Call number: LD2668 .T4 1957 G73 / Master of Science

D.Sc. / Please refer to full text to view abstract

ABSTRACT The present study examined the distribution of six genetic variants (CYP17A1, CYP3A4, SRD5A2, KLK3, AR) in the androgen biosynthesis and metabolism pathway, in 14 sub-Saharan African populations. These polymorphisms have been implicated in several complex diseases, most notably prostate cancer. In order to elucidate the frequencies of these genetic variants, PCR-RFLP and STR based methodologies were employed. Consistent with previously reported results, the frequency distribution of the gene variants in the examined populations greatly coincided with prostate cancer incidence and geographic origin. Populations of African descent had the highest frequencies of the alleles that are postulated to increase risk to prostate cancer, whilst Asian populations had the lowest. Also, there were evident differences in the frequencies of these variants between populations of different continental origin particularly between African and Eurasian populations. The distribution of these genetic variants was further used to assess the spectrum of variation within Africa. The results were greatly aligned with those previously reported, providing further support to the origin and evolution of modern humans from Africa as well as other historic events.

Orientador: Claudio de Oliveira / Banca: Riviane Garcez / Banca: Gleisy Semencio Avelino Santos / Resumo: A ordem Characiformes reúne aproximadamente 1.670 espécies de água doce, das quais pelo menos 1.300 ocorrem no Brasil. Até o momento relativamente poucos estudos genéticos foram realizados com espécies desse grupo, particularmente na Amazônia. Uma questão importante para o momento atual é saber se há algum isolamento entre populações locais separadas por corredeiras ou rápidos na Amazônia, dado o potencial hidrelétrico estimado para esses ambientes. Nesse sentido, no presente estudo, conduzido no âmbito do Programa de Conservação da Ictiofauna da Santo Antônio Energia, foram avaliadas duas populações locais de duas espécies: Pygocentrus nattereri e Potamorhina latior. Empregamos sequências da região controle (D-loop) do DNA mitocondrial, pela maior taxa de mutação que esse gene apresenta em relação aos demais genes. As amostras foram tomadas a montante e a jusante da antiga cachoeira de Teotônio visando testar a hipótese de que essa cachoeira servia de barreira para essas espécies. Foram analisados 54 espécimes de P. nattereri (25 montante e 29 jusante) e 45 de P. latior (25 montante e 20 jusante). Os resultados mostraram que os espécimes da montante de P. nattereri apresentam maior variabilidade genética (haplótipos = 5, Hd = 0,607, π = 0,00105) que os da jusante (haplótipos = 2, Hd = 0,379, π = 0,00046), No caso de P. latior, esses valores foram similares tanto a montante (haplótipos = 23, Hd = 0,993, π = 0,01232) como a jusante (haplótipos = 17, Hd = 0,984, π = 0,01865). Ambas as espécies apresentaram haplótipos compartilhados nas duas localidades. A divergência genética entre as localidades de P. nattereri (0,1%) foi menor que em P. latior (1,9%). A análise de variância molecular revelou diferenças significativas entre as localidades de P. nattereri (Φst = 0,11448, P = 0,018) e P. latior (Φst = 0,16408, P = 0,000). Os resultados sugerem que entre as duas localidades amostradas existia uma ... / Abstract: The order Characiformes gathers approximately 1,670 freshwater species, of which at least 1,300 occur in Brazil. To date relatively few genetic studies have been conducted with species of this group, particularly in the Amazon. An important question for the moment is whether there is some isolation between local populations separated by rapids or fast in the Amazon, given the hydroelectric potential estimated for these environments. Accordingly, in this study, conducted under the Conservation Program Ichthyofauna of Santo Antônio Energia, were evaluated two local populations of two species: Pygocentrus nattereri and Potamorhina latior. We employ sequences of the control region (D-loop) of the mitochondrial DNA, the higher rate of this gene mutation present in relation to other genes. The samples were taken upstream and downstream of the old waterfall Teotônio to test the hypothesis that this waterfall served as a barrier for these species. Were examined 54 specimens of P. nattereri (25 upstream and 29 downstream) and 45 of P. latior (25 upstream and 20 downstream). The results showed that the amount of specimens of P. nattereri have greater genetic variability (Haplotypes = 5, Hd = 0607, π = 0.00105) that the downstream (Haplotypes = 2, Hd = 0379, π = 0.00046). In the case of P. latior, these values were similar both upstream (Haplotypes = 23, Hd = 0993, π = 0.01232) and downstream (Haplotypes = 17, Hd = 0.984, π = 0.01865). Both species have shared haplotypes in the two localities. The genetic divergence between the localities of P. nattereri (0.1%) was lower than in P. latior (1.9%). The analysis of molecular variance revealed significant differences between the localities of P. nattereri (Φst = 0.11448, P = 0.018) and P. latior (Φst = 0.16408, P = 0.000). The results suggest that a possible population structure existed between the two localities sampled both by differences in genetic variability as well as by allelic ... / Mestre

