Solutions for data integration in functional genomics: a critical assessment and case study.

PubMed

Smedley, Damian; Swertz, Morris A; Wolstencroft, Katy; Proctor, Glenn; Zouberakis, Michael; Bard, Jonathan; Hancock, John M; Schofield, Paul

2008-11-01

The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.

Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

USDA-ARS?s Scientific Manuscript database

Modern biological analyses are often assisted by recent technologies making the sequencing of complex genomes both technically possible and feasible. We recently sequenced the tomato genome that, like many eukaryotic genomes, is large and complex. Current sequencing technologies allow the developmen...

Design and characterization of a 52K SNP chip for goats.

PubMed

Tosser-Klopp, Gwenola; Bardou, Philippe; Bouchez, Olivier; Cabau, Cédric; Crooijmans, Richard; Dong, Yang; Donnadieu-Tonon, Cécile; Eggen, André; Heuven, Henri C M; Jamli, Saadiah; Jiken, Abdullah Johari; Klopp, Christophe; Lawley, Cynthia T; McEwan, John; Martin, Patrice; Moreno, Carole R; Mulsant, Philippe; Nabihoudine, Ibouniyamine; Pailhoux, Eric; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Sayre, Brian L; Tircazes, Aurélie; Jun Wang; Wang, Wen; Zhang, Wenguang

2014-01-01

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

Design and Characterization of a 52K SNP Chip for Goats

PubMed Central

Tosser-Klopp, Gwenola; Bardou, Philippe; Bouchez, Olivier; Cabau, Cédric; Crooijmans, Richard; Dong, Yang; Donnadieu-Tonon, Cécile; Eggen, André; Heuven, Henri C. M.; Jamli, Saadiah; Jiken, Abdullah Johari; Klopp, Christophe; Lawley, Cynthia T.; McEwan, John; Martin, Patrice; Moreno, Carole R.; Mulsant, Philippe; Nabihoudine, Ibouniyamine; Pailhoux, Eric; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Sayre, Brian L.; Tircazes, Aurélie; Jun Wang; Wang, Wen; Zhang, Wenguang

2014-01-01

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years. PMID:24465974

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

PubMed

Buckley, Alexandra R; Standish, Kristopher A; Bhutani, Kunal; Ideker, Trey; Lasken, Roger S; Carter, Hannah; Harismendy, Olivier; Schork, Nicholas J

2017-06-12

Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples. We demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glasser, Alan H.

Final technical report on DE-SC0016106. This is the final technical report for a portion of the multi-institutional CEMM project. This report is centered around 3 publications and a seminar presentation, which have been submitted to E-Link.

10 CFR 52.157 - Contents of applications; technical information in final safety analysis report.

Code of Federal Regulations, 2013 CFR

2013-01-01

...; technical information in final safety analysis report. The application must contain a final safety analysis...) Information sufficient to demonstrate compliance with the applicable requirements regarding testing, analysis... 10 Energy 2 2013-01-01 2013-01-01 false Contents of applications; technical information in final...

10 CFR 52.157 - Contents of applications; technical information in final safety analysis report.

Code of Federal Regulations, 2012 CFR

2012-01-01

...; technical information in final safety analysis report. The application must contain a final safety analysis...) Information sufficient to demonstrate compliance with the applicable requirements regarding testing, analysis... 10 Energy 2 2012-01-01 2012-01-01 false Contents of applications; technical information in final...

10 CFR 52.157 - Contents of applications; technical information in final safety analysis report.

Code of Federal Regulations, 2014 CFR

2014-01-01

...; technical information in final safety analysis report. The application must contain a final safety analysis...) Information sufficient to demonstrate compliance with the applicable requirements regarding testing, analysis... 10 Energy 2 2014-01-01 2014-01-01 false Contents of applications; technical information in final...

10 CFR 52.157 - Contents of applications; technical information in final safety analysis report.

Code of Federal Regulations, 2011 CFR

2011-01-01

...; technical information in final safety analysis report. The application must contain a final safety analysis...) Information sufficient to demonstrate compliance with the applicable requirements regarding testing, analysis... 10 Energy 2 2011-01-01 2011-01-01 false Contents of applications; technical information in final...

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

USDA-ARS?s Scientific Manuscript database

Technical Abstract: 20-75 CHARACTER LINES A strategy for a genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into respective genomes. In this study, nucle...

Controversy and debate on clinical genomics sequencing-paper 1: genomics is not exceptional: rigorous evaluations are necessary for clinical applications of genomic sequencing.

PubMed

Wilson, Brenda J; Miller, Fiona Alice; Rousseau, François

2017-12-01

Next generation genomic sequencing (NGS) technologies-whole genome and whole exome sequencing-are now cheap enough to be within the grasp of many health care organizations. To many, NGS is symbolic of cutting edge health care, offering the promise of "precision" and "personalized" medicine. Historically, research and clinical application has been a two-way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations. However, NGS technologies are not simple substitutes for older technologies and need careful evaluation for use as screening, diagnostic, or prognostic tools. We have concerns across three areas. First, at the moment, analytic validity is unknown because technical platforms are not yet stable, laboratory quality assurance programs are in their infancy, and data interpretation capabilities are badly underdeveloped. Second, clinical validity of genomic findings for patient populations without pre-existing high genetic risk is doubtful, as most clinical experience with NGS technologies relates to patients with a high prior likelihood of a genetic etiology. Finally, we are concerned that proponents argue not only for clinically driven approaches to assessing a patient's genome, but also for seeking out variants associated with unrelated conditions or susceptibilities-so-called "secondary targets"-this is screening on a genomic scale. We argue that clinical uses of genomic sequencing should remain limited to specialist and research settings, that screening for secondary findings in clinical testing should be limited to the maximum extent possible, and that the benefits, harms, and economic implications of their routine use be systematically evaluated. All stakeholders have a responsibility to ensure that patients receive effective, safe health care, in an economically sustainable health care system. There should be no exception for genome-based interventions. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome-Enabled Molecular Tools for Reductive Dehalogenation

