The breakthrough of molecular biology in the last century has become the growing point of life science, which has revolutionized the position of life science in natural science. The revelation of the structure, function and relationship of protein, enzyme, nucleic acid and other biological macromolecules has laid a theoretical foundation for studying the nature and activity law of life phenomena. After entering the 2 1 century, the US Department of Energy launched a new strategic plan-GTL (Genomes to Life) plan, which laid the foundation for the application of life science in the fields of energy and environment.

1 GTL project background

"Genomes to Life", with a five-year funding intensity of $6,543.8+billion, was officially launched by the US Department of Energy in July 2002, and was implemented in 65,438+0,994 based on the Human Genome Project and the American Microbiology Plan.

10 On June 3rd, the U.S. Department of Energy announced a new comprehensive plan for biological research-GTL plan road map. The GTL roadmap is extended on the basis of the original GTL research project. Up to now, more than 800 scientists and technical experts have participated in the project.

The goal of the 2 GTL plan

The core goal of GTL project is to understand how thousands of microbial genomes and microbial systems will regulate life activities in the next ten to twenty years, paving the way for solving environmental problems by biological means. GTL roadmap will expand investment in genome projects and help the country solve energy and environmental problems. This research needs to fill the knowledge gap, develop biotechnology and apply bioinformatics to data mining, calculation and storage.

The foundation of GTL plan is to accurately describe all the "molecular machines" of life system, and to understand how "molecular machines" works harmoniously in life. It is necessary to collect a lot of genome data and related data, especially the data of genome expression, and the data of protein's assembly and function in different cells and under different conditions.

The specific objectives of GTL plan include: (1) identifying "molecular machines", mainly protein compounds, and performing the basic functions of life system; (2) Find out the gene regulatory network that controls molecular machines's behavior; (3) Understand the microbial community in the natural environment; (4) Develop the computer technology needed to establish and realize the biological system model.

The significance of 3 GTL plan

2 1 century, human beings are facing a series of urgent problems such as health, energy and environment. The development of biology may be the key to solve these problems, and the study of genomic information is the basis for understanding the molecular composition and regulation mechanism of living systems. It is necessary to understand the way and mechanism of the interaction between the whole biological system and the environment, and use this information to guide the subsequent biological research.

Genes in the genome behave as protein according to certain temporal and spatial laws, and protein needs to interact with other protein or nucleic acids to form an organic "molecular machines". The implementation of GTL plan will promote the intersection and progress of biology, physics and computational science, promote major breakthroughs in experimental equipment, software tools, analytical methods and scientific ideas, lay the foundation for a comprehensive understanding of biology from multiple angles, and apply it to the discussion of the interaction and influence between biology and environment. These are the basis of applying biotechnology to solve energy and environmental problems.

The implementation of this new plan based on the human genome project will focus on the overall understanding and prediction of biological systems such as human body and microorganisms, and provide biotechnology means for solving environmental and energy problems.

(2): GTL road map

In 2002, the US Department of Energy launched the "Genomes to Life", which provided a means for human beings to solve energy and environmental problems by using biotechnology. 10 On June 3rd, the U.S. Department of Energy announced a new GTL plan roadmap, which provided a guiding direction for the specific implementation of GTL.

Key to implementing 1 GTL plan

The GTL roadmap expounds the key points of GTL plan implementation. Prior to this, the Human Genome Project focused on the study of genome expression, but there were few studies on the expression and assembly of protein in cells under different conditions. Knowing and understanding these research contents is the key link to realize GTL plan. Another key link of GTL plan is high performance computing. Using advanced computing tools to manage and integrate the data obtained from the research, establish the cell system model and carry out computer simulation. On this basis, in-depth analysis, and then understand the working mechanism of "molecular machines".

In the research of high performance computing, the main goal of GTL is to establish basic bioinformatics algorithms and methods to simulate processes, determine data standards and develop visualization tools. Many computing tasks in the GTL plan are computationally intensive, requiring a very large computer that performs trillions of floating-point calculations every second.

