Thesis (PhD)--Stellenbosch University, 2004. / ENGLISH ABSTRACT: New agents for the diagnosis, prevention and treatment of tuberculosis are urgently required. Yet, despite extensive tuberculosis research over recent years, no new drugs, vaccines or diagnostics have been identified to date. It is widely speculated that the major obstacle to the identification of new therapies is the lack of understanding of the hostpathogen interaction. This study has investigated whether patterns of antigen expression correlate with molecular epidemiological data and strain virulence through the analysis of protein expression and antigen recognition profiles of different M tuberculosis clinical isolates. Using polyacrylamide gel electrophoresis, enzyme-linked immunosorbent assay, and Western blotting, protein expression and antigen recognition by two genotypically different clinical strains that differed in their frequency in the study population have been compared. In addition to differences in protein expression and antigen recognition between the clinical strains and the reference strain H37Rv, protein expression differences between the clinical strains themselves were observed which may relate to strain frequency and virulence. Differential protein expression by M tuberculosis strains, may explain the heterogeneous host humoral immune response and why no fully effective serodiagnostic test has been developed to date. To explore this hypothesis, the potential of serodiagnosis in this community, where patients are infected with a wide variety of genotypically distinct strains, was investigated. IgG levels to three mycobacterial antigens showed that serodiagnosis of TB is possible in this community, despite infection by a wide variety of genotypically different M tuberculosis strains. Disease episode affected antibody levels, suggesting that care should be taken when evaluating serological diagnosis for repeat episode patients. This study has shown that M tuberculosis protein expression is dynamic and that the bacillus presents a hypervariabie array of antigens to the host immune system. It is likely that different antigens become immunodominant as antituberculosis chemotherapy progresses, and that these differentially expressed antigens may be tracked as predictors of treatment outcome. This hypothesis was tested by correlating Ag85-specific IgG with treatment response, as assessed by sputum smear conversion after two months of antimycobacterial chemotherapy. No significant correlation between antibody levels and treatment responses was observed, suggesting that antibodies may not be useful surrogate markers or that the incorrect antibody type or mycobacterial antigen were selected. Results were consistent with previous findings where patient-to-patient variation dictated the host humoral response. The results obtained in this study have demonstrated that although bacteriological factors may influence strain prevalence due to antigen variation and immune evasion, both bacteriological and host factors affect humoral immunity. Differential protein expression by M tuberculosis strains has potentially important implications for serodiagnosis and the development of subunit or DNA vaccines, by suggesting that multi-antigen cocktails should be used. Differential protein expression may also explain why patients do not develop adequate protective immunity and are susceptible to reinfection. / AFRIKAANSE OPSOMMING: Daar is 'n dringende behoefte vir nuwe middels vir die diagnosering, voorkoming en behandeling van tuberkulose. Ondanks intense tuberkulose navorsing gedurende die afgelope paar jaar, is daar geen nuwe tuberkulose medikasie, vaksines of diagnostiese metodes geïdentifiseer nie. Daar word gespekuleer dat die hoof struikelblok vir die identifisering van nuwe medikasie die onkunde oor die tuberkulose patogeen is. Deur die analise van proteien-uitdrukking en antigeen-erkenning profiele van verskillende M. tuberculosis kliniese isolate is daar tydens hierdie studie ondersoek ingestel of die patroon van antigeen uitdrukking korreleer met molekulêre epidemiologiese data and stam-virulensie. Proteien-uitdrukking en antigeen-erkenning deur twee genotipies verskillende kliniese stamme wat verskil in hul frekwensie in die bestudeerde populasie, is vergelyk deur middel van poli-akrielamied gel elektroforese, ensiem-gekoppelde immuunabsorberende analise en Westelike oordrag. Addisoneel tot die verskille in proteienuitdrukking en antigeen-ekenning tussen kliniese stamme en die verwysingstam H37Rv, is daar ook verskille aangedui tussen die kliniese stamme self wat kan dui op stam frekwensie en virulensie. Differensiële proteien-uitdrukking deur M. tuberculosis stamme, kan moontlik die heterogene gasheer se humorale immuunreaksie verduidelik en daarmee saam die rede waarom daar nie tot op hede 'n effektiewe