History teaches us that novel materials, such as chlorofluorocarbon and asbestos, can have dire unintended consequences to human and environmental health. The exponential growth of the field of nanotechnology and the products developed along the way provide the opportunity for a new paradigm of design thinking, in which human and environmental impacts are considered early on in product development. In particular, nanocellulose is touted as a promising green nanomaterial, as it is sourced from an effectively inexhaustible feedstock of wood-based cellulose and is assumed to be harmless to the environment since it is derived from a natural material and assumed to be biodegradable. The various forms of nanocellulose possess an impressive diversity of properties, making it suitable for a wide variety of applications such as drug delivery, reinforcement, food additives, and iridescent make-up. However, as nanomaterials can have different properties relative to their bulk form, it is questionable whether they are truly environmentally friendly, particularly in terms of their biodegradability and potential impacts to receiving environments. Given the projected mass-scale application of nanocellulose and the inevitability of its subsequent release into environment, the purpose of this study was to determine the biodegradability of nanocellulose and the response of environmentally-relevant microbial communities. Specifically, it was hypothesized that cellulose in the nano size range would display distinct biodegradation patterns and rates, relative to larger forms of cellulose. Further, it was hypothesized that modification of nanocellulose, in terms of morphology and surface properties (e.g., charge), would further influence its biodegradability. Wetlands and anaerobic digesters were selected as two environmentally-relevant receiving environments that also play critical roles in global carbon turnover. To examine the biodegradability of nanocellulose, two distinct microbial consortia were enriched from wetland (W) and anaerobic digester (AD) inocula and applied in parallel experiments. The consortia were grown under anaerobic conditions with microcrystalline cellulose as the sole carbon substrate over a period of 246 days before being aliquoted to microcosms for subsequent biodegradation assays. Various forms of nanocellulose were spiked into the microcosms and compared with microcrystalline cellulose as a non nano reference. Microcosms were sacrificed in triplicate with time to monitor cellulose degradation as well as various measures of microbial community response. Microbial communities were characterized in terms of gene markers for total bacteria (16S rRNA genes) and anaerobic cellulose degraders (glycoside hydrolase family 48 genes, i.e., cel48) as well as high throughput amplicon sequencing of 16S rRNA genes (V4 region). A series of three studies examined: 1) the effect of nanocrystalline versus microcrystalline cellulose; 2) the effects of nanocellulose morphology (crystalline rod versus filament) and surface functionalization (cationic and anionic); and 3) metagenomic characterization of cellulose degrading communities using next-generation DNA sequencing. It was found that the nano- size range did not hinder cellulose degradation, in fact, nanocrystalline cellulose degraded slightly faster than microcrystalline cellulose according to 1st order kinetics (1st order decay constants: 0.62±0.08 wk-1 for anionic nanocrystalline cellulose versus 0.39±0.05 wk-1 for microcrystalline cellulose exposed to AD culture; 0.69±0.04 wk-1 for anionic nanocrystalline cellulose versus 0.58±0.05 wk-1 for microcrystalline cellulose exposed to W). Experiments comparing the effects of surface functionalization indicated that anionic nanocellulose degraded faster than cationic cellulose (1st order decay constants for cationic nanocrystalline cellulose: 0.48±0.06 wk-1 and 0.58±0.07 wk-1 on exposure to AD and W cultures respectively). Measurements of 16S rRNA and cel48 genes were consistent with this trend of greater biological growth and cellulose-degrading potential in the anionic nanocellulose condition, suggesting that surface properties can influence biodegradation patterns. Taxonomic characterization of 16S rRNA gene amplicons suggested that taxa known to contain anaerobic cellulose degraders were enriched in both W and AD consortia, which shifted in a distinct manner in response to exposure to the different cellulosic materials. This suggests that distinct groups of microbes may drive the biodegradation of different forms of cellulose. Further, metagenomic investigation provided new insight into taxonomic and functional aspects of anaerobic cellulose degradation, including identification of enzymatic families associated with degradation of the various forms of cellulose. Overall, the findings of this study advance understanding of anaerobic cellulose degradation and indicate that nanocellulose is likely to readily degrade in receiving environments and not pose an environmental concern. / Ph. D.

