09/30/13 Introduction to Public Genome Projects
Learning Objectives: Students will acquire knowledge concerning Public Genome Projects and societal issues.
All of the following information is provided by the following websites. Students should consult with the instructor regarding the information students are responsible for learning from these sites.
1. DOE Genomic Science Program http://genomicsgtl.energy.gov/
Describe the Genomic Science Program and some of the basic terms related to it.
Natural systems, from simple microbes to complex, highly diverse ecosystems, hold secrets of life that fascinate curious minds, drive scientific inquiry, and offer biological solutions to many energy and environmental challenges facing us today. Even the simplest of these systems, the single microbe, is so complex that we do not yet possess a full understanding of how a living system works, how life processes are regulated at the molecular level, and how organisms interact with and modify their environments. Systems biology is the holistic, multidisciplinary study of complex interactions that specify the function of an entire biological system—whether single cells or multicellular organisms—rather than the reductionist study of individual components in isolation. The target organisms are microbes and plants, highly renewable subjects.
The Department of Energy (DOE) Genomic Science program is driven by a grand challenge in biology: understanding biological systems so well that we can develop predictive models of these systems. By revealing the genetic blueprint and fundamental principles that control plant and microbial systems relevant to DOE missions, the Genomic Science program is providing the foundational knowledge underlying biological approaches to producing biofuels, sequestering carbon in terrestrial ecosystems, and cleaning up contaminated environments.
The DNA code—the genome—is the starting point to understanding any biological system. The genomes of individual organisms and systems of organisms (e.g., plants, microbes, and their communities and ecosystems) contain the information and operating capabilities that determine structure and function across multiple scales of biological organization. Exploring biological systems across all scales in a comprehensive and integrated way is essential to understanding how these systems operate in nature or in more applied contexts related to DOE missions. The biological systems investigated by researchers in the Genomic Science program include protein and other molecular interactions, pathways, and vast interconnected networks within whole cells, communities, and ecosystems.
Research is conducted at national laboratories, national user facilities, and universities and includes single-investigator projects, multi-institutional collaborations, and fundamental research centers. The Genomic Science program is run by the Office of Biological and Environmental Research (BER) within DOE’s Office of Science.
Be able to describe the potential impact areas of this research.
Biofuels:
Alternative fuels from renewable cellulosic (plant cell walls) biomass transformed into fuel (primarily by microbes) are expected to significantly reduce U.S. dependence on imported oil while enhancing national energy security and decreasing the environmental impacts of energy use. In April, 2013, it was announced that the DOE’s three research centers will continue to be funded for the next five years at $25 million per year for each of the centers.
Kbase:
Driven by the ever-increasing wealth of data, systems biology is demanding new computational capabilities. To address this challenge, the Genomic Science program is developing the DOE Systems Biology Knowledgebase (Kbase) which will collect and analyze huge amounts of data. Powerful tools within KBase will allow users to analyze and simulate data to predict biological behavior, generate and test hypotheses, design new biological functions, and propose new experiments. It was first released to the public in February 2013 and was updated several times for ease of use.
Carbon Cycling and Climate:
The global carbon cycle plays a central role in regulating atmospheric carbon dioxide levels and thus Earth’s climate, but our basic understanding of the tightly interlinked biological processes driving the carbon cycle remains limited. Advancing our knowledge of these processes is crucial to predicting potential climate change impacts and informing relevant policy decisions.
Bioremediation:
Polluted and contaminated environments (for example, oil spills and radiation) are a public concern. Research related to bioremediation (using microbes and other living organisms to convert these pollutants into nontoxic forms).
2. Microbial Genome Program http://microbialgenomics.energy.gov/index.shtml
The Microbial Genome Program activities are now performed by the Genomic Science Program centers (see program described above).
This program resulted in the sequencing of hundreds of microbial genomes. Identifying these genes help investigators determine how living systems solve life challenges.
Microbes, which make up most of Earth’s biomass, have evolved for some 3.8 billion years. They have been found in virtually every environment, surviving and thriving in extremes of heat, cold, radiation, pressure, salt, acidity, and darkness, often, where no other forms of life are found. The diversity and range of their environmental adaptations indicate that microbes long ago ‘solved’ many problems for which scientists are still actively seeking solutions. Researchers have only scratched the surface of microbial diversity. Potential applications include:
· Cleanup of toxic-waste sites worldwide.
· Production of novel therapeutic and preventive agents.
· Energy generation and development of renewable energy sources (e.g., methane and hydrogen).
· Production of chemicals to improve efficiency of industrial processes.
· Management of environmental carbon dioxide, which is related to climate change.
· Detection of disease-causing organisms and monitoring of the safety of food and water supplies.
· Use of genetically altered bacteria as living sensors (biosensors) to detect harmful chemicals in soil, air, or water
3. The Human Genome Project (HGP) http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml
Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy (DOE) and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others. Project goals were to
· identify all the approximately 20,500 genes in human DNA,
· determine the sequences of the 3 billion chemical base pairs that make up human DNA,
· store this information in databases,
· improve tools for data analysis,
· transfer related technologies to the private sector, and
· address the ethical, legal, and social issues (ELSI) that may arise from the project.
Though the HGP is finished, analyses of the data will continue for many years.
o Gene Mapping: Finding the location of genes (loci) on the chromosomes.
o Genome: All of the DNA or genes.
o Proteome: All of the proteins.
o Identify the protein machines (the combination of one or more proteins and other molecules) that carry out critical life functions,and understand what controls when and how these protein machines are synthesized.
o Medicine
§ Pharmacogenomics: The study of how an individual's genetic inheritance affects the body's response to drugs. The term comes from the words pharmacology and genomics and is thus the intersection of pharmaceuticals and genetics. Pharmacogenomics holds the promise that drugs might one day be tailor-made for individuals and adapted to each person's own genetic makeup. Environment, diet, age, lifestyle, and state of health all can influence a person's response to medicines, but understanding an individual's genetic makeup is thought to be the key to creating personalized drugs with greater effectiveness and safety.
§ Diagnosing and Predicting Disease and Disease Susceptibility (The risk of acquiring a disease) and Disease Intervention
§ Gene Therapy: Inserting new genes into an organism to treat disease.
o Ethical, Legal and Social Issues
Privacy and confidentiality.
Psychological impact and stigmatization.
Reproductive issues.
Uncertainties associated with gene tests.
Implications regarding responsibility, free will vs. genetic determinism.
Commercialization of products.
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