Constraint-based modelling of metabolism in Arabidopsis thaliana

Plants are the most abundant biomass on Earth. Understanding plant metabolism represents a significant, fundamental challenge, requiring the incorporation of many fields of study. However it also provides potentially significant leverage with which to change the world in which we live. The model organism Arabidopsis thaliana is probably the single best under- stood plant system. The aim of this thesis is to use mathematical modelling to investigate to what extent existing knowledge can describe broad, emergent aspects of the behaviour of metabolism in this system, with particular respect to the metabolism of sulfur, and other nutrients, and to gain insight into the consequences of the structure of its metabolic network. Constraint-based modelling approaches provide a framework for modelling large reaction networks. Although they require various simplifications, and assump- tions, they provide a route for the understanding of large metabolic networks, which is not possible through other approaches. Here, a genome scale model of Arabidopsis metabolism is developed to reflect experimental data, and deployed in the study of nutrient stress, and nutrient requirements. This model predicts changes in gene expression in response to stress, and provides insight into the consequences of the metabolic structure on nutrient use effi�ciency, metabolic flexibility, and the consequences of genetic perturbation

Developing metabolomics for a systems biology approach to understand Parkinson's disease

Neurodegenerative diseases, including Parkinson’s disease (PD), are increasing in prevalence due to the aging population. Despite extensive study, these diseases are still not fully understood and the lack of personalised treatment options that can target the cause of the diseases, rather than the symptoms, has led to a greater demand for improved disease understanding, therapies and diagnostic procedures. In this thesis, we use systems biology approaches to construct disease-specific models intended for biomarker discovery, therapeutic treatment strategy identification and drug repurposing in PD. Systems biology is a mathematical field of research that analyses biological systems via construction of a computational model using experimental data. This is achieved by integration of omics data, including genomics, proteomics, transcriptomics and metabolomics. A specific approach used to identify the physico- and biochemical bounds within a biological system is constraint-based modelling, which requires the input of absolute quantitative metabolomics data. To improve our absolute quantitative coverage of the metabolome, we developed and improved new quantitative metabolomics methods using a targeted mass spectrometry workflow to obtain data intended to be integrated into constraint-based metabolic models for the study of PD. The research was financially supported by the SysMedPD project, which has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement no. 668738.Analytical BioScience

Role of adipose tissue in the pathogenesis and treatment of metabolic syndrome

© Springer International Publishing Switzerland 2014. Adipocytes are highly specialized cells that play a major role in energy homeostasis in vertebrate organisms. Excess adipocyte size or number is a hallmark of obesity, which is currently a global epidemic. Obesity is not only the primary disease of fat cells, but also a major risk factor for the development of Type 2 diabetes, cardiovascular disease, hypertension, and metabolic syndrome (MetS). Today, adipocytes and adipose tissue are no longer considered passive participants in metabolic pathways. In addition to storing lipid, adipocytes are highly insulin sensitive cells that have important endocrine functions. Altering any one of these functions of fat cells can result in a metabolic disease state and dysregulation of adipose tissue can profoundly contribute to MetS. For example, adiponectin is a fat specific hormone that has cardio-protective and anti-diabetic properties. Inhibition of adiponectin expression and secretion are associated with several risk factors for MetS. For this purpose, and several other reasons documented in this chapter, we propose that adipose tissue should be considered as a viable target for a variety of treatment approaches to combat MetS

Metabolic Engineering of Cyanobacteria for Photosynthetic Production of Drop-In Liquid Fuels