DTIC Science & Technology

2011-11-01

Genome-Enabled Molecular Tools for Reductive Dehalogenation - A Shift in Paradigm for Bioremediation - Alfred M. Spormann Departments of Chemical...Genome-Enabled Molecular Tools for Reductive Dehalogenation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...Applications Technical Session No. 3D C-77 GENOME-ENABLED MOLECULAR TOOLS FOR REDUCTIVE DEHALOGENATION PROFESSOR ALFRED SPORMANN Stanford

Genomic science provides new insights into the biology of forest trees

Treesearch

Andrew Groover

2015-01-01

Forest biology is undergoing a fundamental change fostered by the application of genomic science to longstanding questions surrounding the evolution, adaptive traits, development, and environmental interactions of tree species. Genomic science has made major technical leaps in recent years, most notably with the advent of 'next generation sequencing' but...

Henry Taube and Coordination Chemistry

Science.gov Websites

Shifts Caused by Cr++ in Aqueous Solutions, DOE Technical Report, 1962 Reactions of Solvated Ions Final Report, DOE Technical Report, 1962 Isotopic Discrimination of Some Solutes in Liquid Ammonia, DOE Technical Report, 1966 Final Technical Report of Research, DOE Technical Report, 1972 Top Additional Web

George A. Olah, Carbocation and Hydrocarbon Chemistry

Science.gov Websites

. Final Technical Report. [HF:BF{sub 2}/H{sub 2}] , DOE Technical Report, 1980 Superacid Catalyzed Coal Conversion Chemistry. 1st and 2nd Quarterly Technical Progress Reports, September 1, 1983-March 30, 1984 , DOE Technical Report, 1984 Superacid Catalyzed Coal Conversion Chemistry. Final Technical Report

77 FR 46306 - Fluxapyroxad; Pesticide Tolerances Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-03

...; Pesticide Tolerances Technical Amendment AGENCY: Environmental Protection Agency (EPA). ACTION: Final rule; technical amendment. SUMMARY: EPA issued a final rule in the Federal Register of May 14, 2012, concerning.... Inadvertently, the terminology for the oilseed crop group and for dried plums was incorrect. This technical...

New traits in crops produced by genome editing techniques based on deletions.

PubMed

van de Wiel, C C M; Schaart, J G; Lotz, L A P; Smulders, M J M

2017-01-01

One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.

Origins of the Human Genome Project.

PubMed

Watson, J D; Cook-Deegan, R M

1991-01-01

The Human Genome Project has become a reality. Building on a debate that dates back to 1985, several genome projects are now in full stride around the world, and more are likely to form in the next several years. Italy began its genome program in 1987, and the United Kingdom and U.S.S.R. in 1988. The European communities mounted several genome projects on yeast, bacteria, Drosophila, and Arabidospis thaliana (a rapidly growing plant with a small genome) in 1988, and in 1990 commenced a new 2-year program on the human genome. In the United States, we have completed the first year of operation of the National Center for Human Genome Research at the National Institutes of Health (NIH), now the largest single funding source for genome research in the world. There have been dedicated budgets focused on genome-scale research at NIH, the U.S. Department of Energy, and the Howard Hughes Medical Institute for several years, and results are beginning to accumulate. There were three annual meetings on genome mapping and sequencing at Cold Spring Harbor, New York, in the spring of 1988, 1989, and 1990; the talks have shifted from a discussion about how to approach problems to presenting results from experiments already performed. We have finally begun to work rather than merely talk. The purpose of genome projects is to assemble data on the structure of DNA in human chromosomes and those of other organisms. A second goal is to develop new technologies to perform mapping and sequencing. There have been impressive technical advances in the past 5 years since the debate about the human genome project began. We are on the verge of beginning pilot projects to test several approaches to sequencing long stretches of DNA, using both automation and manual methods. Ordered sets of yeast artificial chromosome and cosmid clones have been assembled to span more than 2 million base pairs of several human chromosomes, and a region of 10 million base pairs has been assembled for Caenorhabditis elegans by a collaboration between Washington University and the Medical Research Council laboratory in Cambridge, U.K. This project is now turning to sequencing C. elegans DNA as a logical extension of this work. These are but the first fruits of the genome project. There is much more to come.

Programming biological operating systems: genome design, assembly and activation.

PubMed

Gibson, Daniel G

2014-05-01

The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

Toward genome-enabled mycology.

PubMed

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

32 CFR 37.895 - How is the final performance report to be sent to the Defense Technical Information Center?

Code of Federal Regulations, 2014 CFR

2014-07-01

... How is the final performance report to be sent to the Defense Technical Information Center? (a... 32 National Defense 1 2014-07-01 2014-07-01 false How is the final performance report to be sent to the Defense Technical Information Center? 37.895 Section 37.895 National Defense Department of...

