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The energy supplies of modern society seem to be necessarily associated with risks. In this paper, we address the question as to whether the efficient utilisation of energy in biological systems is also coupled to hazards. Most organisms oxidise highly reduced substrates with molecular oxygen in order to gain energy. In eukaryotes, this process takes place at the inner membrane of specialised organelles, the mitochondria. Interestingly, about 1% of the consumed oxygen molecules are reduced not to water, but to ROS (reactive oxygen species), which are deleterious to many macromolecules, including mitochondrial DNA. As a result, mitochondrial DNA mutations accumulate, in turn affecting the energy supply and inducing degeneration and ageing. / Nach dem heutigen Stand der Technik scheint eine ausreichende Energieversorgung der Gesellschaft stets mit Risiken verbunden zu sein. Wir gehen in dem Artikel der Frage nach, ob auch biologische Systeme bei der Nutzung von Energie Risiken in Kauf nehmen. Zur effizienten Energiegewinnung nutzen Organismen meist Sauerstoff zur Oxidation energiereicher Substrate. In Eukaryonten erfolgt die Energiegewinnung vor allem an der inneren Membran von Mitochondrien. Etwa 1 % des verbrauchten Sauerstoffs wird dabei nicht zu Wasser, sondern zu ROS (reactive oxygen species, reaktive Sauerstoffspezies) reduziert, die unter anderem die mitochondriale DNA schädigen und Mutationen hervorrufen. Diese akkumulieren auf Dauer und führen zu einer Störung der Energiegewinnung, in deren Folge Degenerations- und Alterungsphänomene auftreten.

Thesis (M.S.)--University of Hawaii at Manoa, 2005. / Includes bibliographical references (leaves 64-73). / xi, 73 leaves, bound ill. 29 cm

[Truncated abstract] An ethanol delivery system, consisting of silicone (poly(dimethylsiloxane)) tubing coiled and shaped as mats, was characterised and evaluated for its potential to act as a permeable reactive barrier (PRB), to promote reducing conditions and enable the enhanced bioremediation of a variety of groundwater contaminants in situ. Aqueous ethanol solutions were recirculated through the inner volume of the silicone polymer tubing in the mat, to allow permeation and delivery of ethanol by diffusion through the tubing walls to a target contamination zone. The aim of the system was to provide control over subsurface geochemistry by overcoming carbon source limitations, and as a result stimulate indigenous bacteria to remove contaminants. The physical properties of the silicone tubing were initially characterised, which included the determination of the ethanol sorption and diffusion properties of the tubing. A model for the mass of ethanol transferred via diffusion from an aqueous solution on the inner volume of a length of polymer tubing was developed to enable prediction of the ethanol delivery capacity of the silicone polymer mats. A number of large-scale laboratory column studies were then conducted to validate this ethanol mass delivery model, and to evaluate the use of silicone polymer mats to deliver ethanol and promote the biodegradation of a range of different contaminated groundwaters. The laboratory column experiments were observed to produce ethanol mass flux delivery statistically similar to that predicted by the model; however this was only with the application of an effective diffusion coefficient within the model, which was determined from the model under subsurface-simulated conditions. Ethanol delivery using the silicone tubing polymer mat system was also quantified in a pilot field-scale demonstration. The mass of ethanol delivery in the field was shown to be within the range of model-predicted ethanol delivery; however delivery was not as consistent and predictable as that observed in the column studies. Successful ethanol enhanced nitrate contamination removal (via denitrification) was observed at a field scale. For field applications, this innovative polymer mat amendment delivery system may provide targeted, predictable and cost-effective amendment delivery compared to aqueous injection methods for groundwater bioremediation, however, knowledge and quantification of the hydrogeology of the particular field site is required. Two other ethanol-driven biologically-mediated contaminant removal processes were also investigated in the laboratory-scale soil column studies, and included the assessment of the removal of dissolved metals/sulfate via sulfate reduction and metalsulfide precipitation, and the removal of trichloroethene via reductive dechlorination.

