Hydrothermal liquefaction is a thermochemical technique for obtaining crude bio-oil from lignocellulosic biomass with moderate temperature and pressure. The crude bio-oil can then be upgraded to various biofuels and bioproducts. Hydrothermal liquefaction is amenable to use of biomass feedstocks that have high-moisture. The overall goal of this research is to demonstrate the effectiveness of white rot fungus (WRF) as a pretreatment option in the production of bio-oil from switchgrass through hydrothermal liquefaction. If WRF is an effective pretreatment, it could be a cost-effective option for commercialization, allowing hydrothermal liquefaction to be used on an industrial scale to produce high quality bio-oil capable of replacing some of the fossil fuel liquids used today. This thesis specifically focuses on the investigation of the effects of particle size and culture time on lignin degradation using Phanerochaete chrysosporium as a pretreatment method on switchgrass. In addition, the conversion efficiency of WRF treated switchgrass was compared to that of torrefied switchgrass and untreated switchgrass after the pyrolysis conversion process. The results indicate that WRF outperforms torrefaction as a pretreatment method for the conversion of sugar-based components, thus may be an attractive alternative for fermentation conversion processes, but probably not for thermochemical processes.

This dissertation is composed of two research projects. The first research project is aimed at using synthetic fluorogenic probes to study the possible or dominant linkages in biomass. These probes that mimic the linkages found in lignin-cellulosic biomass are designed to select the optimal fungi from direct evaluation process or could be tested against other microbials to screen candidates which can break ligno-hemicellulose bonds. For the first stage, these probes would be tested against white rot fungi extract. The white rot fungi are used for the first stage to see if releasing or degrading carbohydrates while keeping lignin largely intact is possible or not. These probes can help to answer fundamental questions, such as what could be the dominant linkages between lignin and hemicellulose, and what are the possible mechanisms for the cleavage of carbohydrates in biomasses. Understanding the linkages in these biomass will enable high efficient degradation or release of carbohydrates, primarily hemicelluloses, from biomass. The second project is focused on synthesizing new aminoglycoside analogs and exploring the potential to revive traditional antibacterial kanamycin as new types of antifungal agents. Aminoglycosides are widely used broad spectrum antibiotics. Although mainly used as antibacterial agents, there have been studies to show amphiphilic aminoglycoside derivatives could be possibly employed as antifungal agents. A concise and novel method for site-selective alkylation of tetra-azidokanamycin has been developed that leads to the divergent synthesis of three classes of kanamycin derivatives. These new amphiphilic kanamycin derivatives bearing alkyl chains length of 4, 6, 7, 8, 9, 10, 12, 14，16 have been synthesized and tested against bacteria and fungi. Surprisingly, the antibacterial effect of the synthesized kanamycin derivatives decline or disappear compared with the original kanamycin A, but some of the compounds show very strong activity as antifungal agents.

Biocatalysts are important tools for harnessing the potential of wood fibres since they can perform specific reactions with low environmental impact. Challenges to bioconversion technologies as applied to wood fibres include low accessibility of plant cell wall polymers and the heterogeneity of plant cell walls, which makes it difficult to predict conversion efficiencies. White-rot fungi are among the most efficient degraders of plant fibre (lignocellulose), capable of degrading cellulose, hemicellulose and lignin. Phanerochaete carnosa is a white-rot fungus that, in contrast to many white-rot fungi that have been studied to date, was isolated almost exclusively from fallen coniferous trees (softwood). While several studies describe the lignocellulolytic activity of the hardwood-degrading, model white-rot fungus Phanerochaete chrysosporium, the lignocellulolytic activity of P. carnosa has not been investigated. An underlying hypothesis of this thesis is that P. carnosa encodes enzymes that are particularly well suited for processing softwood fibre, which is an especially recalcitrant feedstock, though a major resource for Canada. Moreover, given the phylogenetic similarity of P. carnosa and P. chrysosporium, it is anticipated that the identification of pertinent enzymes for softwood degradation can be more easily conducted. In particular, this project describes the characterization of P. carnosa in terms of the growth conditions that support lignocellulolytic activity, the effect of enzymes secreted by P. carnosa on the chemistry of softwood feedstocks, and the characterization of the corresponding secretome using proteomic techniques. Through this study, cultivation methods for P. carnosa were established and biochemical assays for protein activity and quantification were developed. Analytical methods, including FTIR and ToF-SIMS were used to characterize wood samples at advancing stages of decay, and revealed preferential degradation of lignin in the early stages of growth on all softwoods analyzed. Finally, an in depth proteomic analysis of the proteins secreted by P. carnosa on spruce and cellulose established that similar sets of enzyme activities are elicited by P. carnosa grown on different lignocellulosic substrates, albeit to different expression levels.