Weaning is defined as the physical separation of the cow-calf pair and the end of milk feeding. Natural weaning occurs between 7 and 14 months and is a gradual process. However, domestic weaning occurs between 6 and 8 months and occurs rapidly. Calves that are abruptly separated from their dam respond with increased vocalization and walking, and decreased eating and resting. The psychological stress the calf undergoes during weaning causes elevated glucocorticoid and catecholamine hormone concentrations that may predispose to increased morbidity and/or mortality from infectious diseases such as Bovine Respiratory Disease Complex. As an attempt to counter these changes, alternative weaning methods have been implemented and normally occur in two stages. Two-stage weaning begins with the cessation of milk feeding for approximately one week with the calf maintaining some contact with their dam and then permanent separation occurs. One of these methods uses a single fence to separate the cow-calf pair; this process allows the calf to see, hear and smell their dam, but does not allow the calf to suckle from its dam. Increases in cortisol, a glucocorticoid, have been linked to immunological alterations. Most notably, elevated cortisol concentrations decrease neutrophil function by down regulating the gene expression of CD62L and Fas. Cortisol also alters lymphocyte phenotype by decreasing ?δ T cells and increasing°? T cells in the circulation. Lastly, increases in cortisol can modify T cell cytokine production. The cytokines IL-12 and IFN? are secreted from T helper 1 cells while T helper 2 cells secrete IL-4 and IL-10; these T cells subsets also inhibit one another. During higher cortisol concentrations, these T cells are biased toward T helper 2 cytokine production. All these changes in immune function can lead to increased susceptibility to disease around the time of weaning. Therefore, two trials were conducted to test the hypotheses that abrupt weaning results in elevated concentrations of cortisol and subsequently alters immunological functions, and that fenceline weaning alleviates the increase in cortisol and alterations to immune function associated with weaning. In the fall of 2008, 12 Angus and Angus-X heifers (186°21 kgs; 174°16 days of age) were blocked by age and weight and randomly allotted into two groups, fenceline and abrupt. Blood samples were taken on day -7, 0, 7, 14, 21, and 42; fecal samples were taken on day -7, 0, and 3. All calves were weighed on day -7, 0, 7, 14, and 42. On day -1 all calves were separated from their dam and transported for 2 hours to another facility. On day 0 all calves were vaccinated with Brucella abortus (strain RB51). Serum was analyzed for IFN? and IL-4 as well as IgG1 and IgG2 specific antibodies to RB51. Fecal samples were analyzed for cortisol metabolites. Both IgG1 and IgG2 antibodies to RB51 increased from day 0 to day 14 (P<0.05), however no differences were detected between treatment groups. Fecal cortisol metabolites were higher on day 0 in abruptly weaned calves (P< 0.001) but did not differ between groups on day -7 or day 3. Fenceline calves had higher concentrations of IFN? in the serum on day -7 and day 0 as compared to the abruptly weaned calves (P<0.04). In the fall of 2009, forty-four Angus and Angus-X calves (19 heifers and 25 steers; 181°27 kgs; 148°17 days old) were blocked by age and gender and randomly allotted within block into two treatment groups, fenceline (FL) and abrupt (AB). Approximately half the fenceline calves were separated from their dams by a single fence at day -7 and the rest of the fenceline group at day -6; all calves were removed from their dam at day 0. Calves were vaccinated with Histophilus somni on day 1. Blood samples were taken at day -6, 1, 3, 8, 15, and 22. Fecal samples were taken on day -7, -6, 1 and 3. All calves were weighed on day -7, 0, 8, and 22. Serum samples were analyzed for IgG1 and IgG2 specific-H. somni antibodies, white blood cells were analyzed for lymphocyte phenotypes, and gene expression using 18S as the housekeeper gene. Fecal samples were analyzed for cortisol metabolites. Abruptly weaned calves had higher concentrations of cortisol metabolites in the feces than fenceline calves at day 1 (P<0.0001). No difference in average daily gain or H. somni specific antibodies between treatment groups was detected. There was a treatment*date interaction in lymphocyte and neutrophil populations (P<0.05); neutrophils from fenceline calves dropped from day -6 to day 1, but increased from