>Magister Scientiae - MSc / Risk factors such as intrauterine and vaginal infection put pregnant women at risk for delivering preterm. Bacterial vaginosis (BV) is a polymicrobial clinical syndrome commonly diagnosed in women of reproductive age, with women of African descent with low socioeconomic status and previous preterm delivery at high risk. Although frequently isolated from healthy women, Gardnerella vaginalis has been most frequently associated with BV. There is limited data available on the prevalence of BV in Southern Africa; therefore, we embarked on a study to determine the prevalence of BV and G. vaginalis in predominantly black communities in the Western Cape, in order to establish the role of G. vaginalis in BV. Women attending various Maternity and Obstetrics units (MOU) in the Cape Peninsula with and without a history of pre-term delivery (PTD) were invited to participate in the study. Several factors were statistically associated with pregnancy history, including location of study population, parity, smoking and presence of clinical symptoms. The presence of G. vaginalis was determined by culture in 51.7% of the preterm delivery group (PTDG) and 44% of the full-term delivery group (FTDG) women. BV was detected in 31.13% of PTDG and 23.67% of FTDG by Gram stained analysis according to Nugent scoring criteria, with age and HIV status posing as risk factors. When comparing PTDG and FTDG for an association between the presence of G. vaginalis and BV, a stronger association was observed in the PTDG but it was not statistically significant. In both PTDG and FTDG, G. vaginalis was isolated significantly more often in women diagnosed with BV at 24.5% (p < 0.05). Antibiogram studies revealed both Metronidazole and Clindamycin resistant strains of G. vaginalis. G. vaginalis Biotype 7 is specifically associated with BV, while Biotype 2 appears to be associated with BV in women with a history of PTD. Accuracy of diagnostic tools were tested and it was determined that Nugent scoring is more sensitive in diagnosing BV (76.04%), but culture for G. vaginalis is more specific (83.21%). Although this study was limited in that we were unable to follow-up pregnancy outcomes, we were able to confirm the perceived role of G. vaginalis in BV. / South Africa

Gram-positive pathogenic bacteria utilize cell-surface anchored proteins to bind and transport heme into the cell. These bacteria acquire iron from host proteins containing heme e.g., hemoglobin. Proteins like HmuT from Corynebacterium diphtheriae bind and help transport heme into the cell. Residues His136 and Tyr235 are utilized as the axial ligands, with a conserved Arg237 residue acting as the hydrogen bonding partner to the axial Tyr235. Similarly, Streptococcus pyogenes utilizes the cell anchored protein Shr to transfer heme into the cell. Shr-NEAT2 is hexacoordinated by two axial methionines and is prone to autoreduction where lysines are the most likely source of electrons. Lastly, PefR of Group A Streptococcus is a DNA transcription factor which regulates protein expression. Preliminary studies indicate a cysteine may coordinate the heme. A combination of UV-visible, resonance Raman, and magnetic circular dichroism spectroscopies shows these proteins play a crucial role heme transport and regulation.

