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93-643: The Department of Energy Organization Act of 1977 established EIA as the primary federal government authority on energy statistics and analysis, building upon systems and organizations first established in 1974 following the oil market disruption of 1973. EIA conducts a comprehensive data collection program that covers the full spectrum of energy sources, end uses, and energy flows; generates short- and long-term domestic and international energy projections; and performs informative energy analyses. EIA disseminates its data products, analyses, reports, and services to customers and stakeholders primarily through its website and

186-416: A " ...central, comprehensive, and unified energy data and information program which will collect, evaluate, assemble, analyze, and disseminate data and information which is relevant to energy resource reserves, energy production, demand, and technology, and related economic and statistical information, or which is relevant to the adequacy of energy resources to meet demands in the near and longer term future for

279-479: A 3'- OH group required for the formation of a phosphodiester bond between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated. The ddNTPs may be radioactively or fluorescently labelled for detection in DNA sequencers . Typically, these machines can sequence up to 96 DNA samples in a single batch (run) in up to 48 runs a day. The high demand for low-cost sequencing has driven

372-642: A Preventive Genomics Clinic in August 2019, with Massachusetts General Hospital following a month later. The All of Us research program aims to collect genome sequence data from 1 million participants to become a critical component of the precision medicine research platform and the UK Biobank initiative has studied more than 500.000 individuals with deep genomic and phenotypic data. The growth of genomic knowledge has enabled increasingly sophisticated applications of synthetic biology . In 2010 researchers at

465-517: A base is incorporated. A microwell containing template DNA is flooded with a single nucleotide , if the nucleotide is complementary to the template strand it will be incorporated and a hydrogen ion will be released. This release triggers an ISFET ion sensor. If a homopolymer is present in the template sequence multiple nucleotides will be incorporated in a single flood cycle, and the detected electrical signal will be proportionally higher. Sequence assembly refers to aligning and merging fragments of

558-467: A combination of experimental and modeling approaches . The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because

651-464: A eukaryote, S. cerevisiae (12.1 Mb), and since then genomes have continued being sequenced at an exponentially growing pace. As of October 2011 , the complete sequences are available for: 2,719 viruses , 1,115 archaea and bacteria , and 36 eukaryotes , of which about half are fungi . Most of the microorganisms whose genomes have been completely sequenced are problematic pathogens , such as Haemophilus influenzae , which has resulted in

744-451: A field of study in biology ending in -omics , such as genomics, proteomics or metabolomics . The related suffix -ome is used to address the objects of study of such fields, such as the genome , proteome , or metabolome ( lipidome ) respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; similarly omics has come to refer generally to the study of large, comprehensive biological data sets. While

837-501: A global level has been made possible only recently through the adaptation of genomic high-throughput assays. Metagenomics is the study of metagenomes , genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures , early environmental gene sequencing cloned specific genes (often

930-657: A gold-colored symbolic sun , atom , oil derrick , windmill , and dynamo . It is crested by the white head of an eagle , atop a white rope. Both appear on a blue field surrounded by concentric circles in which the name of the agency, in gold, appears on a green background." "The eagle represents the care in planning and the purposefulness of efforts required to respond to the Nation's increasing demands for energy . The sun , atom , oil derrick , windmill , and dynamo serve as representative technologies whose enhanced development can help meet these demands. The rope represents

1023-408: A high error rate at approximately 1 percent. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcripts ( ESTs ). Assembly can be broadly categorized into two approaches: de novo assembly, for genomes which are not similar to any sequenced in the past, and comparative assembly, which uses the existing sequence of a closely related organism as

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1116-427: A much longer DNA sequence in order to reconstruct the original sequence. This is needed as current DNA sequencing technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used. Third generation sequencing technologies such as PacBio or Oxford Nanopore routinely generate sequencing reads 10-100 kb in length; however, they have

1209-576: A political appointee of the President of the United States . The Energy Secretary is assisted in managing the department by a United States Deputy Secretary of Energy , also appointed by the president, who assumes the duties of the secretary in the secretary's absence. The department also has three under secretaries, each appointed by the president, who oversee the major areas of the department's work. The president also appoints seven officials with

1302-499: A pronounced bias in their phylogenetic distribution compared to the breadth of microbial diversity. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast ( Saccharomyces cerevisiae ) has long been an important model organism for the eukaryotic cell , while the fruit fly Drosophila melanogaster has been a very important tool (notably in early pre-molecular genetics ). The worm Caenorhabditis elegans

