such as hearing aids or cochlear implants. In the past decade, many studies have highlighted the need for personalized gene therapy or molecular intervention to treat genetic deafness. However, in order to fulfill this vision a comprehensive understanding of the intricate mutation-gene-phenotype nuances and relationships is required.
Toward this goal, we unraveled novel mutation-gene-phenotype associations and mechanisms in four deafness-causing genes (CIB2, COL11A1, CEACAM16 and DFNA5), by using a combination of in-depth phenotyping, human genetics, cutting edge genomic technologies, murine mutant models, and functional assays. These novel insights revealed mutations in CIB2 do not cause Usher Syndrome, mutations in COL11A1 can cause either non-syndromic or syndromic hearing loss, CEACAM16-related deafness is due to two distinct mechanisms, loss of function and gain of function, and coding variants can influence mRNA assembly and cause DFNA5-related hearing loss. Elucidating these novel mutation-gene-phenotype relationships has improved our knowledge of the pathogenic mechanisms underlying hearing loss and provided much needed answers to individuals seeking a diagnosis for their deafness.
Recognizing the complexities associated with genetic hearing loss and the challenges in interpreting the clinical significance of genetic variants, we established the first deafness-specific variant database, the Deafness Variation Database (DVD), which classifies over 876,000 variants across 152 deafness-associated genes. This breadth of data provided us with a unique opportunity to explore the molecular landscape of deafness. We show that over 96% of coding variants are rare and novel and that mutational signatures are unique to each gene and are driven by minor allele frequency thresholds, variant effect, and protein domain. The mutational landscape we define shows complex gene-specific variability, making an understanding of these nuances foundational for improved accuracy in variant interpretation.
Overall the work presented in this thesis improves our understanding of deafness biology, identifies novel targets for therapeutics and enhances clinical decision-making.
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Ostrofsky, Ellen B. "Atrazine biodegradation in agricultural soils : a phenotypic and genotypic analysis /." The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487953567770278.
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Barton, Christopher. "Molecular phylogenetics and genotypic variation in Coleoptera : a bioinformatics approach." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/25134.
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A custom-built bioinformatics pipeline is used to costruct a species-level phylogeny for beetles (Coleoptera) using publicly available sequences from Genbank, including 8441 terminals 5 gene loci. 152 of 189 described beetle families are included, representing 2.17% of described species. The overall structure of publicly available data and its fit with Linnaean classifications are discussed. The dataset is further expanded by the inclusion of additional gene loci and relaxation of concatenation conditions, bringing total species to ~12,000. To overcome incomplete or incorrect identifications, a multi-partite matching algorithm is applied, for concatenation of partially conflicting taxon labels between gene loci, using species-level sequence clusters. The method is modified through the addition of country/specimen weighting between loci, and the incorporation of the the GMYC method of sequence-based species delimitation into the bioinformatics pipeline. GMYC and BlastClust approaches are compared, in terms of accuracy of species delimitation, supermatrix structure and topology of resulting trees. GMYC clusters are used as a framework for broad-scale comparisons of intraspecificvariation across the Coleoptera. The Coleoptera tree is used to illustrate a novel method for estimating total extant diversity by extrapolating from higher-taxon diversification rates, generating an estimate of 3.1 million beetle species globally. The sensitivity of the method to phylogenetic uncertainty within the data, and undersampling of families and subfamilies, is examined. Partial and complete mitochondrial genomes are used to generate the largest and most comprehensive phylogeny ever produced fromthis type of data. This tree is used as the basis for a molecular dating analysis, and the quantification of compositional heterogeneity among genes, taxa and sites within protein-coding genes. Non-homogenous substitution models are applied to help resolve problematic regions of the phylogeny, and the effects on topology and phylogenetic diversity of adding a previously unsampled regional fauna from Borneo are assessed.
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Fitzgerald, Collette Catherine. "The use of high resolution genotyping techniques to investigate the genotypic diversity of Campylobacter spp. isolated from human, animal and environmental sources." Thesis, Lancaster University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264781.
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Svärd, Louise. "Evaluation of phenotypic and genotypic extended-spectrum beta-lactamase detection methods." Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8021.
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The emergence and spread of resistance in Enterobacteriaceae is a growing concern in human medicine today. Enterobacteriaceae producing extended-spectrum β-lactamases (ESBLs) have become efficient at inactivating β-lactam antibiotics especially the newer third generation cephalosporins. In addition, ESBL producing Enterobacteriaceae are frequently resistant to other groups of commonly used non-β-lactam antibiotics such as the fluoroquinolones. Reliable, rapid and low cost methods to detect ESBLs in clinical microbiology laboratories are therefore required.
