Dissertations / Theses on the topic 'Applied microbiology'

Recent advancements in molecular biology such as next generation sequencing and more sensitive and rapid molecular detection methods like qPCR, have historically been developed for clinical applications in human genetics and for health care diagnostic purposes. The high demand for faster and more accurate molecular assays in the health care field has driven rapid development of inexpensive molecular techniques that when applied to the science of environmental microbiology, provides an unprecedented level of understanding of the microbial world around us. The goal of this dissertation is to begin to apply more advanced molecular technologies to problems in applied environmental microbiology. Appendix A is a brief literature review of next generation sequencing technologies for applications in environmental microbiology. Appendix B focuses on the development of a more robust virus nucleic extraction kit for the detection of viral genomes from environmental samples found to contain high concentrations of qPCR inhibitors, such as humic acids or heavy metals. Appendix C summarizes one of the largest virus surveys done in the US, using state of the art qPCR technologies in both wastewater influent and effluent from two wastewater treatment plants in the Southwest. Data suggests that traditional virus indicators may not be a viable tool to evaluate fecally impacted source water or virus removal during water treatment. The third study summarized in Appendix D, provides one of the first insights into the microbial ecology of biofilms utilized as biological treatment media using Roche 454 amplicon sequencing of the 16S rRNA gene.

A resistência de cinco microrganismos presentes na microbiota da área de produção estéril (Cristalização Estéril), frente a ação do gás de peróxido de hidrogênio foi determinada e o valor O obtido para cada microrganismo foi comparado ao valor D do Bacillus stearothermophilus ATCC 12980 exposto ao mesmo agente. Os microrganismos testados foram Bacillus sp, M. luteus, Corynebacterium, Staphylococcus sp e Penicillium sp. Este teste tinha a finalidade de comprovar que a resistência do Bacillus stearothermophilus é maior quando da exposição ao peróxido de hidrogênio se comparada a outros microrganismos presentes na área produtiva. A metodologia consistiu da inoculação de 0,01 mL da suspensão de cada microrganismo na contagem de 102UFC/0,01 mL em cupons de aço inoxidável, previamente esterilizados por calor seco e posterior exposição ao gás de peróxido de hidrogênio. O experimento demonstrou que o valor D obtido para o Bacillus stearothermophilus ésuperior aos obtidos para os outros microrganismos em teste comprovando que a escolha deste microrganismo para o desafio contra o peróxido de hidrogênio é apropriada. Também executou-se o teste que visava garantir que o aço inoxidável é o material de suporte mais recomendado para este fim, utilizando-se suportes de diversos materiais normalmente encontrados no interior dos isoladores (PVC, aço inoxidável, CKC, teflon, polipropileno, látex, silicone, Hypalon, vidro, nylon, saco de alumínio) com 0,01 mL de inóculo de Bacillus stearothermophilus na contagem de 102UFC/O,01 mL, o que foi devidamente comprovado.
The resistance of tive microrganisms found in the sterile production area (Crystallization Area) flora was tested against the hydrogen peroxide gas and the D value of each microrganism was compared to the Bacillus stearothermophilus D Value ATCC 12980 exposed to the same agent. The microrganisms tested were Bacillus sp, M. luteus, Corynebacterium, Staphylococcus sp e Penicillium sp. The purpose of this test was to prove that the resistance of Bacillus stearothermophilus against the exposition the hydrogen peroxide is higher when compared to others microrganisms found in the production area. The methodology consisted in inoculating 0.01 mL of microrganisms suspension with 102UFC/0,01 mL count in stainless steel coupons, treated previously with dry heat and further exposition to the hydrogen peroxide. The experiment demonstrated that the Bacillus stearothermophilus D value is higher against all others microrganisms tested proving that the use of this microrganism for the challenge is appropriate. It was also pertormed a test to guarantee that the stainless steel support is the most recommended one for this purpose, using supports of different materials normally found in the interior of the isolators (PVC, stainless steel, CKC, Teflon, polypropylene, latex, silicon, Hypalon, glass, nylon, aluminum foil) with 0,01 mL Bacillus stearothermophilus inoculum with the count of 102UFC/O,01 mL, that was properly veritied.

A chemically defined medium for Salmonella growth was developed and optimised using supplements of amino acids, nucleosides, vitamins and different carbon sources. The medium developed was compared to commercially available pre-enrichment media BPW and Salmosyst. Growth of Salmonella was significantly higher in BPW and Salmosyst than the medium developed. The amino acid and nucleoside supplement was directly compared with peptone. The results show peptone to be nutritionally superior and promoting better growth of Salmonella. Three different ELISA assays were used to detect Salmonella growing in four different media. The ELISA assay sensitivity was determined and a degree of media interference with the immunoassays was established. Salmonella culture viability was investigated using three different procedures: differential culturing on selective and non-selective media; fluorescence microscopy with BACLIGHT stained cells and flow cytometry analysis of BACLIGHT and BEP stained cells. Flow cytometry was found to be the most consistent, sensitive and rapid procedure for cell viability measurement. Clusters of viable cells unable to grow on solid media and therefore remaining undetectable by cultural methods were identified using flow cytometry. Severely heat injured Salmonella was used to determine media recoverability. The results indicate that media which contain peptone recover injured Salmonella better than chemically defined or other media. Detection of Salmonella was performed using PCR assay after sample pre-enrichment. The amplification of Salmonella DNA extracted using a crude method resulted in an assay sensitivity of 20 Salmonella cells in pure cultures. The specificity of the oligonucleotide primers employed in the PCR assay was confirmed. Non-salmonella organisms present in high numbers interfered with PCR detection of Salmonella. Food components also interfered with PCR amplification and reduced the assay sensitivity. Interference by food components and non-salmonella DNA was eliminated by the use of a 24 hour pre-enrichment followed by a 3 hour secondary enrichment, a rapid DNA extraction and template preparation. Using this system it was possible to detect 3 Salmonella cells per gram of food in the presence of 106 non-salmonella cells within 28 hours.

