The world stocks of fossil fuels are dwindling and may be all but out before the end of the century. Despite this there is increasing demand for them to be used for transport, and the ever increasing green house gases which their use produces. Renewable and less environmentally damaging forms of fuel are needed. Biofuels, particularly bioethanol, are a possibility to subsidise or replace fossil fuels altogether. Ethanol produced from fermentation of starch sugars from corn are already in wide use. As this bioethanol is currently produced from crops such as corn and sugar cane, that puts fuel crops in direct competition for space and resources with food crops. This has led to increases in food prices and the search for more arable land. Hydrolysis of lignocellulosic biomass, a waste by-product of many industries, to produce the sugars necessary for ethanol production would ease many of the problems with current biofuels. Degradation of lignocellulose is not simple and requires expensive chemical pre-treatments and large quantities of enzymes usually from fungal species making it about 10 times more expensive to produce than corn starch bioethanol. The production of a consolidated bioprocessor, an organism able to degrade, metabolise and ferment cellulosic material to produce ethanol or other useful products would greatly reduce the cost currently associated with lignocellulosic biofuel. Cellulomonas fimi ATCC 484 is an actinomycete soil bacterium able to degrade efficiently cellulosic material. The US Department of Energy (DOE) released the genome sequence at the start of 2012. In this thesis the released genome has been searched, for genes annotated as encoding polysaccharide degrading enzymes as well as for metabolic pathways. Over 100 genes predicted to code for polysaccharide hydrolysing enzymes were identified. Fifteen of these genes have been cloned as BioBricks, the standard synthetic biology functional unit, expressed in E. coli and C. freundii and assayed for endo β-1,4-glucanase activity using RBB-CMC, endo β-1,4-xylanase activity using RBB-xylan, β-D-xylosidase activity using ONPX, β-D-cellobiohydrolase activity using ONPC and α-L-arabinofuranosidase activity using PNPA. Eleven enzymes not previously reported from C. fimi were identified as active on a substrate with the strongest activities being for 2 arabinofuranosidases (AfsA+B), 4 β-xylosidases (BxyC, BxyF, CelE and XynH), an endoglucanase (CelA), and 2 multifunctional enzymes CelD and XynF, active as cellobiohydrolases, xylosidases and endoxylanases. Four enzymes were purified from E. coli cell lysates and characterised. It was found that AfsB has an optimum activity at pH 6.5 and 45ºC, BxyF has optimum activity at pH 6.0 and 45ºC and XynH has optimum activity at pH 9.0 and 80ºC. XynF exhibited different optima for the 3 substrates with pH 6.0 and 60ºC for ONPC, pH 4.5 and 50ºC for ONPX and pH 5.5 and 40ºC for RBB-xylan. Searching the genome and screening genes for activities will help genome annotation in the future by increasing the number of positively annotated genes in the databases. The BioBrick format is well suited for rapid cloning and expression of genes to be classified. Searching and screening the genome has also given insights into the complex and large network of enzymes required to fully hydrolyse and metabolise the sugars released from lignocellulose. These enzymes are spread across many different glycosyl hydrolase families conferring different catalytic activities. The characterisation of these novel enzymes points towards a system adapted to not only a broad specificity of substrate but also environmental factors such as high temperature and pH. Genomic analysis revealed gene clusters and traits which could be used in the design of a synthetic cellulolytic network, or for the conversion of C. fimi into a consolidated bioprocessor itself.

Renewable sources such as cellulose derived biofuels are sought after in order to replace fossil fuel sources that are currently used to meet energy demands. Cellulose is a biological polymer composed of a chain of glucose molecules. Hydrolysis of cellulosic materials then has potential to serve as a source of renewable energy in the form of biofuels. The crystalline structure of cellulose is very stable, and current methods of catalyzed hydrolysis are inefficient for industrial application. This project explores the use of phosphomolybdic acid (PMA) in water to catalyze hydrolysis of microcrystalline cellulose. Temperature of hydrolysis was varied from 40 °C – 100 °C. The amount of soluble hydrolysis product was determined through wet oxidative total organic carbon analysis using a Hach method kit. Total organic carbon content is compared between equimolar amounts of PMA and sulfuric acid, the current industry preference. The yield of total organic carbon in parts per thousand (ppt) is directly correlated to increasing temperatures. Across these temperatures, PMA is more efficient than sulfuric acid in hydrolysis of cellulosic materials. Work is ongoing for glucose-specific product detection as well as evaluating the recyclability of the catalyst.