Vias biológicas representam interações entre entidades químicas complexas (proteínas, substratos, metabólitos etc.) que ocorrem no nível molecular das células. A representação e compreensão do comportamento destas vias é o principal alvo de estudos da Biologia Sistêmica. Esta área de estudos envolve a construção de modelos matemáticos que possam simular in silico (computacionalmente) o comportamento destes sistemas biológicos verificados in vivo (experimentalmente). Do ponto de vista computacional é evidente que tais sistemas são complexos para abordar e descrever de modo intuitivo. São necessários modelos com valor preditivo, isto é, que permitam descrever os comportamentos do sistema que são experimentalmente verificáveis. Algumas notações gráficas foram propostas para descrever vias biológicas. Entre elas, os diagramas de processos tem sido amplamente utilizados. Um diagrama de processos é essencialmente um grafo no qual vértices e arestas representam componentes biológicos, e há uma notação gráfica associada com cada elemento. Nesta dissertação propomos uma fundamentação formal para a linguagem dos diagramas de processos definindo a sintaxe usando gramática de grafos. Nós definimos primeiramente um grafo chamado BioProc, descrevendo o meta-modelo dos diagramas de processos. Instâncias do grafo BioProc são portanto diagramas de processos modelando vias biológicas. Para descrever a semântica foi proposta uma tradução algébrica dos grafos BioProc para redes de Petri estocásticas generalizadas (GSPNs) já amplamente utilizadas na modelagem de processos biológicos. O uso de gramática de grafos como formalismo intermediário na tradução habilita a verificação sintática da via com a checagem dos tipos válidos que podem ser definidos para cada reação antes da simulação na rede de Petri e usá-las posteriormente para explorar propriedades estruturais e estocásticas do modelo. Além disso serve como base para a evolução do modelo proposto. Isto é relevante já que modelos frequentemente são construídos incrementalmente para se adaptar a novos requisitos e/ou incluir novas características. / Biological pathways represent interactions between complex chemical entities (proteins, substrates, metabolites, etc.) that occur at the molecular level of cells. The representation and comprehension of biological pathways behavior is the main target of research in the field of Systems Biology. This area investigates the construction of mathematical models that can simulate in silico (computationally) the behavior of biological systems checked in vivo (experimentally). From a computational view point it is clear that such systems are too complex to analyze and describe in an intuitiveway. Models with predictive value are needed, describing the behaviors that are experimentally verifiable. There are some graphical notations to describe biological pathways. Among them, process diagrams have been widely used. A process diagram is essentially a graph in which vertices and edges represent biological components, and there is a graphical notation associated with each element. In this master thesis we give a formal foundation for biological process diagrams, by defining their (concrete and abstract) syntax and semantics using a formalism called graph grammars. We first build a graph called BioProc Graph, describing the meta-model of process diagrams. Instances of this BioProc graph are concrete process diagrams modeling biological pathways. To describe the semantics we proposed a translation of BioProc diagrams to generalized stochastic Petri networks (GSPNs) already widely used in modeling biological processes. The use of graph grammar formalism as a basis for translation enables the syntatic verification to check the valid types that can be defined for each reaction after the simulation of Petri net and before that to explore structural and stochastic properties of the model. In addition it serves as the basis for model evolution proposed. This is relevant because models are often built incrementally to adapt to new requirements and/or include new features.

Vias biológicas representam interações entre entidades químicas complexas (proteínas, substratos, metabólitos etc.) que ocorrem no nível molecular das células. A representação e compreensão do comportamento destas vias é o principal alvo de estudos da Biologia Sistêmica. Esta área de estudos envolve a construção de modelos matemáticos que possam simular in silico (computacionalmente) o comportamento destes sistemas biológicos verificados in vivo (experimentalmente). Do ponto de vista computacional é evidente que tais sistemas são complexos para abordar e descrever de modo intuitivo. São necessários modelos com valor preditivo, isto é, que permitam descrever os comportamentos do sistema que são experimentalmente verificáveis. Algumas notações gráficas foram propostas para descrever vias biológicas. Entre elas, os diagramas de processos tem sido amplamente utilizados. Um diagrama de processos é essencialmente um grafo no qual vértices e arestas representam componentes biológicos, e há uma notação gráfica associada com cada elemento. Nesta dissertação propomos uma fundamentação formal para a linguagem dos diagramas de processos definindo a sintaxe usando gramática de grafos. Nós definimos primeiramente um grafo chamado BioProc, descrevendo o meta-modelo dos diagramas de processos. Instâncias do grafo BioProc são portanto diagramas de processos modelando vias biológicas. Para descrever a semântica foi proposta uma tradução algébrica dos grafos BioProc para redes de Petri estocásticas generalizadas (GSPNs) já amplamente utilizadas na modelagem de processos biológicos. O uso de gramática de grafos como formalismo intermediário na tradução habilita a verificação sintática da via com a checagem dos tipos válidos que podem ser definidos para cada reação antes da simulação na rede de Petri e usá-las posteriormente para explorar propriedades estruturais e estocásticas do modelo. Além disso serve como base para a evolução do modelo proposto. Isto é relevante já que modelos frequentemente são construídos incrementalmente para se adaptar a novos requisitos e/ou incluir novas características. / Biological pathways represent interactions between complex chemical entities (proteins, substrates, metabolites, etc.) that occur at the molecular level of cells. The representation and comprehension of biological pathways behavior is the main target of research in the field of Systems Biology. This area investigates the construction of mathematical models that can simulate in silico (computationally) the behavior of biological systems checked in vivo (experimentally). From a computational view point it is clear that such systems are too complex to analyze and describe in an intuitiveway. Models with predictive value are needed, describing the behaviors that are experimentally verifiable. There are some graphical notations to describe biological pathways. Among them, process diagrams have been widely used. A process diagram is essentially a graph in which vertices and edges represent biological components, and there is a graphical notation associated with each element. In this master thesis we give a formal foundation for biological process diagrams, by defining their (concrete and abstract) syntax and semantics using a formalism called graph grammars. We first build a graph called BioProc Graph, describing the meta-model of process diagrams. Instances of this BioProc graph are concrete process diagrams modeling biological pathways. To describe the semantics we proposed a translation of BioProc diagrams to generalized stochastic Petri networks (GSPNs) already widely used in modeling biological processes. The use of graph grammar formalism as a basis for translation enables the syntatic verification to check the valid types that can be defined for each reaction after the simulation of Petri net and before that to explore structural and stochastic properties of the model. In addition it serves as the basis for model evolution proposed. This is relevant because models are often built incrementally to adapt to new requirements and/or include new features.