sero-diagnostiese toets ontwikkel is nie. Daar is dus ondersoek ingestel na die potensiaal van sero-diagnose in 'n gemeenskap waar pasiënte geïnfekteer is met 'n wye verskeidenheid genotipiese stamme. Die IgG vlakke van drie mikobakteriële antigene het aangedui dat sero-diagnose van tuberkulose moontlik is in hierdie gemeenskap, ten spyte van infektering deur 'n wye verskeidenheid genotipies-verskillende M. tuberculosis stamme. Die tussenspel van die siekte het teenliggaampie-vlakke beïnvloed wat daarop dui dat daar versigtig moet gelet word tydens die evaluering van serologiese diagnose van geïnfekteerde pasiënte wat voorheen siek was. Hierdie studie toon dat M. tuberculosis proteïen-uitdrukking dinamies is en dat die bacillus 'n groot variëteit van antigene tot die immuun sisteem bied. Dit is moontlik dat verskillende antigene immuun dominant kan word soos wat antituberkulose chemoterapie toeneem, en dat hierdie verskillend-uitgedrukte antigene as 'n gevolg daarvan gebruik kan word as voorspellers vir behandeling. Hierdie hipotese is getoets deur die korrelering van Ag85-spesifieke IgG met die reaksie op behandeling soos geëvalueer deur speeksel-monster verandering na twee maande se anti-mikobakteriële chemoterapie. Daar was geen noemenswaardige korrelasie tussen teenliggaampie vlakke en die reaksie op behandeling nie, wat daarop dui dat die teenliggaampies nie toepaslike surrogaat merkers is nie of dat die verkeerde teenliggaampie-tipe of mikobakteriële antigeen geselekteer is. Hierdie resultate bevestig vorige bevindinge waar pasiënt-tot-pasiënt verskille die gasheer se humorale immuunreaksie gedikteer het. Die resultate wat uit hierdie studie volg dui dat alhoewel bakteriologiese faktore die stam-frekwensie kan beïnvloed as gevolg van antigeen-variasie en immuun-ontduiking, kan beide bakteriologiese en gasheer faktore die humorale immuunreaksie beïnvloed. Differensiële proteiën uitdrukking deur 'n verskeidenheid M. tuberculosis stamme het potensieël belangrike toepassings vir sero-diagnose en die ontwikkeling van subeenheid of DNS vaksines wat impliseer dat multi-antigeen mengsels gebruik moet word. Differensiële proteiën uitdrukking mag ook verduidelik waarom pasiënte nie 'n voldoende beskermende immuniteit opbou nie en sodoende ontvanklik is vir her-infeksie.

Thesis (MSc)--Stellenbosch University, 2002. / ENGLISH ABSTRACT: Please see fulltext for abstract. / AFRIKAANSE OPSOMMING: Sien asb volteks vir opsomming.

Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2006. / The focus of this study was the pathways for β-alanine production in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. The major pathway for β-alanine production is the decarboxylation of L-aspartate by L-aspartate-α-decarboxylase (PanD). This enzyme is not essential for the survival for Mtb which implies that an alternative pathway for β-alanine production must exist. We postulated that such a secondary pathway may be based on the oxidation of various polyamines by a polyamine oxidase to give the β-alanine precursor 3-aminopropanal, and therefore set out to find data in support of this hypothesis. Based on sequence homology to the FAD-dependent Saccharomyces cerevisiae polyamine oxidase Fms1, Mtb AofH was identified as a likely candidate. The soluble expression and purification of AofH proved troublesome and lead to the investigation of various techniques to increase protein yield. These methods include fusion to various tags, coexpression with the protein chaperones, addition of scarce codon tRNA’s to the translation mixture and protein refolding. AofH was eventually purified as fusions to the Nus and MBP proteins and its activity determined by analysis of the enzymatic reactions by TLC, reverse phase HPLC, ESI-MS and LC-MS. TLC analysis indicated that 3- aminopropanol formed as a product during polyamine oxidation, but this could not be confirmed by any of the more sensitive analytical techniques. We set out to confirm the presence of the FAD cofactor in the enzyme by various methods and concluded that the AofH fusions did not contain FAD. Efforts to refold the protein in the presence of FAD also failed. From this study it is clear that the biochemical confirmation of the presumed activity of AofH will remain elusive until the enzyme can be purified in its active form, i.e. with FAD bound. A genetic test for activity based on functional complementation studies of Escherichia coli ΔpanD strains proved inconclusive since no difference in growth rate was found between cell transformed with the aofH gene and the negative control. We continued our studies of β-alanine biosynthesis by attempting the design of mechanism-based inhibitors for the PanD enzyme. Various structural analogues were identified and tested by qualitative and quantitative methods. Our results show that β- substituted aspartate analogues may be good potential inhibitors of Mtb’s PanD protein and can thus be used in rational drug design.