1395-475: A protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure. As opposed to traditional structural biology , the determination of a protein structure through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in structural bioinformatics , i.e. determining protein function from its 3D structure. Epigenomics

1488-515: A range of software tools in their automated genome annotation pipeline. Structural annotation consists of the identification of genomic elements, primarily ORFs and their localisation, or gene structure. Functional annotation consists of attaching biological information to genomic elements. The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that computational pipelines have important applications in genomics. Functional genomics

1581-432: A reference during assembly. Relative to comparative assembly, de novo assembly is computationally difficult ( NP-hard ), making it less favourable for short-read NGS technologies. Within the de novo assembly paradigm there are two primary strategies for assembly, Eulerian path strategies, and overlap-layout-consensus (OLC) strategies. OLC strategies ultimately try to create a Hamiltonian path through an overlap graph which

1674-499: A sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the Plus and Minus technique . This involved two closely related methods that generated short oligonucleotides with defined 3' termini. These could be fractionated by electrophoresis on a polyacrylamide gel (called polyacrylamide gel electrophoresis) and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and

1767-629: A specific nuclear device. Wen Ho Lee was accused of stealing nuclear secrets from Los Alamos National Laboratory for the People's Republic of China . Federal officials, including then-Energy Secretary Bill Richardson , publicly named Lee as a suspect before he was charged with a crime. The U.S. Congress held hearings to investigate the Department of Energy's handling of his case. Republican senators thought that an independent agency should be in charge of nuclear weapons and security issues, rather than

1860-434: A substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome: Overall, this method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes. At present there are 24 cyanobacteria for which

1953-628: A total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six Prochlorococcus strains, seven marine Synechococcus strains, Trichodesmium erythraeum IMS101 and Crocosphaera watsonii WH8501 . Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further Prochlorococcus and marine Synechococcus isolates, Acaryochloris and Prochloron ,

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2046-499: A year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop sequencers has come within reach of the average academic laboratory. On the whole, genome sequencing approaches fall into two broad categories, shotgun and high-throughput (or next-generation ) sequencing. Shotgun sequencing

2139-502: Is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects ) to describe gene (and protein ) functions and interactions. Functional genomics focuses on the dynamic aspects such as gene transcription , translation , and protein–protein interactions , as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about

2232-471: Is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun . Since gel electrophoresis sequencing can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain reads . Multiple overlapping reads for

2325-550: Is an executive department of the U.S. federal government that oversees U.S. national energy policy and energy production , the research and development of nuclear power , the military's nuclear weapons program , nuclear reactor production for the United States Navy , energy-related research, and energy conservation . The DOE was created in 1977 in the aftermath of the 1973 oil crisis . It sponsors more physical science research than any other U.S. federal agency,

2418-732: Is an NP-hard problem. Eulerian path strategies are computationally more tractable because they try to find a Eulerian path through a deBruijn graph. Finished genomes are defined as having a single contiguous sequence with no ambiguities representing each replicon . The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to sequences , and consists of three main steps: Automatic annotation tools try to perform these steps in silico , as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification. Ideally, these approaches co-exist and complement each other in

2511-697: Is an often used simple model for multicellular organisms . The zebrafish Brachydanio rerio is used for many developmental studies on the molecular level, and the plant Arabidopsis thaliana is a model organism for flowering plants. The Japanese pufferfish ( Takifugu rubripes ) and the spotted green pufferfish ( Tetraodon nigroviridis ) are interesting because of their small and compact genomes, which contain very little noncoding DNA compared to most species. The mammals dog ( Canis familiaris ), brown rat ( Rattus norvegicus ), mouse ( Mus musculus ), and chimpanzee ( Pan troglodytes ) are all important model animals in medical research. A rough draft of

2604-587: Is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical Research Institute, by Pascal Mayer and Laurent Farinelli. In this method, DNA molecules and primers are first attached on a slide and amplified with polymerase so that local clonal colonies, initially coined "DNA colonies", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. Unlike pyrosequencing,

2697-514: Is focused on a particular energy challenge. Two of the eight hubs are included in the EERE budget and will focus on integrating smart materials, designs, and systems into buildings to better conserve energy and on designing and discovering new concepts and materials needed to convert solar energy into electricity. Another two hubs, included in the DOE Office of Science budget, were created to tackle

2790-486: Is over-sampled is referred to as coverage . For much of its history, the technology underlying shotgun sequencing was the classical chain-termination method or ' Sanger method ', which is based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication . Recently, shotgun sequencing has been supplanted by high-throughput sequencing methods, especially for large-scale, automated genome analyses. However,