32 CFR 37.895 - How is the final performance report to be sent to the Defense Technical Information Center?

Code of Federal Regulations, 2011 CFR

2011-07-01

... How is the final performance report to be sent to the Defense Technical Information Center? (a... 32 National Defense 1 2011-07-01 2011-07-01 false How is the final performance report to be sent to the Defense Technical Information Center? 37.895 Section 37.895 National Defense Department of...

32 CFR 37.895 - How is the final performance report to be sent to the Defense Technical Information Center?

Code of Federal Regulations, 2013 CFR

2013-07-01

... How is the final performance report to be sent to the Defense Technical Information Center? (a... 32 National Defense 1 2013-07-01 2013-07-01 false How is the final performance report to be sent to the Defense Technical Information Center? 37.895 Section 37.895 National Defense Department of...

32 CFR 37.895 - How is the final performance report to be sent to the Defense Technical Information Center?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 1 2012-07-01 2012-07-01 false How is the final performance report to be sent to the Defense Technical Information Center? 37.895 Section 37.895 National Defense Department of... How is the final performance report to be sent to the Defense Technical Information Center? (a...

76 FR 18624 - Research, Technical Assistance and Training Programs: Notice of Final Circular

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-04

... to FTA Circular 6100.1D, Research and Technical Assistance Training Program: Application Instructions... DEPARTMENT OF TRANSPORTATION Federal Transit Administration Research, Technical Assistance and Training Programs: Notice of Final Circular AGENCY: Federal Transit Administration (FTA), DOT. ACTION...

Epigenetic discrimination of identical twins from blood under the forensic scenario.

PubMed

Vidaki, Athina; Díez López, Celia; Carnero-Montoro, Elena; Ralf, Arwin; Ward, Kirsten; Spector, Timothy; Bell, Jordana T; Kayser, Manfred

2017-11-01

Monozygotic (MZ) twins share the same STR profile, demonstrating a practical problem in forensic casework. DNA methylation has provided a suitable resource for MZ twin differentiation; however, studies addressing the forensic feasibility are lacking. Here, we investigated epigenetic MZ twin differentiation from blood under the forensic scenario comprising i) the discovery of candidate markers in reference-type blood DNA via genome-wide analysis, ii) the technical validation of candidate markers in reference-type blood DNA using a suitable targeted method, and iii) the analysis of the validated markers in trace-type DNA. Genome-wide methylation analysis in blood DNA from 10 MZ twin pairs resulted in 19-111 twin-differentially methylated sites (tDMSs) per pair with >0.3 twin-to-twin differences. Considering all top three candidate tDMSs across all pairs in the technical validation based on methylation-specific qPCR, 67.85% generated >0.1 twin-to-twin differences. Of the validated tDMSs, 68.4% showed >0.1 twin-to-twin differences with qPCR in trace-type DNA across 8 pairs. Using an updated marker selection strategy, 8 additional candidate tDMSs were obtained for an example MZ pair, of which 7 showed >0.1 twin-to-twin differences in both reference- and trace-type DNA. Lastly, we introduce a high-resolution melting curve analysis of the entire fragment that can complement the proposed approach. Overall, our study demonstrates the general feasibility of epigenetic twin differentiation in the forensic context and highlights that the number of informative tDMSs in the final trace DNA analysis is crucial, as some candidate markers identified in reference DNA were shown not informative in the trace DNA due to various, including technical, reasons. Future studies will need to address the optimal number of epigenetic markers required for reliable identification of MZ twin individuals including statistical considerations. Copyright © 2017 Elsevier B.V. All rights reserved.

Newborn Sequencing in Genomic Medicine and Public Health

PubMed Central

Agrawal, Pankaj B.; Bailey, Donald B.; Beggs, Alan H.; Brenner, Steven E.; Brower, Amy M.; Cakici, Julie A.; Ceyhan-Birsoy, Ozge; Chan, Kee; Chen, Flavia; Currier, Robert J.; Dukhovny, Dmitry; Green, Robert C.; Harris-Wai, Julie; Holm, Ingrid A.; Iglesias, Brenda; Joseph, Galen; Kingsmore, Stephen F.; Koenig, Barbara A.; Kwok, Pui-Yan; Lantos, John; Leeder, Steven J.; Lewis, Megan A.; McGuire, Amy L.; Milko, Laura V.; Mooney, Sean D.; Parad, Richard B.; Pereira, Stacey; Petrikin, Joshua; Powell, Bradford C.; Powell, Cynthia M.; Puck, Jennifer M.; Rehm, Heidi L.; Risch, Neil; Roche, Myra; Shieh, Joseph T.; Veeraraghavan, Narayanan; Watson, Michael S.; Willig, Laurel; Yu, Timothy W.; Urv, Tiina; Wise, Anastasia L.

2017-01-01

The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening. PMID:28096516

Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure.

PubMed

Gutierrez, Amanda M; Robinson, Jill O; Statham, Emily E; Scollon, Sarah; Bergstrom, Katie L; Slashinski, Melody J; Parsons, Donald W; Plon, Sharon E; McGuire, Amy L; Street, Richard L

2017-11-01

Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.

Genome-wide association studies in maize: praise and stargaze

USDA-ARS?s Scientific Manuscript database

Genome-wide association study (GWAS) has appeared as a widespread strategy in decoding genotype-phenotype associations in many species thanks to technical advances in next-generation sequencing (NGS) applications. Maize is an ideal crop for GWAS and significant progress has been made in the last dec...

Evaluation of Targeted Sequencing for Transcriptional Analysis of Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

EPA Science Inventory

Next-generation sequencing provides unprecedented access to genomic information in archival FFPE tissue samples. However, costs and technical challenges related to RNA isolation and enrichment limit use of whole-genome RNA-sequencing for large-scale studies of FFPE specimens. Rec...

