The sexually transmitted diseases in Mexico have a high prevalence in the population, mostly due to the adopted habits on practicing sexuality, like the absence of protection or multiple sexual partners. Between the most known ITS, three are distinguished for being quite common and highly infectious: human papillomavirus, gonorrhea and chlamydia. On the absence of a clinical test with high specificity and sensibility rates, the use of a molecular technique for the detection of these three diseases is proposed. For this study, 50 genital mucosa samples were used, from a population who suspected from previous infection. The DNA was extracted from the samples and later amplified with a PCR kit. The obtained data was analyzed with the X2 test. The obtained results show that half of the sample population (48%) is infected with one STI, predominantly high risk HPV (59% of the infected subjects). No relationship between HPV and N. gonorrhoeae or C. trachomatis was found. RESUMEN EN ESPA��OL. / Las ETS en M��xico tienen una prevalencia alta en la poblaci��n, sobre todo por las costumbres adoptadas al ejercer la sexualidad, como es la falta de protecci��n o promiscuidad. / (cont.) Entre las ETS m��s conocidas, se distinguen tres por ser muy comunes y altamente infecciosas: papiloma humano, gonorrea y clamidia. Ante la falta de una prueba con ��ndice de especificidad y sensibilidad alto, se propone el uso de una t��cnica molecular para la detecci��n de estas tres enfermedades en una sola prueba, antes de que lleguen a provocar infecci��n. Para este estudio se utilizaron 50 muestras de secreciones genitales de una poblaci��n con sospecha de infecci��n, se les extrajo el ADN y luego se amplific�� con un kit de PCR. A los datos se les analiz�� con la prueba de X2. Como resultados se encuentra que la mitad de la poblaci��n muestra (48%) se encuentra infectada con alguna ETS, predominantemente VPH de alto riesgo (59% de los pacientes infectados). Sin embargo, no se encontr�� alguna relaci��n entre VPH y N. gonorrhoeae o C. trachomatis..

The southern African population of bearded vultures, Gypaetus barbatus, is declining rapidly and plans for windfarm developments within the core of this species' range threaten to accelerate the population's passage to extinction. As an insurance against such a situation a reintroduction has been proposed to establish a second bearded vulture population within their historic South African range. Before such a scheme could occur suitable areas, if present, will first need to be identified and the requirements and best implementation strategy will need to be determined. Therefore, the aims of this study were (1) to identify the most suitable site for such a reintroduction and (2) to provide some insight into the potential outcomes of different release strategies. Habitat modelling and GIS techniques were used to identify potential reintroduction sites, most notably based on the presence of cliffs. Potential reintroduction sites were then compared based on a range of habitat attributes, of which the amount of human settlement and power line density was considered most important. Five potential reintroduction sites were identified with the two highest ranking sites situated mostly within the Eastern Cape Province. Various release strategies ranging from captive breeding prioritization to release prioritization were modelled using stochastic modelling software. Results indicated that straight releases, without any captive breeding support, had a high probability of failure (defined <34 individuals) ranging between 78.3 and 95.7% across different mortality scenarios over a 30 year period. Supplementation from captive breeding reduced this to between 25.5 and 49.8%. Although it is important for mortality rates to be lower at the reintroduced site this study shows that a reintroduction initiative can be valuable even if this is not the case, as a reintroduction initiative can reduce the probability of extinction (one sex remains) of the species in southern Africa after 50 years by approximately 30%. This study concludes that a captive breeding programme is imperative for the success of the reintroduction and is a prudent measure considering the continuing decline of the species. However, a complementary study examining release sites on the ground as well as stakeholder attitudes and the socio-economic impacts of bearded vultures will be required before the reintroduction can be implemented.

No description available.