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2007. / One of the aims of direct observed therapy strategy implemented by the World Health Organization was to prevent the development of drug resistant tuberculosis. However, in recent years a dramatic increase and spread in multidrug resistant tuberculosis has been observed. In this study, a molecular epidemiological approach was used to understand and rapidly detect drug resistance in high incidence tuberculosis communities of the Western Cape, South Africa. Previous studies showed that, drug resistant tuberculosis occurs as a result of spontaneous mutations in particular genes. Using molecular techniques, we developed an algorithm to rapidly detect isoniazid, rifampicin and ethambutol drug resistance in tuberculosis patients from a short term mini culture. Rapid detection of drug resistance is important to prevent future transmission events. In addition, accurate ethambutol resistance testing is of particular importance, since treatment of patients infected with multidrug resistant strains with second line anti-tuberculosis drugs depend on the ethambutol test results. In a comprehensive study, we found that the algorithm performs well when compared to the traditional culture method currently used by the routine laboratories. However, the results showed that more then 90 % of ethambutol resistance is missed by the routine laboratories. This has important implications for the tuberculosis control program, since patients infected with the drug resistant strain may be on inappropriate treatment. In this study, we found that certain strains have a selective advantage to become drug resistant and transmit and this implies that they are more virulent and fit than other strains. This observation has also been made for strains within the same genotype family. The more transmissible drug resistant strains cause large drug resistant outbreaks. This study highlights the complexity of the drug resistant epidemic, and confirms that it is a major problem in local communities. Application of molecular methods has provided us with tools to study how resistance might develop. We have demonstrated how we made use of a newly developed method to detect a multidrug resistant outbreak in the study community. The applications of transcriptomics identified several genes that might play a role in isoniazid resistance. Using this data a model was proposed whereby isoniazid resistant strains can compensate for the toxic effect of the drug. Application of comparative genomics by whole genome sequencing will be used to assist us in the further understanding of the mechanisms of drug resistance. This study also conclude that we should continue in our attempts to develop faster diagnostics for both first and second line drugs and that we must not loose site that all of this research must in the end benefit the patients.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009. / Dissertation presented for the degree of Doctor of Philosophy at Stellenbosch University. / ENGLISH ABSTRACT: This study describes the molecular epidemiology of Mycobacterium tuberculosis strains with the Beijing genotype. This genotype has received clinical prominence due to its global distribution and the hypothesis that these strains have acquired the ability to evade the protective effect of BCG vaccination, spread more readily, acquire drug resistance and cause severe forms of disease. Molecular biological techniques were used in a series of studies to elucidate the genetic evolutionary mechanisms underlying the success of this genotype in Cape Town, South Africa. Using a collection of 40 different markers it was possible for the first time to construct a phylogenetic history of Beijing genotype strains. This phylogeny was characterized by the consecutive evolution of 7 sublineages. Analysis of epidemiological data in relation to these sublineages showed an association between more recently evolved Beijing strains and an increased ability to transmit and cause disease. From these findings it was hypothesized that the pathogenic characteristics of the Beijing genotype were not conserved but rather that strains representative of the different sublineages had evolved unique properties. In order to determine whether these socalled unique properties were associated with either the host population or the genetic background of strains from sublineage 7, a meta-analysis of published Mycobacterial Interspersed Repetitive-Unit (MIRU) typing data (East Asia) was compared with MIRU typing data from the South African strains in the context of their phylogenetic histories. This study showed that Beijing genotype strains in South Africa originated in East Asia following