Biocatalysts are important tools for harnessing the potential of wood fibres since they can perform specific reactions with low environmental impact. Challenges to bioconversion technologies as applied to wood fibres include low accessibility of plant cell wall polymers and the heterogeneity of plant cell walls, which makes it difficult to predict conversion efficiencies. White-rot fungi are among the most efficient degraders of plant fibre (lignocellulose), capable of degrading cellulose, hemicellulose and lignin. Phanerochaete carnosa is a white-rot fungus that, in contrast to many white-rot fungi that have been studied to date, was isolated almost exclusively from fallen coniferous trees (softwood). While several studies describe the lignocellulolytic activity of the hardwood-degrading, model white-rot fungus Phanerochaete chrysosporium, the lignocellulolytic activity of P. carnosa has not been investigated. An underlying hypothesis of this thesis is that P. carnosa encodes enzymes that are particularly well suited for processing softwood fibre, which is an especially recalcitrant feedstock, though a major resource for Canada. Moreover, given the phylogenetic similarity of P. carnosa and P. chrysosporium, it is anticipated that the identification of pertinent enzymes for softwood degradation can be more easily conducted. In particular, this project describes the characterization of P. carnosa in terms of the growth conditions that support lignocellulolytic activity, the effect of enzymes secreted by P. carnosa on the chemistry of softwood feedstocks, and the characterization of the corresponding secretome using proteomic techniques. Through this study, cultivation methods for P. carnosa were established and biochemical assays for protein activity and quantification were developed. Analytical methods, including FTIR and ToF-SIMS were used to characterize wood samples at advancing stages of decay, and revealed preferential degradation of lignin in the early stages of growth on all softwoods analyzed. Finally, an in depth proteomic analysis of the proteins secreted by P. carnosa on spruce and cellulose established that similar sets of enzyme activities are elicited by P. carnosa grown on different lignocellulosic substrates, albeit to different expression levels.

Resumo: O eucalipto é a arbórea mais plantada no Brasil, devido ao seu amplo uso e após seu corte, os tocos e raízes que permanecem no local, dificultam o manejo da cultura. Com base nessa necessidade, o objetivo do presente estudo foi avaliar as características fisiológicas e funcionais de fungos basidiomicotas, isolados de campos de reflorestamento de Eucalyptus spp., com vistas à possibilidade do uso destes na destoca natural. Os fungos Pycnoporus sanguineus, Lentinus bertieri, Xylaria sp. e Lentinula edodes e um isolado não identificado foram estudados. No primeiro experimento, avaliou-se a patogenicidade dos mesmos em plantas de eucalipto urograndis (10 meses de idade), através da inoculação de disco de meio de cultura colonizado e não colonizado (Testemunha). As avaliações foram feitas aos 30 e 60 dias após a inoculação, com base no tamanho das lesões internas e externas. No segundo experimento, avaliou-se o crescimento micelial dos fungos P. sanguineus, L. bertieri, Xylaria sp., L. edodes e S. ostrea, em substrato à base de serragem enriquecida com farelos, e em três composições de meios de cultura, Batata-Dextrose-Ágar (BDA); Malte-Ágar (MA) e Serragem-Dextrose-Ágar (SDA), e incubados a 23, 27 e 31ºC. No terceiro experimento, avaliou-se a produção das enzimas ligninocelulolíticas lacase e celulase, e outras ligadas à degradação de tecidos vegetais, as proteases, pectinases e lipase, em meios de cultura específicos. No quarto experimento, estudou-se, pelo método "soil block", a perda de massa (%) de corpos-de-prova de eucalipto urograndis, inoculados com os fungos P. sanguineus, L. bertieri, Xylaria sp. e L. edodes, mantidos sob dois regimes de umidade (50 e 100%), e avaliados aos 30, 60, 90 e 120 após inoculação. Estudaram-se também as características químicas da madeira, após 120 dias da inoculação / Abstract: The Eucalyptus spp. tree is the most planted in Brazil, due to its widespread use and after its use, the stumps and roots that remains in the area, hinder crop management. Based on this need, the purpose of this work was evaluate the physiological and functional characteristics of basidiomycetes fungi, obtained in reforestation fields of Eucalyptus spp., with the possibility of using the fungi in natural stump removal. Pycnoporus sanguineus, Lentinus bertieri, Xylaria sp., Stereum ostrea and a unidentified isolate, were studied. In the first, was evaluate the fungi pathogenicity in eucalipt urograndis plants (10 months old), by means of disk inoculation into culture medium colonized and non-colonized (control) by fungi. Evaluations were performed at 30 and 60 days after inoculation based on the external and internal size of lesions. In experiment 2, the mycelial growth of P. sanguineus, L. bertieri, Xylaria sp., L. edodes and S. ostrea was evaluated in bran and sawdust-based substrate, as well as in three culture media: Potato-Dextrose-Agar (PDA), Malt-Agar (MA) and Sawdust-Dextrose-Agar (SDA), and at three incubation temperatures, at 23, 27 and 31ºC. In experiment 3, the production of lignolytic enzymes lacase and cellulase, and other enzymes related to degradation of plant tissues, like protease, pectinases and lipase was assessed in specific culture media. In experiment 4, mass loss (%) and chemical features of eucalipt urograndis wood degraded by the soil block method were evaluated by the P. sanguineus, L. bertieri, Xylaria sp. and L. edodes fungi. Thus, test specimens were inoculated with the fungi and kept under two moisture regimes, 50 and 100%, and incubated at 25 ±2ºC. Mass loss was assessed at 30, 60, 90 and 120 days after inoculation. The chemical features of eucalipt urograndis test specimens were only analyzed at 120 days / Orientador: Marli Teixeira de Almeida Minhoni / Coorientador: Edson Luiz Furtado / Banca: Celso Garcia Auer / Banca: Elias Taylor Durgante Severo / Mestre