2 Implementation organization of road map

The U.S. Department of Energy is committed to providing the necessary scientific platform for the implementation of the GTL plan to support the application of scientific research and technological achievements. GTL plans to establish four cutting-edge biological institutions to support the development of related technologies, the research of methods and the improvement of computing capacity, and to establish a public scientific research platform. The platform not only serves the scientific research group, but also serves the industry, thus accelerating the transformation of scientific research achievements or technology transfer. The core of GTL's success is to develop computing and information technology to overcome the obstacles of studying biological functions based on genome sequences. The U.S. Department of Energy will establish an integrated computing environment to integrate all kinds of experimental data, theories, models and new ideas into the discovery of basic biological mechanisms and the development of system biology theories and experiments.

The Science Office of the U.S. Department of Energy is the main coordinating agency for the implementation of GTL roadmap, which is dedicated to providing extraordinary scientific discovery and research tools, changing people's understanding of energy and materials, and improving the level of American economy and energy security. The main tasks of the office include: (1) providing solutions for energy security faced by the country and providing necessary scientific basis for national energy and economic security; (2) With the main support of national physical science, scientific research investment has been made in more than 280 universities, 15 national laboratory and many international research institutions; (three) to provide the most important scientific research tools for the national scientific cause, and to build and operate public scientific research equipment from the perspective of enjoying science; (4) Support core competence building, theoretical construction, experiment and simulation to the maximum extent in the scientific field, so as to maintain the leading position of the United States in the world knowledge innovation field.

The key to the successful implementation of GTL plan is to integrate computing and technology platforms, providing a timely and convenient platform for scientific research and the development of biotechnology plans. In the new development of biology, computing technology and biology itself have become equally important; Therefore, GTL is jointly completed by two departments of the Science Office of the U.S. Department of Energy-the Office of Biological and Environmental Research and the Office of Frontier Scientific Computing Research.

3 GTL roadmap strategy

The strategic goal of GTL is to understand biological systems, develop computational models to study biological mechanisms, and use these models to predict the behavior of living systems. The ultimate goal is to use the biochemical process of microorganisms to serve a series of innovative applications. This needs to be achieved through effective research, production, cost and quality control and efficiency improvement.

Just as the human genome project can stimulate the growth of biomedical and biotechnology industries, the research listed in the GTL roadmap will also accelerate the growth of new biotechnology. Systems biology related to energy and environment is a plan to explore the unknown microbial world. Starting from the coding information of DNA sequence, it aims to find cleaner and safer biological resources, repair toxic wastes, interpret the role of microorganisms in global climate change and develop related emerging sciences. Microorganisms can be used as technology and new products to promote the development of comprehensive economic strength in 2 1 century.

The roadmap describes its specific development path, including the use of emerging technologies, the development of integrated computing technology and the development and use of new research facilities. The realization of these goals depends on the discovery of new microorganisms, the origin and limitation of life and the new understanding of life science research. Microorganisms have extensive heredity and diversity, so their development means the prosperity of the earth's environment, including the environment under extreme temperature, chemistry and pressure. Most of the time, microorganisms live in a wide range of natural environments and form various biological communities. These biological communities have evolved into comprehensive biochemical systems, which have higher selectivity, energy efficiency and less pollution than chemical process systems in any industrial field. GTL roadmap will make use of these microorganisms, paving the way for comprehensive improvement of chemical process system.

(iii): GTL implementation phase

In 2002, the US Department of Energy launched the "Genomes to Life", which provided a means for human beings to solve energy and environmental problems by using biotechnology. 10 On June 3rd, the U.S. Department of Energy announced the road map of GTL, a new generation comprehensive biological research plan, which provided a guiding direction for the concrete realization of GTL.