Bacillus thuringiensis (Bt) is a gram-positive common soil bacterium that produces crystals (Cry) containing proteins that are toxic to certain insects, in particular larvae of Lepidoptera and Diptera. The Bt toxin in the past has been widely used as a bioactive compound for the biological control of mainly lepidopteran pests. Most recently a variety of crops, including cotton and maize, have been genetically modified to express a Bt toxin to confer resistance to lepidopteran pests. However, the effect of abiotic environmental stress, such as drought and heat, which are typical for Africa, on Bt toxin expression in a genetically modified crop has so far not been fully evaluated. This study focuses on the expression and stability of the Cry1Ac insecticidal protein from Bacillus thuringiensis in genetically modified cotton plants under drought and heat stress. These include the physiological and biochemical characterization of the expressed Bt toxin gene under drought stress as well as the biological activity against first-instar larvae of the African cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae). Non-genetically modified cotton (Gossypium hirsutum cv. Opal), as well as genetically modified cotton (cv. Nuopal) expressing the Bt toxin Cry1Ac, were exposed to drought and heat stress. Drought stress was induced by withholding watering plants until the soil moisture content reached 25- 30 % of field capacity. Non-stressed control plants were watered and soil moisture content to 80-100 % of field capacity was maintained. For heat stress, plants were grown at 38 to 32 DC during the day and night, respectively, whereas control plants were grown in a growth cabinet at a 28/25 DC day/night cycle. For growth analysis plants were harvested every second week after planting. At each harvest, different parts of the plant were collected and their fresh and dry weight determined. For biochemical analysis and determining biological activity against first-instar larvae of H. armigera, two types of experiments were carried out, the first experiment four weeks after treatment induction and the second experiment eight weeks after treatment induction. Different plant material (leaves, flowers and immature green bolls) were used for Bt detection as well as for determining biological activity against first-instar larvae of H. armigera. Under drought stress conditions a reduction in leaf area and leaf dry weight were found in both Bt toxin expressing and non-expressing cotton plants, but no significant difference in physiological performance between Bt-expressing and non-expressing cotton plants was found. This study shows that the Bt toxin (Cry1Ac) level decreases in senescent plants and that drought stress did not affect the growth and development of genetically modified Bt plants when compared to non-Bt plants. Although the expression of Bt toxin (Cry1Ac) in Bt cotton plants decreased under drought stress no effect on the efficacy of the toxin against H. armigera was observed. In addition, no significant decrease of Bt toxin content was found in Bt cotton leaves after exposure to heat stress when compared to leaves from nonheat stressed plants. / Dissertation (MSc)--University of Pretoria, 2008. / Plant Science / unrestricted

The increasing emergence and spread of antibiotic-resistant bacteria is a serious threat to public health. Of particular concern are Gram-negative bacteria such as Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae or Pseudomonas aeruginosa. Some of these strains are resistant to a large number of antibiotics and thus our treatment options are rapidly declining. In addition to the increasing number of antibiotic-resistant bacteria, a major problem is that many of the antibiotics at our disposal are ineffective against Gram-negative bacteria. This is partly due to the properties of the outer membrane (OM) which prevents efficient uptake. The overarching goal of this thesis was to investigate how the OM of the Gram-negative bacterium E. coli could be weakened to improve the activity of antibiotics. In the first two papers of my thesis (paper I + II), I investigated the periplasmic chaperone network which consists of the two parallel pathways SurA and Skp/DegP. This network is essential for the integrity of the OM and strains lacking either SurA or Skp are defective in the assembly of the OM, which results in an increased sensitivity towards vancomycin and other antimicrobials. We identified a novel component of the periplasmic chaperone network, namely YfgM, and showed that it operates in the same network as Skp and SurA/DegP. In particular, we demonstrated that deletion of YfgM in strains with either a ΔsurA or Δskp background further compromised the integrity of the OM, as evidenced by an increased sensitivity towards vancomycin. In the remaining two papers of my thesis (paper III + IV), the goal was to characterize small molecules that permeabilize the OM and thus could be used to improve the activity of antibiotics. Towards this goal, we performed a high-throughput screen and identified an inhibitor of the periplasmic chaperone LolA, namely MAC-13243, and showed that it can be used to permeabilize the OM of E. coli (paper III). We further demonstrated that MAC-13243 can be used to potentiate the activity of antibiotics which are normally ineffective against