The cost of deconstructing cellulose into soluble sugars is a key impediment to the commercial production of lignocellulosic biofuels. The use of the quartz crystal microbalance (QCM) to investigate reaction variables critical to enzymatic cellulose hydrolysis is investigated here, extending previous studies of fungal cellulase activity for the first time to whole cell cellulases. Specifically, the activity of the cellulases of Clostridium thermocellum, which are in the form of cellulosomes, was investigated. To clearly differentiate the activity of free cellulosome and cell-bound cellulosome, the distribution of free cellulosome and cell-bound cellulosome in crude cell broth at different growth stages of C. thermocellum (ATCC 27405) was quantified. Throughout growth, greater than 70% of the cellulosome in the crude cell broth was unattached to the cell. The frequency response of the QCM was shown to capture adsorption and hydrolysis of amorphous cellulose films by the whole-cell cellulases. Further, both crude cell broth and free cellulosomes were found to have similar inhibition pattern (within 0 - 10 g/L cellobiose). Thus, kinetic models developed for the cell-free cellulosomes, which allow for more accurate interfacial adsorption analysis by QCM than their cell-attached counterparts, may provide insight into hydrolysis events in both systems.

No description available.

Hydrogen production from abundant renewable biomass would decrease reliance on crude oils, achieve nearly zero net greenhouse gas emissions, create more jobs, and enhance national energy security. Cell-free synthetic pathway biotransformation (SyPaB) is the implementation of complicated chemical reaction by the in vitro assembly of numerous enzymes and coenzymes. Two of the biggest challenges for its commercialization are: effective release of fermentable sugars from pretreated biomass, and preparations of thermostable enzymes with low-cost. The hydrolysis performance of 21 reconstituted bacterial cellulase mixtures containing the glycoside hydrolase family 5 Bacillus subtilis endoglucanase, family 9 Clostridium phytofermentans processive endoglucanase, and family 48 Clostridium phytofermentans cellobiohydrolase was investigated on microcrystalline cellulose (Avicel) and regenerated amorphous cellulose (RAC). The optimal ratios for maximum cellulose digestibility were dynamic for Avicel but nearly fixed for RAC. Processive endoglucanase CpCel9 was most important for high cellulose digestibility regardless of substrate type. These results suggested that the hydrolysis performance of reconstituted cellulase cocktail strongly depended on experimental conditions. Thermobifida fusca YX was hypothesized to have a thermophilic polyphosphate glucokinase. T. fusca YX ORF Tfu_1811 encoding a putative PPGK was cloned and the recombinant protein fused with a family 3 cellulose-binding module (CBM-PPGK) was over expressed in Escherichia coli. By a simple one-step immobilization, the half-life time increased to 2 h, at 50 °C. These results suggest that this enzyme was the most thermostable PPGK reported. My studies would provide important information for the on-going project: high-yield hydrogen production from cellulose by cell-free synthetic enzymatic pathway. / Master of Science

Entropy, first introduced in thermodynamics, is used in a wide range of fields. Chapter 1 discusses some important theoretical and practical aspects of entropy: what is entropy, is it subjective or objective, and how to properly apply it to living organisms. Chapter 2 presents applications of entropy to evolution. Chapter 3 shows how cellulosic biofuel production can be improved. Chapter 4 shows how lattice vacancies influence the thermodynamic properties of materials. To determine the nature of thermodynamic entropy, Chapters 1 and 2 describe the roots, the conceptual history of entropy, as well as its path of development and application. From the viewpoint of physics, thermal entropy is a measure of useless energy stored in a system resulting from thermal motion of