Cyanobacteria are oxygenic phototrophs with great potential as hosts for renewable fuel and chemical production. They grow very quickly (compared with plants) and can use sunlight for energy and CO2 as a carbon source (unlike yeast or E. coli). While cyanobacteria have been engineered to make many chemicals that are native and non-native parts of their metabolism, this work is concerned with the production of heptadecane in Synechocystis sp. PCC 6803. Heptadecane is in a class of natural products produced by all cyanobacteria, but in quantities insufficient for industrialization. Towards this future goal, we have built enabling systems for the overproduction of fuels and chemicals in Synechocystis 6803 and cyanoabacteria generally. These tools include plasmid vectors for the overproduction of heterologous proteins and genome- scale metabolic models that can predict strategies for metabolite overproduction. We have shown that the vectors we developed are helpful in controlling the level and timing of heterologous protein expression using a fluorescent reporter, and have made progress towards heptadecane overproduction. During this process, we have also found that heptadecane is crucial for cold tolerance and modulates cyclic electron flow in photosynthesis. In addition to measuring this phenotype in vivo, we have analyzed it in silico using our genome-scale metabolic model and have gained insight into the role of cyclic electron flow in photosynthesis generally

Laboratory Directed Research and Development Program Activities for FY 2007.

Brookhaven National Laboratory (BNL) is a multidisciplinary laboratory that carries out basic and applied research in the physical, biomedical, and environmental sciences, and in selected energy technologies. It is managed by Brookhaven Science Associates, LLC, (BSA) under contract with the U. S. Department of Energy (DOE). BNL's Fiscal year 2007 budget was $515 million. There are about 2,600 employees, and another 4,500 guest scientists and students who come each year to use the Laboratory's facilities and work with the staff. The BNL Laboratory Directed Research and Development (LDRD) Program reports its status to the U.S. Department of Energy (DOE) annually in March, as required by DOE Order 413.2B, 'Laboratory Directed Research and Development', April 19, 2006, and the Roles, Responsibilities, and Guidelines for Laboratory Directed Research and Development at the Department of Energy/National Nuclear Security Administration Laboratories dated June 13, 2006. In accordance this is our Annual Report in which we describe the Purpose, Approach, Technical Progress and Results, and Specific Accomplishments of all LDRD projects that received funding during Fiscal Year 2007. The goals and objectives of BNL's LDRD Program can be inferred from the Program's stated purposes. These are to (1) encourage and support the development of new ideas and technology, (2) promote the early exploration and exploitation of creative and innovative concepts, and (3) develop new 'fundable' R&D projects and programs. The emphasis is clearly articulated by BNL to be on supporting exploratory research 'which could lead to new programs, projects, and directions' for the Laboratory. We explicitly indicate that research conducted under the LDRD Program should be highly innovative, and an element of high risk as to success is acceptable. In the solicitation for new proposals for Fiscal Year 2007 we especially requested innovative new projects in support of RHIC and the Light Source and any of the Strategic Initiatives listed at the LDRD web site. These included support for NSLS-II, RHIC evolving to a quantum chromo dynamics (QCD) lab, nanoscience, translational and biomedical neuroimaging, energy and, computational sciences. As one of the premier scientific laboratories of the DOE, BNL must continuously foster groundbreaking scientific research. At Brookhaven National Laboratory one such method is through its LDRD Program. This discretionary research and development tool is critical in maintaining the scientific excellence and long-term vitality of the Laboratory. Additionally, it is a means to stimulate the scientific community and foster new science and technology ideas, which becomes a major factor in achieving and maintaining staff excellence and a means to address national needs within the overall mission of the DOE and BNL

