Este trabalho procurou definir a existência de espécies emergentes de micoplasmas (Mycoplasma genitalium, M. fermentans e M. penetrans) em indivíduos HIV-positivos e indivíduos com queixa clínica de retrite, por não haver dados a esse respeito no Brasil. A pesquisa das espécies mais conhecidas (M. hominis e Ureaplasma urealyticum), cuja metodologia para sua detecção já está bem estabelecida, proporcionou uma visão global da participação das espécies de importância clínica conhecidas até o momento. Foram avaliadas amostras de raspado uretral e primeiro jato urinário de 106 indivíduos HIV-positivos e 110 indivíduos HIV-negativos com DST, no total de 212 e 220 amostras do primeiro e do segundo grupo, respectivamente. Deste modo, foram submetidas a análise 432 amostras para pesquisa de micoplasmas por cultura e PCR. Para pesquisa de anticorpos séricos anti- M. penetrans, foram obtidas amostras de soro de cada indivíduo dos dois grupos estudados, bem como de 86 doadores de sangue saudáveis para cálculo do limite de reatividade do ELISA. As taxas de infecção obtidas em nosso estudo, considerando os resultados do cultivo e da PCR, nos indivíduos HIV-positivos, foram: 2,8% para a espécie M. genitalium, 5,7% para M. fermentans, e 6,6% para M. penetrans. Nos indivíduos com queixa de DST, os valores encontrados foram: 9,1% para M. genitalium e 0,9% para M. fermentans, não tendo sido observado nenhum caso positivo para M. penetrans. Estes últimos resultados revelam que, apesar da pouca importância dada até então às três espécies, estas responderam, no total, por taxas de infecção de 15,1% e 10,0%, respectivamente, nos grupos HIV-positivo e DST. Estas taxas são bastante significativas quando comparadas com as observadas para as espécies M. hominis e U. urealyticum, ou seja, 26,4% e 14,5% em cada grupo, respectivamente. Nossos dados demonstraram uma freqüência significativa de anticorpos anti- M. penetrans: 25,5% no grupo de indivíduos HIV-positivos, 17,3% no grupo de DST, e 2,3% no grupo controle para IgG; 3,8%, 9,1% e 5,8% para IgM, e 15,1%,17,3% e 1,2% para IgA, respectivamente. Estes dados, aliados aos resultados de PCR, confirmam a presença de M. penetrans em nosso meio, infectando principalmente os indivíduos HIV-positivos. A presença desta espécie e também de M. fermentans, detectadas por PCR, denotam que muito pouco se conhece sobre o envolvimento destes micoplasmas com o HIV e que ainda não lhes é dada a devida importância na rotina médica. A associação definitiva de sua infecção com a progressão da AIDS, ainda a ser alcançada, e a demonstração em nossa população da infecção por M. genitalium em indivíduos com queixa de uretrite não-gonocócica, abre novos horizontes para o estudo da participação dos micoplasmas na etiologia das doenças humanas no país. / The aim of this work was to define the existence of emergent mycoplasma species, such as Mycoplasma genitalium, M. fermentans and M. penetrans, in HIV-1-infected and HIV-negative individuals with Sexually Trasmitted Diseases (STD), because there are no data concerning this subject in Brazil. The research about well-known species, such as Ureaplasma urealyticum and M. hominis, of wich detection techniques are well established, provided a comprehensive view of the participation of Mollicutes in human disease. We evaluated urethral swabs and urine samples from 106 HIV-1-infected and 110 HIV-negative individuals with clinical symptoms of non-gonococal urethritis, summing up 212 samples from the first group, and 220 from the second. Therefore, we tested a total of 432 samples to mycoplasma detection by culture and PCR. To detection of serum antibodies to M. penetrans, we obtained blood samples of each patient from the groups studied, as well as from 86 healthy blood donors to calculate the ELISA (Enzime Linked Immuno Sorbent Assay) cut-off value. The rates of infection obtained in our study, considering the culture and PCR results, in the HIV-infected individuals were: 2.8% for M. genitalium, 5.7% for M. fermentans, and 6.6% for M. penetrans. In the STD group, the rates were: 9.1% for M. genitalium and 0.9% for M. fermentans. We did not observed any positive case for M. penetrans in this group, and no positive case for M. pneumoniae in both groups, in spite of the existence of some reports of its detection in the genitourinary tract. This results reveal that they account, in the