particles. Thermal entropy is a non-negative objective property. The negentropy concept, while mathematically correct, is physically misleading. This dissertation hypothesizes that concepts from thermodynamics and statistical mechanics can be used to define statistical measurements, similar to thermodynamic entropy, to summarize the convergence of processes driven by random inputs subject to deterministic constraints. A primary example discussed here is evolution in biological systems. As discussed in this dissertation, the first and second laws of thermodynamics do not translate directly into parallel laws for the biome. But, the fundamental principles on which thermodynamic entropy is based are also true for information. Based on these principles, it is shown that adaptation and evolution are stochastically deterministic. Chapter 3 discusses the hydrolysis of cellulose to glucose, which is a key reaction in renewable energy from biomass and in mineralization of soil organic matter to CO2. Conditional thermodynamic parameters, ΔhydG', ΔhydH', and ΔhydS', and equilibrium glucose concentrations are reported for the reaction C6H10O5(cellulose) + H2O(l) ⇄ C6H12O6(aq) as functions of temperature from 0 to 100°C. Activity coefficients of aqueous glucose solution were determined as a function of temperature. The results suggest that producing cellulosic biofuels at higher temperatures will result in higher conversion. Chapter 4 presents the data and a theory relating the linear term in the low temperature heat capacity to lattice vacancy concentration. The theory gives a quantitative result for disordered vacancies, but overestimates the contribution from ordered vacancies because ordering leads to a decreased influence of vacancies on heat capacity.

Made available in DSpace on 2016-06-02T19:56:44Z (GMT). No. of bitstreams: 1 3648.pdf: 4034707 bytes, checksum: d61c1d29df91b4f878b199e7de814791 (MD5) Previous issue date: 2011-03-28 / Universidade Federal de Sao Carlos / This work presents a kinetic study of the enzymatic hydrolysis of three cellulosic substrates: filter paper (FP), used as a de-lignified substrate model; sugarcane bagasse (SB) steam exploded; and acid treated SB, the last two treated with 4% NaOH. All SB were chemically characterized. Hydrolysis experiments to study the influence of agitation and substrate concentration were performed in shaker, using Accellerase® 1500, Genencor, at pH 4.8, in 50mM sodium citrate buffer. To verify the substrate concentration effect, cellulose load (weightsubstrate/weighttotal) was 0.5%-13% (for FP) and 0.99%-9.09% (for SB). For FP, the role of the external mass transport resistance was not significant when the agitation speed was in the range 150-300 rpm. It was possible to fit a pseudo-homogeneous Michaelis-Menten model for substrate concentrations up to 13% (w/w). Preliminary tests fitting the model proposed by Chrastil (CHRASTIL J. Enzymic product formation curves with the normal or diffusion limited reaction mechanism and in the presence of substrate receptors, Int. J. Biochem., v. 20, No. 7, p. 683, 1988) indicated that the role of diffusion through the external film was a more relevant feature for steam exploded SB than for FP, at higher concentrations of substrate. It was possible to fit a pseudo-homogeneous model for steam exploded SB, within a range of cellulose concentrations from 0.99% to 3.85% (w/w). Product inhibition had to be considered by the model. For higher loads of steam exploded SB, a modified Michaelis- Menten model, appropriate for heterogeneous systems with high diffusion resistance, was fitted. Finally, for the highly recalcitrant acid treated SB, Chrastil models were fitted. As expected, the complexity of this system regarding to the substrate and to the pool of enzymes acting in synergy, makes difficult the use of one single lumped parameter model for all hydrolysis operation conditions. / Este trabalho apresenta um estudo cinético da hidrólise enzimática de três substratos celulósicos: papel de filtro (PF), usado como um modelo de substrato