Implementation stage of 1 GTL plan

The implementation of GTL plan is divided into three stages:

The first stage: carry out research on key issues of complex system testing related to energy and environment, develop new technologies and new computing technologies, and improve research facilities;

The second stage: using advanced tools and new technologies to carry out research, quickly understand biological processes, put forward new ideas to solve energy and environmental problems, and collect information on the interaction between global climate and biological processes;

The third stage: quickly transform the knowledge and ability gained in the early stage into revolutionary new processes and products to meet the national energy and environmental needs.

The objectives of the first phase of the 2 GTL plan

The main goal of the first phase of GTL is to lay the foundation for the implementation of GTL plan by starting science, technology and applied technology.

Scientific basis: basic research of genomics in systems biology, research at molecular, cell and community level, key objectives and strategic settings of research.

Technology, computing and facilities: advanced technology development and testing, cutting-edge research, computing and technology upgrading, research, development, design and establishment of institutions/facilities.

Target application: key system selection of target orientation, understanding of the process and interaction between cells and communities, system data and strategy analysis.

The objectives of the first phase of the 3 GTL plan

The main goal of the second phase of GTL is to engineer scientific research results through science, technology and application process.

Scientific basis: Qualcomm quantity research, comparative analysis, system model development, system integration experiment and calculation of key systems and processes.

Technology, computing and facilities: the operation of facilities, the operation of integrating data and computing power, and the ability to quickly collect and apply complete biological system data.

Target application: start the systematic analysis of target mode, understand the strategic objectives of the project, and set specific application strategies.

4. The objectives of the first phase of GTL plan

The third GTL will be further developed in science, technology and applied technology, and will be applied in various fields.

Scientific basis: knowledge integration of target scheme design, development and application of science and technology, scientific innovation and development of next generation concepts.

Technology, calculation and facilities: facilities application, testing, evaluation, monitoring and identification of engineering systems, and engineering design of new functions and concepts.

Target application: design and development of complete engineering system, testing and evaluation of engineering system, development of next generation engineering.

(D): GTL application target

The Genomes to Life (GTL) project put forward by the United States in 2002 aims to study the molecular mechanism and regulatory network of life, understand the functional characteristics of microbial communities in the natural environment at the molecular level, and establish a computer model to understand complex biological systems and predict their behaviors. On this basis, the GTL Roadmap put forward in 2005 expounds how to use biotechnology to solve energy and environmental problems.

Contents of 1 GTL road map

The GTL roadmap is based on the goals of the US Department of Energy. The roadmap strategy integrates genome, systems biology, microbiology, computational science and major institutional goals, and makes a specific timetable and logical framework for the planning of each part in the three stages. Among the specific goals of energy output, environmental restoration and carbon dioxide recovery and absorption, the road map gives the specific areas that biotechnology can support and the challenges that should be faced to achieve these goals. In order to achieve these goals, the roadmap gives a specific research plan and target technology platform, as well as related management, training, ethics and social considerations.

The center of GTL roadmap is integrated bio-computing platform. The development of systems biology needs to increase constraints to narrow the solution space of problems, which is of great help to analyze, explain and even predict the results from experiments. GTL roadmap describes the model, data and data analysis, theory and other related contents, and points out how to realize the establishment of public-oriented application and computing platform, so as to form the "central nervous system" of GTL research project and implement it.

In addition, the GTL roadmap also points out how to effectively manage different institutions, so that they can operate with high level, Qualcomm capacity, high efficiency, high quality and low cost.

2. The application target of biofuels

GTL's scientific plan is consistent with the objectives of the U.S. Department of Energy. The objectives of the U.S. Department of Energy to study biofuels include:

(1) The conversion of cellulose into fuel includes the awareness and improvement of cellulase activity, sugar utilization and alcohol fermentation, and the integration of processes.

(2) Microbial transformation process from solar energy to hydrogen energy fuel, including photolysis cycle production and design of photosynthetic biofuel system.