total, for infection rates of 15.1% and 10%, respectively, in the HIV-infected and the STD groups. These rates are very significant when compared to the ones observed for the species M. hominis and U. urealyticum, i.e., 26.4% and 14.5% in each group, respectively. Our results also show a significant antibody frequency to M. penetrans: 25.5% in the HIV-infected group, 17.3% in the STD group, and 2.3% in the control group for IgG; 3.8%, 9.1% and 5.8% for IgM, and 15.1 %, 17.3% and 1.2% for IgA, respectively. These data, together with the PCR results, confirm the presence of M. penetrans in our population, mainly infecting HIV- positive patients. The presence of this species, and also of M. fermentans, detected by PCR, demonstrate that very little is known about the role of this mycoplasma species in HIV infection, and they are not given the appropriate importance in clinical routine in Brazil. The definitive association between mycoplasma infection and the progression of AIDS is still to be established. The demonstration of M. genitalium infection in individuals with clinical symptoms of non-gonococal urethritis in our population, may open new insights in the study of the role of mycoplamas in the ethiology of human diseases in this country.

Thesis (Master of Engineering in Chemical Engineering)--Cape Peninsula University of Technology, 2018. / Approximately 9 million tonnes of food waste is generated annually in South Africa. Its treatment, including treatment of confectionery waste, is costly because of the high chemical oxygen demand (COD) loads; as a result much of this waste is sent to landfill. South Africa’s confectionery industry contributes to a significant proportion of the country’s economy. Among the confectionery waste entering landfills are defective material, expired sweets and returns. This high COD waste can create breeding grounds for pathogenic microorganisms and anaerobic methanogens, causing negative environmental impacts. Part of the Department of Science and Technology (DST) Waste Research, Development and Innovation (RD&I) roadmap initiative is to minimise waste entering landfills by identifying waste sources from which to produce value that will contribute to social and economic growth. Confectionery waste has a high sugar content which can be used for feedstock to bioprocesses. By placing this bioproduction into a waste biorefinery framework, bio-based raw materials can be used to produce competitively priced products with low environmental impact, thereby optimising remediation and value generation simultaneously. Ongoing research at the Centre for Bioprocess Engineering Research (CeBER) at the University of Cape Town has shown that a wastewater biorefinery approach can use wastewater as feedstock for the generation of products of value. Previous studies have investigated potential products of value based on nutrient loads found in wastewater as well as the nature of the product. Among the organisms selected was the Bacillus species, producing the potential product poly-γ-glutamic acid (PGA), an extracellular poly-amino acid when there is an excess of nutrients. Similarly, this product could potentially be produced from sugar-rich waste candy. The aim of this study was to explore the use of hard candy waste as a feedstock for PGA, and Bacillus licheniformis JCM 2505 was selected as it was characterised in terms of the nutrients needed. The most attractive attribute of this strain was that it did not need L-glutamic acid to synthesise PGA but could do so from sugar. L-glutamic acid is costly. Using a cheaper nitrogen alternative would make the process more cost effective. To investigate this potential, the confectionery waste was characterised to identify the nutrients, namely, sugars, organic nitrogen and key trace elements needed for cell function and PGA production. Results showed that the nitrogen content and trace element concentrations were insignificant, as it was determined that the waste consisted mostly of sucrose. This therefore had to be supplemented with a basal medium containing the supplementation needed for cell function and PGA production. The growth of B. licheniformis was profiled in Erlenmeyer shake flasks using candy waste supplemented with the basal medium, with sucrose supplemented with basal medium as a control. The results showed similar trends on candy waste and sucrose.