delignificado; bagaço de cana (BC) explodido a vapor e BC tratado com ácido, os dois últimos tratados com NaOH 4%. Todos os BC foram caracterizados. Experimentos de hidrólise para estudar a influência da agitação e da concentração do substrato foram realizados em shaker, usando Accellerase ® 1500, Genencor, em pH 4,8, em tampão citrato de sódio 50mM. Para verificar o efeito da concentração do substrato, a carga de celulose (m / m) foi de 0,5% -13% (para PF) e 0,99% - 9,09% (para o BC). Para o PF, o papel da resistência externa ao transporte de massa não foi significativo quando a velocidade de agitação foi na faixa de 150-300 rpm, em shaker. Foi possível ajustar um modelo pseudo-homogêneo de Michaelis-Menten para concentrações de substrato até 13% (m / m). Testes preliminares através do ajuste do modelo proposto por Chrastil (CHRASTIL J. Enzymic product formation curves with the normal or diffusion limited reaction mechanism and in the presence of substrate receptors, Int. J. Biochem., v. 20, No. 7, p. 683, 1988) indicaram que o papel da difusão através da película externa era uma característica mais relevante para o BC explodido a vapor que para o PF, em altas concentrações de substrato. Foi possível ajustar um modelo pseudo-homogêneo para o BC explodido a vapor, dentro de uma faixa de concentrações de celulose de 0,99% a 3,85% (m / m). Inibição pelo produto teve de ser considerada pelo modelo. Para cargas maiores de BC explodido a vapor, um modelo modificado de Michaelis-Menten, adequado para sistemas heterogêneos, com alta resistência à difusão, foi ajustado. Finalmente, para BC tratado com ácido (altamente recalcitrante), modelos de Chrastil foram ajustados. Como esperado, a complexidade deste sistema em relação ao substrato para o pool de enzimas agindo em sinergia, torna difícil o uso de um modelo único para todas as condições operacionais de hidrólise.

Abstract New methods are being sought for the production of chemicals, fuels and energy from renewable biomass. Lignocellulosic biomass consists mainly of cellulose, hemicellulose and lignin. Cellulose and hemicellulose can be converted to their building blocks, i.e. sugars, via hydrolysis. This thesis is focused on glucose production from cellulose by dilute acid hydrolysis. Acid hydrolysis has the drawback of limited glucose yields, but it has the potential to become a short-term solution for biochemical production. During acid hydrolysis, the cellulose chain is split into glucose, which undergoes further decomposition reactions to hydroxymethylfurfural, levulinic acid, formic acid and by-products like insoluble humins. The present thesis aims to increase our knowledge on complicated acid-catalysed hydrolysis of cellulose. Glucose decomposition and cellulose hydrolysis were studied independently in laboratory experiments. Kinetic modelling was used as a tool to evaluate the results. The effect of the hydrogen ion on the reactions was evaluated using formic or sulphuric acid as a catalyst. This thesis provides new knowledge of cellulose hydrolysis and glucose decomposition in formic acid, a novel catalyst for high-temperature dilute acid hydrolysis. Glucose yields from cellulose hydrolysed in formic or in sulphuric acid were comparable, indicating that a weak organic acid could function as a cellulose hydrolysis catalyst. Biomass fibres in the form of wheat straw pulp were hydrolysed more selectively to glucose than a model component, microcrystalline cellulose, using formic acid. Glucose decomposition took place similarly in formic and sulphuric acid when the temperature dependence of the hydrogen ion concentration was taken into account, but a significant difference was found between the reaction rates of cellulose hydrolysis in formic acid and in sulphuric acid. The observations can be explained by changes in the cellulose hydrolysis mechanism. Thus, it is proposed in this thesis that side-reactions from cellulose to non-glucose compounds have a more significant role in the system than has earlier been understood. / Tiivistelmä Uusia menetelmiä etsitään