Vias biológicas representam interações entre entidades químicas complexas (proteínas, substratos, metabólitos etc.) que ocorrem no nível molecular das células. A representação e compreensão do comportamento destas vias é o principal alvo de estudos da Biologia Sistêmica. Esta área de estudos envolve a construção de modelos matemáticos que possam simular in silico (computacionalmente) o comportamento destes sistemas biológicos verificados in vivo (experimentalmente). Do ponto de vista computacional é evidente que tais sistemas são complexos para abordar e descrever de modo intuitivo. São necessários modelos com valor preditivo, isto é, que permitam descrever os comportamentos do sistema que são experimentalmente verificáveis. Algumas notações gráficas foram propostas para descrever vias biológicas. Entre elas, os diagramas de processos tem sido amplamente utilizados. Um diagrama de processos é essencialmente um grafo no qual vértices e arestas representam componentes biológicos, e há uma notação gráfica associada com cada elemento. Nesta dissertação propomos uma fundamentação formal para a linguagem dos diagramas de processos definindo a sintaxe usando gramática de grafos. Nós definimos primeiramente um grafo chamado BioProc, descrevendo o meta-modelo dos diagramas de processos. Instâncias do grafo BioProc são portanto diagramas de processos modelando vias biológicas. Para descrever a semântica foi proposta uma tradução algébrica dos grafos BioProc para redes de Petri estocásticas generalizadas (GSPNs) já amplamente utilizadas na modelagem de processos biológicos. O uso de gramática de grafos como formalismo intermediário na tradução habilita a verificação sintática da via com a checagem dos tipos válidos que podem ser definidos para cada reação antes da simulação na rede de Petri e usá-las posteriormente para explorar propriedades estruturais e estocásticas do modelo. Além disso serve como base para a evolução do modelo proposto. Isto é relevante já que modelos frequentemente são construídos incrementalmente para se adaptar a novos requisitos e/ou incluir novas características. / Biological pathways represent interactions between complex chemical entities (proteins, substrates, metabolites, etc.) that occur at the molecular level of cells. The representation and comprehension of biological pathways behavior is the main target of research in the field of Systems Biology. This area investigates the construction of mathematical models that can simulate in silico (computationally) the behavior of biological systems checked in vivo (experimentally). From a computational view point it is clear that such systems are too complex to analyze and describe in an intuitiveway. Models with predictive value are needed, describing the behaviors that are experimentally verifiable. There are some graphical notations to describe biological pathways. Among them, process diagrams have been widely used. A process diagram is essentially a graph in which vertices and edges represent biological components, and there is a graphical notation associated with each element. In this master thesis we give a formal foundation for biological process diagrams, by defining their (concrete and abstract) syntax and semantics using a formalism called graph grammars. We first build a graph called BioProc Graph, describing the meta-model of process diagrams. Instances of this BioProc graph are concrete process diagrams modeling biological pathways. To describe the semantics we proposed a translation of BioProc diagrams to generalized stochastic Petri networks (GSPNs) already widely used in modeling biological processes. The use of graph grammar formalism as a basis for translation enables the syntatic verification to check the valid types that can be defined for each reaction after the simulation of Petri net and before that to explore structural and stochastic properties of the model. In addition it serves as the basis for model evolution proposed. This is relevant because models are often built incrementally to adapt to new requirements and/or include new features.