It is recognized that microbial transformations are the primary mechanism of organic contaminant removal in natural and constructed wetland systems. However, not much is known about urban wetland microbial communities or their functional capacity to process contaminants. The objective of this research was to first characterize the physiological and phylogenetic diversity of microbial communities of different urban wetland types using the BIOLOG™ method and through DGGE of 16S rRNA sequences. The capacity of urban wetlands to attenuate model chlorinated aromatic compounds (2,4-D and 3-CBA) was assessed by UPLC biodegradation and 14C mineralization experiments. Toxicity tests were conducted to assess microbial tolerance to pollutant addition. In general, results indicate that urbanization has a homogenizing effect on microbial community structure and distribution within urban wetland systems, regardless of type. Urban wetlands also appear to have a limited capacity to remove chlorinated organic pollutants. Microbial community tolerance to chlorinated organic pollutants is relatively high, whereas heavy metal tolerance was found to coincide with history of contaminant exposure. / UOIT

In the face of ever increasing atmospheric CO₂ a better understanding of soil properties and processes and the effect of management practices, such as the application of nitrogen fertilizer is of importance and could potentially improve our ability to sustainably manage forestry systems. With that in mind this study was conducted in order to investigate the effects of tree species and fertilization on soil carbon and the soil microbial community. To this end, soil from fertilized and unfertilized plots at Berwick forest, under stands of Pinus radiata and Sequoia sempervirens at Hanmer and under six different tree species at Holt forest was sampled. Two glasshouse pot trials were established using soil collected from the Hanmer and Berwick forest sites and seedlings of Pinus radiata, Sequoia sempervirens, and Eucalyptus nitens were grown. Soil properties were determined from both the field sites and pot trials including soil organic matter, carbon, nitrogen, and microbial biomass by chloroform fumigation extraction. Biolog ecoplates were used to determine the relative differences in diversity based on substrate utilization patterns of the soil microbial communities in soil sampled from the glasshouse pot trials. Soil microbial biomass carbon, nitrogen and the ratio of microbial biomass carbon:nitrogen differed significantly between Pinus radiata and the other tree species sampled at Holt forest. Significant effects of fertilization and tree species on soil carbon and microbial biomass were observed in both pot trials. Soil carbon differed significantly between Eucalyptus nitens and both Pinus radiata and Sequoia sempervirens in the first pot trial and relative to both, E. nitens contributed significantly more carbon. No significant effect of either fertilization or tree species on the catabolic diversity of the soil microbial community in both glasshouse pot trials was observed. The results demonstrated the effects that fertilization and tree species can have. Particularly notable was the short-time period in which tree species effects became apparent coupled with the absence of any aboveground inputs to the soil.

Submitted by MILENA TAVARES LIMA null (milena.tavares@hotmail.com) on 2018-02-22T20:53:15Z No. of bitstreams: 1 tese.docx: 10715432 bytes, checksum: 43d05c474d46b9a07105fe43fdc08920 (MD5) / Rejected by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: O arquivo para ser submetido no repositório deve ser em formato pdf como descrito no item 13 do tutorial do repositório: 13. Para enviar o arquivo contendo sua dissertação ou tese é necessário que:  o arquivo esteja no formato Portable Document Format (PDF);  o arquivo não esteja protegido;  o trabalho (dissertação ou tese) esteja reunido em um único arquivo, inclusive os apêndices e anexos. Agradecemos a compreensão on 2018-02-23T13:51:33Z (GMT) / Submitted by MILENA TAVARES LIMA null (milena.tavares@hotmail.com) on 2018-02-23T13:57:19Z No. of bitstreams: 1 Tese_Milena_Tavares_Lima_Constancio.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-02-23T17:32:08Z (GMT) No. of bitstreams: 1 constancio_mtl_dr_jabo.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) / Made available in DSpace on 2018-02-23T17:32:08Z (GMT). No. of bitstreams: 1 constancio_mtl_dr_jabo.