O lodo de esgoto é um resíduo semissólido, pastoso e de natureza predominantemente orgânica gerado em estações de tratamento de esgotos. Esse resíduo pode exibir características indesejáveis, como instabilidade biológica, possibilidade de transmissão de patógenos e grandes volumes. O lodo é uma importante fonte de matéria orgânica, micro e macronutriente. Quando aplicado ao solo pode conferir maior capacidade de retenção de água, maior resistência à erosão, diminuição do uso de fertilizantes minerais e, possivelmente, propiciando maior resistência da planta aos fitopatógenos. No entanto, a presença de metais pesados e microrganismos patogênicos no biossólido podem comprometer o seu uso agrícola. A destinação deste lodo residual que é gerado nas estações de tratamento de esgotos é um grande problema ambiental para as empresas de saneamento, públicas ou privadas e existem possibilidades de tecnologias para o uso sustentável do lodo. / Sewage sludge is a semisolid, pasty and predominantly organic nature residual generated in sewage treatment plants. This waste may exhibit undesirable characteristics such as biological instability, possibility of pathogen transmission and large volumes. The sludge is an important source of organic matter, micro and macronutrients. Upon applying it to the soil it makes water holding capacity higher, resistance to erosion greater, decreased use of mineral fertilizers, and it may provide higher plant resistance to pathogens. However, the presence of heavy metals and pathogens in biosolids could compromise its agricultural use. The disposal of the residual sludge that is generated in sewage treatment plants is a major environmental problem for public or private water utilities, but it may also mean possibilities of technologies for sustainable use of sludge.

Microbial infections of medical implants occur in 10% of the more than 20 million surgical procedures carried out annually in the United States. The additional treatments required to address these infections generate more than $11 billion in additional patient costs, increase recovery time, and decrease overall patient quality of life. As the population ages, the number of necessary and voluntary surgical procedures increases; The rate of infection increases proportionately. While treatments are available, the biofilm mode of growth confers resistance to antimicrobial therapies up to 500 times greater than that of planktonic microbes. Currently, the only guaranteed method of removing an established microbial implant infection is through surgical excision of the implant and surrounding tissues. While removing the original infection, additional colonization and pathogenesis may take place. This research explores the a priori assumption that a medical implant infection cannot occur unless a microbial cell is capable of adhering to the implant surface. From that assumption, the following sections will focus primarily on identifying the necessary and sufficient factors influencing microbial adhesion, discretizing those factors into measurable quantities, and developing methods by which those factors may be mitigated or eliminated. Following is a brief summary of each major topic treated within this research period. Development of a Benchmark System: We have characterized the interactions between Pseudomonas aeruginosa ATCC 10145 and Candida parapsilosis ATCC 90018 using a novel method of cellular immobilization, which emphasizes minimal chemical modification of the cell surface. This research describes the very different force-separation interactions seen between C. parapsilosis and both a common medical implant material (viz., silicone rubber) and a nascent P. aeruginosa biofilm grown on the same material. This study was the first step in developing an ab initio technique which may be used to determine the relative affinity of a microbial cell for an implant material surface. The Role of the Substrate: Microbial adhesion to a medical implant device involves two major components, being the microbe itself, and the substrate to which it adheres. Each of the two has specific and unique surface chemical and textural characteristics which, when combined, allow for microbial colonization and subsequent infection. The goal of this study was to identify correlations between the adhesive strength of Staphylococcus epidermidis to a variety of chemically and texturally distinct substrates, and common surface characterization parameters (e.g., surface roughness and water contact angle). Relationships to adhesive strength did not demonstrate statistically significant or consistent trends. To extend upon the correlation parameters, we have employed a Discrete Bonding Model, which characterizes the surface texture according to Mandelbrot fractal theory. Correlations between the adhesive strength and the observational scale show stronger relationships, indicating a significant contribution of the surface texture to a microbe's ability to colonize a surface. Finding a Surface That Cannot Be Touched: Historically, AFM force-separation curves demonstrating only repulsive behavior on extension of the piezoactuator have been largely ignored, in terms of quantitative modeling of the interactions. In bacterial systems, such behavior describes the majority of the force profiles recorded by the instrument. As a result of the former lack of study, the latter data sets have remained unanalyzed and unanalyzable. Building on existing mathematical models, we have developed an analytical method by which the point of zero separation between a surface (viz., the microbial cell wall) coated with a polymer brush and an AFM probe may be quantitatively identified.