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Doctor of Philosophy / Dental caries continues to be a significant public health problem affecting mankind in many parts of the world. Microbial activities include the progressive localised destruction of teeth that without treatment, would eventually result in infection of the dental pulp and surrounding periapical tissues. Although the bacteria responsible for caries initiation and early caries progression have been extensively studied, the microbiology of dentine caries is reported to show considerable diversity and has not yet been fully identified. Few studies have analysed the microbiology of deep caries or examined the relationship between the microflora and the histopathy of chronic pulpits in symptomatic teeth. Matched carious dentine samples and dental pulps were obtained from teeth without evidence of periodontal disease but with coronal caries and symptoms of pulpits. Bacteria were cultured from the carious dentine samples under both anaerobic and microaerophilic conditions. Real-time polymerase chain reaction (PCR) technology was also used to identify and enumerate the bacteria. Development of the techniques for the efficient extraction of bacterial DNA from both Gram-negative and Gram-positive bacteria found in carious dentine was an essential prerequisite for molecular analysis. In addition, the dental pulps were processed and categorised into one of four groups on the basis of dominant pathology of the tissue (minimal inflammation, soft tissue degeneration, hard tissue degeneration, inflammatory degeneration). Analysis of the culture data indicated a predominance of Gram-positive bacteria, particularly lactobacilli, while Gram-negative bacteria were also present in significant numbers with Prevotella species the most numerous anaerobic group cultured. Real-time PCR indicated a greater anaerobic microbial load than that determined by colony counting. The total number of anaerobes detected by PCR was 41-fold greater, while Prevotella spp. and Fusobacterium ssp. were 82-fold and 2.4-fold greater respectively. PCR also identified the presence of Micromonas micros, Porphyromonas endodontalis and Porphyromonas gingivalis in 71%, 60% and 52% of carious dentine samples, respectively. Correlation matrices from the real-time PCR data revealed significant multiple associations involving Fusobacterium spp. in combination with P. endodontalis, M. micros and/or Prevotella in the tissue response categories of minimal inflammation, soft and hard disuse degeneration. A positive correlation was also observed between M. micros and P. endodontalis for the category of inflammatory degeneration of the dental pulp. These anaerobes have been strongly implicated in the endodontic infections that occur as sequelae to carious pulpitis. Accordingly, the data suggest that the presence of threshold levels of these bacteria in carious dentine may be indicative of irreversible pulpitis. Knowledge of the microbial predictors associated with irreversible pulpitis creates potential for the development of a diagnostic tool, and for restorative materials with antimicrobial properties.

Abstract not available

Nototodarus sloanii is an important component of the Southern Ocean fauna, and the basis of a large commercial fishery. Despite this, much is unknown about the biology of this species. This study examines some aspects of the biology of N. sloanii. Stomach contents analysis identified no significant differences in diet between male and female squid. Sixteen putative species, including 12 identifiable teleosts, 2 crustaceans, and 2 cephalopods were identified in the diet of this species. The euphausid, Nyctiphanes australis was the most important prey item, Lanternfish, Lampanyctodes hectoris, and Pearlside, Maurolicus muelleri, were of secondary importance. Squid were aged using counts of statolith micro-increments and back-calculation from the date of capture showed that hatching occurred between August and February, with a peak in the austral winter/spring and another smaller peak in the austral summer. Growth rate for male squid differed depending on whether squid were hatched in the winter/spring or summer. Growth rates were more variable in the winter/spring-hatched individuals, and they attained larger size than summer-hatched squid. This was not the case for female squid. Mean age for immature winter/spring-hatched squid was significantly higher than for summer-hatched squid, although there was no significant difference in mean mantle length or body mass. No significant differences between mean age, mantle length, or body mass for same-gender mature squid, regardless of hatch season, were apparent. However, mature female squid hatched in the winter/spring season were significantly longer (ML) than mature male squid hatched in winter/spring. No squid was found to be older than 211 days. All squid had started to mature by 91-120 days old and all were fully mature at 180 days. Validation experiments run on juvenile squid using calcein markers were inconclusive, however the increments in the statoliths were very similar to those found in other validated species of ommastrephid squid, thus for the purposes of this study they were assumed to be of daily periodicity. Gladius increments identify a gender difference in growth rate, with female squid having a shorter initial slow growth phase than male squid. Gonadosomatic indices (GSIs) were calculated for male and female squid. These were low (7.12%�0.3% for females and 1.9%�0.2% for males) suggesting that these squid are intermittent spawners. This is further supported by a histological examination, which found germinal cells of different stages present in the same gonad. Lack of mature individuals in this study means that these results are suggestive rather than definitive; more examination of the reproductive process of this squid is required. Histological examination was also used to validate the Lipinski maturity scale for use with this species, while some misidentification occurred the scale is useful to place squid into the broad categories of immature, maturing, or mature. New maturity scales were created for N. sloanii utilising these broad categories. Finer-scale identification is not possible using this scale, as maturation appears to be a continuous process. Morphometric measurements were taken from both hard and soft tissues and were analysed using non-metric multidimensional scaling and analysis of similarity. Divisions were only apparent in the hard structure measurements. They did not appear to be age, dietary or reproductive differences.