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) Previous issue date: 2018-01-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O interesse no estudo de comunidades microbianas de ambientes pouco avaliados, impactados e/ou extremos tem aumentado significativamente. Dentre os ambientes estudados, encontram-se as águas residuais de áreas de mineração. Com o grande número de cavas e lagoas de rejeitos gerados através da atividade mineradora e o pouco estudo deste tema no Brasil, foi desenvolvido este trabalho, onde avaliamos a taxonomia e capacidade funcional da comunidade microbiana. As amostras de água foram coletadas de uma cava de mineração e uma lagoa de rejeitos de uma região anteriormente utilizada para extração de minério de ferro no Centro de Biodiversidade (CeBio) da empresa VALE/SA, em Sabará/MG. Análises do perfil de atividade metabólica indicaram um excelente desempenho quanto à degradação de diferentes compostos. Além disso, o isolamento com métodos tradicionais de cultivo mostrou que algumas bactérias apresentam capacidade em produzir diferentes enzimas de interesse biotecnológico. O DNA foi extraído e sequenciado através de técnicas metagenômicas, o sequenciamento do gene de 16S rRNA foi realizado na plataforma Ion PGM™. Esta análise, além de revelar a taxonomia da comunidade presente na água da cava e lagoa, identificou o perfil funcional indicando enriquecimento de subsistemas importantes para ambas as amostras. Adicionalmente para a água da cava de mineração, foi realizado o sequenciamento do DNA total na plataforma Ion Proton™, que através de análises com o banco de dados SEED revelou genes associados à manutenção celular e ao ciclo do nitrogênio, sugerindo que a comunidade microbiana está bem adaptada ao processo de recuperação da área. Além disso, as ORfs preditas do metagenoma foram utilizadas para uma análise no banco de dados BacMet, que revelou uma abundância de genes relacionados a resistência a metais. Assim, nossos dados expandem os conhecimentos sobre a estrutura e capacidade funcional das comunidades microbianas de ambientes aquáticos impactados, fornecendo uma melhor compreensão do papel dos micro-organismos em processos de remediação natural. / The interest in the study of microbial communities of low evaluated, impacted or extreme environments has increased significantly. Among the studied environments, there is the wastewater from mining areas. Due to the large number of reject pits and lagoons generated by the mining activity and the lack of study of this theme in Brazil, this study was developed to evaluate the taxonomy and functional capacity of the microbial community. The water samples were collected from a mining pit and a reject lagoon from a region formerly used for iron extraction at the Biodiversity Center (CeBio) from VALE/SA, in Sabará/MG. Analyzes of the metabolic activity profile indicated an excellent performance regarding the degradation of different compounds. Moreover, the isolation with traditional methods of culture showed that some bacteria have the capacity to produce different enzymes of biotechnological interest. The DNA was extracted and sequenced using metagenomic techniques, the 16S rRNA gene sequencing was performed on the Ion PGM™ platform. This analysis, in addition to revealing the taxonomy of the community present in the water of the pit and the lagoon, identified the functional profile indicating enrichment of important subsystems for the studied samples. In addition to the water from the mining pit, the total DNA sequencing was carried out on the ION Proton™ platform, which, through analysis with the SEED database, revealed genes associated with cell maintenance and the nitrogen cycle, suggesting that the microbial community is well adapted to the recovery process of the area. Also, the predicted ORfs from metagenomic were used for an analysis in the BacMet database that revealed an abundance of genes related to resistance to metals. Thus, our data expand the knowledge about the structure and functional capacity of microbial communities in impacted aquatic environments, providing a better understanding of the role of microorganisms in natural remediation processes. / FAPESP: 2014/07592-3

The need for new antibiotics has been highlighted recently with the increasing pace of emergence of drug resistant pathogens (MRSA, XDR-TB, etc.). Modification of existing antibiotics with the additions of side chains or other chemical groups and genomics based drug targeting have been the preferred method of drug development at the corporate level in recent years. These approaches have yielded few viable antibiotics and natural products are once again becoming an area of interest for drug discovery. We examined the antimicrobial "Red Soils" of the Hashemite Kingdom of Jordan that have historically been used to prevent infection and cure rashes by the native peoples. Antimicrobial producing bacteria were present in these soils and found to be the reason for their antibiotic activity. After isolation, these bacteria were found to excrete their antimicrobials into the liquid culture media which we could then attempt to isolate for further study. Adsorbent resins were employed to capture the antimicrobial compounds and then elute them in a more concentrated solution. As part of a drug discovery