E. coli. In the last paper of my thesis (paper IV), we undertook a more specific approach and wanted to identify an inhibitor against the glycosyltransferase WaaG. This enzyme is involved in the synthesis of LPS and genetic inactivation of WaaG results in a defect in the OM, which leads to an increased sensitivity to various antibiotics. In this paper, we identified a small molecular fragment (compound L1) and showed that it can be used to inhibit the activity of WaaG in vitro. To summarize, this thesis provides novel insights into how the OM of the Gram-negative bacterium E. coli can be weakened by using small molecules. We believe that the two identified small molecules represent important first steps towards the design of more potent inhibitors that could be used in clinics to enhance the activity of antibiotics. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

Rapidly emerging strains of bacteria resistant to most advanced antibiotics have become issues of very important public health concern. Research currently directed towards marine actinomycetes presents a vast potential for new compounds that could be able to safely and effectively target resistant species. In this regard, ten putative Streptomyces strains isolated from the Nahoon beach were selected and assessed for antibiotic production and activity against a wide range of bacteria including reference strains, environmental strain and clinical isolates. The ethyl acetate extracts of the putative Streptomyces isolates showed activities against at least 6 and up to 26 of the 32 test bacteria. Inhibition zones were found to range between 9-32 mm diameters at a concentration of 10 mg/ml. The minimum inhibitory concentrations (MICs) of the crude extracts ranged from 0.039 - 10 mg/ml and the least minimum bactericidal concentration (MBC) demonstrated was 0.625 mg/ml against a reference strain Staphylococcus aureus ATCC 6538. Time kill kinetics of all extracts revealed bacteristatic and bactericidal activities. Average Log reductions in viable cell counts for all the extracts ranged from 0.86 Log10 and 3.99 Log10 cfu/ml after 3 h interaction and 0.01 Log10 and 4.86 Log10 after 6 h interaction at MIC, 2 × MIC, 3 × MIC and 4 × MIC concentrations. Most of the extracts were speedily bactericidal at 3 × MIC and 4 × MIC resulting in over 50 % elimination of most of the test bacteria within 3 h and 6 h interaction. The partial characterization of the crude extracts by IR spectral analysis revealed possibility of terpenoid, long chain fatty acids and secondary amine derivatives compounds in the extracts. It is therefore recommended that further investigation should address the relationship between the structure of the active component of the extracts and the broad spectrum activity, as well as a rapid method for large scale production and purification and whether this group of antibiotics has any application in managing human infectious disease.

Stenotrophomonas maltophilia is increasingly emerging as an opportunistic pathogen of global concern. Due to its inherent resistance to several classes of antibiotics including carbapenems and its ability to acquire mobile resistance elements, treatment of infections caused by S. maltophilia is a constant challenge for clinicians. Trimethoprim-sulphamethoxazole (TMP-SMX) is the generally accepted antibiotic of choice for the treatment of infections caused by this organism, but resistance to the drug is increasingly being reported; hence, the need for alternative therapeutic options. In this study, the antimicrobial susceptibility profile of 110 commensal S. maltophilia isolates obtained from Nkonkobe municipality, Eastern Cape Province, Republic of South Africa was investigated. Twenty-one antibiotics including TMP-SMX and the newer fluoroquinolones; levofloxacin, gatifloxacin and moxifloxacin were included in the antibiotic panel. About 63.4 percent of the isolates were susceptible to TMP-SMX with a resistance rate of 28.2 percent. The fluoroquinolones were more effective with susceptibilities ranging from 76 percent to 94.7 percent. Resistance to the fluoroquinolones ranged from 1.3 percent to 2.7 percent. Levofloxacin was the most effective fluoroquinolone tested. Phenotypic dectection of extended spectrum β-lactamases (ESBLs) showed double disc synergy test (DDST) positivity in 59.5 percent of the isolates. Cefepime was the most sensitive indicator cephalosporin in the DDST with 77.3 percent of suspected ESBL-producing isolates showing cefepime-clavulanic acid synergy. Isolates exhibited nine different ESBL phenotypes, however, PCR amplification of the bla genes revealed four isolates that possessed genes belonging to the CTX-M group (CTX-M-1 and CTX-M-8 groups). ESBL genes are usually carried on mobile elements such as plasmids and transposons which may also bear genes that mediate resistance to aminoglycosides, tetracyclines, TMP-SMX and fluoroquinolones. ESBL positive isolates appeared more susceptible to the fluoroquinolones compared to TMP-SMX but there was no significant relationship between ESBL production and susceptibility to these drugs (p > 0.05). The newer fluoroquinolones are a possible alternative treatment option for S. maltophilia infections in this environment but further studies and clinical investigations are needed to determine the in vivo efficacy of these drugs.

