Genetic diversity and differentiation in natural Plasmodium falciparum populations inferred by molecular typing of the merozoite surface proteins 1 and 2

Genetic diversity and differentiation, inferred by typing the polymorphic genes coding for the merozoite surface proteins 1 (Msp-1) and 2 (Msp-2), were compared for 345 isolates belonging to seven Plasmodium falciparum populations from three continents. Both loci yielded similar estimates of genetic diversity for each population, but rather different patterns of between-population differentiation, suggesting that natural selection on these loci, rather than the transmission dynamics of P. falciparum, determines the variation in allele frequencies among populations.

Understanding the microbial ecology and ecophysiology of enhanced biological phosphorus removal processes through metabolic modelling and experimental studies

Dissertation to obtain the degree of Master in Chemical and Biochemical Engineering

Energy-efficient diversity combining for different access schemes in a multi-path dispersive channel

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e Computadores

Constraint-based modelling of mixed microbial populations: Application to polyhydroxyalkanoates production

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Enrichment of a PHA producing microbial community in a continuous bioreactor setup

Polyhydroxyalkanoates (PHAs) are biosynthetic polyesters, biodegradable and biocompatible making them of great interest for industrial purposes. The use of low value substrates with mixed microbial communities (MMC) is a strategy currently used to decrease the elevated PHA production costs. PHA production process requires an important step for selection and enrichment of PHA-storing microorganisms which is usually carried out in a Sequencing Batch Reactor (SBR). The aim of this study was to optimize the PHA accumulating culture selection stage using a 2-stage Continuous Stirrer Tank Reactor (CSTR) system. The system was composed by two separate feast and famine bioreactors operated continuously, mimicking the feast and famine phases in a SBR system. Acetate was used as carbon source and biomass seed was highly enriched in Plasticicumulans acidivorans obtained from activated sludge. The system was operated under two different sets of conditions (setup 1 and 2), maintaining a system total retention time of 12 hours and an OLR of 2.25 Cmmol/L.h-1. An average PHB-content of 3.3 % wt was obtained in setup 1 and 4.8% wt in setup 2. Several other experiments were performed in order to better understand the continuous system behaviour, using biomass from the continuous system. With the fed-batch experiment a maximum of 8.1% PHB was stored and the maximum substrate uptake and specific growth rates obtained in the growth experiment (1.15 Cmol Cmol-1.h-1 and 0.53 Cmol Cmol-1.h-1) were close to the ones from continuous system (1.12 Cmol Cmol-1.h-1 and 0.59 Cmol Cmol-1.h-1). The microbial community was characterized trough microscopic visualization, Denaturing Gradient Gel Electrophoresis (DGGE) analysis and Fluorescent in situ hybridization (FISH). The last studied performed mimicked the continuous system by building up a SBR system with all the same operational conditions while adding an extra acetate dosage during the 12 h cycle, simulating the substrate passing from the feast to the famine reactors under continuous operation. It was shown that possibly the continuous system was not able to efficiently select for PHB storing organisms under the operational conditions imposed, although the selected culture was capable of consuming the substrate and grow fast. This main conclusion might have resulted from two major factors affecting the system performance: the ammonium concentration in the Feast reactor and the amount of substrate leaching from the Feast to the Famine reactor.

Novel ready-to-eat mango product using gellan gum as gelling agent: physico-chemical, microbial and sensory characteristics

Este trabalho foi efectuado com o apoio da Universidade de Lisboa, Instituto Superior de Agronomia com o Centro de Engenharia dos Biossistemas (CEER

Genetic diversity of dengue virus serotypes 1 and 2 in the State of Paraná, Brazil, based on a fragment of the capsid/premembrane junction region

INTRODUCTION: The precise identification of the genetic variants of the dengue virus is important to understand its dispersion and virulence patterns and to identify the strains responsible for epidemic outbreaks. This study investigated the genetic variants of the capsid-premembrane junction region fragment in the dengue virus serotypes 1 and 2 (DENV1-2). METHODS: Samples from 11 municipalities in the State of Paraná, Brazil, were provided by the Central Laboratory of Paraná. They were isolated from the cell culture line C6/36 (Aedes albopictus) and were positive for indirect immunofluorescence. Ribonucleic acid (RNA) extracted from these samples was submitted to the reverse transcription polymerase chain reaction (RT-PCR) and nested PCR. RESULTS: RT-PCR revealed that 4 of the samples were co-infected with both serotypes. The isolated DENV-1 sequences were 95-100% similar to the sequences of other serotype 1 strains deposited in GenBank. Similarly, the isolated DENV-2 sequences were 98-100% similar to other serotype 2 sequences in GenBank. According to our neighbor-joining tree, all strains obtained in this study belonged to genotype V of DENV-1. The DENV-2 strains, by contrast, belonged to the American/Asian genotypes. CONCLUSIONS: The monitoring of circulating strains is an important tool to detect the migration of virus subtypes involved in dengue epidemics.