Minnesota Deaf-Blind Technical Assistance Project. Final Report.

ERIC Educational Resources Information Center

Kloos, Eric

This final report describes activities and accomplishments of the 3-year federally supported Minnesota Deaf-Blind Technical Assistance Project. The project provided training and technical assistance, information sharing, and support services to families of children with deaf-blindness. Activities and accomplishments included: collaboration with…

75 FR 56857 - Pilot, Flight Instructor, and Pilot School Certification

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-17

... of part 141. Discussion of Technical Amendment Section 141.5(d) establishes the quality of training... Certification AGENCY: Federal Aviation Administration, DOT. ACTION: Final rule; technical amendment. SUMMARY: The Federal Aviation Administration (FAA) is making minor technical changes to a final rule published...

77 FR 29247 - Federal Motor Vehicle Safety Standards; Occupant Crash Protection

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-17

...). ACTION: Final rule; technical amendments. SUMMARY: This final rule makes technical amendments to Federal... advanced air bag requirements. As written now, the general warning label requirements contain an explicit... equipment requirements for restraint systems. This document makes technical amendments to several of the...

Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case

USDA-ARS?s Scientific Manuscript database

Prokaryotic taxonomy is the underpinning of microbiology, providing a framework for the proper identification and naming of organisms. The 'gold standard' of bacterial species delineation is the overall genome similarity as determined by DNA-DNA hybridization (DDH), a technically rigorous yet someti...

Mapping Our Genes: The Genome Projects: How Big, How Fast

DOE R&D Accomplishments Database

1988-04-01

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for ?writing the rules? of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. The Office of Technology Assessment (OTA) prepared this report with the assistance of several hundred experts throughout the world.

Human Genome: DOE Origins

Science.gov Websites

Health and Environmental Research [OHER], the program that supported most Biology in the Department. The origins of DOE's biology program traced to the Manhattan Project, the World War II program that produced Technical Report; 1964 Impact of Radiation Biology on Fundamental Insights in Biology; DOE Technical Report

Utilization of TALEN and CRISPR/Cas9 technologies for gene targeting and modification

PubMed Central

Pu, Jiali; Zhang, Baorong; Feng, Jian

2015-01-01

The capability to modify the genome precisely and efficiently offers an extremely useful tool for biomedical research. Recent developments in genome editing technologies such as transcription activator-like effector nuclease and the clustered regularly interspaced short palindromic repeats system have made genome modification available for a number of organisms with relative ease. Here, we introduce these genome editing techniques, compare and contrast each technical approach and discuss their potential to study the underlying mechanisms of human disease using patient-derived induced pluripotent stem cells. PMID:25956682

Newborn Sequencing in Genomic Medicine and Public Health.

PubMed

Berg, Jonathan S; Agrawal, Pankaj B; Bailey, Donald B; Beggs, Alan H; Brenner, Steven E; Brower, Amy M; Cakici, Julie A; Ceyhan-Birsoy, Ozge; Chan, Kee; Chen, Flavia; Currier, Robert J; Dukhovny, Dmitry; Green, Robert C; Harris-Wai, Julie; Holm, Ingrid A; Iglesias, Brenda; Joseph, Galen; Kingsmore, Stephen F; Koenig, Barbara A; Kwok, Pui-Yan; Lantos, John; Leeder, Steven J; Lewis, Megan A; McGuire, Amy L; Milko, Laura V; Mooney, Sean D; Parad, Richard B; Pereira, Stacey; Petrikin, Joshua; Powell, Bradford C; Powell, Cynthia M; Puck, Jennifer M; Rehm, Heidi L; Risch, Neil; Roche, Myra; Shieh, Joseph T; Veeraraghavan, Narayanan; Watson, Michael S; Willig, Laurel; Yu, Timothy W; Urv, Tiina; Wise, Anastasia L

2017-02-01

The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening. Copyright © 2017 by the American Academy of Pediatrics.

The Glyphosate-Based Herbicide Roundup Does not Elevate Genome-Wide Mutagenesis of Escherichia coli.

PubMed

Tincher, Clayton; Long, Hongan; Behringer, Megan; Walker, Noah; Lynch, Michael

2017-10-05

Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup Concentrate Plus. The genome-wide mutation rate decreases as GBH concentration increases, suggesting that even long-term GBH exposure does not compromise the genome stability of bacteria. Copyright © 2017 Tincher et al.

The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery.

PubMed

Bradley, Anthony R; Echalier, Aude; Fairhead, Michael; Strain-Damerell, Claire; Brennan, Paul; Bullock, Alex N; Burgess-Brown, Nicola A; Carpenter, Elisabeth P; Gileadi, Opher; Marsden, Brian D; Lee, Wen Hwa; Yue, Wyatt; Bountra, Chas; von Delft, Frank

2017-11-08

The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets. © 2017 The Author(s).

77 FR 30512 - Native American Career and Technical Education Program; Final Waivers and Extension of Project...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-23

... DEPARTMENT OF EDUCATION Native American Career and Technical Education Program; Final Waivers and... American Career and Technical Education Program Catalog of Federal Domestic Assistance (CFDA) Number: 84.101A. SUMMARY: For 60-month projects funded in fiscal year (FY) 2007 under the Native American Career...

48 CFR 1852.235-73 - Final Scientific and Technical Reports.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Final Scientific and Technical Reports. 1852.235-73 Section 1852.235-73 Federal Acquisition Regulations System NATIONAL..., including recommendations and conclusions based on the experience and results obtained. The final report...