their introduction during the early 18th century. A significant association was observed between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (p <0.0001). Based on these findings it was proposed that either the host population (South African) had selected for a particular Beijing sublineage (i.e. sublineage 7) or that strains from that sublineage had adapted to be more successful in the South African population. In a subsequent study, using the methodology developed in the above studies, it was shown that strains from the ancestrally positioned lineage (termed “atypical” Beijing genotype) were over-represented in drug resistant isolates in the Eastern Cape region. This contradicts current dogma which suggests that “atypical” Beijing genotype strains are attenuated in their ability to transmit. However, this phenomenon may be ameliorated in immune-compromised patients as review of the clinical records showed that transmission was associated with HIV co-infection. These findings highlight the need to improve tuberculosis control in vulnerable populations as strains which would normally not contribute significantly to the epidemic now become a cause for concern especially if they are associated with drug resistance. To improve our understanding of the evolution of the Beijing genotype, the genomic stability of an additional 27 polymorphic markers were analysed. These markers have recently been proposed as the new standard in molecular epidemiological studies and were based on MIRU-Variable Number Tandem-Repeats (VNTR) sequences. Superimposition of the MIRU-VNTR data onto the phylogenetic tree showed excellent concordance thereby demonstrating that these alleles were largely stable over time. It is currently not known how the alleles that do change could influence pathogenicity. The results of this study also demonstrated discordance between strains defined by IS6110 DNA fingerprinting and those defined by MIRU-VNTR typing thereby demonstrating that these markers evolve independently and at different rates. Furthermore, the MIRU-VNTR typing method was unable to predict transmission of drug resistant strains which contradict previous reports from low incidence settings. This has significant implications for the use of this typing method in high incidence settings. Using an improved PCR-based method it was possible for the first time, to identify the 5 most prominent phylogenetic lineages in primary cultures of adult tuberculosis patients resident in a high HIV/TB co-infection setting. The results of this study showed that 15% of the study population was infected with two or more strains and Beijing genotype strains were over-represented in these mixed infections. Furthermore, drug susceptibility tests showed that one patient was co-infected with both a drug sensitive and a drug resistant strain. Since mixed infections have been implicated in treatment failure, these findings demonstrate the epidemiological importance of detecting mixed infections in vulnerable populations. This PCR-based method was further applied to cultures of paediatric tuberculosis patients to classify strains which spoligotyping was unable to define. The result of this study showed three mixed infections which otherwise would have been missed. In order to determine whether clinical disease presentation of patients infected with strains of the Beijing genotype were different from that of patients infected with non-Beijing genotype strains, clinical and demographic data of these two groups were analysed. This study showed that patients infected with strains of the Beijing genotype were highly infectious as defined by the increased bacterial load in sputum specimens. However, this finding could not be validated by lung pathology according to chest radiographs of infected patients. / AFRIKAANSE OPSOMMING: Hierdie studie beskryf die molekulêre epidemiologie van Mycobacterium tuberculosis rasse met die Beijing genotipe. Hierdie genotipe is van groot kliniese belang weens hul globale verspreiding en die hipotese dat hierdie rasse die vermoë ontwikkel het om die beskermende effek van BCG vaksinasie te vermy, om meer geredelik te versprei, middelweerstandigheid te ontwikkel en erger vorms van siekte te veroorsaak. Molekulêre biologiese tegnieke is gebruik in ‘n reeks studies om die genetiese evolusionêre meganismes onderliggend tot die sukses van hierdie genotipe in Kaapstad, Suid-Afrika te verklaar. Deur ‘n versameling van 40 verskillende merkers te gebruik, was dit moontlik om vir die eerste keer ‘n filogenetiese stamboom van die Beijing ras genotipe te skep. Hierdie filogenie word gekenmerk deur die opeenvolgende evolusie van 7 ras sublyne. Met die analise van epidemiologiese data in verhouding tot hierdie ras sublyne, is ‘n assosiasie tussen die mees onlangs ontwikkelde Beijing rasse en die verhoogde vermoë