2883-679: Is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome . Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p. 475). Two of the most characterized epigenetic modifications are DNA methylation and histone modification . Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis . The study of epigenetics on

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2976-411: The 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its power to reveal

3069-633: The J. Craig Venter Institute announced the creation of a partially synthetic species of bacterium , Mycoplasma laboratorium , derived from the genome of Mycoplasma genitalium . Population genomics has developed as a popular field of research, where genomic sequencing methods are used to conduct large-scale comparisons of DNA sequences among populations - beyond the limits of genetic markers such as short-range PCR products or microsatellites traditionally used in population genetics . Population genomics studies genome -wide effects to improve our understanding of microevolution so that we may learn

3162-525: The Jackson Laboratory ( Bar Harbor, Maine ), over beers with Jim Womack, Tom Shows and Stephen O’Brien at a meeting held in Maryland on the mapping of the human genome in 1986. First as the name for a new journal and then as a whole new science discipline. Following Rosalind Franklin 's confirmation of the helical structure of DNA, James D. Watson and Francis Crick 's publication of

3255-500: The World Institute for Nuclear Security (WINS), an international non-governmental organization designed to provide a forum to share best practices in strengthening the security and safety of nuclear and radioactive materials and facilities. The department announced a reorganization with new names of under secretaries in 2022. The department is under the control and supervision of a United States Secretary of Energy ,

3348-519: The earth itself, and gold represents the creation of energy in the release of natural forces. By invoking this symbolism , the color scheme represents the Nation's commitment to meet its energy needs in a manner consistent with the preservation of the natural environment ." The Department of Energy operates a system of national laboratories and technical facilities for research and development, as follows: Other major DOE facilities include: Airstrip: The DOE/ NNSA has federal responsibility for

3441-475: The human genome was completed by the Human Genome Project in early 2001, creating much fanfare. This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared "finished" (less than one error in 20,000 bases and all chromosomes assembled). In the years since then, the genomes of many other individuals have been sequenced, partly under

3534-442: The phylogenetic history and demography of a population. Population genomic methods are used for many different fields including evolutionary biology , ecology , biogeography , conservation biology and fisheries management . Similarly, landscape genomics has developed from landscape genetics to use genomic methods to identify relationships between patterns of environmental and genetic variation. Conservationists can use

3627-439: The 1980 Nobel Prize in chemistry with Paul Berg ( recombinant DNA ). The advent of these technologies resulted in a rapid intensification in the scope and speed of completion of genome sequencing projects . The first complete genome sequence of a eukaryotic organelle , the human mitochondrion (16,568 bp, about 16.6 kb [kilobase]), was reported in 1981, and the first chloroplast genomes followed in 1986. In 1992,

3720-416: The DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity; with an optimal configuration, the ultimate throughput of

3813-651: The DOE. All but one of the 59 charges against Lee were eventually dropped because the investigation proved the plans the Chinese obtained could not have come from Lee. Lee filed suit and won a $ 1.6 million settlement against the federal government and news agencies. The episode eventually led to the creation of the National Nuclear Security Administration , a semi-autonomous agency within the department. In 2001, American Solar Challenge

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3906-400: The Department of Energy with the goal of promoting energy conservation and energy independence, and developing alternative sources of energy to reduce the use of fossil fuels . With international energy's future uncertain for America, Carter acted quickly to have the department come into action the first year of his presidency. This was an extremely important issue of the time as the oil crisis

3999-729: The Department of Energy. The new agency, which began operations on October 1, 1977, consolidated the Federal Energy Administration , the Energy Research and Development Administration , the Federal Power Commission , and programs of various other agencies. Former Secretary of Defense James Schlesinger , who served under Presidents Nixon and Ford during the Vietnam War , was appointed as the first secretary. President Carter proposed

4092-561: The EIA's information online each month. Some of the EIA's products include: The Federal Energy Administration Act of 1974 created the Federal Energy Administration (FEA), the first U.S. agency with the primary focus on energy and mandated it to collect, assemble, evaluate, and analyze energy information. It also provided the FEA with data collection enforcement authority for gathering data from energy producing and major consuming firms. Section 52 of

4185-783: The FEA Act mandated establishment of the National Energy Information System to "… contain such energy information as is necessary to carry out the Administration's statistical and forecasting activities …" The Department of Energy Organization Act of 1977 , Public Law 95-91, created the Department of Energy. Section 205 of this law established the Energy Information Administration (EIA) as the primary federal government authority on energy statistics and analysis to carry out