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

PubMed

Alberti, Claudio; Daniels, Noah; Hernaez, Mikel; Voges, Jan; Goldfeder, Rachel L; Hernandez-Lopez, Ana A; Mattavelli, Marco; Berger, Bonnie

2016-01-01

This paper provides the specification and an initial validation of an evaluation framework for the comparison of lossy compressors of genome sequencing quality values. The goal is to define reference data, test sets, tools and metrics that shall be used to evaluate the impact of lossy compression of quality values on human genome variant calling. The functionality of the framework is validated referring to two state-of-the-art genomic compressors. This work has been spurred by the current activity within the ISO/IEC SC29/WG11 technical committee (a.k.a. MPEG), which is investigating the possibility of starting a standardization activity for genomic information representation.

Pooled-BAC sequencing of a black pod resistance region (cBPQTL12) in T. cacao

USDA-ARS?s Scientific Manuscript database

Whole genome sequencing (WGS) is an expensive and technically challenging endeavor. An alternative to WGS is to sequence specific chromosomal segments of biological interest (e.g. a QTL interval). This method is cheaper than WGS and reduces the risk of misassembly from distal parts of the genome. Us...

Coosa River Storage Annex, Talladega, Alabama Environmental Investigation, Final Management and Resources Utilization Plan

DTIC Science & Technology

1991-02-01

to adequately assess the health and environmental risks associated with the closure and transfer of the Annex forI other use; and 3) identification of...1990); Draft Final Technical Plan, Draft Final Sampling Design Plan and Draft Final Health and Safety Plan, USATHAMA, June 1990. 2.1.2 Draft Final...Final Technical Plan, Sampling Design Plan and Health and Safety Plan) supplied by USATHAMA. The estimate may be revised, with USATHAMA approval, as

Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States

PubMed Central

Wang, Shuang; Jiang, Xiaoqian; Singh, Siddharth; Marmor, Rebecca; Bonomi, Luca; Fox, Dov; Dow, Michelle; Ohno-Machado, Lucila

2016-01-01

Accessing and integrating human genomic data with phenotypes is important for biomedical research. Making genomic data accessible for research purposes, however, must be handled carefully to avoid leakage of sensitive individual information to unauthorized parties and improper use of data. In this article, we focus on data sharing within the scope of data accessibility for research. Current common practices to gain biomedical data access are strictly rule based, without a clear and quantitative measurement of the risk of privacy breaches. In addition, several types of studies require privacy-preserving linkage of genotype and phenotype information across different locations (e.g., genotypes stored in a sequencing facility and phenotypes stored in an electronic health record) to accelerate discoveries. The computer science community has developed a spectrum of techniques for data privacy and confidentiality protection, many of which have yet to be tested on real-world problems. In this article, we discuss clinical, technical, and ethical aspects of genome data privacy and confidentiality in the United States, as well as potential solutions for privacy-preserving genotype–phenotype linkage in biomedical research. PMID:27681358

Technical Report: Algorithm and Implementation for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLoughlin, Kevin

2016-01-11

This report describes the design and implementation of an algorithm for estimating relative microbial abundances, together with confidence limits, using data from metagenomic DNA sequencing. For the background behind this project and a detailed discussion of our modeling approach for metagenomic data, we refer the reader to our earlier technical report, dated March 4, 2014. Briefly, we described a fully Bayesian generative model for paired-end sequence read data, incorporating the effects of the relative abundances, the distribution of sequence fragment lengths, fragment position bias, sequencing errors and variations between the sampled genomes and the nearest reference genomes. A distinctive featuremore » of our modeling approach is the use of a Chinese restaurant process (CRP) to describe the selection of genomes to be sampled, and thus the relative abundances. The CRP component is desirable for fitting abundances to reads that may map ambiguously to multiple targets, because it naturally leads to sparse solutions that select the best representative from each set of nearly equivalent genomes.« less

Sensitivity to sequencing depth in single-cell cancer genomics.

PubMed

Alves, João M; Posada, David

2018-04-16

Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of previously published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection. Five single-cell whole-genome and whole-exome cancer datasets were independently downscaled to 25, 10, 5, and 1× sequencing depth. For each depth level, ten technical replicates were generated, resulting in a total of 6280 single-cell BAM files. The sensitivity of variant detection, including structural and driver mutations, genotyping, clonal inference, and phylogenetic reconstruction to sequencing depth was evaluated using recent tools specifically designed for single-cell data. Altogether, our results suggest that for relatively large sample sizes (25 or more cells) sequencing single tumor cells at depths > 5× does not drastically improve somatic variant discovery, characterization of clonal genotypes, or estimation of single-cell phylogenies. We suggest that sequencing multiple individual tumor cells at a modest depth represents an effective alternative to explore the mutational landscape and clonal evolutionary patterns of cancer genomes.