program, we sought a way to quickly characterize other soils for potential antibiotic producing bacteria. The community level physiologic profile was examined to determine if this approach would allow for a rapid categorizing of soils based on their probability of containing antimicrobial producing microorganisms. This method proved to have a high level of variability that could not be overcome even after mixing using a commercial blender. The role of these antimicrobial producing bacteria within their natural microbial community has largely been confined to microbe-plant interactions. The role of antimicrobial-producing microorganisms in driving the diversity of their community has not been a focus of considerable study. The potential of an antimicrobial-producing bacterium to act as a driver of diversity was examined using an artificial microbial community based in a sand microcosm. The changes in the microbial assemblage indicate that antimicrobial-producing bacteria may act in an allelopathic manner rather than in a predatory role. / Ph. D.

Biofumigation is an important crop protection practice that uses a plant’s natural defence mechanisms to control agricultural crop pathogens and diseases. Glucosinolates are volatile compounds found in most Brassica species and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. Research suggests that biofumigation is a good alternative to chemical fumigants as it is effective in controlling plant pests but with lower health and environmental risks. Several studies have confirmed the effectiveness of the breakdown products, especially isothiocyanates, as fungicidal, bactericidal and nematicidal products against a series of plant pests. However, very little information is available on the effects of glucosinolates and its breakdown products on non-target and beneficial soil organisms. Negative effects on beneficial soil organisms can have serious negative impacts on soil quality especially when essential ecosystem functions such as nutrient cycling and soil bioturbation are affected. Three biofumigants, broccoli, mustard and oilseed radish, and two chemical fumigants, metham sodium and cadusafos, were investigated for possible effects on non-target and essential soil organisms such as earthworms and the soil microbial community. Sublethal endpoints, including growth and reproductive success of the earthworms, were monitored. The genotoxicity of the biologically active compounds found in the fumigants, towards earthworms, was evaluated by means of the comet assay. The DNA damage was quantified by tail intensity parameters. Furthermore, the changes in the soil microbial community function and structure were evaluated by means of community level physiological profiling (CLPP) and phospholipid fatty acid (PLFA) analyses respectively. All exposures were done in artificial soil prepared according to the OECD standard guidelines. In the biofumigant treated soils, results varied and different effects were observed on the non-target soil organisms. Broccoli reduced cocoon production and the number of hatchlings while mustard induced more DNA strand breaks in earthworm cells compared to the control. All the biofumigants stimulated microbial growth but broccoli and oilseed radish changed the microbial functional diversity. Mustard had no lasting effect on the functional diversity but altered the microbial community structure. The chemical fumigants had a marked negative impact on the survival, growth, reproduction and the genotoxicity of the earthworms with metham sodium causing greater harm than cadusafos. The effects on the microbial community varied. Both chemicals had an inhibitory effect on the microbial growth in terms of the viable biomass determined by PLFA and the average well colour development in the Biolog™ Ecoplates. No lasting effects were observed in the community structure. Overall, cadusafos had a more pronounced effect on the microbial community functional diversity than metham sodium. Results indicated that each bioindicator species illustrates effects at their own level of organisation / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Biofumigation is an important crop protection practice that uses a plant’s natural defence mechanisms to control agricultural crop pathogens and diseases. Glucosinolates are volatile compounds found in most Brassica species and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. Research suggests that biofumigation is a good alternative to chemical fumigants as it is effective in controlling plant pests but with lower health and environmental risks. Several studies have confirmed the effectiveness of the breakdown products, especially isothiocyanates, as fungicidal, bactericidal and nematicidal products against a series of plant pests. However, very little information is available on the effects of glucosinolates and its breakdown