Diversity and dynamics of airborne fungi in São Luis, State of Maranhão, Brazil

Introduction: This study aimed to identify airborne fungi in São Luis, Maranhão, Brazil, to determine the prevalent genera and to correlate these genera with the area and season. Methods: In total, 1,510 colony-forming units (CFUs) of airborne fungi were isolated from the north, south, east and west sides and from the center of the city from January to December 2007. The samples were collected on Petri dishes that were exposed to the fungi by the gravitational method. Results: Twenty genera of fungi were isolated; the most common were Aspergillus (33.5%), Penicillium (18.8%), Cladosporium (14.2%), Curvularia (10.6%) and Fusarium (7.6%). The CFUs of the fungi were statistically significant (p < 0.0001). Fungal biological diversity was present all year, without any large seasonal variations but with slight increases in May, August and September. Conclusions: The fungal genera identified in this study were correlated with natural systems and could be useful when evaluating the impact of environmental changes on the region.

The influence of the area of the Serra da Mesa Hydroelectric Plant, State of Goiás, on the frequency and diversity of anophelines (Diptera: Culicidae): a study on the effect of a reservoir

INTRODUCTION: Bioecological aspects of anophelines (Diptera: Culicidae) near areas under the direct influence of the hydroelectric plant reservoir of Serra da Mesa in Goiás, Brazil, were analyzed. METHODS: Samples were collected at the surrounding dam area during the phases before and after reservoir impoundment. The influence of climatic and environmental factors on the occurrence of Anopheles darlingi, Anopheles albitarsis, Anopheles triannulatus, Anopheles oswaldoi and Anopheles evansae was assessed using Pearson's correlations with indicators for richness and diversity as well as the index of species abundance (ISA) and the standardized index of species abundance (SISA). RESULTS: The highest anopheline density occurred during the phase after filling the tank; however, no direct correlation with the climatic factors was observed during this stage. The reservoir formation determined the incidence of the anopheline species. An. darlingi was the predominant species (SISA = 1.00). CONCLUSIONS: The significant difference (p < 0.05) observed between the species incidence during the different reservoir phases demonstrates the environmental effect of the reservoir on anophelines.

Impact of carbon/nitrogen feeding strategy on polyhydroxyalkanoates production using mixed microbial cultures

Polyhydroxyalkanoates (PHA) production using mixed microbial cultures (MMC) requires a multi-stage process involving the microbial selection of PHA-storing microorganisms, typically operated in sequencing batch reactors (SBR), and an accumulation reactor. Since low-cost renewable feedstocks used as process feedstock are often nitrogen-deficient, nutrient supply in the selection stage is required to allow for microbial growth. In this context, the possibility to uncouple nitrogen supply from carbon feeding within the SBR cycle has been investigated in this study. Moreover, three different COD:N ratios (100:3.79, 100:3.03 and 100:2.43) were tested in three different runs which also allowed the study of COD:N ratio on the SBR performance. For each run, a synthetic mixture of acetic and propionic acids at an overall organic load rate of 8.5 gCOD L-1 d-1 was used as carbon feedstock, whereas ammonium sulfate was the nitrogen source in a lab-scale sequence batch reactor (SBR) with 1 L of working volume. Besides, a sludge retention time (SRT) of 1 d was used as well as a 6 h cycle length. The uncoupled feeding strategy significantly enhanced the selective pressure towards PHA-storing microorganisms, resulting in a two-fold increase in the PHA production (up to about 1.3 gCOD L-1). A high storage response was observed for the two runs with the COD:N ratios (gCOD:gN) of 100:3.79 and 100:3.03, whereas the lowest investigated nitrogen load resulted in very poor performance in terms of polymer production. In fact, strong nitrogen limitation caused fungi to grow and a very poor storage ability by microorganisms that thrived in those conditions. The COD:N ratio also affected the polymer composition, indeed the produced poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) showed a variable HV content (1-20 %, w/w) among the three runs, lessening as the COD:N increased. This clearly suggests the possibility to use the COD:N ratio as a tool for tuning polymer properties regardless the composition of the feedstock.