Final technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edward DeLong

2011-10-07

Our overarching goals in this project were to: Develop and improve high-throughput sequencing methods and analytical approaches for quantitative analyses of microbial gene expression at the Hawaii Ocean Time Series Station and the Bermuda Atlantic Time Series Station; Conduct field analyses following gene expression patterns in picoplankton microbial communities in general, and Prochlorococcus flow sorted from that community, as they respond to different environmental variables (light, macronutrients, dissolved organic carbon), that are predicted to influence activity, productivity, and carbon cycling; Use the expression analyses of flow sorted Prochlorococcus to identify horizontally transferred genes and gene products, in particular those thatmore » are located in genomic islands and likely to confer habitat-specific fitness advantages; Use the microbial community gene expression data that we generate to gain insights, and test hypotheses, about the variability, genomic context, activity and function of as yet uncharacterized gene products, that appear highly expressed in the environment. We achieved the above goals, and even more over the course of the project. This includes a number of novel methodological developments, as well as the standardization of microbial community gene expression analyses in both field surveys, and experimental modalities. The availability of these methods, tools and approaches is changing current practice in microbial community analyses.« less

Azolla--a model organism for plant genomic studies.

PubMed

Qiu, Yin-Long; Yu, Jun

2003-02-01

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

Mapping our genes: The genome projects: How big, how fast

DOE Office of Scientific and Technical Information (OSTI.GOV)

none,

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate,more » focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.« less

The Paris-Sud yeast structural genomics pilot-project: from structure to function.

PubMed

Quevillon-Cheruel, Sophie; Liger, Dominique; Leulliot, Nicolas; Graille, Marc; Poupon, Anne; Li de La Sierra-Gallay, Inès; Zhou, Cong-Zhao; Collinet, Bruno; Janin, Joël; Van Tilbeurgh, Herman

2004-01-01

We present here the outlines and results from our yeast structural genomics (YSG) pilot-project. A lab-scale platform for the systematic production and structure determination is presented. In order to validate this approach, 250 non-membrane proteins of unknown structure were targeted. Strategies and final statistics are evaluated. We finally discuss the opportunity of structural genomics programs to contribute to functional biochemical annotation.

77 FR 50589 - Agreements and Memoranda of Understanding Between the Food and Drug Administration and Other...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

...: Final rule. SUMMARY: This final rule makes technical changes that will update a requirement that many of the written agreements and memoranda of understanding (MOUs) between the Food and Drug Administration.... This final rule, accordingly, eliminates it. We are making these technical changes to conserve Agency...

77 FR 30514 - Native Hawaiian Career and Technical Education Program; Final Waiver and Extension of Project Period

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-23

... DEPARTMENT OF EDUCATION Native Hawaiian Career and Technical Education Program; Final Waiver and.... ACTION: Notice. Overview Information Final Waiver and Extension of Project Period for the Native Hawaiian.... SUMMARY: For 36-month projects funded in fiscal year (FY) 2009 under the Native Hawaiian Career and...

2005 v4.3 Technical Support Document

EPA Pesticide Factsheets

Emissions Modeling for the Final Mercury and Air Toxics Standards Technical Support Document describes how updated 2005 NEI, version 2 emissions were processed for air quality modeling in support of the final Mercury and Air Toxics Standards (MATS).

The Center for Space Telemetering and Telecommunications Systems

NASA Technical Reports Server (NTRS)

Horan, S.; DeLeon, P.; Borah, D.; Lyman, R.

2003-01-01

This report comprises the final technical report for the research grant 'Center for Space Telemetering and Telecommunications Systems' sponsored by the National Aeronautics and Space Administration's Goddard Space Flight Center. The grant activities are broken down into the following technology areas: (1) Space Protocol Testing; (2) Autonomous Reconfiguration of Ground Station Receivers; (3) Satellite Cluster Communications; and (4) Bandwidth Efficient Modulation. The grant activity produced a number of technical reports and papers that were communicated to NASA as they were generated. This final report contains the final summary papers or final technical report conclusions for each of the project areas. Additionally, the grant supported students who made progress towards their degrees while working on the research.

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

PubMed Central

Meloche, Caroline; Andrade, Danielle M.; Lafreniere, Ron G.; Gravel, Micheline; Spiegelman, Dan; Dionne-Laporte, Alexandre; Boelman, Cyrus; Hamdan, Fadi F.; Michaud, Jacques L.; Rouleau, Guy; Minassian, Berge A.; Bourque, Guillaume; Cossette, Patrick

2018-01-01

Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases. PMID:29649218

Promotion of the Equal Access of Girls and Women to Technical and Vocational Education. Studies on Technical and Vocational Education 7.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France).

This monograph includes the final report of the International Expert Meeting on the Promotion of Equal Access of Girls and Women to Technical and Vocational Education (TVE) held in Seoul, Republic of Korea, and country discussion papers. The final report is composed of an introduction that proposes that many Member States require special measures…

Air Quality Modeling Technical Support Document for the Final Cross State Air Pollution Rule Update

EPA Pesticide Factsheets

In this technical support document (TSD) we describe the air quality modeling performed to support the final Cross State Air Pollution Rule for the 2008 ozone National Ambient Air Quality Standards (NAAQS).

7 CFR 614.7 - Preliminary technical determinations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 6 2010-01-01 2010-01-01 false Preliminary technical determinations. 614.7 Section... Preliminary technical determinations. (a) A preliminary technical determination becomes final 30 days after... purpose of gathering additional information and discussing the facts relating to the preliminary technical...

Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States.