We can now manipulate the genetic material of living organism routinely and cheaply. This has inspired a burgeoning field of synthesis based on DNA as a building block. The development of this new synthetic field has mirrored the trajectory of synthetic organic chemistry from small molecular systems to complex macromolecular assemblies. At first, this field of synthetic biology delivered recombinant proteins that enhanced our understanding of the structure-function relationship of biological macromolecules. Now, as the synthetic tools and analysis methods have come of age, synthetic whole-cell and multicellular systems have come within reach. In Chapter 1 we review the significant advances in DNA synthesis and analysis that have brought us to this point. In this work, we first ask what practical applications will benefit most from the unique qualities of synthetic whole-cell system, such as their ability to replicate, sense and respond with molecular specificity. In Chapter 2, we implement a pathogen detection platform based solely on genetically modified yeast. This approach holds the potential to deliver ultra low-cost sensors that can be used and produced at the point-of-care. In Chapter 3, we develop methods to target these yeast-based sensors for the detection of any peptide biomarker of choice. We next look forward to the potential of synthetic multicellular systems. While natural multicellular systems can be directly manipulated, our ability to rationally build multicellular systems from the bottom-up is still in its infancy. There still remain gaps in the available tools to make and analyze such synthetic systems. In Chapter 4, we leverage the explosion of available genomic databases to uncover a highly extensible set of cell-cell signaling modules. In Chapter 5, we implement ratiometric fluorescent tags to track mixed cell populations in multiplex. Together these components will be useful in implementing and analyzing synthetic communication networks that will be key components of advanced synthetic multicellular systems.

Este trabalho procurou definir a existência de espécies emergentes de micoplasmas (Mycoplasma genitalium, M. fermentans e M. penetrans) em indivíduos HIV-positivos e indivíduos com queixa clínica de retrite, por não haver dados a esse respeito no Brasil. A pesquisa das espécies mais conhecidas (M. hominis e Ureaplasma urealyticum), cuja metodologia para sua detecção já está bem estabelecida, proporcionou uma visão global da participação das espécies de importância clínica conhecidas até o momento. Foram avaliadas amostras de raspado uretral e primeiro jato urinário de 106 indivíduos HIV-positivos e 110 indivíduos HIV-negativos com DST, no total de 212 e 220 amostras do primeiro e do segundo grupo, respectivamente. Deste modo, foram submetidas a análise 432 amostras para pesquisa de micoplasmas por cultura e PCR. Para pesquisa de anticorpos séricos anti- M. penetrans, foram obtidas amostras de soro de cada indivíduo dos dois grupos estudados, bem como de 86 doadores de sangue saudáveis para cálculo do limite de reatividade do ELISA. As taxas de infecção obtidas em nosso estudo, considerando os resultados do cultivo e da PCR, nos indivíduos HIV-positivos, foram: 2,8% para a espécie M. genitalium, 5,7% para M. fermentans, e 6,6% para M. penetrans. Nos indivíduos com queixa de DST, os valores encontrados foram: 9,1% para M. genitalium e 0,9% para M. fermentans, não tendo sido observado nenhum caso positivo para M. penetrans. Estes últimos resultados revelam que, apesar da pouca importância dada até então às três espécies, estas responderam, no total, por taxas de infecção de 15,1% e 10,0%, respectivamente, nos grupos HIV-positivo e DST. Estas taxas são bastante significativas quando comparadas com as observadas para as espécies M. hominis e U. urealyticum, ou seja, 26,4% e 14,5% em cada grupo, respectivamente. Nossos dados demonstraram uma freqüência significativa de anticorpos anti- M. penetrans: 25,5% no grupo de indivíduos HIV-positivos, 17,3% no grupo de DST, e 2,3% no grupo controle para IgG; 3,8%, 9,1% e 5,8% para IgM, e 15,1%,17,3% e 1,2% para IgA, respectivamente. Estes dados, aliados aos resultados de PCR, confirmam a presença de M. penetrans em nosso meio, infectando principalmente os indivíduos HIV-positivos. A presença desta espécie e também de M. fermentans, detectadas por PCR, denotam que muito pouco se conhece sobre o envolvimento destes micoplasmas com o HIV e que ainda não lhes é dada a devida importância na rotina médica. A associação