om te versprei en siekte te veroorsaak, getoon. Vanweë hierdie bevindinge, is ‘n hipotese daargestel dat die patogeniese kenmerke van die Beijing genotipe nie in alle raslyne voorkom nie, maar eerder dat verteenwoordigende rasse van die verskillende sublyne unieke eienskappe deur evolusie ontwikkel het. ‘n Metaanalise van gepubliseerde MIRU tipering data van Oos-Asië is vergelyk met MIRU tipering data van Suid-Afrikaanse rasse in die konteks van hul filogenetiese geskiedenis om te bepaal watter van hierdie sogenoemde unieke eienskappe geassosieer is met die gasheerpopulasie en watter eienskappe geassosieer is met die genetiese agtergrond van die sublyn 7 rasse. Hierdie studie het getoon dat die Beijing ras genotipe van Suid-Afrika hul oorsprong gekry het van Oos-Asië en vir die eerste keer waargeneem is in die vroeë 18de eeu. ‘n Betekenisvolle assosiasie is waargeneem tussen die frekwensie waarteen die rasse van ‘n bepaalde Beijing sublyn voorkom en die menslike populasie van wie hulle geïsoleer is (p < 0.0001). Gebaseer op hierdie bevindinge is dit voorgestel dat die menslike populasie (Suid-Afrikaners) vir ‘n spesifieke Beijing sublyn geselekteer het (bv. Sublyn 7) of dat rasse van hierdie sublyn aangepas het om meer suksesvol te wees in die Suid-Afrikaanse populasie In ‘n daaropvolgende studie is, deur gebruik te maak van die metodiek wat ontwikkel is vir die bogenoemde studies, getoon dat die voorouerlike sublyn (bekend as die“atipiese” Beijing genotipe) die mees verteenwoordigende sublyn was onder middelweerstandige isolate van die Oos-Kaap gebied. Dit is teenstrydig met die bestaande dogma wat bepaal dat die “atipiese” Beijing genotipe rasse hulle vermoë om te versprei verloor het. Hierdie verskynsel kan egter versterk word in immuun inkompetente pasiënte aangesien hersiening van die kliniese rekords aangedui het dat verspreiding geassosieer was met HIV ko-infeksie. Hierdie bevindinge bring die behoefte om TB beheer in vatbare populasies te verbeter, na vore, omrede rasse wat gewoonlik `n onbetekenisvolle bydrae tot die epidemie lewer, nou ‘n rede vir kommer is veral as hulle met middelweerstandigheid geassosieer is. Om ons insig rakende die evolusie van die Beijing genotipe te verbeter, is die genomiese stabiliteit van ‘n addisionele 27 polimorfiese merkers geanaliseer. Daar is onlangs voorgestel dat hierdie merkers, wat gebaseer is op MIRU-VNTR volgordes,die nuwe standaard vir molekulêre studies is. Die MIRU-VNTR data is op die filogenetiese boom geplaas en het uitstekende ooreenstemming getoon wat die allele se stabiliteit oor tyd gedemonstreer het. Dit is tans nie duidelik hoe van die allele wat wel verander, die patogenisiteit beïnvloed nie. Die resultate van die studie wys ook onenigheid tussen rasse wat deur IS6110 DNA tipering gedefinieer is en dié wat deur MIRU-VNTR tipering gedefinieer is. Dit impliseer dus dat die evolusie van merkers onafhanklik van mekaar plaasvind en teen verskillende tempos. Verder was die MIRU-VNTR tipering metode nie in staat om verspreiding van middelweerstandige rasse te voorspel nie, wat teenstrydig is met vorige verslae waar lae insidensie omgewings bestudeer is. Dit het noemenswaardige implikasies vir die gebruik van hierdie tipering metode in hoë insidensie omgewings. ‘n Verbeterde PKR-gebaseerde metode is vir die eerste keer gebruik om die 5 mees prominente filogenetiese sublyne in primêre kulture van volwasse tuberkulose pasiënte van ‘n hoë MIV/TB ko-infeksie omgewing, te identifiseer. Die resultate van hierdie studie het gewys dat 15% van die studiepopulasie geïnfekteer is met twee of meer rasse en dat die Beijing genotipe ras die meeste voorgekom het in gemengde infeksies. Verder het middelweerstandige toetse gewys dat een pasiënt geïnfekteer was met beide ‘n middelsensitiewe en ‘n middelweerstandige ras. Gemengde infeksies is al vantevore gekoppel aan onsuksesvolle behandeling en dus demonstreer hierdie bevindinge die epidemiologiese belang van die opsporing van gemengde infeksies in vatbare populasies. Hierdie PKR-gebaseerde metode is verder gebruik om rasse wat voorkom in kulture van pediatriese pasiënte, wat spoligotipering nie kon klassifiseer nie, te klassifiseer. Die resultate het drie gemengde infeksies gewys wat sonder die PKR-gebaseerde metode, nie geïdentifiseer sou gewees het. Om te bepaal of die kliniese beeld van pasiënte wat geïnfekteer is met rasse van die Beijing genotipe verskil van dié van pasiënte wat geïnfekteer is met rasse van die nie-Beijing genotipe, is die kliniese en demografiese data van die twee groepe pasiënte geanaliseer. Hierdie studie wys dat pasiënte wat geïnfekteer is met rasse van die Beijing genotipe hoogs aansteeklik is (gedefinieer op grond van hoë bakteriële lading in sputum monsters). Hierdie bevindinge kon egter nie met behulp van long patologie op borskas X-strale bevestig word nie.