PubMed

Wang, Shuang; Jiang, Xiaoqian; Singh, Siddharth; Marmor, Rebecca; Bonomi, Luca; Fox, Dov; Dow, Michelle; Ohno-Machado, Lucila

2017-01-01

Accessing and integrating human genomic data with phenotypes are important for biomedical research. Making genomic data accessible for research purposes, however, must be handled carefully to avoid leakage of sensitive individual information to unauthorized parties and improper use of data. In this article, we focus on data sharing within the scope of data accessibility for research. Current common practices to gain biomedical data access are strictly rule based, without a clear and quantitative measurement of the risk of privacy breaches. In addition, several types of studies require privacy-preserving linkage of genotype and phenotype information across different locations (e.g., genotypes stored in a sequencing facility and phenotypes stored in an electronic health record) to accelerate discoveries. The computer science community has developed a spectrum of techniques for data privacy and confidentiality protection, many of which have yet to be tested on real-world problems. In this article, we discuss clinical, technical, and ethical aspects of genome data privacy and confidentiality in the United States, as well as potential solutions for privacy-preserving genotype-phenotype linkage in biomedical research. © 2016 New York Academy of Sciences.

Proteomics technique opens new frontiers in mobilome research.

PubMed

Davidson, Andrew D; Matthews, David A; Maringer, Kevin

2017-01-01

A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons. In a recent paper, we overcame these technical hurdles using a technique called "proteomics informed by transcriptomics" (PIT), and thus published the first unbiased global mobilome-derived proteome for any organism (using cell lines derived from the mosquito Aedes aegypti ). In this commentary, we describe our methods in more detail, and summarise our major findings. We also use new genome sequencing data to show that, in many cases, the specific genomic element expressing a given protein can be identified using PIT. This proteomic technique therefore represents an important technological advance that will open new avenues of research into the role that proteins derived from transposons and other repetitive and sequence diverse genetic elements, such as endogenous retroviruses, play in health and disease.

Missing data and technical variability in single-cell RNA-sequencing experiments.

PubMed

Hicks, Stephanie C; Townes, F William; Teng, Mingxiang; Irizarry, Rafael A

2017-11-06

Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands of cells to produce reliable measurements. Recent technical advances permit genome-wide gene expression measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is the most widely used and numerous publications are based on data produced with this technology. However, RNA-seq and scRNA-seq data are markedly different. In particular, unlike RNA-seq, the majority of reported expression levels in scRNA-seq are zeros, which could be either biologically-driven, genes not expressing RNA at the time of measurement, or technically-driven, genes expressing RNA, but not at a sufficient level to be detected by sequencing technology. Another difference is that the proportion of genes reporting the expression level to be zero varies substantially across single cells compared to RNA-seq samples. However, it remains unclear to what extent this cell-to-cell variation is being driven by technical rather than biological variation. Furthermore, while systematic errors, including batch effects, have been widely reported as a major challenge in high-throughput technologies, these issues have received minimal attention in published studies based on scRNA-seq technology. Here, we use an assessment experiment to examine data from published studies and demonstrate that systematic errors can explain a substantial percentage of observed cell-to-cell expression variability. Specifically, we present evidence that some of these reported zeros are driven by technical variation by demonstrating that scRNA-seq produces more zeros than expected and that this bias is greater for lower expressed genes. In addition, this missing data problem is exacerbated by the fact that this technical variation varies cell-to-cell. Then, we show how this technical cell-to-cell variability can be confused with novel biological results. Finally, we demonstrate and discuss how batch-effects and confounded experiments can intensify the problem. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Stepanauskas, Ramunas

2018-02-06

DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Technical and Policy Approaches to Balancing Patient Privacy and Data Sharing in Clinical and Translational Research

PubMed Central

Malin, Bradley; Karp, David; Scheuermann, Richard H.

2010-01-01

Clinical researchers need to share data to support scientific validation and information reuse, and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics resources in the form of centralized databases to ensure widespread availability of data derived from sponsored research. The widespread use of such open databases is contingent on the protection of patient privacy. In this paper, we review several aspects of the privacy-related problems associated with data sharing for clinical research from technical and policy perspectives. We begin with a review of existing policies for secondary data sharing and privacy requirements in the context of data derived from research and clinical settings. In particular, we focus on policies specified by the U.S. National Institutes of Health and the Health Insurance Portability and Accountability Act and touch upon how these policies are related to current, as well as future, use of data stored in public database archives. Next, we address aspects of data privacy and “identifiability” from a more technical perspective, and review how biomedical databanks can be exploited and seemingly anonymous records can be “re-identified” using various resources without compromising or hacking into secure computer systems. We highlight which data features specified in clinical research data models are potentially vulnerable or exploitable. In the process, we recount a recent privacy-related concern associated with the publication of aggregate statistics from pooled genome-wide association studies that has had a significant impact on the data sharing policies of NIH-sponsored databanks. Finally, we conclude with a list of recommendations that cover various technical, legal, and policy mechanisms that open clinical databases can adopt to strengthen data privacy protections as they move toward wider deployment and adoption. PMID:20051768

The re-emergence of natural products for drug discovery in the genomics era.

PubMed

Harvey, Alan L; Edrada-Ebel, RuAngelie; Quinn, Ronald J

2015-02-01

Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.

Programs of Study as a State Policy Mandate: A Longitudinal Study of the South Carolina Personal Pathways to Success Initiative. Final Technical Report: Major Findings and Implications

ERIC Educational Resources Information Center

Hammond, Cathy; Drew, Sam F.; Withington, Cairen; Griffith, Cathy; Swiger, Caroline M.; Mobley, Catherine; Sharp, Julia L.; Stringfield, Samuel C.; Stipanovic, Natalie; Daugherty, Lindsay

2013-01-01

This is the final technical report from the National Research Center for Career and Technical Education's (NRCCTE's) five-year longitudinal study of South Carolina's Personal Pathway to Success initiative, which was authorized by the state's Education and Economic Development Act (EEDA) in 2005. NRCCTE-affiliated researchers at the National…

Direct Final Rule: Nonroad Diesel Technical Amendments and Tier 3 Technical Relief Provision

EPA Pesticide Factsheets

Rule making certain technical corrections to the rules establishing emission standards for nonroad diesel engines and amending those rules to provide manufacturers with a production technical relief provision for Tier 3 equipment.