Cocos nucifera belong to the family Aracaceae (palm Family). The English name is coconut and it is used extensively as medicinal remedies against infections such as urinary tract infections, gastro intestinal infections, skin and wound infections. The in vitro antibacterial (including anti-listerial and anti-vibrio) properties as well as the evaluation of the combination potentials of the plant extract with six front-line antibiotics were evaluated in this study using standard procedures. The in vitro anti-listerial properties of the crude aqueous and n-Hexane extract of the husk of Cocos nucifera were carried out against 37 Listeria isolates. Twenty-nine of the test organisms were susceptible to the aqueous extract while thirty were susceptible to the n-Hexane extract both at the screening concentration of 25 mg/ml. Minimum Inhibitory Concentration (MIC) values for all the susceptible bacteria ranged between 0.6 - 5.0 mg/ml. For the aqueous extract, average log reduction in viable cell count ranged between 0.32 Log10 and 4.8 Log10 CFU/ml after 8 hours interaction in 1 × MIC and 2 × MIC. For the n-Hexane extract, the log reduction ranged between 2.4 Log10 and 6.2 Log10 CFU/ml after 8 hours interaction in 1 × MIC and 2 × MIC. The time-kill characteristics of the two extracts suggest that at higher concentration (2 × MIC) and longer duration of interaction (8 hr), more bacteria were killed. In vitro anti-vibrio and antibacterial properties experiment revealed that of all the 45 vibrio and 25 bacteria strains that was tested, 37 were susceptible to the aqueous extract and 38 to the n-Hexane extract, while 17 were susceptible to the aqueous extract and 21 to the n-Hexane extract. Minimum Inhibitory Concentration (MIC) values for all the susceptible bacteria ranged between 0.3 - 5.0 mg/ml. viii The time kill studies revealed that for the aqueous extract, average log reduction in viable cell count in time kill assay ranged between 0.12 Log10 and 4.2 Log10 CFU/ml after 8 hr interaction at 1 × MIC and 2 × MIC. For the n-Hexane extract, the log reduction ranged between 0.56 Log10 and 6.4 Log10 CFU/ml after 8 hr interaction in 1 × MIC and 2 × MIC. In the test for the combination interactions, the checkerboard method revealed synergy of 67% and indifferent of 33%, while the time kill assay detected synergy in 72% and indifferent in 28% of the combinations tested. The synergy detected was not specific to any of the antibiotics or the Gram reaction of the bacteria, and no antagonism was detected. We conclude that the aqueous and n-Hexane extract of the husk of C. nucifera contains potential broad spectrum antibiotics resistance modulating compounds that could be relevant in the treatment of infections caused by these pathogens. In addition, the husk which is being discarded as agro waste will opens up a vista of opportunities for utilization for therapeutic purposes

The stem bark of Peltophorum africanum and Bridelia micrantha are used in South Africa traditional medicine for treatment of intestinal parasites, relieve problems and human immunodeficiency virus/ acquired immune deficiency syndrome (HIV/AIDS). The growing problem of antibiotic resistance by Helicobacter pylori the major etiological agent in gastritis, gastric cancer, peptic and gastric ulcer demands the search for novel compounds from plant based sources. This study was aimed to determine the antimicrobial activity of five solvent (ethylacetate, acetone, ethanol, methanol and water) extracts of the stem bark of P. africanum and B. micrantha on clinical strains of H. pylori in a bid to identify potential sources of cheap starting materials for the synthesis of new drugs. H. pylori strains were isolated from patients presenting with gastric related morbidities at the Livingstone Hospital, Port Elizabeth for endoscopy and confirmed following standard microbiology procedures. The plant extracts including clarithromycin were tested against 31 clinical strains of H. pylori by the agar well diffusion method. The most potent extract was evaluated by the microdilution method to determine the Minimum Inhibitory Concentration (MIC50&90), followed by the rate of