definitiva de sua infecção com a progressão da AIDS, ainda a ser alcançada, e a demonstração em nossa população da infecção por M. genitalium em indivíduos com queixa de uretrite não-gonocócica, abre novos horizontes para o estudo da participação dos micoplasmas na etiologia das doenças humanas no país. / The aim of this work was to define the existence of emergent mycoplasma species, such as Mycoplasma genitalium, M. fermentans and M. penetrans, in HIV-1-infected and HIV-negative individuals with Sexually Trasmitted Diseases (STD), because there are no data concerning this subject in Brazil. The research about well-known species, such as Ureaplasma urealyticum and M. hominis, of wich detection techniques are well established, provided a comprehensive view of the participation of Mollicutes in human disease. We evaluated urethral swabs and urine samples from 106 HIV-1-infected and 110 HIV-negative individuals with clinical symptoms of non-gonococal urethritis, summing up 212 samples from the first group, and 220 from the second. Therefore, we tested a total of 432 samples to mycoplasma detection by culture and PCR. To detection of serum antibodies to M. penetrans, we obtained blood samples of each patient from the groups studied, as well as from 86 healthy blood donors to calculate the ELISA (Enzime Linked Immuno Sorbent Assay) cut-off value. The rates of infection obtained in our study, considering the culture and PCR results, in the HIV-infected individuals were: 2.8% for M. genitalium, 5.7% for M. fermentans, and 6.6% for M. penetrans. In the STD group, the rates were: 9.1% for M. genitalium and 0.9% for M. fermentans. We did not observed any positive case for M. penetrans in this group, and no positive case for M. pneumoniae in both groups, in spite of the existence of some reports of its detection in the genitourinary tract. This results reveal that they account, in the total, for infection rates of 15.1% and 10%, respectively, in the HIV-infected and the STD groups. These rates are very significant when compared to the ones observed for the species M. hominis and U. urealyticum, i.e., 26.4% and 14.5% in each group, respectively. Our results also show a significant antibody frequency to M. penetrans: 25.5% in the HIV-infected group, 17.3% in the STD group, and 2.3% in the control group for IgG; 3.8%, 9.1% and 5.8% for IgM, and 15.1 %, 17.3% and 1.2% for IgA, respectively. These data, together with the PCR results, confirm the presence of M. penetrans in our population, mainly infecting HIV- positive patients. The presence of this species, and also of M. fermentans, detected by PCR, demonstrate that very little is known about the role of this mycoplasma species in HIV infection, and they are not given the appropriate importance in clinical routine in Brazil. The definitive association between mycoplasma infection and the progression of AIDS is still to be established. The demonstration of M. genitalium infection in individuals with clinical symptoms of non-gonococal urethritis in our population, may open new insights in the study of the role of mycoplamas in the ethiology of human diseases in this country.

The most important priority for the management of Australian drinking water catchments is the control of pathogen loads delivered to raw water reservoirs and treatment plant intakes. A process-based mathematical model was developed to estimate pathogen catchment budgets (PCB) for Cryptosporidium, Giardia and E. coli loads generated within and exported from catchments. The model quantified key processes affecting the generation and transport of microorganisms from humans and animal excreta using land use and hydrologic data, and catchment specific information including point sources such as sewage treatment plants and on-site systems. The PCB model was applied in the Wingecarribee catchment, Sydney and used to predict and rank pathogen and indicator loads in dry weather, intermediate (<30 mm in 24 h) and large wet weather events (100mm in 24 h). Sensitivity analysis identified that pathogen excretion rates from animals and humans, and manure mobilisation rates were the most significant factors determining the output of the model. Comparison with water quality data indicated that predicted dry weather loads were generally within 1-2 log10 of the measured loads for Cryptosporidium and E. coli and within 1 log10 for Giardia. The model was subsequently used to predict and rank pathogen and indicator loads for the entire (16 000 km2) Sydney drinking water catchment.