Actualment s’observa un increment en la utilització de tècniques de cocció a temperatures moderades com la cuina al buit. Donada la possibilitat d’utilitzar aquestes tècniques per a preparar menjars amb antelació i considerant que les dades sobre el comportament microbià en el rang entre 40 i 60 ºC són escasses, hi ha un gran interès en definir la seva seguretat microbiològica. Aquesta tesi doctoral té com a objectiu avaluar l’efecte de la cocció al buit a temperatures moderades sobre L. monocytogenes i Salmonella spp. inoculades en llom de porc. Es van realitzar assajos d’inoculació (challenge test) en llom de porc, amb dues soques de Salmonella (S. enterica subsp. enterica serovar Enteritidis CECT 4300 i Senftenberg CECT 4565) i Listeria monocytogenes (CECT 4031 i Scott A), avaluades de forma individual o combinada. Les porcions de carn inoculada es van envasar al buit i es van cuinar en un forn de vapor a dues temperatures (55 i 60 ºC) durant 30, 60 o 90 minuts. Es va determinar la letalitat i la recuperació microbiana durant l’emmagatzematge a 4 i 8 ºC fins al dia 30 post-cocció. L’evolució en el recompte es va modelitzar utilitzant les eines predictives Bioinactivation FE per a la inactivació tèrmica i DMFit pel creixement durant l’emmagatzematge. Es va aplicar el mètode Monte Carlo per incorporar la variabilitat observada en els models predictius. L’heterogeneïtat dels resultats va ser important, i una de les seves fonts va ser probablement el funcionament del forn a les temperatures d’assaig. En general, Salmonella spp. es mostrà més termoresistent que L. monocytogenes, però el seu creixement durant l’emmagatzematge va ser més limitat. Per tant, l’avaluació de la seguretat microbiològica d’aquests tractaments moderats ha de considerar tant la letalitat com la capacitat de recuperació durant l’emmagatzematge. Tenint en compte tots dos factors, es van obtenir tres escenaris diferents. El primer vas ser d’inactivació completa (S. Enteritidis i L. monocytogenes Scott A i CECT 4031 a 60 ºC) és a dir, no es van detectar les soques inoculades en cap rèplica durant tot el període d’emmagatzematge. L’escenari de viabilitat es va observar en casos en què totes les rèpliques van mostrar recomptes superiors al límit de quantificació (5 CFU/g), amb o sense creixement (S. Senftenberg, L. monocytogenes Scott A, còctel de soques de L. monocytogenes a 55 ºC i còctel de soques de Salmonella spp. a 55ºC durant 30 min). Finalment, l’escenari de "creixement/no creixement", es va caracteritzar per diferents proporcions de mort, viabilitat i lesió a nivell cel·lular. Aquesta circumstància es va produir en mostres inoculades cuinades a 60 ºC (S. Senftenberg, còctel de L. monocytogenes) i 55 ºC (còctel de Salmonella spp. i L. monocytogenes CECT 4031). En conclusió, la seguretat microbiològica dels processos de cocció al buit a temperatura moderada ha de ser curosament avaluada cas per cas. El nostre estudi indica que els tractaments a 60 ºC durant 90 minuts aplicats al llom de porc es podrien considerar raonablement segurs, sempre que no es produeixi un abús de temperatura durant la vida útil. Els tractaments a 60 ºC durant 30 i 60 minuts es podrien utilitzar només en cas de servei immediat després de la cocció. La cocció de llom de porc a 55 ºC durant 30, 60 i 90 minuts no es pot considerar segura en relació a S. Senftenberg i L. monocytogenes Scott A, donat que les cèl·lules supervivents poden créixer a 8 ºC. Aquest tractament s’ha d’utilitzar només per a sistemes de servei immediat. Aquest estudi proporciona dades útils per a futures avaluacions del risc aplicades a la cocció al buit de carn a temperatures moderades.
A raising interest has been detected nowadays in relation to the use of cooking techniques at moderate temperatures like sous-vide cooking. Given the possibility of using these techniques to prepare food in advance, and considering that data on behaviour of bacteria in the range of 40 to 60 °C is scarce, there is great concern in accurately define the microbiological safety of this food. The aim of this doctoral thesis was to characterize the effect of mild temperature vacuum cooking treatments on two main food pathogens, L. monocytogenes and Salmonella spp. inoculated in raw pork meat. Challenge studies were conducted using two bacterial strains of Salmonella (S. enterica subsp. enterica serovar Enteritidis CECT 4300 and Senftenberg CECT 4565), and Listeria monocytogenes (CECT 4031 and Scott A), inoculated either individually or in combination. Pork loin pieces were inoculated, vacuum packed and cooked in a steam oven at two different temperatures (55 and 60 ºC) during 30, 60 or 90 minutes. Lethality caused by each treatment was determined just after cooking. Further recovery of injured cells was evaluated during storage at 4 and 8 ºC until the 30th day after treatments. Evolution of microbial counts were modelled using the predictive tools Bioinactivation FE for thermal inactivation and DMFit for growth through the storage time. The Monte Carlo method was applied in order to incorporate the variability observed between replicates in the predictive models of inactivation and growth. The heterogeneity of results was important. One source of this variability was probably the steam oven performance between 55 and 60 ºC. At these cooking temperatures, Salmonella spp. was more heat resistant than L. monocytogenes, but it was less able to growth during cold storage. Microbiological safety evaluation of sous-vide mild heat treatments must be based both on lethality and on the capability of recovery during storage. Considering both factors, three different scenarios were obtained: complete inactivation, presence of viable cells and a growth/no growth interface. In case of a complete inactivation (S. Enteritidis and L. monocytogenes Scott A and CECT 4031 cooked at 60 ºC), inoculated strains were not detected in any replicate during all the storage period. In case of viability, all replicates showed counts above the quantification limit (5 CFU/g), whether growth was observed or not (S. Senftenberg, L. monocytogenes Scott A, cocktail of L. monocytogenes strains at 55 ºC, and cocktail of Salmonella spp. strains at 55 ºC during 30 min). Finally, in some experimental conditions a “growth/no growth” behaviour, with different proportions of death, viable and injured cells, was observed. This circumstance took place in inoculated samples cooked at 60 ºC (S. Senftenberg, cocktail of L. monocytogenes) and 55 ºC (cocktail of Salmonella spp. and L. monocytogenes CECT 4031). In conclusion, the microbiological safety of sous-vide mild heat processes have to be accurately assessed on a case-by-case basis. Heat treatments at 60 ºC for 90 min applied to pork loin could be considered reasonably safe and suitable for “cook-chill” systems in relation to Salmonella spp. and L. monocytogenes strains included in the essay, as long as no temperature abuse occurs during shelf-life. Treatments at 60 ºC during 30 and 60 minutes must be used only for “cook-serve” systems. Sous-vide cooking of pork loin at 55 ºC during 30, 60 and 90 minutes cannot be considered safe in relation to S. Senftenberg and L. monocytogenes Scott A due to the presence of survivor cells that can growth at 8 ºC. This treatment must be used only for “cook-serve” systems. This study provides useful data for future risk assessment studies applied to meat sous-vide cooked at mild temperatures.

Limestone built heritage is at risk from the effects of biofilms, a microbial community encapsulated in a matrix of sugars, protein and extracellular DNA. Although biofilm research has been carried out in Mediterranean regions, few studies cover temperate Northern Europe climates, or the UK. This study concentrates on bacterial colonisation of Lincoln limestone, a highly vulnerable building material, and identifies the species, their role in biodeterioration and the efficacy of biocides against them. As part of this study the core species which comprise the bacterial component of the limestone microbiome have been characterised for the first time; this has allowed the identification of non-core species which are significantly associated with damaged and undamaged surfaces. Four mechanisms of biodeterioration have been identified, one previously unidentified, and isolated species have been characterised as to whether they are biodeteriorative and the mechanisms of biodeterioration that they employ. Two species, Curtobacterium flaccumfaciens and Solibacillus silvestris, have been characterised as producing biofilm matrix which actively causes biomechanical damage to the oolitic limestone structure as opposed to the passive enhancement of physical weathering which has been previously associated with biofilm matrix. Species capable of biodeterioration have also been shown to be present on both damaged and undamaged surfaces, something which has not been previously investigated. Environmental sampling, species identification and characterisation of species for biodeterioration have all combined to identify markers of biodeterioration, ie both physical markers and biomarkers. Specifically, a surface pH of 5.5 or lower and the presence of B. licheniformis is indicative of biodeterioration with a proportionally higher level of M. luteus when comparing damaged and undamaged stone. Finally this study brings the literature on conservation methods up to date by testing biocides which are in current usage, as many biocides in the literature are discontinued. This study is also the first in the field to show their efficacy against biofilm encapsulated bacteria and their propensity for chemically disrupting the biofilm matrix.

Os tipos de cassete cromossômico estafilocócico mec (SCCmec) encontrados em cepas de Staphylococcus aureus resistente a oxacilina (ORSA) isoladas em ambiente hospitalar são denominados I, II e III. Um novo SCCmec, tipo IV, foi identificado em cepas isoladas de pacientes que não tinham conexão aparente com hospitais. Essas cepas, denominadas ORSA adquiridas na comunidade ou CA-ORSA, não costumam conter genes de resistência a antimicrobianos além do gene mecA, porém, são mais virulentas. Com a finalidade de conhecer a diversidade estrutural do SCCmec de cepas ORSA brasileiras, foram estudadas 50 cepas ORSA, entre elas algumas S. aureus com resistência intermediária a vancomicina (VISA) e S. aureus com resistência heterogênea intermediária a vancomicina (HVISA). As cepas foram isoladas entre 1995 e 2000, provenientes de hospitais de 13 Estados brasileiros, pertencentes a diversos clones de PFGE. As cepas foram analisadas quanto ao perfil de sensibilidade, RFLP do gene da coagulase, fagotipagem e tipagem do SCCmec. A maioria das cepas é pertencente ao clone endêmico brasileiro, que carrega o SCCmec tipo III, também presente em outros clones de PFGE. O SCCmec tipo IV, encontrado em 3 cepas (clones J, L e D), mostrou suscetibilidade a um maior número de antimicrobianos pertencentes a diferentes classes, em comparação aos outros tipos de SCCmec. O SCCmec tipo IV está presente entre os ORSA brasileiros e pode estar disseminando na comunidade e hospitais do país.
The types of SCCmec found in nosocomial methicillin-resistant Staphylococcus aureus (MRSA) strains can be designated type I, II or III. A novel type of SCCmec, designated type IV, was identified in strains isolated in outpatients. These strains, called community-acquired MRSA or CA-MRSA, do not contain antimicrobial resistance genes other than mecA, however, they are more virulent. In order to characterise the structural diversity of SCCmec in Brazilian MRSA strains, 50 MRSA strains were studied, including some vancomycin intermediate resistant S. aureus (VISA) and heterogeneous vancomycin intermediate S. aureus (HVISA) strains. All strains were isolated between 1995-2000, in hospitaIs in 13 Brazilian States, and belonged to different PFGE clones. Strains were analysed as to their susceptibility profile, RFLP of the coagulase gene, phagetype and SCCmec type. The majority of strains belonged to the Brazilian Endemic Clone, which carries an type IH SCCmec, which in turn, was also found in other PFGE clones. The type IV SCCmec was found in 3 strains (belonging to the J, L and D clones) and presented a susceptibility profile to a number of drugs of different antimicrobial classes. The type IV SCCmec is present among Brazilian MRSA strains and can be disseminated in the community and in hospitaIs throughout the country.

