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De Vries, Ronald P. - One of the best experts on this subject based on the ideXlab platform.

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens
    'American Society for Microbiology', 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.Peer reviewe

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens.
    eScholarship University of California, 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production

Daly Paul - One of the best experts on this subject based on the ideXlab platform.

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens
    'American Society for Microbiology', 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.Peer reviewe

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens.
    eScholarship University of California, 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production

Yuji Naka - One of the best experts on this subject based on the ideXlab platform.

  • Superstructure-based design and operation for Biomass Utilization networks
    Computers & Chemical Engineering, 2009
    Co-Authors: Nasser Ayoub, Hiroya Seki, Yuji Naka
    Abstract:

    This paper is providing a design and evaluation methodology for Biomass Utilization networks (B-NETs) planning in local areas. The methodology is an effort to integrate various exertions of many researchers as well as stakeholders in the Biomass field including process technologies, local area classification and renewable energy mechanisms to design and evaluate B-NETs. The proposed design methodology has three steps: classification, problem formulation and suggesting solution methods. The core part of planning the B-NETs Utilization methodology is the superstructure that is a super class model for the processes of Biomass Utilization networks that has to be built for the local area. The Biomass Utilization superstructure (BUSS) relates the Biomass resources to their products, available processes, and possible future processes of Utilization in static manner. Although the local area BUSS is static in nature, it shows the decision makers what kinds of B-NETs are, or can be, available in their area. It is important to note that for each super class process there exists a number of elemental technologies, or what we call unit process (UP), that can perform the job under the same condition with different processing constraint. To support the design and operation process a technological information infrastructure (TII) needs to be built to work as an information pool and simulation tool. With the support of TII and the BUSS different scenarios can be synthesized, analyzed and compared. Scenarios development enables the designer to check processing alternatives as well as Biomass promotion mechanisms that fit the concerns of various stakeholders. The results of the methodology application can be given in the form of suggestions of a specific network class(es) or scenarios that can be applied in a class of localities with the same characteristics. Following to methodology configuration, a proposal for optimization methods is discussed and a case study for comparing Biomass network scenarios in mountainous city is introduced.

  • A methodology for designing and evaluating Biomass Utilization Networks
    Computer Aided Chemical Engineering, 2008
    Co-Authors: Nasser Ayoub, Hiroya Seki, Yuji Naka
    Abstract:

    Abstract This paper presents a methodology for designing and evaluating Biomass Utilization Networks, BUN, in local areas. Therefore, the proposed methodology assumes the great importance of establishing the BUN superstructure for the area under study, which relates the Biomass resources to their products, available processes and possible future processes of Utilization. Using the developed network superstructure, the quantitative data of the local Biomass resources, the bioproducts demands, the redundant resources and processes, due to low amount, low demand, or technical problems, are excluded. Then two types of network structures were set upped, the first is the reference models that show the current situation with its possibilities for improvements and the second type is future network structures that can be established excluding or partly including, the current Utilization strategy. The resulted network structures are used as a blue print for different scenarios of integrated Biomass Utilization systems that can be evaluated in comparison to the reference scenario. Optimizing the different scenarios allows us to define the bottlenecks in the Biomass Utilization system that limits its total throughput. Solving the optimization problem of the selected network structure in the local level needs high rank of details where each resource's supply chain includes wide range of Unit Processes, UPs, that meet domestic circumstances e.g. logistics, production facilities, and so on. The GA was used to solve this optimization problem as a powerful tool in solving such combinatorial problems considering three optimization criterions, e.g. costs, emissions, energy consumption to congregate the different economical and environmental burdens of the established BUN.

Prapita Thanarak - One of the best experts on this subject based on the ideXlab platform.

  • supply chain management of agricultural waste for Biomass Utilization and co2 emission reduction in the lower northern region of thailand
    Energy Procedia, 2012
    Co-Authors: Prapita Thanarak
    Abstract:

    Abstract Biomass plays an important role as renewable energy resource for electricity generation and biofuel. It is necessary to study the commercial Biomass in 9 provinces of the northern region of Thailand. Information on the status of Biomass Utilization was applied from Biomass fuel project management that approach to the use of renewable energy in macrolevel. The study presents that there is low potential of biofuel in this region. Then, explore the cost of raw fuel, collection and processing cost, transportation costs, electricity prices, prices of agricultural products, price level of agricultural waste, fuel prices, employment and the business of producing Biomass energy. After that developed a mathematical model is needed to present the impact of the expansion of the production of Biomass to changes in economic variables, using the regression model to plan and manage the forecasts. The study of carbon dioxide emissions using the calculations of Annex 12 Methodological tool (version 01.1) “Tool to calculate the emission factor for an electricity system” and create a database, which is the concept of business strategy for new economic era. This is a practical guide to implementing an effective supply chain management for Biomass in the lower northern region of Thailand.

Makela, Miia R. - One of the best experts on this subject based on the ideXlab platform.

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens
    'American Society for Microbiology', 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.Peer reviewe

  • Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens.
    eScholarship University of California, 2019
    Co-Authors: Daly Paul, Peng Mao, Di Falco Marcos, Lipzen Anna, Wang Mei, Ng Vivian, Grigoriev Igor, Tsang Adrian, Makela, Miia R., De Vries, Ronald P.
    Abstract:

    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for Utilization of plant Biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant Biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant Biomass Utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production