day 1 to day 3, while abrupt calves decreased from day -6 to day 3. Lymphocytes from fenceline calves increased from day -6 to day 1, but decreased from day 1 to day 3, while lymphocytes from abrupt calves increased from day -6 to day 3. No difference in treatment groups was detected for lymphocyte phenotypes or gene expression; however, a date effect was detected. The CD4 and CD8 cell populations increased over time (P<0.0001) and WC1 and TcR1 decreased over time (P=0.0243 and P=0.0027 respectively) for both treatment groups. A decrease was detected over time for expression of GAPDH and CD62L (P<0.0001). The gene expression for the cytokines IFN?, IL-4 and IL-10 had no change over time. Results from the two studies suggest that fenceline weaning decreases the cortisol response associated with cow-calf separation, but does not have a significant effect on immunological parameters measured in this study. / Master of Science

The Tobacco mosaic virus (TMV) is a positive sense single stranded RNA virus and is found across the world. TMV can impact the overall yield and quality of the crop resulting in an economic loss. Plants that are infected with TMV show a variety of symptoms such as mosaic pattern, mottling, necrotic lesions and stunted growth. Historically, TMV has caused controversy on whether this economically significant virus is seedborne or seed transmitted. The objective of this study is to track TMV infection from infected seeds to seedlings to determine the percentage of seed transmission. This experiment used three pods from three different TMV infected cultivar K 326 flue-cured tobacco plants. Seeds from each pod were germinated in a growth chamber for approximately ten days. Samples were separated into seed coat, root and leaves after germination. Total RNA was extracted from each part and synthesized into cDNA for analysis. A quantitative real-time PCR (RT-qPCR) assay was used to determine TMV concentration of each sample. Endpoint RT-PCR was used to determine a conservative threshold value from the RT-qPCR results. These results demonstrated that TMV influenced percent germination with a range from 94% to 50%. Seed coats had a significantly higher virus titer concentration (P < 0.05) when compared to the roots and leaves. Statistical analysis revealed highly significant (P < 0.0001) differences among pods for virus titer and there is a highly significant plant by pod interaction (P < 0.0001). Endpoint RT-PCR confirmed TMV infection in leaves, roots and seed coats. Percent infection in leaves ranged from 2% to 24% and percent infection for roots ranged from 8% to 40%. Results demonstrate that TMV is seed transmitted in flue-cured tobacco. / Master of Science / The Tobacco mosaic virus (TMV) is an RNA virus that occurs globally in areas where tobacco is grown. TMV is a tobamovirus and infects over 350 plant species. TMV can reduce the yield and quality of the crop which will result in an economic loss for the grower. Plants that are infected with TMV show a variety of symptoms such as mosaic pattern, necrotic lesions, and stunted growth, and there are no effective ways to eradicate the virus. There has been controversy on whether to categorize TMV as a seedborne virus or a seed-transmitted virus because the location of the virus within a seed is unknown. This study examined seeds from three pods grown on three different TMV-infected flue-cured tobacco plants of cultivar K 326 to track TMV infection from infected seeds to seedlings. Seeds from each pod were germinated in a growth chamber for ten days and samples were separated into leaves, root and seed coat. Each sample had total RNA extracted and synthesized into cDNA for analysis. A quantitative real-time PCR (RT-qPCR) assay was used to determine TMV concentration of each sample since this technology can detect small amounts of virus. Endpoint RT-PCR was used to conservatively determine an infection threshold value from the RT-qPCR results. Percent germination of TMV infected seeds ranged from 94% to 50%. Seed coats had a significantly higher virus titer (P < 0.05) when compared to the roots and leaves in each pod. Statistical analysis showed (P < 0.0001) differences among pods for virus titer and there is a highly significant plant by pod interaction (P < 0.0001). Endpoint RT-PCR confirmed TMV infection in leaves, roots and seed coats. Percent infection in iv leaves ranged from 2% to 24% and percent infection for roots ranged from 8% to 40%. Therefore, results show that TMV is seed-transmitted in flue-cured tobacco.