Memoria para optar al Título Profesional de Médico Veterinario / Con el fin de pesquisar y describir las lesiones pulmonares en Lobos marinos (Otaria flavescens), se realizó un estudio radiográfico simple de tórax a 20 ejemplares cachorros y juveniles. También se realizaron lavados traqueales para la obtención de muestras que fueron analizadas para la búsqueda de bacterias del Complejo Mycobacterium tuberculosis, mediante la prueba de Reacción de Polimerasa en Cadena (PCR), con el objetivo de investigar la presencia de tuberculosis pulmonar. Para ambos estudios los animales se encontraban bajo anestesia general mediante la utilización de Isofluorano, con buena respuesta a la inducción y recuperación. Se logró estandarizar la técnica radiográfica, kVp y mAs, y se extrapoló técnica de lavados traqueales de caninos a lobos marinos. Los resultaron mostraron que 11 animales (55%) presentaban algún tipo de lesión pulmonar, en 10 individuos (50%) se observó un infiltrado del parénquima pulmonar, en 5 de ellos este infiltrado es de tipo difuso, mientras que en los 5 restantes es de tipo celular. En cuanto a la presencia de broncogramas aéreos positivos (BAP), éste estuvo presente en 9 de los individuos en estudio (45%). En lo referente la prueba de PCR, ésta arrojó resultados negativos en la totalidad de los animales, probablemente, debido a que los animales no se hayan encontrado infectados con alguna bacteria del complejo M. tuberculosis

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Submitted in fulfillment for the Degree of Doctor of Philosophy (Biotechnology), Durban University of Technology, Durban, South Africa, 2016. / Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB) has infected approximately one-third of the world population, with 9.6 million TB cases in 2014. The emergence of multi-drug resistant (MDR) and extensively-drug resistant (XDR) strains of MTB has further complicated the problem of TB control. It is now imperative that novel antimycobacterial compounds are discovered in order to treat infections and reduce the duration of current TB therapy courses. For centuries, medicinal plants have been used globally worldwide for the treatment and prevention of various ailments. This occurs particularly in developing countries where infectious diseases are endemic and modern health facilities and services are inadequate. In recent years, the use and search for plant drug derivatives have been fast-tracked. Ethnopharmacologists, botanists, microbiologists, and natural product chemists are trying to discover phytochemicals which could be developed for the treatment of infectious diseases, especially TB. Plants are rich in a wide variety of secondary metabolites, such as tannins, terpenoids, alkaloids, and flavonoids, which have been found in vitro to have antimycobacterial activity. In the search for new lead compounds, nine medicinal plant species, Buddleja saligna, Capparis tomentosa, Carpobrotus dimidiatus, Dichrostachys cinerea, Ekerbergia capensis, Ficus Sur, Gunnera perpensa, Leonotis leonurus and Tetradenia riparia were collected in Kwa-Zulu Natal (KZN) following report of their therapeutic use in traditional medicine to treat symptoms and infections related to TB. They were tested in vitro for their activity against Mycobacterium smegmatis, Mycobacterium tuberculosis H37Rv (ATCC 25177) and three well-characterized clinical isolates of MDR-TB and XDR-TB using the agar incorporation method. The minimum inhibitory concentration of the active plant extracts was determined using the broth microdilution method. Our findings show that five of the nine plants screened have antimycobacterial activity with concentrations ranging from 125 µg/ml to 1000 µg/ml. The aqueous extracts of G. perpensa and T. riparia; and the methanolic extracts of B. saligna, C. tomentosa, and C. dimidiatus possessed significant activity against M. smegmatis, M. tuberculosis H37Rv (ATCC 25177) and the three well-characterized clinical isolates of MDR-TB and XDR-TB. The cytotoxic effect of the active plant extracts was evaluated against the mouse BALB/C monocyte-macrophage (J774.2) and peripheral blood mononuclear cells (PBMCs). The toxic effects of the active plant extracts were evaluated using the brine shrimp lethality assay. Except for a