4278-449: The N 2 -fixing filamentous cyanobacteria Nodularia spumigena , Lyngbya aestuarii and Lyngbya majuscula , as well as bacteriophages infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into

4371-425: The Nation's economic and social needs." The same law established that EIA's processes and products are independent from review by Executive Branch officials. The majority of EIA energy data surveys are based on the general mandates set forth above. However, there are some surveys specifically mandated by law, including: United States Department of Energy The United States Department of Energy ( DOE )

4464-462: The Office of Energy Efficiency and Renewable Energy would be lowered to $ 696 million under the plan, down from $ 1.3 billion in fiscal year 2017. Overall, the department's energy and related programs would be cut by $ 1.9 billion. Energy Savings Performance Contracts (ESPCs) are contracts under which a contractor designs, constructs, and obtains the necessary financing for an energy savings project, and

4557-481: The Sanger method remains in wide use, primarily for smaller-scale projects and for obtaining especially long contiguous DNA sequence reads (>500 nucleotides). Chain-termination methods require a single-stranded DNA template, a DNA primer , a DNA polymerase , normal deoxynucleosidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation. These chain-terminating nucleotides lack

4650-643: The United States at the time the guarantee is issued". In loan guarantees, a conditional commitment requires to meet an equity commitment, as well as other conditions, before the loan guarantee is completed. In September 2008, the DOE, the Nuclear Threat Initiative (NTI), the Institute of Nuclear Materials Management (INMM), and the International Atomic Energy Agency (IAEA) partnered to develop and launch

4743-496: The approval of any other officer or employee of the Department in connection with the collection or analysis of any information; nor shall the Administrator be required, prior to publication, to obtain the approval of any other officer or employee of the United States with respect to the substance of any statistical or forecasting technical reports which he has prepared in accordance with law." More than two million people use

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4836-575: The auspices of the 1000 Genomes Project , which announced the sequencing of 1,092 genomes in October 2012. Completion of this project was made possible by the development of dramatically more efficient sequencing technologies and required the commitment of significant bioinformatics resources from a large international collaboration. The continued analysis of human genomic data has profound political and social repercussions for human societies. The English-language neologism omics informally refers to

4929-411: The availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved homologs. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to

5022-567: The challenges of devising advanced methods of energy storage and creating fuels directly from sunlight without the use of plants or microbes. Yet another hub was made to develop "smart" materials to allow the electrical grid to adapt and respond to changing conditions. In 2012, the DOE awarded $ 120 million to the Ames Laboratory to start a new EIH, the Critical Materials Institute, which will focus on improving

5115-449: The cohesiveness in the development of the technologies and their link to our future capabilities. The lightning bolt represents the power of the natural forces from which energy is derived and the Nation's challenge in harnessing the forces." "The color scheme is derived from nature, symbolizing both the source of energy and the support of man's existence. The blue field represents air and water , green represents mineral resources and

5208-479: The complete nucleotide-sequence of bacteriophage MS2-RNA (whose genome encodes just four genes in 3569 base pairs [bp]) and Simian virus 40 in 1976 and 1978, respectively. In addition to his seminal work on the amino acid sequence of insulin, Frederick Sanger and his colleagues played a key role in the development of DNA sequencing techniques that enabled the establishment of comprehensive genome sequencing projects. In 1975, he and Alan Coulson published

5301-577: The customer contact center. Located in Washington, D.C. , EIA has about 325 federal employees and a budget of $ 126.8 million in fiscal year 2021. By law, EIA's products are prepared independently of policy considerations. EIA neither formulates nor advocates any policy conclusions. The Department of Energy Organization Act allows EIA's processes and products to be independent from review by Executive Branch officials; specifically, Section 205(d) says: "The Administrator shall not be required to obtain

5394-476: The design, testing and production of all nuclear weapons. NNSA in turn uses contractors to carry out its responsibilities at the following government owned sites: On May 7, 2009 President Barack Obama unveiled a $ 26.4 billion budget request for DOE for fiscal year (FY) 2010, including $ 2.3 billion for the DOE Office of Energy Efficiency and Renewable Energy (EERE). That budget aimed to substantially expand

5487-448: The development of high-throughput sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences at once. High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis operations may be run in parallel. The Illumina dye sequencing method