Fiber-yielding plants is an area of increased interest due to the potential use in a variety of green-based materials. These biocomposites can be incorporated into multiple uses; for example, to replace building materials and interior vehicular paneling. The research here aims to focus in on the crop Hibiscus cannabinus for utilization into these functions. H. cannabinus is economically attractive due to the entire process being able to be accomplished here in the United States. The plant can be grown in a relatively short growth period (120-180 days), and then processed and incorporated in a biocomposite. The plant fiber must first be broken down into a useable medium. This is accomplished by the retting process, which occurs when microbial constituents breakdown the heteropolysaccharides releasing the fiber. The research aims to bridge the gap between the primitive process of retting and current techniques in molecular and microbiology. Utilizing a classical microbiological approach, which entailed enrichment and isolation of pectinase-producing bacteria for downstream use in augmented microbial retting experiments. The tracking of the bacteria was accomplished by using the 16S rRNA which acts as “barcodes” for bacteria. Next-generation sequencing can then provide data from each environment telling the composition and microbial diversity of each tested variable. The main environments tested are: a natural environment, organisms contributed by the plant material solely, and an augmented version in which pectinase-producing bacteria are added. In addition, a time-course experiment was performed on the augmented environment providing data of the shift to an anaerobic environment. Lastly, a drop-in set was performed using each isolate separately to determine which contributes to the shift in microbial organization. This research provided a much needed modernization of the retting technique. Previous studies have been subject to simple clone libraries and growth plate assays and next-generation sequencing will bring the understanding of microbial retting into the 21st century.

Neste trabalho foi feito um estudo para obtenção de formulações multiparticuladas, formadas por micropartículas de polímeros naturais, solúveis em água, não tóxicos e biodegradáveis. Os polímeros utilizados foram: Caseína, Hidroxietilcelulose (HEC), Hidroxipropilmetilcelulose (HPMC), Alginato de sódio e Quitosana. As técnicas utilizadas para obtenção das micropartículas foram o spray drying e a atomização de alginato de sódio em uma solução de CaCl2, para gelificação das gotículas formadas, com uma complexação ou não com quitosana. O estudo de micropartículas secas de alginato de cálcio e alginato de cálcio recoberta com uma membrana de quitosana revelou que diferentes procedimentos e variáveis de processo influenciavam nas características das micropartículas obtidas. O diâmetro médio das micropartículas de alginato e alginato-quitosana variou de 60 a 553 µm. A superfície de micropartículas com quitosana se mostrou mais rugosa, com uma grande quantidade de poros menores que 1 µm. As micropartículas com diâmetro médio de 60 µm apresentaram uma boa esfericidade e uma distribuição de tamanho de partícula uniforme. O teor de cálcio apresentou variações, diminuindo em processos com quitosana. A maioria das micropartículas de alginato e alginato-quitosana eram estáveis em água, mas instáveis em soro fisiológico e tampão fosfato 0,1M. Após a realização do estudo das características destas micropartículas foram incorporados a elas materiais com atividade bioinseticida (Bacillus thuringiensis var. krusfaki (Btk) e de Baculovirus (Bv)). As micropartículas obtidas com alginato de cálcio formaram pós contendo sistemas matriciais capazes de microencapsular e reter microrganismos entomopatogênicos, inclusive após redispersão em água. Os processos de microencapsulação de desenvolvidos e avaliados demonstraram ser adequados para a manutenção da viabilidade de Btk e da integridade dos poliedros de Bv, assim como, a conservação da capacidade bioinseticida destes microrganismos. As micropartículas obtidas com as misturas poliméricas Caseína/HEC e Caseína/HPMC pelo processo de spray drying revelaram-se inadequadas na medida que se dissolviam rapidamente depois de dispersas em água e não poderiam assim proteger o material bioinseticida no meio ambiente.
The aim of this work was to develop powder formulations containing microparticles, to be used as multiparticulate delivery systems. Two different methods were investigated : 1) the preparation of microparticles by spray drying using casein, hydroxyethylcellulose (HEC) and hydroxypropilmetilcellulose (HPMC) and 2) the preparation of calcium alginate and chitosan-alginate microparticles by using an atomizer device. Different experimental procedures to prepare calcium alginate and chitosanalginate microparticles were evaluated and variables beHeved to be important for the membrane formation were examined. The mean particles diarneter ranged from 60 to 553 µm. When a comparison was made between the surface morphology of calcium alginate and alginate-chitosan microparticles, remarkable roughness and more porous structure was observed in the chitosan-alginate microparticles. Some properties of the microparticles depended on the method and the procedure conditions of forming the chitosan-alginate complex. Calcium alginate and chitosan-alginate microparticles containing two different bioinsecticides were also prepared: 1) a spore/δ-endotoxinscomplex of Bacillus thuringiensis var.kurstaki (Btk) and 2) polyhedra of Baculovirus anticarsia (Bv), a viral insecticide. The results shown that the encapsulation of suspensions of Btk containing spore/toxin complex or polyhedra of B. anticarcia in calcium alginate and chitosan-alginate microparticles did not decrease the larvicidal activity of these biopesticides against lepidopterous pests. The formulations developed in this study remained unchanged, did not swell, did not release the spores (Btk) or the polyhedra (Bv), when dispersed in water and could be useful to be applied by aqueous spray as bioinsecticides in agriculture. On the other hand, casein, HEC and HPMC microparticles prepared by spray drying were not suitable to encapsulate bioinsecticides because they dissolved fastly after dispersion in water.

The effects of inhaled air pollution particles on lung clearance mechanisms is an important factor in understanding how the mammalian lung deals with such pollutants and, as such, how exposure to these pollutants can be regulated. The nanoparticle(diameter S lOOnm) and transition metal components of PMIO (particulate matter with a diameter less than lO~m) have been implicated as playing major roles in the impairment of alveolar macrophage function and the subsequent retention of particles in the respiratory system. The aim of this study was to investigate the effects of components of PMIO on macrophage functions both directly, by examining macrophage phagocytosis and migration, and indirectly, by studying peripheral factors affecting macrophagefunction such as recruitment by type II cells and complement based mechanisms. We hypothesised that the alveolar epithelial type II cell line would release leukocyte chemoattractants in response to particle exposure and that this could be measured by use of a macrophage migration assay. A sub-toxic dose (125 ~g/ml)of surrogate air pollutionparticles (fine and nanoparticle carbon black and titanium dioxide) was established by measuring LOH release from a murine alveolar macrophage cell line (1774.2) and an alveolar epithelial type II cell line (L-2) in response to particle exposure. Optimisation ofa chemotaxis assay and measurement of macrophage migration towards conditioned medium obtained from the particle-exposed type II cells was conducted and it was determined that carbon black nanoparticles induced type II cells to secrete a chemoattractant that resulted in significant increases in macrophage migration compared to the negative control. This was in contrast to other particle types tested in this study which did not induce any increases in macrophage migration. It was also hypothesised that complement proteins could be involved in macrophage recruitment to sites of particle deposition and, as such, the migration of macrophages towards particle exposed blood serum was examined in vitro. Foetal bovine serum (FBS) was exposed to fine and nanoparticle caroon black and titanium dioxide (l-Smg/ml) for 2 hours. It was found, in accord with the previous study involving type II cells, that carbon black nanoparticles could activate the generation of chemotactic factors in serum that could subsequently induce significant increases (p < 0.001) in macrophage migration when serum was diluted to 10% using serum-free RPMI 1640 culture medium. This effect could be ameliorated by co-incubating the particle-treated serum in the presence of the antioxidant Trolox suggesting that oxidative stress played a role in the generation of the chemoattractant molecules. However, incubation of the serum with a pure oxidant at a range of doses did not result in the generation of chemotactic molecules suggesting that another factor could be involved in the chemoattractant generation. Further investigation to determine the exact molecular mechanism behind the chemoattractant generation is warranted. In contrast to the previous studies, we have also found evidence that components of PM₁₀ can cause decreased efficacy of macrophage clearance mechanisms in vivo and in vitro. It was hypothesised that PM₁₀ instillation would result in a decrease in macrophage phagocytic potential and an increase in chemotactic potential ex vivo. Rats were instilled with 125 and 250μg of PM₁₀ collected from North Kensington, London or sterile saline (negative control). Post-instillation (18 hours), significantly elevated concentrations of TNFa were detected in the BAL fluid together with a significant increase in the number of BAL neutrophils. Phagocytosis and chemotaxis assays conducted with BAL macrophages ex vivo showed that macrophage migration towards a positive chemoattractant, Zymosan Activated Serum (ZAS), was significantly lower than the macrophages obtained from the negative control rats. Macrophage phagocytosis of latex beads ex vivo was also found to be significantly decreased when PM₁₀ was visible inside the cell. An in vitro study where a macrophage cell line (J774.Al) was exposed to a low dose of nanoparticle carbon black (31.25μg) together with varying concentrations (100μM - 100nM) of zinc chloride (ZnCl₂) was also conducted. Exposure of macrophages to nanoparticle carbon black and zinc chloride alone induced a decrease in macrophage phagocytosis. It was found that when macrophages were co-exposed to nanoparticle carbon black and ZnCl₂, there was an additive decrease in macrophage phagocytic potential. The results contained within this manuscript demonstrate that the components of PM₁₀ can induce adverse effects on specific aspects of macrophage clearance mechanisms, but that nanoparticles can also stimulate the production of chemoattractants to aid in the recruitment of phagocytes and subsequent particle clearance. Although a contrary relationship appears to exist between these findings, the recruitment of leukocytes in response to particulate exposure is a mechanism that supports particle clearance. However, the retardation of phagocytic and chemotactic mechanisms in particle exposed macrophages may help to explain the increased toxicity, inflammation and retention time observed with nanoparticle inhalation.