Basic Research Needs for Geosciences: Facilitating 21st Century Energy Systems

Executive Summary Serious challenges must be faced in this century as the world seeks to meet global energy needs and at the same time reduce emissions of greenhouse gases to the atmosphere. Even with a growing energy supply from alternative sources, fossil carbon resources will remain in heavy use and will generate large volumes of carbon dioxide (CO2). To reduce the atmospheric impact of this fossil energy use, it is necessary to capture and sequester a substantial fraction of the produced CO2. Subsurface geologic formations offer a potential location for long-term storage of the requisite large volumes of CO2. Nuclear energy resources could also reduce use of carbon-based fuels and CO2 generation, especially if nuclear energy capacity is greatly increased. Nuclear power generation results in spent nuclear fuel and other radioactive materials that also must be sequestered underground. Hence, regardless of technology choices, there will be major increases in the demand to store materials underground in large quantities, for long times, and with increasing efficiency and safety margins. Rock formations are composed of complex natural materials and were not designed by nature as storage vaults. If new energy technologies are to be developed in a timely fashion while ensuring public safety, fundamental improvements are needed in our understanding of how these rock formations will perform as storage systems. This report describes the scientific challenges associated with geologic sequestration of large volumes of carbon dioxide for hundreds of years, and also addresses the geoscientific aspects of safely storing nuclear waste materials for thousands to hundreds of thousands of years. The fundamental crosscutting challenge is to understand the properties and processes associated with complex and heterogeneous subsurface mineral assemblages comprising porous rock formations, and the equally complex fluids that may reside within and flow through those formations. The relevant physical and chemical interactions occur on spatial scales that range from those of atoms, molecules, and mineral surfaces, up to tens of kilometers, and time scales that range from picoseconds to millennia and longer. To predict with confidence the transport and fate of either CO2 or the various components of stored nuclear materials, we need to learn to better describe fundamental atomic, molecular, and biological processes, and to translate those microscale descriptions into macroscopic properties of materials and fluids. We also need fundamental advances in the ability to simulate multiscale systems as they are perturbed during sequestration activities and for very long times afterward, and to monitor those systems in real time with increasing spatial and temporal resolution. The ultimate objective is to predict accurately the performance of the subsurface fluid-rock storage systems, and to verify enough of the predicted performance with direct observations to build confidence that the systems will meet their design targets as well as environmental protection goals. The report summarizes the results and conclusions of a Workshop on Basic Research Needs for Geosciences held in February 2007. Five panels met, resulting in four Panel Reports, three Grand Challenges, six Priority Research Directions, and three Crosscutting Research Issues. The Grand Challenges differ from the Priority Research Directions in that the former describe broader, long-term objectives while the latter are more focused

Laboratory Directed Research and Development Program FY 2005 Annual Report

The Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD) Program reports its status to the U.S. Department of Energy (DOE) in March of each year. The program operates under the authority of DOE Order 413.2A, 'Laboratory Directed Research and Development' (January 8, 2001), which establishes DOE's requirements for the program while providing the Laboratory Director broad flexibility for program implementation. LDRD funds are obtained through a charge to all Laboratory programs. This report describes all ORNL LDRD research activities supported during FY 2005 and includes final reports for completed projects and shorter progress reports for projects that were active, but not completed, during this period. The FY 2005 ORNL LDRD Self-Assessment (ORNL/PPA-2006/2) provides financial data about the FY 2005 projects and an internal evaluation of the program's management process. ORNL is a DOE multiprogram science, technology, and energy laboratory with distinctive capabilities in materials science and engineering, neutron science and technology, energy production and end-use technologies, biological and environmental science, and scientific computing. With these capabilities ORNL conducts basic and applied research and development (R&D) to support DOE's overarching national security mission, which encompasses science, energy resources, environmental quality, and national nuclear security. As a national resource, the Laboratory also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Work For Others (WFO) program. Information about the Laboratory and its programs is available on the Internet at <http://www. ornl.gov/>. LDRD is a relatively small but vital DOE program that allows ORNL, as well as other multiprogram DOE laboratories, to select a limited number of R&D projects for the purpose of: (1) maintaining the scientific and technical vitality of the Laboratory; (2) enhancing the Laboratory's ability to address future DOE missions; (3) fostering creativity and stimulating exploration of forefront science and technology; (4) serving as a proving ground for new research; and (5) supporting high-risk, potentially high-value R&D. Through LDRD the Laboratory is able to improve its distinctive capabilities and enhance its ability to conduct cutting-edge R&D for its DOE and WFO sponsors. To meet the LDRD objectives and fulfill the particular needs of the Laboratory, ORNL has established a program with two components: the Director's R&D Fund and the Seed Money Fund. As outlined in Table 1, these two funds are complementary. The Director's R&D Fund develops new capabilities in support of the Laboratory initiatives, while the Seed Money Fund is open to all innovative ideas that have the potential for enhancing the Laboratory's core scientific and technical competencies. Provision for multiple routes of access to ORNL LDRD funds maximizes the likelihood that novel and seminal ideas with scientific and technological merit will be recognized and supported