kill. Preliminary phytochemical analysis was carried out. The one way ANOVA test was used to statistically analyse the results. All the extracts demonstrated anti-H. pylori activity with zone diameters of inhibition that ranged from 0 to 23 mm for the extracts and 0 to 35 mm for clarithromycin. Marked susceptibility (100%) was recorded for the ethyl acetate extract of P. africanum (P. afr. EA) and the acetone extract of B. micrantha (B. mic. A), which were statistically significant (P < 0.05) compared to all other extracts and clarithromycin. For B. micrantha ethyl acetate extract, 93.5 percent susceptibility was observed while for the control iv antibiotic, clarithromycin it was 58.1 percent. The MIC50 ranged from 0.0048 to 0.313 mg/mL for P. afr. EA, and from 0.0048 to 0.156 mg/mL for B. mic. EA; MIC90 ranged from 0.156 mg/mL to 0.625 mg/mL and 0.0048 to 2.5 mg/mL for P. afr. EA and B. mic. EA respectively. There was a significant statistical difference observed in potency of both P. afr. EA and B. mic. A compared to the two antibiotics (P < 0.05). One hundred percent killing by P. afr EA was observed at 0.05 mg/mL (½ x MIC) and 0.2 mg/mL (2 x MIC) in 66 h for strain PE466C and PE252C respectively. For B. mic. EA, 100 percent killing effect of both strains (PE430C and PE369C) was observed at 0.1 mg/mL (2 x MIC) in 66 h. Qualitative phytochemical analysis confirmed the presence of alkaloids, flavonoids, steroids, tannins and saponins in the ethyl acetate extracts of both plants, which could be a potential template of lead molecule for the design of new anti- Helicobacter pylori therapies.

In practice, most approaches for text error detection and correction are based on a conventional domain-dependent background dictionary that represents a fixed and static collection of correct words of a given language and, as a result, satisfactory correction can only be achieved if the dictionary covers most tokens of the underlying correct text. Again, most approaches for text correction are for only one or at best a very few types of errors. The purpose of this thesis is to propose an unsupervised approach to detecting and correcting text errors, that can compete with supervised approaches and answer the following questions: Can an unsupervised approach efficiently detect and correct a text containing multiple errors of both syntactic and semantic nature? What is the magnitude of error coverage, in terms of the number of errors that can be corrected? We conclude that (1) it is possible that an unsupervised approach can efficiently detect and correct a text containing multiple errors of both syntactic and semantic nature. Error types include: real-word spelling errors, typographical errors, lexical choice errors, unwanted words, missing words, prepositional errors, article errors, punctuation errors, and many of the grammatical errors (e.g., errors in agreement and verb formation). (2) The magnitude of error coverage, in terms of the number of errors that can be corrected, is almost double of the number of correct words of the text. Although this is not the upper limit, this is what is practically feasible. We use engineering approaches to answer the first question and theoretical approaches to answer and support the second question. We show that finding inherent properties of a correct text using a corpus in the form of an n-gram data set is more appropriate and practical than using other approaches to detecting and correcting errors. Instead of using rule-based approaches and dictionaries, we argue that a corpus can effectively be used to infer the properties of these types of errors, and to detect and correct these errors. We test the robustness of the proposed approach separately for some individual error types, and then for all types of errors. The approach is language-independent, it can be applied to other languages, as long as n-grams are available. The results of this thesis thus suggest that unsupervised approaches, which are often dismissed in favor of supervised ones in the context of many Natural Language Processing (NLP) related tasks, may present an interesting array of NLP-related problem solving strengths.