Population numbers of bumblebees has been on a steady decline leading to the endangerment of several species that are critical to the growth and pollination of crops and plants. Varying factors have contributed to this situation, one key factor being pathogens wiping out colonies. Studying pathogens that diminish bumblebee populations is vital to understanding how to combat the decline of these important species effectively. The aim of this study was to analyse five of the most common pathogens that exist in the abdomen of five different species of bumblebees. This was achieved by extracting DNA, from 176 previously acquired frozen samples, through homogenisation and varying washing steps before an analysis of the resulting nucleic acids. The analysis was done with quantitative polymerase chain reactions to quantify the amounts of each pathogen, as well as a passive reference nucleic acid, to then be able to calculate the absolute total -amount of pathogen carried by each individual bumblebee. The results showed that almost half of the bumblebees were infected by Nosema, one sixth were infected by Crithidia and Apicystis while only a small number of individuals had been infected by Bombus Densovirus and the Apis Mellifera Filamentous Virus. Bombus Lapponicus was the most infected species. The conclusion based on the results is that future research could put a focus on the more commonly found parasites Nosema, Crithidia and Apicystis. Additional research should also be undertaken into the factors contributing to the less common pathogens Bombus Densovirus and the Apis Mellifera Filamentous Virus.

Conventional techniques within the beef cattle industry involve weaning the calf from the dam when the calf is about 205 days of age. Weaning induces a stress-response that is implicated in reducing the health and productivity of newly weaned calves. Our goal was to evaluate the impact of weaning on the stress immune responses of beef calves. To that end, we 1) evaluated novel methods to quantify physiological markers of stress, 2) compared immune function and growth of calves grazing legume versus grass forages, and 3) compared the effects of abrupt versus two-stage weaning on calves. In study 1, calf, yearling, and adult beef cattle were used to assess the accuracy and precision of handheld glucometers in quantifying bovine blood glucose concentration. Precision Xtra® and ReliOn® glucometers were used chute side to quantify blood glucose concentrations in cattle and were compared to an accepted plasma glucose analysis on the same samples for validation. The Precision Xtra® glucometer was more accurate and precise than the ReliOn® glucometer. In study 2, weaned heifers were used to compare the immunomodulatory effects of grazing alfalfa versus fescue over a 30 day grazing period. No differences were detected in the interferon gamma (IFNγ) production and weight gain between the heifers on alfalfa and fescue. In study 3, effects of two-stage (fenceline) and abrupt weaning were compared. Calf weights, immune cell function, antibody production, blood glucose concentrations, fecal cortisol concentrations, and gene expression (FAS, IL-4,IL-10, and IFNγ) were measured pre- and post-weaning. On the day after weaning, the abruptly weaned calves had higher blood glucose concentrations than fenceline weaned calves. Fecal cortisol concentration and gene expression of FAS and IL-4 increased in both groups after weaning, but no differences were detected between the weaning treatments. Gene expression of IL-10 and IFNγ did not change over time. No date, treatment or treatment*date effect was detected for total weight gain or IFNγ production within the non-stimulated and the mitogen-stimulated whole blood samples. / Master of Science

Cancer is increasingly prevalent globally and influenced by factors such as obesity and smoking. Cancer itself and chemotherapies, like cisplatin, can affect our reproductive organs and increase the risk of involuntary childlessness. In the ovaries there are oocytes that are surrounded by cumulus cells (CC) and the CC provides the oocyte with nutrients like pyruvate, which is important for the oocytes ability to mature. If the oocyte does not receive sufficient amount of nutrients the ovulation may be compromised. The CC are not well studied, and few prior studies have been done specifically to observe the impact of chemotherapies on CC. Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) is important for the mitochondrial biogenesis in cells. The purpose of the project was to evaluate a method for RNA extraction in CC and observe the impact of cisplatin exposure on the PPARGC1A expression. CCs were aspirated from bovine ovaries and exposed to cisplatin during in vitro maturation. RNA was eluted using the QIAcube and then quality assured. The primer β2 microglobulin (B2M) was used as an endogenous control in the qPCR. The results showed that PPARGC1A was minimally expressed in bovine CC and was inadequate for use when evaluating if cisplatin changes the RNA expression in CC. However, the QIAcube proved to be a suitable method for RNA extraction from bovine CC and B2M showed to be suitable as an endogenous control in bovine CC.