kemikaalien, polttoaineiden ja energian valmistamiseen uusiutuvasta biomassasta. Eräs biomassa, ns. lignoselluloosa, koostuu pääasiassa selluloosasta, hemiselluloosasta ja ligniinistä. Selluloosa ja hemiselluloosa voidaan muuttaa hydrolyysin avulla niiden rakennuspalikoikseen eli sokereiksi. Tämä väitöskirja keskittyy glukoosin tuottamiseen selluloosasta laimean happohydrolyysin menetelmällä. Happohydrolyysi kärsii rajoittuneesta glukoosin saannosta, mutta sillä on potentiaalia tulla lyhyen aikavälin ratkaisuksi biokemikaalien tuotannossa. Happohydrolyysin aikana selluloosaketju pilkkoutuu glukoosiksi, joka reagoi edelleen hajoamisreaktioiden kautta hydroksimetyylifurfuraaliksi, levuliini- ja muurahaishapoiksi ja kiinteäksi sivutuotteeksi. Tämän tutkimuksen tavoitteena on kasvattaa ymmärrystämme monimutkaisesta happokatalysoidusta selluloosan hydrolyysistä. Glukoosin hajoamista ja selluloosan hydrolyysiä tutkittiin erikseen laboratoriokokein. Kineettistä mallinnusta käytettiin työkaluna arvioimaan tuloksia. Vety-ionien vaikutus reaktioihin arvioitiin käyttämällä muurahais- ja rikkihappoja katalyytteinä. Tämä väitöskirja antaa uutta tietoa selluloosan hydrolyysistä ja glukoosin hajoamisreaktioista muurahaishapossa, joka on uusi katalyytti korkean lämpötilan laimean hapon hydrolyysissä. Glukoosisaannot muurahaishappo-hydrolysoidusta selluloosasta olivat vertailukelpoisia vastaaviin rikkihappo-hydrolyysi saantoihin. Tämä viittaa siihen, että heikko orgaaninen happo voisi toimia selluloosahydrolyysin katalyyttinä. Kun katalyyttinä käytettiin muurahaishappoa, vehnän oljesta tehdyt kuidut hydrolysoituivat selektiivisemmin glukoosiksi kuin mallikomponenttina toimineen mikrokiteisen selluloosan. Kun vetyionikonsentraation lämpötilariippuvuus otettiin huomioon, glukoosi hajosi samalla tavalla sekä muurahais- että rikkihappokatalyytissä, mutta merkittävä ero havaittiin selluloosahydrolyysin reaktionopeudessa. Havainnot voidaan selittää selluloosahydrolyysin mekanismissa tapahtuvilla muutoksilla. Väitöskirjassa esitetään, että sivureaktioilla selluloosasta ei-glukoosi-tuotteiksi on merkittävä vaikutus systeemiin.

Cellulose is the most abundant biopolymer on Earth as it is found in every plant cell wall; therefore, it represents one of the most promising natural resources for the fabrication of sustainable materials. In plants, cellulose is mainly used for structural integrity, however, some species organise cellulose in helicoidal nano-architectures generating strong iridescent colours. Recent research has shown that cellulose nanocrystals, CNCs, isolated from natural fibres, can spontaneously self-assemble into architectures that resemble the one producing colouration in plants. Therefore, CNCs are an ideal candidate for the development of new photonic materials that can find use to substitute conventional pigments, which are often harmful to humans and to the environment. However, various obstacles still prevent a widespread use of cellulose-based photonic structures. For instance, while the CNC films can display a wide range of colours, a precise control of the optical appearance is still difficult to achieve. The intrinsic low thermal stability and brittleness of cellulose-based films strongly limit their use as photonic pigments at the industrial scale. Moreover, it is challenging to integrate them into composites to obtain further functionality while preserving their optical response. In this thesis, I present a series of research contributions that make progress towards addressing these challenges. First, I use an external magnetic field to tune the CNC films scattering response. Then, I demonstrate how it is possible to tailor the optical appearance and the mechanical properties of the films as well as to enhance their functionality, by combining CNCs with other polymers. Finally, I study the thermal properties of CNC films to improve the retention of the helicoidal arrangement at high temperatures and to explore the potential use of this material in industrial fabrication processes, such as hot-melt extrusion.