Submitted by Reginaldo Soares de Freitas (reginaldo.freitas@ufv.br) on 2015-11-06T13:56:13Z No. of bitstreams: 1 texto completo.pdf: 4206218 bytes, checksum: 1ab8811fdfb49e96c8403829a66a38e2 (MD5) / Made available in DSpace on 2015-11-06T13:56:13Z (GMT). No. of bitstreams: 1 texto completo.pdf: 4206218 bytes, checksum: 1ab8811fdfb49e96c8403829a66a38e2 (MD5) Previous issue date: 2013-07-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Diante do contínuo aumento mundial de doenças como o câncer do tipo melanoma e infecções causadas por Staphylococus aureus resistentes à meticilina, a pesquisa por novos fármacos tem ganhado importância cada vez maior no mundo científico. O Brasil é um dos países com maior biodiversidade vegetal no mundo. Entretanto, muito pouco ainda se sabe sobre as propriedades terapêuticas desse patrimônio vegetal. O objetivo desse estudo foi avaliar, in vitro, o potencial citotóxico dos extratos hidroalcoólcios de Inga subnuda subsp. Luschnathiana (Benth.) T.D.Penn. (ingá) e Rollinia dolabripetala (Raddi) R.E. Fr. (araticum, marolo), dos flavonóides naringina e morina e de xantonas, sobre o câncer de pele do tipo melanoma, realizando um comparativo com a atividade do fármaco comercial 5-Fluoracil (5-FU). Os extratos também tiveram sua eficácia testada, in vitro, quanto ao seu potencial antioxidativo e potencial bactericida principalmente em cepas Gram-positivas. A avaliação da citotoxicidade foi baseada na linhagem B16F10 submetida ao ensaio colorimétrico do MTT. O extrato de I. subnuda apresentou ação bactericida contra todas as cepas bacterianas testadas, enquanto o extrato de R. dolabripetala apresentou atividade apenas contra S. aureus ATCC 29213. O extrato de I. subnuda desempenhou atividade antioxidante estatísticamente maior (p < 0,05) que os extratos de Gingko biloba (controle) e R. dolabripetala, tanto no teste do DPPH quanto no de peroxidação lipídica. No teste de citotoxicidade, a naringina foi considerada uma substância inativa para este tipo de câncerpatologia e a morina promoveu maior citotoxicidade no período de 72 horas (98,48% ± 0,71) com diferença significativa em relação ao controle (α < 0,05). Contudo, assim como a 1,7- dihidroxixantona, o potencial uso terapêutico da morina dificilmente será considerado devido a alta concentração necessária para desempenhar atividade citotóxica relevante (1,25x103 μg/mL). Assim, o extrato de ingá foi considerado o mais efetivo por, no tempo de 24, 48 e 72 horas, desencadear mais de 80% de citotoxicidade com a menor concentração (78,13 μg/mL). Os resultados indicam que ambos os extratos apresentam atividade antioxidante, antibacteriana e citotóxica, mas estudos posteriores são necessários para uma melhor compreensão das promissoras atividades biológicas dos extratos. / The increasing world-wide rates of deseases such as melanoma skin cancer and infections caused by methicillin-resistant strains of Staphylococcus aureus has historically attracted the attention of researchers about the development of new drugs. Brazil has one of the world's greatest biodiversity; nevertheless, the majority of plants with therapeutic potential still unclear. The aim of present study was to evaluate the in vitro antiproliferative activity of naringin, morin, xanthones and hydroalcoholic extracts of Inga subnuda subsp. Luschnathiana (Benth.) T.D.Penn. and Rollinia dolabripetala (Raddi) R.E. Fr., compared of Fluorouracil (5-FU). Both extracts were evalueted about their antioxidant capability and about their antimicrobial activity mainly against Gram- positive bacterias. The cytotoxicity test methodology was based on the MTT colorimetric assay and was performed on B16-F10 melanoma cells. The I. subnuda extract was effective against the three strains of bacteria, whereas the R. dolabripetala extract was effective just against S. aureus ATCC 29213. The I. subnuda extract performed a statistical higher antioxidant activity (p < 0,05) than the Gingko biloba (control) and R. dolabripetala extracts in both antioxidative tests. The naringin was considered as inactive substance against this cancer cell and the morin bring about the higher citotoxity in 72 hours (98,48% ± 0,71) with statistically significant difference compared to the control group (α < 0,05). On the other hand, as 1,7-dihydroxyxanthone, the therapeutic use of the morin for this porpose could be disregarded due the high concentration required for relevant citotoxity activity (1,25x10 3 μg/mL of both). Thus, the I. subnuda extract was regarded as the most effective tested substance by his up to 80% citotoxity capability under all treatment periodo (24, 48, 72 hours). Moreover, the citotoxity test of I. subnuda extract required the lowest concentration for a effective result (78,13 μg/mL). The experiments reported tha both extracts play a role as an antioxidant, an antibacterial and a cytotoxic agent. However, further studies are required for a better understanding about their biological activities.