The overall objective of this project was to investigate the effects of the symbiotic association of plants with vesicular - arbuscular mycorrhizal fungi on the intensity of intraspecific competition and its consequences on population structure I performed four main glasshouse experiments using a non - cultivated species, Rhodanthe chlorocephala ssp rosea, or a cultivated species, Trifolium subterraneum. I grew the plants at different plant densities, under different levels of resources ( phosphorus and / or light ), in environments with homogeneous and / or patchy distribution of phosphorus ( P ). In pots with homogeneous distribution of P, the addition of P to R. chlorocephala and mycorrhizal infection in T. subterraneum increased plant biomass of single plants. However, these beneficial effects were reduced by increasing plant density. Shading of plants of T. subterraneum did not generally alter these effects. Mycorrhizal symbiosis and the addition of P always increased the intensity of plant intraspecific competition. In trays with patchy or homogeneous distribution of P, mycorrhizal infection and patchy distribution of P increased the total biomass and size inequality of populations of plants of T. subterraneum. Individual biomass was determined by the local soil P concentration in patchy environments and by mycorrhizal infection in low density treatments. Mycorrhizal infection, but not patchy P distribution, increased relative competition intensity. Asymmetric or symmetric distribution of resources between plants will change these size hierarchies. The distinction between these two types of distributions has lead to two different models explaining the interaction between competition and size inequality ( degree to which the biomass is concentrated within a small fraction of the population &# 40 Weiner and Thomas 1986 ) ) the resource depletion and resource pre - emption models ( Weiner and Thomas 1986, Weiner 1988b ). In the first model ( resource depletion ) competition reduces the relative growth rate of all the individuals by the same proportion, reduces variance of growth rates and reduces variation in sizes. Thus, in this model resource acquisition is proportional to plant size ( Weiner 1990 ). This model is also called symmetric or two - sided competition and applies when competition for nutrients predominates. It predicts that at high density, plants will be smaller but the population will have less inequality than at low density ( Weiner and Thomas 1986 ). In the second model ( resource pre - emption ), competition increases the variation in relative growth rates and increases variation in sizes. Large plants obtain a more than proportional share of the resources ( relative to sizes ) ( Weiner 1990 ) and this increases their competitive ability which results in a positive feedback on plant size. This phenomenon is also called snowball cumulation, asymmetric or one - sided competition and it was observed only when competition for light was predominant ( Wilson 1988a ). This second model predicts that at high density plant populations will have more inequality than at low density ( Weiner and Thomas 1986 ). Although these two models are generally accepted, alternative analyses and recent experiments show that the degree of asymmetry of the interaction depends on the spatial and temporal distribution of the resource, the spatial distribution of the individuals in the population, neighbourhood competition and the mobility of the resource ( Huston 1986 ; Miller and Weiner 1989, Weiner 1990, Bonan 1991 ). Weiner ( 1990 ) suggested that if nutrients are distributed homogeneously and the uptake is proportional to root size, the competitive interaction will be more symmetric, whereas if patches with more nutrients can be reached by large individuals, asymmetric competition will predominate. This hypothesis has not been tested yet. Turner and Rabinowitz ( 1983 ) found that populations with an initial random spatial distribution of individuals had an unexpected increase in size inequality. My results emphasise that the main effects of mycorrhizas at the individual level cannot be expected to be apparent at the population level, because of the influence of density - dependent processes. However, infected individuals with a strong response to the symbiosis would have an advantage in situations of competition. This scenario can explain the maintenance of the symbiotic ability even under conditions such as dense populations, where there is no obvious advantage of the symbiosis at the population level. / Thesis (Ph.D.)--Department of Soil and Water, 1998.