The plant pathogen, Phytophthora dnnamomi, is a cause of dieback disease observed in sclerophyll vegetation in Australia, The effects of P. dnnamomi on flora and fauna were studied at two locations in heathland vegetation near the coastal town of Anglesea, Victoria. The pathogen was isolated from soils beneath diseased heathland plants. The extent of diseased vegetation was assessed by the presence and absence of highly sensitive indicator species, Xanthorrhoea australis and hopogon ceratophyllus. The characteristics of heathland vegetation exhibiting dieback disease associated with the presence of P. dnnamomi were investigated. Plant species richness was similar between diseased and non-diseased areas however diseased areas were characterised by significant declines in the cover and frequency of susceptible species, increases in resistant species and increases in percent cover of open ground. Compared to non-diseased areas, diseased areas exhibited fewer shrub species and decreased shrub cover. The percentage cover and number of species of sedges, lilies and grasses were higher in diseased areas. Structural differences were significant between 0-0.6 m with decreased cover of vegetation in diseased areas. Differences in structure between diseased and non-diseased areas were not as great as expected due to increases in the cover of resistant species. A number of regenerating X australis were observed in post-disease areas. Cluster analysis of floristic data could clearly separate diseased and non-diseased trap stations. The population dynamics and habitat use of eight small mammal species present were compared in diseased and non-diseased areas using trapping and radio-tracking techniques. The number of small mammal species captured in post-disease areas was significantly lower than non-diseased areas. Mean captures of Antechinus stuartii and Rattus fiisdpes were significantly lower in diseased areas on Grid B. Mean captures of Rattus lutreolus were significantly lower in diseased areas on both study grids. Significant differences were not observed in every season over the two year study period. Radio tracking revealed more observations of Sminthopsis leucopus in non-diseased vegetation than in diseased. Cercartetus nanus was frequently observed to utilise the disease susceptible X. australis for nesting. At one location, the recovery of vegetation and small mammal communities in non-diseased and diseased vegetation after fuel reduction burning was monitored for three years post-fire. Return of plant species after fire in both disease classes were similar, reaching 75% of pre-fire richness after three years. Vegetation cover was slower to return after fire in diseased areas. Of the seven small mammal species captured pre-fire, five were regularly captured in the three years after fire. General linear model analysis revealed a significant influence of disease on capture rates for total small mammals before fire and a significant influence of fire on capture rates for total small mammals after fire. After three years, the influence of fire on capture rates was reduced no significant difference was detected between disease classes. Measurements of microclimate indicate that diseased, burnt heathland was likely to experience greater extremes of temperature and wind speed. Seeding of diseased heathland with X. australis resulted in the establishment of seedlings of this sensitive species. The reported distributions of the mamma] species in Victoria were analysed to determine which species were associated with the reported distribution of dieback disease. Twenty-two species have more than 20% of their known distribution in diseased areas. Five of these species, Pseudomys novaehollandiae, Pseudomys fumeust Pseudomys shortridgei, Potorous longipes and Petrogale pencillata are rare or endangered in Victoria. Four of the twenty-two species, Sminthopsis leucopus, Isoodon obesulus, Cercartetus nanus and Rottus lutreolus am observed in Victorian heathlands. Phytophthora cinnamomi changes both the structure and floristics of heathland vegetation in the eastern Qtway Ranges. Small mammals respond to these changes through decreased utilisation of diseased heathland. The pathogen threatens the diversity of species present and future research efforts should be directed towards limiting its spread and rehabilitating diseased areas.

Thesis (Ph. D.)--University of Chicago, Committee on Immunology, June 2003. / Includes bibliographical references. Also available on the Internet.

AbstractFive bacteria, Escherichia coli, Serratia marcescens, Bacillus subtilis,, Bacillus cereus, and Sarcina flava, were tested for establishment in the yellow mealworm, Tenebrio molitor, using a fluorescent screening technique. Through literature research some of the above bacteria were known to establish in the mealworm.The various test bacteria were dyed with Calcofluor white, a fluorescent dye, and introduced to the mealworm by several techniques. Oral injection, anal injection, drop on head, and petri dish methods were attempted. The best method of bacterial entry into the insect was found to be the drop on head. Since few bacteria were ingested by the insect, a quantitative analysis was impossible.It was found that as the dyed bacteria grew, fluorescence decreased. This was substantiated by allowing dyed Sarcina flava to grow at 37 degrees C. in nutrient broth and examining every hour for ten hours.Although this study did not show a definite screening technique for bacterial establishment in Tenebrio molitor Linnaeus, the results from this project could aid researchers in developing such a technique.Ball State UniversityMuncie, IN 47306