Made available in DSpace on 2014-06-11T19:28:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-07-06Bitstream added on 2014-06-13T18:58:01Z : No. of bitstreams: 1 negrao_dr_me_botfca.pdf: 3707396 bytes, checksum: a86257bbc964f1d5be2cd0c00ddf6c80 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O eucalipto é a arbórea mais plantada no Brasil, devido ao seu amplo uso e após seu corte, os tocos e raízes que permanecem no local, dificultam o manejo da cultura. Com base nessa necessidade, o objetivo do presente estudo foi avaliar as características fisiológicas e funcionais de fungos basidiomicotas, isolados de campos de reflorestamento de Eucalyptus spp., com vistas à possibilidade do uso destes na destoca natural. Os fungos Pycnoporus sanguineus, Lentinus bertieri, Xylaria sp. e Lentinula edodes e um isolado não identificado foram estudados. No primeiro experimento, avaliou-se a patogenicidade dos mesmos em plantas de eucalipto urograndis (10 meses de idade), através da inoculação de disco de meio de cultura colonizado e não colonizado (Testemunha). As avaliações foram feitas aos 30 e 60 dias após a inoculação, com base no tamanho das lesões internas e externas. No segundo experimento, avaliou-se o crescimento micelial dos fungos P. sanguineus, L. bertieri, Xylaria sp., L. edodes e S. ostrea, em substrato à base de serragem enriquecida com farelos, e em três composições de meios de cultura, Batata-Dextrose-Ágar (BDA); Malte-Ágar (MA) e Serragem-Dextrose-Ágar (SDA), e incubados a 23, 27 e 31ºC. No terceiro experimento, avaliou-se a produção das enzimas ligninocelulolíticas lacase e celulase, e outras ligadas à degradação de tecidos vegetais, as proteases, pectinases e lipase, em meios de cultura específicos. No quarto experimento, estudou-se, pelo método “soil block”, a perda de massa (%) de corpos-de-prova de eucalipto urograndis, inoculados com os fungos P. sanguineus, L. bertieri, Xylaria sp. e L. edodes, mantidos sob dois regimes de umidade (50 e 100%), e avaliados aos 30, 60, 90 e 120 após inoculação. Estudaram-se também as características químicas da madeira, após 120 dias da inoculação / The Eucalyptus spp. tree is the most planted in Brazil, due to its widespread use and after its use, the stumps and roots that remains in the area, hinder crop management. Based on this need, the purpose of this work was evaluate the physiological and functional characteristics of basidiomycetes fungi, obtained in reforestation fields of Eucalyptus spp., with the possibility of using the fungi in natural stump removal. Pycnoporus sanguineus, Lentinus bertieri, Xylaria sp., Stereum ostrea and a unidentified isolate, were studied. In the first, was evaluate the fungi pathogenicity in eucalipt urograndis plants (10 months old), by means of disk inoculation into culture medium colonized and non-colonized (control) by fungi. Evaluations were performed at 30 and 60 days after inoculation based on the external and internal size of lesions. In experiment 2, the mycelial growth of P. sanguineus, L. bertieri, Xylaria sp., L. edodes and S. ostrea was evaluated in bran and sawdust-based substrate, as well as in three culture media: Potato-Dextrose-Agar (PDA), Malt-Agar (MA) and Sawdust-Dextrose-Agar (SDA), and at three incubation temperatures, at 23, 27 and 31ºC. In experiment 3, the production of lignolytic enzymes lacase and cellulase, and other enzymes related to degradation of plant tissues, like protease, pectinases and lipase was assessed in specific culture media. In experiment 4, mass loss (%) and chemical features of eucalipt urograndis wood degraded by the soil block method were evaluated by the P. sanguineus, L. bertieri, Xylaria sp. and L. edodes fungi. Thus, test specimens were inoculated with the fungi and kept under two moisture regimes, 50 and 100%, and incubated at 25 ±2ºC. Mass loss was assessed at 30, 60, 90 and 120 days after inoculation. The chemical features of eucalipt urograndis test specimens were only analyzed at 120 days

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