Burkholderia sacchari é uma nova espécie bacteriana do solo brasileiro que tem a capacidade de crescer em sacarose e acumular grânulos intracelulares de poliésteres pertencentes à família dos polihidroxiaIcanoatos (PHA). Quando cultivado em sacarose, o homopolímero poli-3¬hidroxibutirato é acumulado por esta bactéria, que é usado como um plástico biodegradável e biocompatível. Quando sacarose e ácido propiônico são fornecidos como fontes de carbono, as células de B. sacchari acumulam o copolímero poli-3-hidroxibutirato-co-3-hidroxivalerato (P3HB-co-3HV). Entretanto, uma pequena porcentagem do ácido propiônico fornecido é convertido a unidades 3HV devido à eficientes vias catabólicas que convertem este substrato preferencialmente a biomassa, CO2 e água, reduzindo portanto a eficiência da produção do polímero. Ao menos duas vias do catabolismo de propionato foram previamente propostas em B. sacchari: a-oxidação e ciclo do 2-metilcitrato (2MCC), sendo somente a última confilmada no nível molecular. Mutantes UV, obtidos anteriormente, foram incapazes de crescer em propionato (prp) e também apresentaram fenótipo afetado no crescimento em intermediários da a-oxidação. No presente trabalho, após uma busca em bibliotecas genômicas de B. sacchari, uma delas construída também no presente trabalho, três diferentes fragmentos de DNA presentes nos clones AI, PI e P2 foram capazes de restaurar o fenótipo prp+ aos mutantes. Experimentos quantitativos revelaram que AI somente restaurou parcialmente a conversão de propionato a unidades 3HV aos mutantes. PI foi capaz de restaurar a capacidade de crescimento em propionato, e em outros intermediários da a-oxidação, a um dos mutantes. Um DNA de 1.2 Kb, subfragmento de PI, ainda capaz de complementar mutantes prp, foi subclonado e seqüenciado, demonstrando similaridade a seqüências de DNA codificadoras de reguladores transcricionais do tipo LysR de várias bactérias, incluindo espécies de Bllrkholderia. Regiões adjacentes a LysR em diferentes genomas de Burkholderia são anotados como codificadores de acil-CoA desidrogenases, ao lado de proposta acil-CoA transferases/carnitina desidrogenases e de uma permease do facilitador maior da superfamília MFS-l. Após confirmação das mesmas regiões adjacentes em B. sacchari e também a sua específica deleção, será possível provar a presença da via do catabolismo de propionato indicada neste trabalho.
Burkholderia sacchari is a new bacterial species from brazilian soil, able to grow in sucrose, accumulating intracellular granules of polyester belonging to the polyhydroxyalkanoate family (PHA). When cultivated on sucrose, the homopolymer poly-3-hydroxybutyrate is accumulated by this bacterium, which is used as biodegradable and biocompatible plastic. When sucrose and propionic acid are supplied as carbon sources, B. sacchari cells accumulate the copolymer poly-3-hydroxybutyrate-co-3-hydroxyvalerate (P3HB-co-3HV). However, a small percentage ofthe propionic acid supplied is converted to 3HV units, because efficient catabolic pathways convert this substrate preferentially to biomass, CO2 and water, thus reducing the efficiency of polymer production. At least two propionate catabolic pathways have been previously indicated in B. sacchari: a-oxidation and the 2-methylcitric acid (2MCC), the latter confirmed at molecular leveI. UV mutants previously obtained were unable to grow in propionate (prp) and also showed the phenotype affected concerning grow on intermediates of propionate a-oxidation. In the present work, after a screening in B. sacchari genomic libraries, one ofthem constructed also in the present work, the prp + phenotype was restored to the mutants by three different DNA fragments harbored by dones A), PI and P2. Quantitative experiments revealed that AI restored only partially the quantitative conversion of propionate to 3HV units to the mutants. PI restored the ability to grow in propionate and in other intermediates of a-oxidation to one prp mutant. A DNA 1.2 Kb subfragment of PI, still able to complement prp mutants, was subcloned and sequenced, showing similarity to DNA sequences encoding to LysR-type transcriptional regulators of various bacteria, including BlIrkholderia species. Adjacent regions to LysR in different genomes of BlIrkholderia are annotated as encoding to acyl-CoA dehydrogenases, neighboring a predicted acyl-CoA transferases/carnitine dehydratase and a permease ofthe major facilitator superfamily MFS-1. After confirmation ofthe same adjacent regions in B. sacchari and also their especific deletion, it will be possible to prove the presence of the pathway indicated here in the catabolism of propionate.

A micologia marinha é uma ciência relativamente recente e pouco se conhece sobre a diversidade das suas comunidades. Assim, o isolamento, triagem e preservação de fungos derivados do mar podem levar à descoberta de novas tecnologias. O objetivo deste estudo foi conhecer a diversidade de fungos filamentosos derivados marinhos e selecionar isolados capazes de produzir enzimas celulolíticas. Para tanto, foram isolados seletivamente fungos filamentosos a partir de amostras de macro-organismos marinhos coletados em 2007 e 2008. Os resultados demonstraram uma ampla diversidade de fungos potencialmente celulolíticos, pertencentes ao filo Basidiomycota e Ascomycota. Nos experimentos de produção de celulases, 17 apresentaram resultados satisfatórios de CMCase e FPase e foram selecionados para a avaliação da Celobiase. Os experimentos de cinética enzimática apresentaram os melhores resultados de produção de celulases em meio contendo farelo de trigo. O trabalho demonstra o potencial para aplicação biotecnológica dos fungos e estimula novos estudos com as celulases.
The Marine mycology is a relatively recent and little is known about the diversity of its communities. Thus, the isolation, separation and preservation of fungi derived from the sea can lead to the discovery of new technologies. The aim of this study was the diversity of filamentous fungi isolates derived marine and select capable of producing cellulolytic enzymes. It had been selectively isolated filamentous fungi from samples of marine macro-organisms collected in 2007 and 2008. The results showed a wide range of potential cellulolytic fungi, belonging to the phylum Basidiomycota and Ascomycota. In the experiments to produce cellulases, 17 had satisfactory results of CMCase and FPase and were selected for evaluation of cellobiase. The enzyme kinetics experiments showed better results for the production of cellulases in a medium containing wheat bran. The work demonstrates the potential for biotechnological application of fungi and stimulate further research with cellulases.

Chlamydia trachomatis (CT) replicates in macrophages, but is inhibited by IFN-$\gamma$ or LPS. IFN-$\gamma$ and/or LPS induced nitrite production in mouse peritoneal macrophages, macrophage cell lines (RAW264.7 and J774A.1) and McCoy cells. Kinetic studies indicated that peak production occurred 48 hours post-treatment. CT infection itself was insufficient to induce nitrite production, but resulted in enhancement of nitrite production in IFN-$\gamma$-treated cells. Treatment with IFN-$\gamma$ or LPS resulted in significant inhibition of CT replication in these cells. Strong correlation between nitrite production and inhibition of CT replication was observed in RAW264.7 and J774A.1 cells (correlation coefficients: $-$0.93 and $-$0.94, p $<$ 0.001). N$\sp{\rm g}$- monomethyl-L-arginine (L-NMMA) specifically inhibited nitrite production and partially reversed inhibition of CT replication in macrophage cell lines. NOS mRNA was measured in RAW264.7 cells by Northern blot and Dot blot hybridization. Strong correlation between NOS mRNA expression and inhibition of CT replication (correlation coefficient: $-$0.97, p $<$ 0.05) was observed. Anti-TNF-$\alpha$ antibody completely neutralized the biological activity of TNF-$\alpha$ secreted by LPS-treated RAW264.7 cells, yet the antibody neither reduced nitrite production nor restored CT replication. Combination of the antibody and L-NMMA significantly enhanced restoration of CT replication. In peritoneal macrophages, inhibition of CT replication induced by IFN-$\gamma$ was partially restored by L-NMMA or anti-TNF-$\alpha$ antibody. In McCoy cells, inhibition of CT replication induced by IFN-$\gamma$ and LPS was not significantly restored by L-NMMA. Great restoration of CT replication by 1 mM L-NMMA was observed in LPS-treated J774A.1 cells (31%), but not in IFN-$\gamma$-treated cells (5%). Our data indicate that (1) NO production is one of the mechanisms for inhibition of CT replication in IFN-$\gamma$-activated peritoneal macrophages and RAW264.7 cells; (2) NO plays a significant role in CT inhibition in LPS-treated macrophage cell lines, but not peritoneal macrophages; (3) TNF-$\alpha$ may be associated with inhibition, but the mechanism(s) may not involve NO production; (4) NO production may not be the mechanism for CT inhibition in McCoy cells treated with IFN-$\gamma$ and LPS.