The aim of this project was to evaluate the phenotypic and genotypic detection methods for ESBLs and to examine the optimum antimicrobial agent(s) for ESBL detection. A comparison with the CLSI susceptibility test and the ESBL screen test was performed using a number of clinical isolates of E. coli and Klebsiella spp. suspected to contain ESBLs. Two confirmatory tests, the double disc synergy test and the combination disc test for ESBLs were also compared. Single and multiplex PCR assays were established using primers for the TEM-, SHV- and OXA-type β-lactamases. The results of this study show that ESBL screening is required in routine laboratories for successful detection of ESBLs. The best indicator cephalosporin for detection of ESBLs in E. coli was cefpodoxime whilst the best indicators for detection of ESBLs in K. pneumoniae were cefpodoxime and ceftazidime. The combination disc confirmatory test demonstrated the highest rate of detection. The multiplex PCR assay was found to be a rapid and cost-effective method for ESBL detection. However, nucleotide sequencing is required to confirm ESBL production amongst these organisms.
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Aspelmeier, Stella. "Genotypic variation in drought response of silver birch (Betula pendula Roth)." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=964913461.
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Devane, Megan (P M. L. ). "The isolation and genotypic characterisation of campylobacter jejuni from environmental matrices." Thesis, University of Canterbury. Biological Sciences, 2006. http://hdl.handle.net/10092/1297.
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Infection by Campylobacter is the most notified gastrointestinal disease in New Zealand. Reliable recovery and identification of campylobacters is challenging. Improved and validated methods are needed to increase the power of subtyping and epidemiological studies to trace the sources and transmission routes of Campylobacter. An enrichment-PCR method for the isolation and detection of C. jejuni and C. coli was developed and sensitivity levels determined in 13 environmental matrices, including animal faeces, food and water. Less than ten cells per sample of either C. jejuni or C. coli could be detected, except for rabbit faeces where the minimum number of cells detected per sample was greater than ten cells for C. coli (range 3-32 cells). The sensitivity of the method was comparable to that determined for the conventional methods in the same matrices. Application of the method to retail chicken carcasses (n =204) determined a prevalence of 27.5% C. jejuni and 1% C. coli. River water assays (n = 293) found 55.3% of samples to contain C. jejuni and 4.1% C. coli. Furthermore, the enrichment-PCR assay was shown to identify up to three subtypes in individual water samples. It was proposed that the identification of non-dominant subtypes carried by a chicken carcass may aid the identification of subtypes implicated in human cases of campylobacteriosis. An average of twenty-three C. jejuni isolates from each of ten retail chicken carcass were subtyped by PFGE using the two restriction enzymes SmaI and KpnI. Fifteen subtypes, in total, were identified from the ten carcasses. One subtype was identified on three carcasses. Five carcasses carried a single subtype, three carcasses carried two subtypes each and two carcasses carried three subtypes each. Some of the subtypes carried by an individual carcass were shown to be clonally related raising the question of in vivo recombination events during host passage. Comparison of C. jejuni subtypes from chickens with those isolated from human clinical cases revealed three of the fifteen subtypes correlated with those from human cases. None of the minority subtypes were identified in human case isolate data, suggesting that the lack of identification of non-dominant subtypes from chicken carcasses may not hinder the investigation of campylobacteriosis outbreaks.
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Schoenbaum, Elizabeth. "Genotypic Characterization of Phytophthora cinnamomi from Ornamental Crops in North Carolina." NCSU, 2008. http://www.lib.ncsu.edu/theses/available/etd-11042008-100454/.
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Forty-two Phytophthora cinnamomi isolates from Camellia spp., Ilex spp., Juniperus spp., and Rhododendron spp. were characterized for mating type, mefenoxam fungicide sensitivity, and aggressiveness on Rhododendron âHino de Giriâ. Isolates collected from Camellia spp. were of the A1 mating type, while isolates from the other host plants were A2. All isolates were sensitive to mefenoxam at 100 ppm and all but one was sensitive at 1 ppm. Isolates from Rhododendron spp. scored higher average foliar disease and root rot ratings, while A1 isolates from Camellia spp. had the lowest average foliar disease and root rot ratings. The population sample of 42 isolates was also examined for DNA sequence polymorphisms in two nuclear loci, beta-tubulin (Btu) and a portion of the intergenic spacer (IGS) region of the nuclear rDNA repeat, and one mitochondrial DNA locus, cytochrome c oxidase subunit 1 (COX 1). Six base substitutions were found among the 42 isolates with a multi-locus data set. Isolates grouped into four haplotypes. Haplotype grouping corresponded to isolate mating type, plant host, and heterozygosity in the Btu locus. Our inferred multilocus rooted gene genealogy revealed a putative ancestral lineage representing the most frequently sampled haplotype in the population. This haplotype contained A2 isolates collected from Ilex spp., Juniperus spp., and Rhododendron spp.. Isolates of the A1 mating type diverged more recently in the genealogy. There is an increase in heterozygosity at the Btu locus that coincides with the appearance of the A1 mating type. These findings increase our understanding of the population structure of P. cinnamomi.