high concentration of G. perpensa none of the other plants which possessed antimycobacterial activity showed any toxic or cytotoxic activity. The active plant extracts were thereafter assessed to determine if they had any effect on the survival or death of mycobacterial species, M. smegmatis, bound within the macrophage (J774.2) cell line at a concentration of 100 µg/ml. B. saligna had inactivated most of the phagocytosed bacilli after 24 hours of treatment therefore, it has a bactericidal effect on the mycobacteria located within the mouse macrophage. A phytochemical investigation of the leaves of B. saligna led to the isolation of two isomeric pentacyclic triterpene compounds namely Oleanolic Acid (OA) and Ursolic Acid (UA) using thin layer chromatography followed by silica gel column chromatography. The structures of these compounds were fully characterized by detailed NMR investigations, which included 1H and 13C NMR. Ursolic acid was isolated from this plant for the first time. Two-dimensional (2D) and three-dimensional (3D) quantitative structure-activity relationship (QSAR) studies were carried out to provide insight on the interaction of the compounds with the enzyme. Molecular docking studies predicted the free binding energy of the triterpenes inside the steroid binding pocket of Mycobacterium tuberculosis fadA5 thiolase compared to a reported inhibitor. Thus, their ability to inhibit the growth of Mycobacterium tuberculosis was predicted and was confirmed to possess significant antimycobacterial activity when tested against M. smegmatis, M. tuberculosis H37Rv (ATCC 25177), clinical isolates of MDR-TB and XDR-TB using the Microplate Alamar Blue Plate (MABA) assay. The present study has scientifically validated the traditional use of medicinal plant B. saligna. / D

The DNA glycosylases function in the first step of the base excision repair (BER) process, that is responsible for removing base lesions resulting from oxidation, alkylation or deamination. The DNA glycosylases that recognize oxidative base damage fall into two general families: the Fpg/Nei family and the Nth superfamily. Based on protein sequence alignments, we identified four putative Fpg/Nei family members as well as a putative Nth protein in Mycobacterium tuberculosis H37Rv, the causative agent of tuberculosis. While Fpg proteins are widely distributed among the bacteria and plants, Nei homologs are sparsely distributed across phyla, and are only found in γ-proteobacteria, actinobacteria and metazoans. Interestingly, M. tuberculosis H37Rv harbors two proteins (Rv2464c and Rv3297) from the Nei clade and two (Rv2924c and Rv0944) from the Fpg clade. All four Fpg/Nei proteins were successfully overexpressed by using a novel bicistronic vector, which theoretically prevented stable mRNA secondary structure(s) surrounding the translation initiation region (TIR) thereby improving translation efficiency. Additionally, MtuNth (Rv3674c) was also overexpressed in soluble form. The substrate specificities of the purified enzymes were characterized in vitro with oligonucleotide substrates containing single lesions. Some were further characterized by gas chromatography/mass spectrometry (GC/MS) analysis of products released from γ-irradiated DNA. MtuFpg1 (Rv2924c) has a substrate specificity similar to that of EcoFpg and recognizes oxidized purines. Both EcoFpg and MtuFpg1 are more efficient at removing spiroiminodihydantoin (Sp) than 7,8-dihydro-8-oxoguanine (8-oxoG); however, MtuFpg1 has a substantially increased opposite base discrimination compared to EcoFpg. The Rv0944 gene encodes MtuFpg2, which contains only the C-terminal domain of an Fpg protein and has no detectable DNA binding activity or DNA glycosylase/lyase activity and thus appears to be a pseudogene. MtuNei1 (Rv2464c) recognizes oxidized pyrimidines not only on doublestranded DNA but also on single-stranded DNA. It also exhibits uracil DNA glycosylase activity as well as weak activity on FapyA and FapyG. MtuNth recognizes a variety of oxidized bases, such as urea, 5,6-dihydrouracil (DHU), 5-hydroxyuracil (5- OHU), 5-hydroxycytosine (5-OHC) and methylhydantoin (MeHyd) as well as FapyA, FapyG and 8-oxoadenine (8-oxoA). Both MtuNei1 and MtuNth excise thymine glycol (Tg); however, MtuNei1 strongly prefers