5580-623: The evolutionary origin of photosynthesis , or estimation of the contribution of horizontal gene transfer to the genomes that have been analyzed. Genomics has provided applications in many fields, including medicine , biotechnology , anthropology and other social sciences . Next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study populations. When combined with new informatics approaches that integrate many kinds of data with genomic data in disease research, this allows researchers to better understand

5673-433: The federal agency makes payments over time to the contractor from the savings in the agency's utility bills. The contractor guarantees the energy improvements will generate savings, and after the contract ends, all continuing cost savings accrue to the federal agency. Energy Innovation Hubs are multi-disciplinary , meant to advance highly promising areas of energy science and technology from their early stages of research to

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5766-422: The first eukaryotic chromosome , chromosome III of brewer's yeast Saccharomyces cerevisiae (315 kb) was sequenced. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8 Mb [megabase]) in 1995. The following year a consortium of researchers from laboratories across North America , Europe , and Japan announced the completion of the first complete genome sequence of

5859-473: The following quarter-century of research. In the same year Walter Gilbert and Allan Maxam of Harvard University independently developed the Maxam-Gilbert method (also known as the chemical method ) of DNA sequencing, involving the preferential cleavage of DNA at known bases, a less efficient method. For their groundbreaking work in the sequencing of nucleic acids, Gilbert and Sanger shared half

5952-514: The function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain. The field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within

6045-430: The function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "gene-by-gene" approach. A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created

6138-480: The genetic bases of drug response and disease. Early efforts to apply the genome to medicine included those by a Stanford team led by Euan Ashley who developed the first tools for the medical interpretation of a human genome. The Genomes2People research program at Brigham and Women’s Hospital , Broad Institute and Harvard Medical School was established in 2012 to conduct empirical research in translating genomics into health. Brigham and Women's Hospital opened

6231-571: The genome. From the Greek ΓΕΝ gen , "gene" (gamma, epsilon, nu, epsilon) meaning "become, create, creation, birth", and subsequent variants: genealogy, genesis, genetics, genic, genomere, genotype, genus etc. While the word genome (from the German Genom , attributed to Hans Winkler ) was in use in English as early as 1926, the term genomics was coined by Tom Roderick, a geneticist at

6324-425: The growth in the use of the term has led some scientists ( Jonathan Eisen , among others ) to claim that it has been oversold, it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the constituents of a system. In the study of symbioses , for example, researchers which were once limited to the study of a single gene product can now simultaneously compare

6417-438: The information gathered by genomic sequencing in order to better evaluate genetic factors key to species conservation, such as the genetic diversity of a population or whether an individual is heterozygous for a recessive inherited genetic disorder. By using genomic data to evaluate the effects of evolutionary processes and to detect patterns in variation throughout a given population, conservationists can formulate plans to aid

6510-467: The instrument depends only on the A/D conversion rate of the camera. The camera takes images of the fluorescently labeled nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle. An alternative approach, ion semiconductor sequencing, is based on standard DNA replication chemistry. This technology measures the release of a hydrogen ion each time

6603-476: The majority of which is conducted through its system of National Laboratories . The DOE also directs research in genomics , with the Human Genome Project originating from a DOE initiative. The department is headed by the secretary of energy , who reports directly to the president of the United States and is a member of the Cabinet . The current secretary of energy is Jennifer Granholm , who has served in

6696-515: The new Nuclear Regulatory Commission , which was charged with regulating the nuclear power industry, and the Energy Research and Development Administration , which was assigned to manage the nuclear weapon, naval reactor, and energy development programs. The 1973 oil crisis called attention to the need to consolidate energy policy. In 1977, President Jimmy Carter signed into law the Department of Energy Organization Act , which established

6789-412: The organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze

6882-497: The point that the risk level will be low enough for industry to commercialize the technologies. The Consortium for Advanced Simulation of Light Water Reactors (CASL) was the first DOE Energy Innovation Hub established in July 2010, for the purpose of providing advanced modeling and simulation (M&S) solutions for commercial nuclear reactors. The 2009 DOE budget includes $ 280 million to fund eight Energy Innovation Hubs, each of which

6975-661: The position since February 2021. The department's headquarters are in southwestern Washington, D.C. , in the James V. Forrestal Building , with additional offices in Germantown, Maryland . In 1942, during World War II , the United States started the Manhattan Project to develop the atomic bomb under the U.S. Army Corps of Engineers . After the war, in 1946, the Atomic Energy Commission (AEC)

7068-415: The possibility for the field of functional genomics , mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics . Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome . This genome-based approach allows for a high-throughput method of structure determination by

7161-433: The previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology . Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced

7254-505: The rank of Assistant Secretary of Energy who have line management responsibility for major organizational elements of the department. The Energy Secretary assigns their functions and duties. Excerpt from the Code of Federal Regulations , in Title 10: Energy : The official seal of the Department of Energy "includes a green shield bisected by a gold-colored lightning bolt, on which is emblazoned

7347-660: The same annotation pipeline (also see below ). Traditionally, the basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on homologues. More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl ) rely on both curated data sources as well as

7440-517: The stimulus spending was in the form of grants and contracts. For fiscal year 2013, each of the operating units of the Department of Energy operated with the following budgets: In March 2018, Energy Secretary Rick Perry testified to a Senate panel about the Trump administration's DOE budget request for fiscal year 2019. The budget request prioritized nuclear security while making large cuts to energy efficiency and renewable energy programs. The proposal

7533-473: The structure of DNA in 1953 and Fred Sanger 's publication of the Amino acid sequence of insulin in 1955, nucleic acid sequencing became a major target of early molecular biologists . In 1964, Robert W. Holley and colleagues published the first nucleic acid sequence ever determined, the ribonucleotide sequence of alanine transfer RNA . Extending this work, Marshall Nirenberg and Philip Leder revealed

7626-470: The structure, function, evolution, mapping, and editing of genomes . A genome is an organism's complete set of DNA , including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics , which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on

7719-574: The supply of rare earth elements . ARPA-E was officially created by the America COMPETES Act , authored by Congressman Bart Gordon , within the United States Department of Energy (DOE) in 2007, though without a budget. The initial budget of about $ 400 million was a part of the economic stimulus bill of February 2009. Genomics Genomics is an interdisciplinary field of molecular biology focusing on

7812-405: The target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing is a random sampling process, requiring over-sampling to ensure a given nucleotide is represented in the reconstructed sequence; the average number of reads by which a genome

7905-507: The total complement of several types of biological molecules. After an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation. Historically, sequencing was done in sequencing centers , centralized facilities (ranging from large independent institutions such as Joint Genome Institute which sequence dozens of terabases

7998-538: The triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in their experiments. In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent ( Ghent , Belgium ) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein. Fiers' group expanded on their MS2 coat protein work, determining

8091-565: The use of renewable energy sources while improving energy transmission infrastructure. It also proposed significant investments in hybrids and plug-in hybrids , smart grid technologies, and scientific research and innovation. As part of the $ 789 billion economic stimulus package in the American Recovery and Reinvestment Act of 2009, Congress provided Energy with an additional $ 38.3 billion for fiscal years 2009 and 2010, adding about 75 percent to Energy's annual budgets. Most of

8184-507: Was a bacteriophage . However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that

8277-510: Was a $ 500 million increase in funds over fiscal year 2017. It "promotes innovations like a new Office of Cybersecurity, Energy Security, and Emergency Response (CESER) and gains for the Office of Fossil Energy. Investments would be made to strengthen the National Nuclear Security Administration and modernize the nuclear force, as well as in weapons activities and advanced computing." However, the budget for

8370-492: Was a big improvement, but was still very laborious. Nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the single-stranded bacteriophage φX174 , completing the first fully sequenced DNA-based genome. The refinement of the Plus and Minus method resulted in the chain-termination, or Sanger method (see below ), which formed the basis of the techniques of DNA sequencing, genome mapping, data storage, and bioinformatic analysis most widely used in

8463-628: Was causing shortages and inflation . With the Three Mile Island accident , Carter was able to intervene with the help of the department. Through the DOE, Carter was able to make changes within the Nuclear Regulatory Commission , including improving management and procedures, since nuclear energy and weapons are responsibilities of the department. In December 1999, the FBI was investigating how China obtained plans for

8556-506: Was created to control the future of the project. The Atomic Energy Act of 1946 also created the framework for the first National Laboratories . Among other nuclear projects, the AEC produced fabricated uranium fuel cores at locations such as Fernald Feed Materials Production Center in Cincinnati, Ohio . The Energy Reorganization Act of 1974 split the responsibilities of the AEC into

8649-530: Was sponsored by the DOE and the National Renewable Energy Laboratory . After the 2005 race, the DOE discontinued its sponsorship. Title XVII of Energy Policy Act of 2005 authorizes the DOE to issue loan guarantees to eligible projects that "avoid, reduce, or sequester air pollutants or anthropogenic emissions of greenhouse gases " and "employ new or significantly improved technologies as compared to technologies in service in

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