products on non-target and beneficial soil organisms. Negative effects on beneficial soil organisms can have serious negative impacts on soil quality especially when essential ecosystem functions such as nutrient cycling and soil bioturbation are affected. Three biofumigants, broccoli, mustard and oilseed radish, and two chemical fumigants, metham sodium and cadusafos, were investigated for possible effects on non-target and essential soil organisms such as earthworms and the soil microbial community. Sublethal endpoints, including growth and reproductive success of the earthworms, were monitored. The genotoxicity of the biologically active compounds found in the fumigants, towards earthworms, was evaluated by means of the comet assay. The DNA damage was quantified by tail intensity parameters. Furthermore, the changes in the soil microbial community function and structure were evaluated by means of community level physiological profiling (CLPP) and phospholipid fatty acid (PLFA) analyses respectively. All exposures were done in artificial soil prepared according to the OECD standard guidelines. In the biofumigant treated soils, results varied and different effects were observed on the non-target soil organisms. Broccoli reduced cocoon production and the number of hatchlings while mustard induced more DNA strand breaks in earthworm cells compared to the control. All the biofumigants stimulated microbial growth but broccoli and oilseed radish changed the microbial functional diversity. Mustard had no lasting effect on the functional diversity but altered the microbial community structure. The chemical fumigants had a marked negative impact on the survival, growth, reproduction and the genotoxicity of the earthworms with metham sodium causing greater harm than cadusafos. The effects on the microbial community varied. Both chemicals had an inhibitory effect on the microbial growth in terms of the viable biomass determined by PLFA and the average well colour development in the Biolog™ Ecoplates. No lasting effects were observed in the community structure. Overall, cadusafos had a more pronounced effect on the microbial community functional diversity than metham sodium. Results indicated that each bioindicator species illustrates effects at their own level of organisation / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Carrion decomposition is an essential ecosystem function as it is an important component of nutrient cycling. Carrion decomposition has primarily been attributed to insect consumption, with little attention given to microbial communities or their potential interactions with insects. The first objective was to use passive insect-trapping methods to assess primary colonizer communities on swine carcasses between two treatments: 1) carrion with access to insects and 2) carrion excluded from insect access for five days using exclusion cages. Despite similarities between succession patterns within each treatment, carcasses initially exposed to insects had significantly fewer insect taxa. Therefore, collections of adult insect communities associated with carrion are promising as an indication of whether or not there has been a delay in insect colonization of a resource. There has yet to be a study documenting bacterial communities during carrion decomposition. The second objective was to describe bacterial community succession and composition during decomposition in the presence and absence of naturally occurring insects. Total genomic DNA was used to identify bacterial community composition via a modified bacterial tagged encoded FLX amplicon pyrosequencing. I obtained 378,904 sequences and documented distinct bacterial community successional trajectories associated with insect access and exclusion carcasses. By the fifth day of decomposition, Proteus was the dominant (72%) bacterial genus on exclusion carcasses while Psychrobacillus (58%) and Ignatzschineria (18%) were dominant bacterial genera on insect carcasses. These data are the first to document bacterial community composition and succession on carrion. My final objective was to assess microbial community function in response to carrion insect colonization using metabolic profiling. I characterized microbial community metabolic function in the presence and absence of the primary necrophagous insects. I documented significant microbial community metabolic profile changes during active decomposition of carcasses. Mean carcass microbial community metabolic function with insect access continuously decreased over decomposition during both field seasons. Thus demonstrating microbial metabolic activity may have discriminatory power to differentiate early and late stages of decomposition. Overall, my data contributes to an understudied area of microbial research important to organic matter decomposition, forensic entomology, and microbial-insect ecological interactions.