In this project, an outgrowth and optical density (OD) measurement step was developed and validated for an established protocol for antibiotic treatment of Anopheles stephensi mosquitoes. This step allows the elimination of uncleared mosquitoes from experimental pools. Our findings suggest that, as previously demonstrated, antibiotic treatment reduced the mosquito microbiome to an extent, as evidenced by decreased bacterial growth observed through OD readings of our experimental samples. Additionally, qPCR analysis of 16S abundance provided quantitative data on bacterial abundance, which further supported the effectiveness of antibiotic treatment. Finally, a comparison of mosquito samples pooled randomly or with high OD individuals removed showed a significant improvement in bacterial clearance in samples with our refinement step included. The method established here can generate experimental samples for third-generation sequencing with minimal bacterial contamination for robust hypothesis testing. The addition of OD measurement is a rapid, cost-effective step that can potentially improve hypothesis testing on large pools of samples. This study contributes to our understanding of the impact of antibiotic treatment on mosquito microbiomes. Improvements in molecular and bench-level techniques can greatly contribute to our ability to gain insights into the role of microbes in mosquito biology.

Em cana-de-açúcar, a colonização do caule por fungos oportunistas, como Fusarium verticillioides e Colletotrichum falcatum, está diretamente ligada ao ataque da lagarta Diatraea saccharalis (Lepidoptera: Crambidae). Duas proteínas, SUGARWIN1 e SUGARWIN2 são produzidas em cana-de-açúcar, em resposta ao dano mecânico e ao ataque de D. saccharalis, porém estas proteínas não afetam o inseto, e sim ocasionam alterações fisiológicas e morfológicas em F. verticillioides e C. falcatum, ocasionando a morte destes fungos por apoptose. Dietas artificiais suplementadas com estes fungos oportunistas ocasionaram o ganho de peso da D. saccharalis. Esses dados indicam uma interação mais íntima entre o inseto e estes patógenos de cana, sendo que, neste estudo procuramos identificar relações simbióticas entre os indivíduos, analisando se a forma de transmissão desses fungos é mediado pela D. saccharalis. Os resultados mostraram a presença do F. verticillioides em todas as fases de desenvolvimento da D. saccharalis após contato com o fungo, ou seja, depois de se alimentarem em dieta suplementada por F. verticillioides no 4º instar, permaneceram infectadas pelo fungo ao longo de toda a fase pupal e adulta, em ambos os sexos. Além disso, o F. verticillioides foi transmitido para os descendentes de D. saccharalis, sendo que o fungo foi detectado nos ovos, ou seja, um caso original de transmissão vertical. Por meio de microscopia, também foi possível verificar a alta intensidade de F. verticillioides no interior do intestino de lagartas. Estes dados inferem em uma relação simbiótica entre F. verticillioides e D. saccharalis, onde o simbionte é transferido verticalmente para as gerações subsequentes. As respostas obtidas com o fungo C. falcatum diferiram daquelas obtidas com F. verticillioides, uma vez que não se detectou a presença do fungo a partir da fase pupal. Neste caso, a relação de simbiose entre o fungo e o inseto pode resultar em uma transmissão horizontal. Com este estudo foi possível identificar diferentes formas de transmissão por D. saccharalis para dois fungos envolvidos em podridão de colmo em cana-de-açúcar. Estes dados mudam a forma como é vista a transmissão de F. verticillioides por D. saccharalis em cana-de-açúcar, podendo influenciar a forma de manejo da podridão de Fusarium e da broca nos canaviais. / In sugarcane, stem colonization by opportunistic fungi, such as Fusarium verticillioides and Colletotrichum falcatum, is directly linked to the attack of Diatraea saccharalis (Lepidoptera: Crambidae) caterpillar. Two proteins, SUGARWIN1 and SUGARWIN2 are produced in sugarcane, in response to mechanical damage and attack of D. saccharalis, however these proteins do not affect the insect, but cause physiological and morphological changes in F. verticillioides and C. falcatum, causing the death of these fungi by apoptosis. Artificial diets supplemented with these opportunistic fungi caused the weight gain of D. saccharalis. These data indicate a more intimate interaction between the insect and the sugarcane pathogens. In this study, we sought to identify symbiotic relationship among individuals, analyzing whether the transmission of these fungi is mediated by D. saccharalis. The results showed the presence of F. verticillioides in all stages of D. saccharalis development after contact with the fungus, in the 4th instar. The caterpillars remained infect by the fungus throughout the pupal and adult phase, in both sexes. In addition, F. verticillioides was transmitted to D. saccharalis offspring, being detected in eggs, an original case of vertical transmission. Through the microscopy results, it was also possible to verify the high intensity of F. verticillioides inside the intestines of caterpillar. These data infer in a symbiotic relationship between F. verticillioides and D. saccharalis, where the symbiont is transferred vertically to the offspring. The responses obtained with C. falcatum differed from those obtained with F. verticillioides, since the presence of the fungus was not detected from the pupal phase. In this case, the symbiont relationship between fungus and insect can result in a horizontal transmission. With this study was possible to identify different forms of fungi transmission by D. saccharalis. These data change the way the transmission of F. verticillioides by D. saccharalis in sugarcane is viewed, and may influence the management of Fusarium rot and sugarcane borer attack in sugarcane.