Tendo em vista a importância do processo esterilizante aplicado a produtos farmacêuticos e aos produtos médico-hospitalares, distintos métodos foram desenvolvidos de forma a possibilitar sua aplicação, inclusive a materiais termossensíveis. Neste contexto, o processo que se tornou mais amplamente empregado consiste naquele utilizando o óxido de etileno. Este agente, devido às características de inflamabilidade e explosividade, tem sido usado diluído em gases inertes, predominantemente os clorofluorcarbonos (CFCs), que contornam tais problemas. Conhecimentos recentemente adquiridos e consenso internacional quanto ao risco da depleção da camada de ozônio da estratosfera ocasionaram a busca de alternativas, dentre as quais a adoção dos hidroclorofluorcarbonos (HCFCs). O delineamento do presente trabalho objetivou a comparação da eficácia esterilizante de misturas de óxido de etileno em CFC 12 (Oxyfume 12R), e em HCFCs 22 e 124 (Oxyfume 2002R), quando aplicadas em diferentes concentrações (450 mg/L e 600mg/L) e sob distintas temperaturas (45°C, 55°C e 65°C). Procedeu-se a desafios subletais (3, 6 ,9, 12 e 15 minutos de exposição), empregando a cada ciclo seis indicadores biológicos laboratorialmente preparados, com esporos de Bacillus subtilis var. niger ATCC 9372 obtidos em garrafas de Roux contendo meio de esporulação, sendo a seguir padronizados, inoculados em suportes celulósicos e acondicionados em embalagens filme-papel, perfazendo um total de 1080 monitores. Paralelamente foram também submetidos a desafios indicadores biológicos de aquisição comercial (AttestR 1264, 3M), dois a cada ciclo, perfazendo 360 unidades. Os resultados de resistência obtidos (valor D) nos 180 ciclos privilegiaram estes últimos, levando tal resultado a considerações quanto ao procedimento de purificação da suspensão de esporos e diferenças existentes entre suportes e acondicionamentos empregados. A eficácia esterilizante de ambas as misturas, Oxyfume 12R e Oxyfume 2002R, revelou-se equivalente, mesmo em diferentes concentrações. Além de observações que evidenciaram os efeitos significantes quanto à preparação dos indicadores biológicos, foi evidente e estatisticamente significante ( p=1% ) o efeito do aumento da temperatura, promovendo efeito mais intenso sobre a letalidade dos esporos. Numa outra abordagem, de conotação ocupacional, procedeu-se também no decorrer do trabalho experimental à monitoração do ambiente quanto a resíduos de óxido de etileno, usando bomba e tubos de detecção da DragüerR: os resultados obtidos nas diferentes posições e momentos, inferiores a 1 ppm, proporcionaram a conclusão de que, respeitando a adoção dos conceitos de engenharia indicados na Portaria Interministerial nº 482 de 16 de abril de 1999, publicada no Diário Oficial da União do dia 19 do mesmo mês e ano, é obtida condição compatível com a presença humana. É portanto gratificante que se possa concluir o trabalho com o sentimento de que efetivamente se tenha constituído em contribuição no sentido de permitir a manutenção de emprego do processo esterilizante em pauta, conferindo segurança ao paciente no uso de produtos, sem entretanto comprometer a vida humana em nosso planeta.
Taking into account the importance of the sterilization process applied to medicines and medical devices, different kinds of methods have been developed, also applicable to heat sensitive materiais. Ethylene oxide is the process most widely applied to medical devices. Due its explosiveness and inflamability, it has been used associated to non active gases, wich inhibit these properties, mainly the chlorofluorocarbons (CFCs). Recent knowledge about ozone-depleting gases and an international consensus on the need of reducing their effects are promoting a search for alternative chemicals. From these, one of the most interesting are the hydrochlorofluorocarbons (HCFCs) which, besides having this role, can also be used as transitional compounds while more environmentally suitable compounds are not available. This paper aims to compare two ethylene oxide sterilization mixtures: Oxyfume 12R (using CFC 12) and Oxyfume 2002R (using HCFCs 22 and 124), under different concentrations (450mg/L and 600mg/L) and different temperatures (45°C, 55°C and 65°C). To accomplish this procedure, sub-Iethal challenges were performed (3, 6, 9, 12 and 15 minutes of exposition), in a total of 180 cycles, using six biological indicators per cycle prepared in a laboratory, in a total of 1080 units, as well as two others purchased from an American supplier (AttestR 1264, 3M), in a total of 360 units. The former indicators were obtained using Bacillus subtilis var. niger ATCC 9372 in Roux bottles, innoculated on paper carriers and wrapped up on protective packaging. The posterior lethality study and D value calculation highlighted the highest resistance of AttestR indicators in comparison with the laboratory ones. This can be explained by different leveIs of spores purification, alongside with the differences between the carriers and packaging used in both cases. The sterilizing efficacy of Oxyfume 12R and Oxyfume 2002R revealed equivalent results, even in different concentrations. The influence of higher temperatures was efficient (p=1,0). Aiming at occupational safety, environmental monitoration was also performed related to ethylene oxide, using DragüerR detection tubes and foley pump. The results, obtained in different positions and moments under 1 ppm, confirmed that the engineering concepts indicated by the Portaria Interministerial nº 482 from 16 april 1999, published on the 19th of the same month in the Diário Oficial, offer residual safe levels compatible with human presence. It is therefore gratifying to conclude that the sterilization process using Oxyfume 2002R is both an efficient contribution to a safe utilization of products and, at the same time, to preserve the animallife on Earth.

Micro-organismos fotossintetizantes, incluído aqui o gênero Arthrospira, vêm sendo amplamente produzidos em larga escala em vários países, detendo um mercado que gera mais de 1 bilhão de dólares ao ano. A produção industrial utiliza grande volume de água com alta concentração salina para produzir milhares de toneladas de biomassa microalgal. É crescente a utilização de tratamento de águas por processo de separação por membranas, demonstrando ser uma técnica que gera água de ótima qualidade, de instalação compacta e de fácil automação. No presente trabalho, foi avaliada esta tecnologia para o reaproveitamento do meio de cultura em novos cultivos de micro-organismos fotossintetizantes, visando contribuir para a sustentabilidade deste processo produtivo. O efluente do cultivo de Arthrospira platensis oriundo de processo descontínuo em minitanques foi submetido a tratamento por membranas de filtração tangencial, incluindo microfiltração (MF) (porosidades de 0,65 µm e de 0,22 µm) e ultrafiltração (UF) (peso molecular de corte de 5.000 Da), em pressões transmembrana (TMP) de 22,5 a 90 kPa. Os processos de MF levaram a reduções médias de 53,9±1,3 % e 93,1±1,1 % de matéria orgânica natural (NOM) e pigmentos nos meios residuais, respectivamente. Com o uso de processos de UF, cujos meios foram previamente tratados por MF (0,22 µm e 22,5 kPa), as reduções médias de NOM e pigmentos foram de 57,2±0,5 % e 94,0±0,8 %, respectivamente. Os processos de MF com TMP de 22,5 kPa levaram a concentrações celulares máximas (Xm) equivalentes às obtidas com meio novo. O uso de membrana de 0,65 µm e TMP de 22,5 kPa levou a uma perda média de 2,9 %, 22,7 % e 16,4% dos nutrientes carbonato, fosfato e nitrato, respectivamente, mas a correção desses valores aos mesmos do meio padrão levou à obtenção dos mais altos valores de Xm (3586,6±80 mg L-1), produtividade em células (505,0±11,6 mg L-1 d-1) e fator de conversão de nitrogênio em células (29,6±0,7 mg mg-1). O teor protéico da biomassa foi estatisticamente igual ao da biomassa obtida de cultivo com meio padrão novo. Os dados deste trabalho evidenciam que processos de filtração por membrana são promissores para o reuso de meio de micro-organismos fotossintetizantes.
Photosynthetic microorganisms, including here the genus Arthrospira, have been produced worldwide in large scale, in a market which generates more than $ 1 billion a year. The industrial production uses huge volume of water with high salinity to produce thousands of tons of microalgal biomass. It is increasing the use of membrane separation process in water treatment, proving to be a technique that generates high quality water, compact and easy both installation and automation. In this study, it was evaluated this technology for the recycling of the culture medium to produce photosynthetic microorganisms, aiming to contribute to the sustainability of this production process. The effluent from Arthrospira platensis culture originating from batch process in laboratory-scale open raceway tanks was treated by tangential flow filtration with microfiltration (MF) (membrane pore size of 0.65 µm and 0.22 µm) and ultrafiltration (UF) (molecular weight cut-off of 5,000 Da), using transmembrane pressure (TMP) from 22.5 up to 90 kPa. MF processes led to average reductions of 53,9±1.3% and 93.1±1.1% of natural organic matter (NOM) and pigments in the exhausted media, respectively. With the use of UF process, whose media were pre-treated by MF (0.22 µm and 22.5 kPa), the average NOM and pigments reductions were 57.2±0.5% and 94.0±0.8%, respectively. The MF process with TMP of 22.5 kPa led to maximum cell concentrations (Xm) equivalent to those obtained with the new medium. The use of membrane of 0.65 µm under TMP of 22.5 kPa led to an average loss of 2.9%, 22.7% and 16.4% of the nutrients carbonate, phosphate and nitrate, respectively, but correcting the concentration of these nutrients to those values present in the standard medium led to obtain the highest Xm (3586.6±80 mg L-1), cell productivity (505.0±11.6 mg L-1 d-1) and nitrogen-to-cell conversion yield (29.6±0.7 cells mg mg-1). The protein content of this biomass was statistically equal to that one obtained from cultivation with standard new medium. Data from this study show that membrane filtration processes are promising for reuse media in cultivation of photosynthetic microorganisms.