the (5R) isomers of Tg, whereas MtuNth recognizes only the (5S) isomers. The other Nei paralog, MtuNei2 (Rv3297), did not demonstrate activity in vitro as a recombinant protein, but when expressed in Escherichia coli, the protein decreased the spontaneous mutation frequency of both the fpg mutY nei triple and nei nth double mutants, suggesting that MtuNei2 is functionally active in vivo recognizing both guanine and cytosine oxidation products. The kinetic parameters of the MtuFpg1, MtuNei1 and MtuNth proteins on selected substrates were also determined and compared to those of their E. coli homologs. Since pathogenic bacteria are often exposed to an oxidative environment, such as in macrophages, our data, together with previous observations, support the idea that the BER pathway is of importance in protecting M. tuberculosis against oxidative stress, as has been observed with other pathogens .

P450s are heme containing enzymes which affect oxidation of substrates via catalytic intermediates having transient lifetimes. These oxidative catalytic intermediates are formed by a sequential interplay of electrons and protons at the active site of the enzyme bearing molecular dioxygen. The proton transfer to the active site from bulk solvent is coordinated by an “acid-alcohol” pair of active site residues which are conserved in all P450s. Sterol 14α-demethylases (CYP51) are P450 enzymes which catalyze oxidative deformylation of lanosterol in the cholesterol/ergosterol biosynthetic pathway. Both cholesterol and ergosterol are important regulators of membrane fluidity. CYP51 differs from other P450s in that the acid in the acid-alcohol pair in the active site is replaced by a His residue. This enzyme is present in tuberculosis (TB) causing pathogen Mycobacterium tuberculosis (Mtb). This finding was significant for primarily two reasons. The first one being the baffling presence of CYP51 in Mtb, as Mtb is not known to have any endogenous sterol biosynthetic pathways. The second being that CYP51 is a validated drug target in treating fungal infections. Thus given the global resurgence of multidrug resistant strains of Mtb and the deadly coexsistence of Mtb in immunocompromised HIV patients, CYP51 may be an ideal drug target for new generation of antimycobacterial drugs. The Mtb CYP51 enzyme was chosen to study the proton transfer pathways in the active site based on the outcome of explicit solvent molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations performed in our laboratory. Based on these calculations of CYP51 catalysis, Glu173 was implicated to be the proton source. Proton transfer to the active site occurred by a coordinated shuttling via four water molecules, His259 and Thr260. To experimentally verify the roles of Glu173, His259 and Thr260 they were mutated to alanine and biophysically characterized. Ferredoxin, an accessory protein required to shuttle electrons from NADPH to the CYP51 active site for catalysis, was also cloned using ligation independent cloning. We were successfully able to reconstitute the electron transport chain for CYP51. The mutants were found to differentially bind type I and type II enzymes. Based on biophysical characterization, Thr260 can be implicated to have a role in modulating the spin state of the enzyme. The Mtb CYP51 enzyme was chosen to study the proton transfer pathways in the active site based on the outcome of explicit solvent molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations performed in our laboratory. Based on these calculations of CYP51 catalysis, Glu173 was implicated to be the proton source. Proton transfer to the active site occurred by a coordinated shuttling via four water molecules, His259 and Thr260. To experimentally verify the roles of Glu173, His259 and Thr260 they were mutated to alanine and biophysically characterized. Ferredoxin, an accessory protein required to shuttle electrons from NADPH to the CYP51 active site for catalysis, was also cloned using ligation independent cloning. We were successfully able to reconstitute the electron transport chain for CYP51. The mutants were found to differentially bind type I and type II enzymes. Based on biophysical characterization, Thr260 can be implicated to have a role in modulating the spin state of the enzyme.