O Brasil é o maior produtor mundial de maracujá azedo (Passiflora edulis f. flavicarpa) sendo esta a espécie de maior expressão comercial dentre as passifloras cultivadas. A bacteriose do maracujazeiro, causada por Xanthomonas axonopodis pv. passiflorae (Xap), é uma das doenças mais severas da cultura, acarretando grandes prejuízos aos produtores. Atualmente, é incipiente o conhecimento sobre a interação maracujá azedo-Xap. Diante disso, a identificação e a caracterização dos genes envolvidos no processo de defesa são passos importantes para dar suporte ao desenvolvimento de variedades resistentes. Assim, o objetivo deste trabalho foi identificar e caracterizar genes de maracujá azedo diferencialmente expressos durante a resposta de defesa à Xap, bem como mensurar a sua expressão. Para isso, foram construídas duas bibliotecas subtrativas de cDNA (forward e reverse) usando o método SSH a partir de transcritos de folhas, que foram inoculadas com o patógeno ou solução salina (controle). Após o sequenciamento dos clones, o processamento e a montagem das sequências, as unisequências foram anotadas através da Plataforma PLAZA e do programa computacional Blast2GO. Genes envolvidos em diversos processos biológicos foram selecionados para a validação das bibliotecas por PCR quantitativo. Usando a Plataforma PLAZA, 78 % (764) das unisequências mostraram similaridade com proteínas de Arabidopsis thaliana, enquanto 87 % (866) delas apresentaram similaridade com proteínas putativas de diversas espécies vegetais, quando se utilizou Blast2GO. Na biblioteca forward, foram identificadas 73 proteínas relacionadas à resposta de defesa, dentre as quais estão proteínas envolvidas na sinalização intracelular, na ativação da transcrição e regulação da expressão de genes de defesa, bem como proteínas de defesa, de resistência e relacionadas à patogênese (PRs). Dentre os 22 transcritos validados, 95 % foram diferencialmente expressos em pelo menos um dos três períodos avaliados; os genes mais expressos em resposta à infecção pelo patógeno são os que codificam as enzimas lipoxigenase, (+)-neomentol desidrogenase e quitinase, as quais participam diretamente nas respostas de defesa vegetal. Dos genes cuja expressão foi mais reprimida, dois codificam proteínas relacionadas à fotossíntese e dois codificam proteínas envolvidas na detoxificação da amônia e do H2O2. Nossos resultados sugerem que a planta utiliza um arsenal de transcritos para responder à infecção; entretanto, este arsenal não é eficiente para impedir a ação do patógeno e, consequentemente, o desenvolvimento da bacteriose nas condições estudadas. Nosso estudo é inédito e gerou informações sobre a reprogramação transcricional durante a interação maracujá azedo-Xap, o que constitui um importante passo para o melhor entendimento sobre este patossistema. / Brazil is the main producer of yellow passion fruit (Passiflora edulis f. flavicarpa) worldwide, which is the most widely commercialized crop among the cultivated passifloras. The bacterial leaf spot induced by Xanthomonas axonopodis pv. passiflorae (Xap) is one of the most severe diseases of the crop, causing great losses to producers. Currently, we understand very little about the yellow passion fruit-Xap interaction. Therefore, the identification and characterization of genes involved in the defense process are important steps to support the development of resistant varieties. Thus, the objective of this study was identify and characterize differentially expressed genes during the defense response to Xap, as well as to measure their expression. For that, we constructed two subtractive cDNA libraries (the forward and the reverse) by performing the SSH method from leaf transcripts, which were inoculated with the pathogen or saline solution (control). After sequencing the clones and sequence data processing, sequences were assembled into unique sequences, which were annotated using the PLAZA Platform and the computational program Blast2GO. Genes involved in several biological processes were selected to validate the libraries by quantitative PCR. When PLAZA was used for sequence similarity searches, 78 % (764) of the yellow passion