The performance of fibrous biomass support media (Ringlace) and porous spongelike biomass support media (Captor) was evaluated for enhanced nitrification and denitrification in a pilot-scale Virginia Initiative Project (VIP) biological nutrient removal (BNR) process. Four separate pilot-scale treatment trains were constructed and operated during this research. Three of the four treatment trains were operated with fixed film media (Ringlace/Captor) incorporated in the aerobic zone of the system and are referred to as the Integrated Fixed Film Activated Sludge (IFAS) systems. A fourth treatment train (Control train) was operated without any fixed film media. All experiments in this research were performed using domestic wastewater from Blacksburg, Virginia, and the Virginia Tech campus. Enhanced nitrification was observed in the IFAS system containing porous biomass support media (Captor) that was freely suspended in the mixed liquor of the aerobic zone. Near-complete nitrification was observed in the IFAS system containing Captor media even at total suspended growth MCRTs as low as 5.6 days and a 12°C liquid temperature. Significantly higher nitrification rates were observed in the IFAS system containing Captor media compared to both the IFAS system containing Ringlace media and the control train. However, there was less denitrification in the aerobic zone of the IFAS systems containing Captor media compared to the Ringlace media systems. Enhanced nitrification could not be statistically shown in the IFAS system containing Ringlace media. The overall nitrification rates in the Ringlace media system were about the same as the control train for the MCRTs and temperatures used during this research. However, a significantly greater amount of denitrification was observed in the aerobic zone of the IFAS system containing Ringlace media compared to both the IFAS system containing Captor media and the control system. Microscopic examination of the growth on the fixed film media (Ringlace and Captor) showed that red worms always grew on the Ringlace media, and were detrimental to performance on at least one occasion. Methods for controlling the worms were developed and applied successfully. During certain operating phases, lower sludge productions and observed sludge yields were measured in the IFAS system containing Ringlace media. However, a Statistical difference could not be calculated between the sludge production in the Ringlace media system and the control system. Lower sludge production and observed sludge yield were also observed in the IFAS system containing Captor media, but only two data points were available and a Statistical t-test analysis was not possible. / Master of Science

Chitin in shrimp waste is tightly associated with proteins, lipids, pigments and mineral deposits. Therefore, these source materials have to be pretreated to remove these components. For a long time, chemical process has been used widely for extraction of chitin from shrimp waste. The chemical process however led to severe environmental damage and low chitin quality. The biological process has been shown promising to replace the harsh chemical process to reduce the environment impact. In our previous study chitin recovery from sterilized shrimp waste by Lactobacillus plantarum NCDN4 was investigated. However in large scale it is uneconomical to sterilize the shrimp waste. For that reason, in this study the microbial process using Lactobacillus plantarum NCDN4 for chitin recovery from unsterilezed shrimp waste has been investigated. Factors affecting the demineralization by this strain such as inoculum size, glucose concentration, initial pH, NaCl concentration and fermentation time were investigated. It was found that when unsterilized shrimp waste fermented with 20% L. plantarum inoculum, 12,5% glucose, and pH 6 for 4 days at 30oC, 99. 28% emineralization and 48.65% deproteination could be achieved. The ash and protein content of fermented residues were 1.33% and 22.46% respectively. Compared to sterilized condition the efficiency of demineralization and deproteination was similar. / Chitin trong phế liệu tôm liên kết chặt chẽ với protein, sắc tố và khoáng. Do vậy để thu được chitin cần có các bước tiền xử lí để loại các thành phần không phải chitin ra. Phương pháp hóa học được sử dụng rộng rãi từ lâu để tiền xử lí chitin. Tuy nhiên do phương pháp hóa học gây hại cho môi trường và tạo ra chitin chất lượng thấp, các nhà khoa học nỗ lực nghiên cứu tìm ra các phương pháp thay thế. Phương pháp sinh học được xem là rất khả quan để thay thế phương pháp hóa học. Trong nghiên cứu trước của chúng tôi, quá trình lên men phế liệu tôm thanh trùng bằng Lactobacillus plantarum NCDN4 đã được nghiên cứu. Tuy nhiên việc thanh trùng phế liệu tôm không kinh tế. Trong nghiên cứu này quá trình lên men phế liệu tôm không thanh trùng bằng Lactobacillus plantarum NCDN4 đã được khảo sát. Các yếu tố như tỷ lệ giống, nồng độ đường glucose, nồng độ NaCl, pH ban đầu của môi trường lên men và thời gian lên men đã được nghiên cứu. Kết quả cho thấy ở điều kiện 20% giống theo thể tích, 12,5% dịch đường glucose, 2% muối theo khối lượng, pH ban đầu 6, sau 5 ngày lên men lượng khoáng và protein trong nguyên liệu giảm tương ứng 99.28% và 48.65%. Lượng khoáng và protein còn lại tương ứng 1.33% và 22.46% (tính theo trọng lượng khô). So với phế liệu tôm không thanh trùng, hiệu quả loại khoáng và protein là tương đương.