Apesar da industrialização no setor farmacêutico, o emprego de drogas vegetais constitui desafio atual quando considerado alternativa terapêutica para as populações de baixa renda ou aquelas que apresentam tradição no uso dessas drogas. Além disso, tendências modernas valorizam a variedade de espécies com propriedades curativas, em particular as espécies brasileiras, desafiando os pesquisadores a intensificar investigações nessa área e induzindo à população um crescente consumo. Assim, questões relacionadas à qualidade dessas drogas apresentam fundamental importância. Devido à origem, a carga microbiana detectada nas mesmas é normalmente elevada, oferecendo riscos potenciais ao usuário. Desta forma, a avaliação de sua qualidade sanitária constitui etapa obrigatória no que se refere ao aspecto de segurança ao consumidor. Além disso, a eficácia terapêutica pode igualmente ser comprometida por decomposição de componentes, decorrente da ação de microrganismos. Com o objetivo de eliminar os efeitos decorrentes da biocarga presente nas drogas vegetais, agentes descontaminantes, de natureza física ou química, têm sido empregados. A utilização de tais procedimentos de descontaminação, prevista na legislação vigente, requer estudos relacionados à estabilidade dos princípios ativos após exposição ao agente selecionado. Dentre os agentes destaca-se a irradiação gama, amplamente utilizada em função de sua aplicabilidade na ausência de água e de temperatura elevada, além de apresentar alta penetrabilidade e reduzir, com eficácia, a carga microbiana viável. Os objetivos do presente trabalho foram avaliar os efeitos de diferentes doses de radiação ionizante sobre a carga microbiana de quatro espécies de drogas vegetais: alcachofra (Cynara scolymus L.), camomila (Matricaria recutita L.), ginkgo (Ginkgo biloba L.) e guaraná (Paullinia cupana H.B.K.), bem como detectar possíveis alterações provocadas pela radiação sobre os teores de seus princípios ativos. As análises microbiológicas e químicas foram realizadas antes e após irradiação com doses médias de 5,5 kGy, 11,4 kGy e 17,8 kGy. Os resultados obtidos anteriormente à irradiação revelaram elevados níveis de contaminação: média de 4,1 x106 para microrganismos aeróbicos totais e 3,3x105 para fungos. Após descontaminação, a dose média de 11,4 kGy, reduziu a carga de microrganismos aeróbicos totais a níveis menores ou iguais a 102 em todas as drogas, com exceção da camomila proveniente do fornecedor B (3,2x104). Para os fungos, a menor dose aplicada (5,5 kGy) foi suficiente para reduzir a contagem a níveis da ordem de 10. Com relação à determinação dos marcadores nas drogas vegetais, os resultados obtidos não revelaram alterações significativas nos teores de cafeína no guaraná e de glicosídeos flavonoídicos no ginkgo. Para a camomila, as amostras antes a após irradiação, apresentaram o mesmo teor de óleo volátil bem como ausência de diferenças significativas no teor de α-bisabolol. Em contraste, observou-se redução no teor de 7-glicosil apigenina após submissão à radiação ionizante, indicando degradação decorrente do processo. Com relação à alcachofra, permanece ainda desconhecida a influência da radiação devido à ausência de metodologias adequadas para extração e determinação da cinarina.
Despite industrialization in the pharmaceutical area, the use of vegetable drugs is being considered a therapeutical alternative either for underprivileged people or for those who are already used to their consumption. Furthermore there is presently a tendency to value those species with healing property, mainly the Brazilian ones, what is stimulating research and their increasing consumption. Thus, issues concerning the quality of such drugs are extremely important, mainly due to the fact that their microbial load offers potential risks to consumers. Consequently, the evaluation of their sanitary conditions has become fundamental, also owing to the fact that their therapeutical efficacy can be harmed by the decomposition of their components, as a result of the action of microorganisms. Therefore, physical or chemical decontamination has been employed as a measure to reduce the bioburden. Although these procedures are being legally performed they require studies concerning the stability of the active principles after the process. Gamma irradiation has been one of the most important decontaminating agents, widely used due to its applicability in the absence of water or high temperature and to its property of presenting high penetration and efficiently reducing the viable microbial load. This work aimed at evaluating the effects of different radiation doses over the microbial burden of four kinds of vegetable drugs: artichoke (Cynara scolymus L.), chamomile (Matricaria recutita L.), ginkgo (Ginkgo biloba L.) and guarana (Paullinia cupana H.B.K.). The detection of possible alterations provoked by radiation on the contents of their active principies has also been a goal of this study. The microbiological and chemical analyses were performed before and after irradiation with average doses of 5,5 kGy, 11,4 kGy and 17,8 kGy. The results revealed high contamination levels: average of 4,1 x106 for total aerobic microorganisms and 3,3x105 for fungi. After decontamination the average dose of 11,4 kGy reduced the total aerobic microbial count to levels below or equal to 102 in all drugs, except the chamomile provided by supplier B (3,2x104). For fungi, the lowest dose applied (5,5 kGy) was enough to reduce the count to a level of 10. As to the determination of markers in vegetable drugs, the results obtained presented no significant alterations in cafein contents of guarana or in flavonol glycosides of ginkgo. The samples of chamomile, both prior to and after radiation presented the same yield of essential oil as well as absence of significant differences in the contents of α-bisabolol. On the other hand, a reduction in the concentration of apigenin-7-glycoside after irradiation was observed, what indicates degradation caused by the process. The influence of radiation over artichoke remains unknown due to the absence of adequate methods of extraction and determination of cinarin.

Thesis (Ph.D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Biological activity has shaped the surface of the earth in numerous ways, but life's most pervasive and persistent global impact has been the secular oxidation of the surface environment. Through primary production - the biochemical reduction of carbon dioxide to synthesize biomass - large amounts of oxidants such as molecular oxygen, sulfate and ferric iron have accumulated in the ocean, atmosphere and crust, fundamentally altering the chemical environment of the earth's surface. This thesis addresses aspects of the role of marine microorganisms in driving this process. In the first section of the thesis, biomarkers (hydrocarbon molecular fossils) are used to investigate the early history of microbial diversity and biogeochemistry. Molecular fossils from the Transvaal Supergroup, South Africa, document the presence in the oceans of a diverse microbiota, including eukaryotes, as well as oxygenic photosynthesis and aerobic biochemistry, by ca. 2.7Ga. Experimental study of the oxygen requirements of steroid biosynthesis suggests that sterane biomarkers in late Archean rocks are consistent with the persistence of microaerobic surface ocean environments long before the initial oxygenation of the atmosphere. In the second part, using Prochlorococcus (a marine cyanobacterium that is the most abundant primary producer on earth today) as a model system, we explored how microbes use the limited nutrient resources available in the marine environment to make the protein catalysts that enable primary production. Quantification of the Prochlorococcus proteome over the diel cell-division cycle reveals that protein abundances are distinct from transcript-level dynamics, and that small temporal shifts in enzyme levels can redirect metabolic fluxes. This thesis illustrates how molecular techniques can contribute to a systems-level understanding of biogeochemical processes, which will aid in reconstructing the past of, and predicting future change in, earth surface environment
by Jacob Richard Waldbauer.
Ph.D.