Coupling organic substrate removal to methane production in a fully biological microbial electrolysis cell

Microbial electrolysis cells (MECs) are an innovative and emerging technique based on the use of solid-state electrodes to stimulate microbial metabolism for wastewater treatment and simultaneous production of value-added compounds (such as methane). This research studied the performance of a two-chamber MEC in terms of organic matter oxidation (at the anode) and methane production (at the cathode). MEC‟s anode had been previously inoculated with an activated sludge, whereas the cathode chamber inoculum was an anaerobic sludge (containing methanogenic microorganisms). During the experimentation, the bioanode was continuously fed with synthetic solutions in anaerobic basal medium, at an organic load rate (OLR) of around 1 g L-1 d-1, referred to the chemical oxygen demand (COD). At the beginning (Run I), the feeding solution contained acetate and subsequently (Run II) it was replaced with a more complex solution containing soluble organic compounds other than acetate. For both conditions, the anode potential was controlled at -0.1 V vs. standard hydrogen electrode, by means of a potentiostat. During Run I, over 80% of the influent acetate was anaerobically oxidized at the anode, and the resulting electric current was recovered as methane at the cathode (with a cathode capture efficiency, CCE, accounting around 115 %). The average energy efficiency of the system (i.e., the energy captured into methane relative to the electrical energy input) under these conditions was over 170%. However, reactor‟s performance decreased over time during this run. Throughout Run II, a substrate oxidation over 60% (on COD basis) was observed. The electric current produced (57% of coulombic efficiency) was also recovered as methane, with a CCE of 90%. For this run the MEC‟s average energy efficiency accounted for almost 170 %. During all the experimentation, a very low biomass growth was observed at the anode whereas ammonium was transferred through the cationic membrane and concentrated at the cathode. Tracer experiments and scanning electron microscopy analyses were also carried out to gain a deeper insight into the reactor performance and also to investigate the possible reasons for partial loss of performance. In conclusion, this research suggests the great potential of MEC to successfully treat low-strength wastewaters, with high energy efficiency and very low sludge production.

Local diversity of tropical and temperature ant faunas (Hymenoptera, Formicidae)

Qualitative and quantitative collections of ants made in the region of Manaus, Brazil (evergreen tropical humid forest), and in western North Carolina, USA (deciduous temperate/wet forest), were undertaken to investigate. latitudinal patterns of ant diversity and community organization on regional and local scales. We have found to date 307 ant species in the Municipality of Manaus. Totals ranging from 134 to 270+ species have been reported in the literature for other tropical regions of less than 10,000km2. In contrast, temperate ant surveys generally report only SO to 150 species in similar or larger areas. Sampling at sardine baits set 10m apart on square grids, we found forest ecosystems near Manaus to be much richer and more diverse in ants than those sampled in North Carolina: 28 species vs. 5-10 species in 50 collections and 16 vs. 3 previously unrecorded species discovered with each doubling of sample size. Room's (1975a) results from climatically simllar Papua New Guinea forest agree closely with those from Manaus. We suggest that one important factor contributing to the increased diversity of tropical, omnivorous ants may be greater variety of nest sites available for specialization.

Amazon landforms and soils in relation to biological diversity

Thirteen main landform units are distinguished for the whole of the forested Amazon region, each with its specific soil pattern and vegetation structure. These landform-soil-vegetation units are delineated on a small-scale map and illustrated by a schematic cross-section. Floristic diversity of the gamma type is to be highest on the steepland-and-valley complexes of the Andean fringe, on the crystalline shield uplands, on the inselberg complexes, and on the eutric variant of the western sedimentary plains. Endemism is expected to be highest on the sandy plains, and parts of the table lands and inselberg complexes. Speciation, linked to the concept of forest refuge areas, is likely to be highest on the sandstone table lands, on the stretches of Amazon planalto, and in the areas of relict valleys, in view of the prolonged geomorphological stability of these units.

Effects of residues on the degradation of PHA produced from mixed microbial cultures and processed in extrusion

Thermal degradation upon melting is one of the major drawbacks reported for polyhydroxyalkanoates (PHA). However, the role of residues originating from the fermentation and the extraction steps on the thermal stability of this class of biopolymers still needs to be clarified. In the particular case of PHA produced from mixed microbial cultures (MMC), this topic is even less documented in the literature. Here, two polyhydroxy(butyrate-co-valerate) (PHBV) produced from MMC enriched in PHA accumulating organisms and fed with cheese whey were studied. A micro extrusion line is used to produce filaments and assess the processability and the degradation of processed PHBV. The prototype micro extrusion line allows for studying grams of materials. The two PHBV contain 18 mol% HV. PHBV was recovered with 11 wt% residues, and further submitted to a purification procedure resulting in a second biopolyester containing less than 2 wt% impurities. The thermorheological characterization of the two PHBV is first presented, together with their semicrystalline properties. Then the processing windows of the two biopolyesters are presented. Finally, the properties of extruded filaments are reported and the thermomechanical degradation of PHBV is extensively studied. The structure was assessed by wide angle X-ray diffraction, mechanical and rheological properties are reported, thermal properties are studied with differential scanning calorimetry and thermogravimetric analysis, whereas Fourier Transform Infrared spectroscopy was used to assess the impact of the extrusion on PHBV chemical structure. All results obtained with the two PHBV are compared to assess the effects of residues on both PHBV processability and degradation.

Biofunctionalization of titanium surfaces for dental implants: osteogenic, anti-microbial and tribocorrosion resistant surfaces

PhD thesis in Biomedical Engineering