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Lawrence, Lorna Margaret. "The genotypic characterisation of Listeria monocytogenes within the food processing environment." Thesis, Queen's University Belfast, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284274.
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Walker, Paul L. "Genotypic and phenotypic aspects of metal tolerance in Holcus lanatus L." Thesis, University of Sheffield, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284588.
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Smejkal, Christopher Wayne. "The genotypic and metabolic variation of chlorophenoxyalkanoic acid herbicide degrading bacteria." Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366613.
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Rotundo, José Luis. "Physiological bases of environmental and genotypic effects on soybean seed composition." [Ames, Iowa : Iowa State University], 2009.
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Saxenborn, Patricia. "Sepsis : Genotypic analysis of clinical Klebsiella spp. using next-generation sequencing." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-15842.
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Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response system and can occur when the immune system over- or under- reacts to an infection. Klebsiella spp. has been found to be one of the leading causes of sepsis, and the increasing occurrence of antibiotic resistance observed has become a major concern in clinical care. To study the genome and increase knowledge of the biodiversity of K. pneumoniae, K. variicola, and K. oxytoca, bacterial isolates were collected from blood, urine, nasopharynx, and wounds of patients with suspected sepsis. Next-generation sequencing was performed, and the presence of antibiotic resistance genes and plasmids were studied. Furthermore, a prediction of traits for each phylogroup was performed and the results from whole-genome sequencing were compared to phenotypic results. Among the K. pneumoniae isolates obtained, almost half had been misidentified by standard phenotypic methods and were found to be K. variicola, K. quasipneumoniae, and K. quasivariicola. A significant difference in the number of antibiotic resistance genes were observed between K. pneumoniae and K. variicola compared to K. oxytoca, however no significant difference was observed between K. pneumoniae and K. variicola, suggesting the underestimated pathogenicity of K. variicola. A genetic agreement was observed between the type of beta-lactamase harboured and presence or absence of nitrogen-fixation genes to the phylogroup, providing a way of species identification. Further studies should be conducted on the pathogenicity and virulence of K. variicola and K. quasipneumoniae to avoid misidentification, find organism-specific treatments, and narrow down the antibiotic prescription.Biodiversitet vid Sepsis
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Tiao, Narry. "Phenotypic And Genotypic Characterization Of Staphylococci From Dairy In Northeast Brazil." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1222093339.
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Thulin, Hedberg Sara. "Antibiotic susceptibility and resistance in Neisseria meningitidis : phenotypic and genotypic characteristics." Doctoral thesis, Örebro universitet, Hälsoakademin, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-8652.
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Neisseria meningitidis, also known as the meningococcus, is a globally spread obligate human bacterium causing meningitis and/or septicaemia. It is responsible for epidemics in both developed and developing countries. Untreated invasive meningococcal disease is often fatal, and despite modern intensive care units, the mortality is still remarkably high (approximately 10%). The continuously increasing antibiotic resistance in many bacterial pathogens is a serious public health threat worldwide and there have been numerous reports of emerging resistance in meningococci during the past decades. In paper I, the gene linked to reduced susceptibility to penicillins, the penA gene, was examined. The totally reported variation in all published penA genes was described. The penA gene was highly variable (in total 130 variants were identified). By examination of clinical meningococcal isolates, the association between penA gene sequences and penicillin susceptibility could be determined. Isolates with reduced susceptibility displayed mosaic structures in the penA gene. Two closely positioned nucleotide polymorphisms were identified in all isolates with reduced penicillin susceptibility and mosaic structured penA genes. These alterations were absent in all susceptible isolates and were successfully used to detect reduced penicillin susceptibility by real-time PCR and pyrosequencing in paper II. In papers III and IV, antibiotic susceptibility and characteristics of Swedish and African meningitis belt meningococcal isolates were comprehensively described. Although both populations were mainly susceptible to the antibiotics used for treatment and prophylaxis, the proportion of meningococci with reduced penicillin susceptibility was slightly higher in Sweden. A large proportion of the African isolates was resistant to tetracycline and erythromycin. In paper V, the gene linked to rifampicin resistance, the rpoB gene, was examined in meningococci from 12 mainly European countries. Alterations of three amino acids in the RpoB protein were found to always and directly lead to rifampicin resistance. A new breakpoint for rifampicin resistance in meningococci was suggested. The biological cost of the RpoB alterations was investigated in mice. The pathogenicity/virulence was significantly lower in rifampicin resistant mutants as compared with susceptible wild-type bacteria.
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O'Hanlon, Karen Ann. "Studies on the enzyme DNA-dependent RNA polymerase." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266340.
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