2,4,6-trinitrotoluene (TNT) is a toxic and recalcitrant pollutant contaminating soils and groundwater. Therefore, characterization of microbial populations of TNT-contaminated soils and isolation of bacteria degrading this pollutant are of primordial importance. Comparison of hybridizations of 16S rRNA derived from uncontaminated and TNT-contaminated soil samples required the development of a functional ANOVA model. Specifically, a statistical tool was necessary to compare dissociation curves obtained from thermal dissociation analysis of RNA hybridizations to DNA microarrays, and to determine if the dissociation curves significantly differed. To test and validate the model, we used dissociation curves from in vitro transcribed 16S rRNA amplified from two environmental samples hybridized to a phylogenetic microarray. Detection and rejection of outlier curves was important for appropriate discrimination between curves. The identification of significantly different curves was more efficient with the model than approaches relying on measurements at a single temperature. This functional ANOVA analysis was used to improve discrimination between hybridizations of two soil microbial communities. Following hybridization of in vitro transcribed 16S rRNA derived from an uncontaminated and a TNT-contaminated soil sample to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and mismatch (MM) variants, thermal dissociation was used to analyze the nucleic acid bound to each PM-MM probe set. Functional ANOVA of the dissociation curves generally discriminated PM-MM probe sets when values of Td (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than Td. Comparison of signal intensities measured prior to dissociation analysis from hybridizations of the two soil samples revealed significant differences in domain-, group-, and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridizations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. These differences in hybridizations between the two soil samples were likely the result from the presence of TNT. The effect of TNT on soil microbial communities was further investigated with additional uncontaminated and TNT-contaminated soil samples using 16S rRNA PCR-DGGE and cultivation-dependent techniques. In all contaminated soil samples, the amount of DNA extracted was lower than in the uncontaminated ones. Analysis of bacterial diversity by DGGE showed a predominance of Pseudomonadaceae and Xanthomonadaceae in the TNT-contaminated soil samples compared to the uncontaminated ones. Caulobacteraceae were also present in several contaminated soil samples. The culturable microflora of these soils was studied by plate counts on agar supplemented with dilute nutrient broth. The number of CFUs was lower in a TNT-contaminated soil inoculum than in an uncontaminated one. In the former, most of the CFUs belonged to Pseudomonadaceae, and to a lesser extent, to Caulobacteraceae. In addition to the above contaminated soil samples, a pristine soil was artificially contaminated with different concentrations of TNT and incubated for 4 months. The amount of DNA extracted decreased in the highly contaminated soil samples (1.4 and 28.5 g TNT/kg soil). After 7 days of incubation of these soil samples, there was a clear shift of their original flora to a population dominated by Pseudomonadaceae, Xanthomonadaceae, Comamonadaceae and Caulobacteraceae. When the TNT concentration was lower (140 mg TNT/kg soil), a moderate shift in the bacterial population was observed. These results indicate that TNT affects soil bacterial diversity and richness by selecting for a narrow range of bacterial species that belong mostly to Pseudomonadaceae and Xanthomonadaceae. TNT-contaminated soil samples probably contained TNT-degrading bacteria. In order to isolate bacteria that can denitrate TNT, enrichment cultures were carried out with TNT as sole nitrogen source and in the absence of oxygen. These cultures were established starting with an uncontaminated or a TNT-contaminated soil inoculum, in the presence or absence of ferrihydrite. A significant release of nitrite was observed in the liquid culture containing TNT, ferrihydrite and inoculum from a TNT-contaminated soil. Under these conditions, Pseudomonas aeruginosa was the predominant bacterium in the enrichment, leading to the isolation of P. aeruginosa ESA-5 as a pure strain. The isolate had TNT denitration capabilities as confirmed by nitrite release in oxygen-depleted cultures containing TNT and ferrihydrite. Concomitantly, TNT-reduced compounds were detected as well as unidentified polar metabolites. The concentration of nitrite released from TNT was proportional to the concentration of ferrihydrite in the medium. The release of nitrite was lower when the concentration of initially spiked TNT was reduced by one order of magnitude. Under these conditions, the concentration of nitrite peaked and then its concentration slowly decreased and production of ferrous ions was detected. A decrease of nitrite concentration and production of ferrous ion were observed when TNT was omitted and nitrite and ferrihydrite were provided. These results suggest that nitrite-reducing conditions were initially achieved, followed by iron-reducing conditions. When grown aerobically on a chemically defined medium, P. aeruginosa strain ESA-5 produced a greenish extracellular compound. This product was identified as phenazine-1-carboxylic acid (PCA). When purified PCA was incubated with TNT in the presence of NADH, nitrite was released. The concentration of nitrite released was dependent on the concentration of NADH and PCA. Denitration also occurred with two TNT-related molecules, 2,4,6-trinitrobenzaldehyde and 2,4,6-trinitrobenzyl alcohol. The release of nitrite was coupled with the formation of two polar metabolites and mass spectrometry analyses indicated that each of these compounds had lost two nitro groups from the trinitroaromatic parent molecule. The results obtained with the PCA mediated denitration of TNT in the presence of inhibitors of oxygen reactive species suggested the involvement of superoxide (O2.-). When exogenous PCA was added to a P. aeruginosa ESA-5 liquid culture containing TNT as sole nitrogen source, bacterial growth was significantly enhanced compared to cultures containing TNT without PCA.