O tratamento antimicrobiano pode destruir o equilíbrio da microbiota gastrintestinal, podendo induzir sintomas clínicos, principalmente a diarréia. A influência de Lactobacillus casei Shirota sobre a microbiota intestinal foi avaliada em um estudo prospectivo, randomizado, duplo-cego e controlado. Sessenta e três crianças hospitalizadas com idade de 2 a 14 anos, sob tratamento com antibióticos β-lactâmicos, foram randomizadas para receber o leite fermentado por L. casei Shirota, 108-9 UFC/mL, ou o placebo, durante o tratamento antimicrobiano. As amostras de fezes foram colhidas antes da administração do leite fermentado, durante o tratamento antibiótico e uma semana após o término do tratamento com o antimicrobiano e a ingestão do leite fermentado. O número de L. casei Shirota aumentou significativamente (p<0,001) durante o período de ingestão do leite fermentado. Foi observado na microbiota do grupo que recebeu o placebo um aumento na contagem de Pseudomonas aeruginosa (p<0,05) e Clostridium sp (p<0,05), principalmente no último período da terapia antimicrobiana. A alteração da microbiota intestinal em decorrência do tratamento antibiótico foi constatada pela diminuição de acetato (p<0,05), butirato (p<0,05) e formato (p<0,05). Embora nenhuma criança deste estudo tenha apresentado diarréia, na avaliação geral, a microbiota daquelas que receberam o leite fermentado mostrou uma recuperação precoce da microbiota intestinal. Foi observado que a variação da contagem bacteriana realizada não foi significativa para as crianças do grupo que recebeu o leite fermentado, enquanto que no grupo placebo a contagem bacteriana ficou alterada, mostrando desequilíbrio da microbiota. Cerca de 50% das crianças ainda apresentaram L. casei Shirota nas fezes após uma semana da ingestão do leite fermentado. Este estudo mostrou que a ingestão do leite fermentado contendo L. casei Shirota promoveu um reequilíbrio mais rápido da microbiota intestinal quando comparada com a do grupo que ingeriu o placebo.
Antimicrobial treatment can destroy the balance of gastrointestinal microflora, which may induce clinical symptoms, mainly diarrhoea. The influence of Lactobacillus casei Shirota on the intestinal microflora was assessed in a prospective, randomised, double-blind controlled study. Sixty-three hospitalised children, with ages between 2 and 14 years, under treatment with β-lactam antibiotics were randomised to receive milk fermented by L. casei Shirota, 108-9 CFU/mL, or placebo during the antimicrobial treatment. Stool samples were collected before the administration of fermented milk, during the antibiotic treatment, and one week after the end of treatment with the antimicrobial agent and the ingestion of fermented milk. The number of L. casei Shirota increased significantly (p<0.05) during the period in which fermented milk was ingested. An increase in the Pseudomonas aeruginosa (p<0.05) and Clostridium sp (p<0.05) count was observed in the microflora of the group that received placebo, mainly in the last period of antimicrobial therapy. The alteration of intestinal microflora as a result of antibiotic treatment was found by the reduction of acetate (p<0.05), butyrate (p<0.05) and formate (p<0.05). The variation in bacterial count proved not to be significant for the children under antimicrobial treatment who received fermented milk, while the placebo group showed imbalance of microflora with the result of the altered bacterial count. About 50% of the children still presented L. casei Shirota in their stools after interrupting the ingestion of fermented milk for one week. This study showed that ingestion of fermented milk containing L. casei Shirota promoted a much faster re-balance of the intestinal microflora when compared to the group that ingested a placebo.

O Brasil é um dos maiores produtores mundiais de suco de laranja, da mesma forma que a produção é elevada, a geração de resíduos também é significativa. Sabe-se que estes resíduos, os quais incluem sementes, cascas e restos de polpa são ricos em nutrientes que poderiam ser utilizados como substrato por micro-organismos, seja para o crescimento ou para a obtenção de subprodutos. Esporos de Bacillus atrophaeus ATCC 9372 são utilizados como indicadores biológicos, IBs, em processos térmicos por formarem esporos termorresistentes. O objetivo deste trabalho foi avaliar o uso de resíduos do processamento de suco de laranja como um meio de cultura alternativo para obtenção de esporos de B. atrophaeus, para serem aplicados em processos industriais. Ao bagaço de laranja (de 1,0 g a 20,0 g), obtido por processamento em centrífuga de frutas, foram adicionados 100 mL de água, e incubados a 150 rpm / 37 ºC por até 6 dias. Evidenciada a viabilidade de crescimento celular (µmáx = 0,0238 h-1 e Px = 0,0787 g/L.h, para 5,0 g de bagaço) procedeu-se ao estudo de planejamento experimental fatorial 22 em formato estrela com 6 pontos centrais, considerando a concentração de bagaço e o volume de meio. Foram determinados os valores de pH, de biomassa, de esporos viáveis e a resistência térmica dos mesmos a 102 ºC. Observou-se que houve aumento nos valores de pH após o cultivo e que as maiores concentrações de esporos foram de 1,73 x 109 esporos /mL e 5,75 x 109 esporos /mL após 3 e 6 dias de cultivo e os tempos de redução decimal determinados variaram de D102C = 0,92 min a D102C = 2,71 min e de D102C = 1,34 min a D102C = 3,98 min após 3 e 6 dias de cultivo, respectivamente. Com base no planejamento proposto e a análise de regressão, o desenvolvimento de esporos em bagaço segue a relação: Esporos = {-1,15 + 0,0303* [bagaço (g)] - 0,00611* [volume (mL)] + 0,611* [tempo (dias)]}, p=0,000, R2 =0,452, sendo o tempo (p=0,000) o fator de maior influência na formação de esporos. Os meios preparados com bagaço de laranja apresentaram-se viáveis para a produção de esporos de B. atrophaeus termorresistentes, produto de interesse farmacêutico e industrial, agregando valor ao resíduo que seria descartado.
Brazil is one of the world´s largest producers of oranges juice, in the same way that the production is high the amount of generated waste is also significant. It is well known that these residues, which include seeds, peel and pulp, are rich in nutrients that could be used as substrate by microorganisms whether for growth or for obtaining by-products. Bacillus atrophaeus ATCC 9372 spores are used as biological indicators, BIs, in thermal processes due to their ability to form heat-resistant spores. This study aimed to evaluate the use of orange juice processing waste as an alternative culture media to obtain B. atrophaeus spores, to be applied in industrial processes. To orange\'s bagasse (from 1.0 g to 20.0 g), obtained by processing in a fruit\'s centrifuge, 100 mL of water was added, and sterilized at 121 ºC. An aliquot of 0.1g/L of Bacillus atrophaeus spores was inoculated to bagasses\'s media and incubated at 150 rpm / 37 ºC up to 6 days. As cells (µmáx = 0.0238 h-1 and Px = 0.0787 g/L.h, for 5.0 g of bagasse) were obtained, a factorial experimental design 22, with star-shaped model and 6 central points, was performed considering the bagasse concentration and the media volume used. Values of pH, biomass, viable spores and their thermal resistance at 102 ºC were determined. It was observed that pH increased after cultivation and major values of spore concentration achieved were 1.73 x 109 spores /mL and 5.75 x 109 spores /mL after 3 and 6 days, respectively. Decimal reduction times determined ranged from D102C = 0.92 min to D102C = 2.71 min and from D102C = 1.34 min to D102C = 3.98 min after 3 and 6 days of incubation, correspondingly. The regression analysis showed that the development of spores in bagasse can be defined by the equation: Spores = , p=0.000, R2 =0.452 and time has a positive influence in the spore formation. Results demonstrated media prepared with oranges\' bagasse were capable to grow and to develop B. atrophaeus heat-resistant spores, being an alternative to add value to a waste that would be discarded, generating a product of great importance in the pharmaceutical field.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2008.
Includes bibliographical references (leaves 52-56).
Functional screening of environmental genomic libraries permits the identification of clones expressing activities of interest without requiring prior knowledge of the genes responsible. In this study, protocols were optimized for the construction of mid-size DNA insert, inducible expression environmental genomic plasmid libraries for this purpose. A library with a mean insert size of 5.2 kilobases was constructed with environmental DNA isolated from surface ocean water collected at Hawaii Ocean Time-series station ALOHA in plasmid cloning vector pMCL200 under the inducible control of the PLAC promoter. To begin to evaluate the utility of such libraries for gene expression-based screens, this library was screened phenotypically for clones expressing genes that confer fluorescence or distinctive coloration on colonies of host Escherichia coli cells, and results were compared to those for a fosmid library constructed from the same marine microbial DNA sample. Ecologically relevant sequences were identified in both libraries, and each was observed to offer both advantages and disadvantages. Results of this study suggest that mid-size insert plasmid libraries under the control of inducible promoters can provide a useful and complementary approach for both functional screening and shotgun sequencing of environmental genomic libraries.
by Jennifer C. Braff.
S.M.