3 Application objectives of environmental restoration

The objectives of the US Department of Energy's environmental restoration research include:

(1) Reduce the content of toxic metals through microbial processes, including understanding the interaction between microorganisms and metals and designing remediation processes.

(2) The role of surface microbial community in pollutant transfer includes understanding the results and impacts of pollutant transfer and supporting the remediation process.

4 Carbon dioxide circulation and absorption

The research objectives of the US Department of Energy on carbon dioxide cycle and absorption include:

(1) The position and function of marine microbial community in biological carbon dioxide pump, including the understanding of C, N, P, O and S cycles, the prediction of climate change and the impact assessment of carbon dioxide absorption;

(2) The position and role of terrestrial microbial communities in the global carbon cycle, including the understanding of C, N, P, O and S cycles, the prediction of carbon change and climate change, and the assessment of carbon dioxide absorption.

(v) ㈤GTL Scientific Roadmap and Systems Biology

The breakthrough of molecular biology in the last century has become the growing point of life science, which has revolutionized the position of life science in natural science. The revelation of the structure, function and relationship of protein, enzyme, nucleic acid and other biological macromolecules has laid a theoretical foundation for studying the essence and activity law of life phenomena. In 2005, the US Department of Energy announced the road map of the GTL project, pointing out the application of systems biology in solving energy and environmental problems.

1 GTL scientific road map

GTL's scientific roadmap includes:

(1) Description of genes, protein, biomolecules, biological pathways and systems, including genome research and comparison, basic research of natural systems with new functions, generation and location of protein, and analysis of interactions and complexes in life process.

(2) Understand the function and regulation, including the measurement of molecular reaction and the realization of functional test.

(3) Development of mechanism prediction model, including experimental design, molecular design and operation, and utilization of cell system.

(4) Population and its potential function analysis, including genome sequencing and comparison, natural system screening of the process, and protein production and location.

(5) Understand the community response and regulation, including the comparison of carbon dioxide, nutrition and biogeochemical cycles, the molecular investigation of cells and populations, and the function test of populations.

(6) Predicting reaction and influence, including establishing interaction and prediction models and applying natural and artificial processes.

The target outputs of these plans are:

(1) system engineering, including strategy of system design and development, life system and extracellular system, identification and analysis.

(2) Strong policy and engineering science foundation, including model ecosystem response of natural events and efficiency and impact analysis of intervention strategies.

2 From genome to organism, systematic biology research

Traditional biology is mainly based on reductionism and solves problems through experiments. However, the organism is a complex system, which is not just a collection of genes and protein. It is not possible to fully understand the characteristics of the system just by sketching their relationship. On the basis of a large number of data collection and analysis, system biology uses software tools, analytical methods and new scientific ideas to study the dynamic behavior of biological systems and fully understand the mechanism behind their stability and robustness.

From Genome to Life (GTL) project, spanning molecules, cells, tissues and organs, systems to life, is a research project that truly reflects the changes of life science from analysis to synthesis, from reductionism to overall research. GTL project is a new research project based on human genome project, which embodies this feature. Systems biology studies molecules with different structures and functions and their interactions on the whole level of molecules, cells, tissues, organs and organisms, and completes the research from life code to the whole process of life on the basis of genome sequence; From the recognition and interaction of various molecules in organisms to the study of biological pathways, molecular networks and functional modules, the road map of the whole life activity is finally completed. The introduction of GTL road map points out the specific ways to apply these specific plans to solve energy and environmental problems, and is an example of applying biotechnology to solve the bottlenecks of resources, energy and environment faced by mankind.

The most important feature of a complex life system lies not in its very complex individual components, but in the relationship between the components and the dynamics that form this relationship. The synthesis of system functions is higher than the analysis of each sub-component. Developing life science and biotechnology is an effective way to solve the problems of resources, energy, environment and health faced by human development. From the implementation of GTL roadmap, it can be seen that it is the development direction of life science and biotechnology to achieve this goal by developing system biology and related technologies.