fruit unique sequences showed similarity to proteins of Arabidopsis thaliana; when Blast2GO was used, 87 % (866) of the unique sequences showed similarities to putative proteins of several plant species. For the forward library, 73 proteins related to defense response were identified, such as those involved in intracellular signaling, transcription activation and regulation of defense gene expression, as well as defense and resistance proteins, and pathogenesis-related proteins (PRs). Of the 22 validated transcripts, 95 % were differentially expressed during at least one of the three periods evaluated; the genes up-regulated in response to the pathogen infection were those that code for the enzymes lipoxygenase, (+)-neomenthol dehydrogenase and chitinase, which participate directly in plant-defense responses. Out of down-regulated genes, two code for photosynthesis-related proteins, and two for ammonia and H2O2 detoxification. Our results suggest the plant uses an arsenal of transcripts to respond to infection; however, this arsenal is not effective to prevent pathogen action and consequently the occurrence of bacterial leaf spot under the evaluated conditions. The present study is the first to produce information on the transcriptional reprogramming during the passion fruit-Xap interaction, which represents an important step for a better understanding of this pathosystem.

A digestão anaeróbia tem se apresentado como um processo de grande interesse sob a ótica da potencial produção de energia renovável (H2 e CH4), considerando-se a ampla variedade de compostos orgânicos que podem ser utilizados. Neste estudo desejou-se avançar na compreensão do sistema de reatores anaeróbios de duas fases (acidogênico seguido de metanogênico) operados em condições termofílicas (55&#176;C), alimentados com melaço da cana-de-açúcar, subproduto da indústria sucroalcooleira. Os experimentos foram conduzidos em reatores anaeróbios de leito fixo estruturado com fluxo ascendente e o melaço foi diluído com água de abastecimento, para adequação da concentração aos processos de tratamento de águas residuárias. Na 1ª Etapa dois reatores acidogênicos foram operados em paralelo para avaliar diferentes formas de inoculação e meios suportes, a fim de manter a produção continua e estável de hidrogênio. Para isso foram aplicadas diferentes cargas orgânicas (2,5, 5 e 10 gDQO.L-1) que resultam em COV de 30, 60 e 120 g.DQO.Lreator1.dia-1, com TDH fixo de 2 horas. A expressão do gene hidrogenase foi detectado em ambos os reatores, mas em maior proporção no reator inoculado com lodo de reator UASB e usando como material suporte a espuma de poliuretano. Sequencialmente a este reator, foi acoplado um reator metanogênico, alimentado com efluente do reator acidogênico, estabilizado nas condições apresentadas, e operado com COV crescentes de 1, 2, 5, 7, 14, 17 e 26,5 gDQO.Lreator-1.dia-1 e consequente diminuição do TDH de 240, 96, 48, 32, 24, 16 e 12 horas. O reator acidogênico na 2ª etapa foi operado por 417 dias consecutivos e COV de 120 g.DQO.Lreator1.dia-1, produzindo hidrogênio continuamente, alcançado valores de produção bruta de H2 de 7,60 LH2.dia-1. O reator metanogênico foi operado por 251 dias consecutivos, produzindo metano e alcançado valores de produção bruta de CH4 de 5,90 LCH4.dia-1. A eficiência de remoção de DQO do sistema de reatores foi de aproximadamente 90&#37;, com contribuição aproximadamente de 10&#37; para o reator acidogênico e contribuição aproximadamente de 80&#37; para o reator metanogênico. O reator acidogênico alcançou rendimento de produção de hidrogênio por kg de melaço aplicado de 392 LH2.kgmelaço-1 e o reator metanogênico de 387 LCH4.kgmelaço-1. Para finalidade de comparações e aplicabilidade, o ganho energético global do sistema de reatores de duas fases foi de aproximadamente 5,7 kWh.kgmelaço-1 (1,4 kWh.kgmelaço-1 para o reator acidogênico e 4,3 kWh.kgmelaço-1 para o reator metanogênico). A produção continua de H2 obtida neste estudo está relacionada à associação das vias dos ácidos produtores de hidrogênio já consolidados pela literatura pertinente (acético e butírico) e pela produção de hidrogênio pela rota do