A análise da qualidade microbiana de matérias-primas e de produtos por meio da técnica convencional de contagem de microrganismos exige demanda elevada de trabalho e fornece resultados em período de tempo não compatível com o desenvolvimento da tecnologia. A indústria farmacêutica e cosmética necessita de liberação rápida de seus produtos, assim métodos alternativos podem reduzir o tempo de trabalho e custo. O método de ATP bioluminescência detecta a presença ou ausência de microrganismos em até 24 horas. O método baseia-se na reação do ATP (adenosina trifosfato) provenientes do microrganismo com o complexo luciferina - luciferase, produzindo luz. Os componentes da formulação de produtos cosméticos, como os corantes e os pigmentos podem interferir na reação e influenciar na leitura da Unidade Relativa de Luz (URL). O objetivo do experimento foi validar método de ATP bioluminescência para avaliação da qualidade microbiana do pigmento Green Nº 7 e dos corantes FD&C Blue Covanor e o FD&C Red Nº 5, usados em produtos cosméticos, verificando se esses podem interferir na reação de ATP-bioluminescência , utilizando os meios de cultura TAT(Tryptone-Azolectin-Tween) , DE ( Dey Engly Neutralization Broth) e LB (Letheen Broth) . A primeira etapa da validação do sistema ATP bioluminescência foi determinar o Efeito da Amostra nas suspensões o qual verifica a presença de ATP não microbiano. A sensibilidade do ensaio foi analisada por meio do teste de limite de detecção inoculando-se os microorganismos Escherichia coli ATCC 8739, Burkholderia cepacea ATCC 25416, Staphylococcus aureus ATCC 6538, Candida albicans ATCC 10231 na suspensão das amostras. Para C. albicans não foi possível a detecção pois houve a necessidade de tempo maior de incubação. O meio de cultura TAT sem acréscimo de polissorbato 80 apresentou as melhores condições para a validação do pigmento Green Nº 7. Para corantes há necessidade ainda de uma investigação mais criteriosa, estudando outros meios de cultura, reagentes e condições que propiciem resultados adequados em conformidade com as especificações para a validação.
The analysis of the microbiology quality of raw materiais and finished products by means of the conventional technique of counting of microorganism demands high time of work and supplies resulted in period of not compatible time with the development of the technology. The rapid methods provide reliable and cost effective analysis for the microbiological evaluation the pharmaceutical and cosmetic industry. The ATP Bioluminescence detect the presence or absence of microorganisms the reduction in detection times and analysis from 72 hours to 24 hours. The bioluminescence assay is based upon the light-producing enzyme luciferase that will hydrolyze ATP to produce light. Light production is detected by a luminometer and recorded as relative light units (RLU). The purpose of this investigation was to develop and validate the use an ATP bioluminescence assay for detection microbial contamination in artificially contaminated commercial Green Nº 7 pigment and FD&C Blue Covanor e o FD&C Red Nº 5 dyes with some microbial cultures, TAT (Tryptone-Azolectin-Tween) , DE (Dey Engly Neutralization Broth) e LB (Letheen Broth), and to compare the results against standard microbiological analysis. The first step in validation of the ATP bioluminescence system was to determine the sample effect of the sample suspensions on the bioluminescence reaction where analyzed to determine whether the sample contained nonmicrobial ATP. The sensitivity of the assay to detect different levels of Escherichia coli ATCC 8739, Burkholderia cepacea ATCC 25416, Staphylococcus aureus ATCC 6538, Candida albicans ATCC 10231 was analyzed by spiking into the samples suspensions. For C. albicans contamination detection has not been possible because it has required more time than bacteria. The microbial culture TAT without addition of polissorbato 80 has presented the best conditions for the validation of the Green pigment n° 7. For dyes has still been necessity of studying other microbial culture, reagents and conditions that they propitiate resulted adequate in compliance with the specifications for the validation.

Human Papillomavirus (HPV) is the cause of cervical cancers (among these, adenocarcinoma, AdCa) and is associated to a subgroup of oropharyngeal carcinomas (OPSCCs). Even if the risk for cancer development is linked to the infection by some viral genotypes, mainly HPV16 and 18, viral DNA alone seems not to be sufficient for diagnosis. Moreover, the role of the virus in OPSCCs has not been totally clarified yet. In the first part of the thesis, the performances concerning viral genotyping in clinical cervical samples of a new pyrosequencing-based test and a well-known hybridization-based assay have been compared. Similar results between the methods have been obtained. However, the former showed advantages in detecting intratype variants, higher specificity and a broader spectrum of detectable HPV types. The second part deals with the evaluation of virological markers (genotyping, viral oncoproteins expression, viral load, physical state and CpG methylation of HPV16 genome) in the diagnosis/prognosis of cervical AdCa and HPV-associated OPSCCs. HPV16 has been confirmed the most prevalent genotype in both the populations. Interestingly, the mean methylation frequency of viral DNA at the early promoter showed the tendency to be associated to invasion for cervical AdCa and to a worse prognosis for OPSCCs, suggesting a promising role as diagnostic/prognostic biomarker. The experiments of the third part were performed at the DKFZ in Heidelberg (Germany) and dealt with the analysis of the response to IFN-k transfection in HPV16-positive cervical cancer and head&neck carcinoma cell lines to evaluate its potential role as new treatment. After 24h, we observed increased IFN-b expression which lead to the up-regulation of genes involved in the antigens presentation pathway (MHC class I and immunoproteasome) and antiviral response as well, in particular in cervical cancer cell lines. This fact suggested also the presence of different HPV-mediated carcinogenic pathways between the two anatomical districts.
Il Papillomavirus umano (HPV) è causa dei carcinomi della cervice uterina (tra cui adenocarcinomi, AdCa) ed è associato ad un sottogruppo di tumori dell’orofaringe (OPSCCs). Nonostante il rischio di sviluppo di tumore sia associato all’infezione da parte di alcuni genotipi virali, principalmente HPV16 e 18, il DNA virale da solo sembra non essere sufficiente in campo diagnosico. Inoltre, per tumori orofaringei il ruolo del virus non è ancora del tutto chiaro. Nella prima parte della tesi, sono state confrontate le performance riguardo la genotipizzazione di HPV su campioni clinici cervicali di una tecnica innovativa, basata su amplificazione e pirosequenziamento, e una di routine, basata su amplificazione e ibridazione inversa. Lo studio ha evidenziato performance simili tra le due metodiche, sottolineando per il sequenziamento una maggiore specificità e capacità di rilevare varianti intratipo. Nella seconda parte sono stati analizzati marker virologici (genotipizzazione, espressione delle oncoproteine virali, carica virale, stato fisico e metilazione del genoma di HPV16) in funzione dei dati clinici disponibili, per un possibile impiego nella diagnosi/prognosi di AdCa cervicali e OPSCCs HPV-associati. HPV16 si è confermato il genotipo prevalente in entrambe le popolazioni. La frequenza di metilazione nel promotore precoce virale ha mostrato una tendenza ad essere associata ad invasione negli AdCa, e ad una prognosi peggiore negli OPSCCs, emergendo come il più promettente marker diagnostico/prognostico. La terza parte, svolta presso il DKFZ di Heidelberg (Germania), ha visto l’analisi della risposta alla transfezione di IFN-k in linee cellulari tumorali HPV16-positive della cervice uterina e della regione testa-collo, per valutarne l’impiego terapeutico. Dopo 24h, è stato osservato un incremento dell’espressione di IFN-b e, di conseguenza, una up-regolazione dei geni coinvolti nella presentazione antigenica (MHC classe I ed immunoproteasoma) e nella risposta antivirale, specialmente nelle cellule cervicali, suggerendo la presenza di diversi meccanismi patogenetici tra tumori HPV-positivi dei due distretti anatomici.

Células transformadas de E.coli DH5-α expressando a proteína verde fluorescente (GFPuv, pico de excitação e emissão de 394nm e 509nm) foram submetidas a extração pelo método de partição de três fases (TPP) e o extrato obtido purificado por cromatografia de interação hidrofóbica (HIC). O objetivo principal deste trabalho foi estudar a termoestabilidade da GFPuv extraída, para avaliar a sua possível utilização como indicador biológico econômico, de resposta rápida e precisa para processos térmicos de esterilização utilizando o calor úmido. A estabilidade térmica da proteína foi estudada em diferentes soluções-tampão (acetato, fosfato e tris-HCI 10mM) no intervalo de valor de pH de 5,O a 9,0 e, em temperaturas entre 75° e 95°C. Os parâmetros de resistência térmica determinados foram: o tempo de redução decimal (Valor D - min), valor z (°C), coeficiente Q10 e valor de energia de ativação (kcal/mol). A termoestabilidade da GFPuv, expressa em valor D, mostrou correlação linear para valores de pH ≥ 5,50, em tampão acetato. Em tampão fosfato, para valores de pH ≥ 7,50 a estabilidade térmica da proteína foi independente do valor de pH da solução. Em tampão tris-HCI, o valor D mostrou-se inconstante ao aumento do valor de pH da solução. No intervalo de temperatura estudada, em tampão acetato a GFPuv apresentou melhor termoestabilidade (Ea de 19,27 kcal/mol) do que em tampão fosfato (Ea de 26,18 kcal/mol ao valor de pH 6,S) e em tampão tris-HCI (Ea 28,19 kcallmol ao valor de pH 7,0). Em tampão acetato e tris-HCI ao valor de pH 7,0, a termoestabilidade da proteína mostrou-se equivalente. Entretanto, em tampão fosfato aos valores de pH 7,5 e 8,0 e em tampão tris-HCI aos valores de pH 8,0 e 8,5 a GFPuv apresentou menor estabilidade térmica A GFPuv apresenta potencialidade para ser utilizada como indicador biológico em processos térmicos que utilizam calor úmido às temperaturas inferiores a 100°C.
Transformed cells of Escheríchía coli DH5-α expressing recombinant green fluorescent protein (GFPuv, excitation and emission peaks at 394nm and 509nm), were subjected to the three-phase partitioning (TPP) method and the release extracts were eluted through methyl HIC column with a buffer solution (10 mM Tris-HCI, 10mM EDTA, pH=8.0). The purpose of this work was to study the thermal stability of the TPP-extracted recombinant protein, GFPuv, to determine its utility as a quick, accurate and economical biological indicator for moist heat-treatments. The thermal stability of the extracted GFPuv was studied in different buffer solutions (acetate, phosphate and tris-HCI 10mM) in the range of pH between 5.0 and 9.0 and at temperature between 75-95°C. The thermal resistance parameters determinated were: decimal reduction times (D-values, min), z-value (۰C), Q