ácido lático, devido a associação entre as comunidades de microrganismos estabelecidas no reator. O sequenciamento massivo MiSeq mostrou a seleção de diversos gêneros de microrganismos com redundância funcional e pertencentes principalmente aos Filos Firmicutes, Proteobacteria e Thermotogae, tais como Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium e Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella e Petrobacter (Proteobacteria) e Fervidobacterium (Thermotogae). Microrganismos produtores de ácido lático também foram selecionados tais como: Lactobacillus, Leuconostoc, Sporolactobacillus e Trichococcus. Dos pontos de vista científico e tecnológico este estudo deu mais um passo para a compreensão dos bioprocessos envolvidos nos sistemas anaeróbios em dois estágios produzindo H2 e CH4 continuamente por longo período de tempo. / Anaerobic digestion has shown as an interesting process for renewable energy production (H2 and CH4), for a wide variety of organic compounds (carbon source). This study aimed to advance the understanding of a two-stage process anaerobic system (acidogenic bioreactor followed by methanogenic bioreactor) under thermophilic condition (55&#176;C) fed with molasses, a sugarcane industry by-product. The experiments were conducted at up-flow structured bed reactors and sugarcane molasses was diluted with tap water, to adjust the concentration to the wastewater treatment. At first stage two acidogenic reactors were operated in parallel to evaluate different source of inocula and support bed, to obtain continuous and stable hydrogen production. It was applied 2.5, 5 and 10 gCOD.L-1 resulting in OLR of 30, 60 and 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours of hydrogenase gene was detected in both reactors but with higher number of copies of the gene in the reactor that showed higher hydrogen production: the reactor sed with sludge of UASB reactor and using polyurethane foam as support material. To this reactor was coupled a methanogenic reactor fed with effluent from acidogenic reactor and operated with increasing OLR (1, 2, 5, 7, 14, 17 e 26,5 gCOD.Lreactor-1.day-1) decreasing the HRT (240, 96, 48, 32, 24, 16 and 12 hours). The acidogenic reactor was operated during 471 days with OLR of 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours, with continuous hydrogen production with a gross production of 7.60 LH2.day-1. The methanogenic reactor was operated for 251 days, with continuous methane production of up to 5.90LCH4.day-1. The COD removal efficiency using the two-stage system was approximately 90&#37; , with 10&#37; contribution by the acidogenic reactor and 80&#37; contribution by the methanogenic reactor. The acidogenic reactor achieved hydrogen yield per kg of applied molasses equal to 392 LH2.kgmolases-1. The methanogenic reactor achieved methane yield per kg of applied molasses equal to 387 LCH4.kgmolasses-1. For comparison and applicability purposes, the overall energy yield using the two stage reactor system was approximately 5.7 kWh.kgmolasses-1 (Acidogenic reactor 1.4 kWh.kgmolasses-1 and Methanogenic reactor 4.3 kWh.kgmolasses-1). The continuous production of H2 obtained in this study is related to the association of the hydrogen producer acids pathway established by the relevant literature (acetic and butyric) and the hydrogen production by the lactic acid pathway due to the microorganisms association established in the reactor. Metagenomic analysis by MiSeq Plataform revealed that hydrogen production was due the selection of microorganisms with functional redundancy mainly of Phyla Firmicutes, Proteobacteria and Thermotogae, such as Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium, Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella and Petrobacter (Proteobacteria) and Fervidobacterium (Thermotogae). Genera of acid latic producers, such as Lactobacillus, Leuconostoc, Sporolactobacillus and Trichococcus, were also selected. From the scientific and technological point of view this study has taken another step towards the understanding of bioprocesses involving two stage anaerobic systems for a long term continuous production of H2 and CH4.