The business value and cost-effectiveness of genomic medicine.

PubMed

Crawford, James M; Aspinall, Mara G

2012-05-01

Genomic medicine offers the promise of more effective diagnosis and treatment of human diseases. Genome sequencing early in the course of disease may enable more timely and informed intervention, with reduced healthcare costs and improved long-term outcomes. However, genomic medicine strains current models for demonstrating value, challenging efforts to achieve fair payment for services delivered, both for laboratory diagnostics and for use of molecular information in clinical management. Current models of healthcare reform stipulate that care must be delivered at equal or lower cost, with better patient and population outcomes. To achieve demonstrated value, genomic medicine must overcome many uncertainties: the clinical relevance of genomic variation; potential variation in technical performance and/or computational analysis; management of massive information sets; and must have available clinical interventions that can be informed by genomic analysis, so as to attain more favorable cost management of healthcare delivery and demonstrate improvements in cost-effectiveness.

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

PubMed

Lan, Freeman; Demaree, Benjamin; Ahmed, Noorsher; Abate, Adam R

2017-07-01

The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

Arizona Deafblind Project, 1995-1999. Final Report.

ERIC Educational Resources Information Center

Arizona State School for the Deaf and Blind, Tucson.

This final report describes accomplishments of the four-year federally funded Arizona Deafblind Project which attempted to: (1) identify all deafblind children in Arizona; (2) deliver technical assistance to families; (3) deliver technical assistance to service providers; and (4) enhance community oversight, coordination, and collaboration with…

Technical Desiderata for the Integration of Genomic Data into Electronic Health Records

PubMed Central

Masys, Daniel R.; Jarvik, Gail P.; Abernethy, Neil F.; Anderson, Nicholas R.; Papanicolaou, George J.; Paltoo, Dina N.; Hoffman, Mark A.; Kohane, Isaac S.; Levy, Howard P.

2012-01-01

The era of “Personalized Medicine,” guided by individual molecular variation in DNA, RNA, expressed proteins and other forms of high volume molecular data brings new requirements and challenges to the design and implementation of Electronic Health Records (EHRs). In this article we describe the characteristics of biomolecular data that differentiate it from other classes of data commonly found in EHRs, enumerate a set of technical desiderata for its management in healthcare settings, and offer a candidate technical approach to its compact and efficient representation in operational systems. PMID:22223081

Crowdsourcing in biomedicine: challenges and opportunities

PubMed Central

Khare, Ritu; Good, Benjamin M.; Leaman, Robert; Su, Andrew I.

2016-01-01

The use of crowdsourcing to solve important but complex problems in biomedical and clinical sciences is growing and encompasses a wide variety of approaches. The crowd is diverse and includes online marketplace workers, health information seekers, science enthusiasts and domain experts. In this article, we review and highlight recent studies that use crowdsourcing to advance biomedicine. We classify these studies into two broad categories: (i) mining big data generated from a crowd (e.g. search logs) and (ii) active crowdsourcing via specific technical platforms, e.g. labor markets, wikis, scientific games and community challenges. Through describing each study in detail, we demonstrate the applicability of different methods in a variety of domains in biomedical research, including genomics, biocuration and clinical research. Furthermore, we discuss and highlight the strengths and limitations of different crowdsourcing platforms. Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine. PMID:25888696

PRODORIC2: the bacterial gene regulation database in 2018

PubMed Central

Dudek, Christian-Alexander; Hartlich, Juliane; Brötje, David; Jahn, Dieter

2018-01-01

Abstract Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de. PMID:29136200

Joint Common Architecture Demonstration (JCA Demo) Final Report

DTIC Science & Technology

2016-07-28

approach for implementing open systems [16], formerly known as the Modular Open Systems Approach (MOSA). OSA is a business and technical strategy to... TECHNICAL REPORT RDMR-AD-16-01 JOINT COMMON ARCHITECTURE DEMONSTRATION (JCA DEMO) FINAL REPORT Scott A. Wigginton... Modular Avionics .......................................................................... 5 E. Model-Based Engineering

International Standards for Genomes, Transcriptomes, and Metagenomes

PubMed Central

Mason, Christopher E.; Afshinnekoo, Ebrahim; Tighe, Scott; Wu, Shixiu; Levy, Shawn

2017-01-01

Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine. PMID:28337071

Complex multi-enhancer contacts captured by genome architecture mapping.

PubMed

Beagrie, Robert A; Scialdone, Antonio; Schueler, Markus; Kraemer, Dorothee C A; Chotalia, Mita; Xie, Sheila Q; Barbieri, Mariano; de Santiago, Inês; Lavitas, Liron-Mark; Branco, Miguel R; Fraser, James; Dostie, Josée; Game, Laurence; Dillon, Niall; Edwards, Paul A W; Nicodemi, Mario; Pombo, Ana

2017-03-23

The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses.

PubMed

Chandra, Amaresh; Jain, Radha; Solomon, Sushil; Shrivastava, Shiksha; Roy, Ajoy K

2013-02-04

Sugarcane is an important cash crop, providing 70% of the global raw sugar as well as raw material for biofuel production. Genetic analysis is hindered in sugarcane because of its large and complex polyploid genome and lack of sufficiently informative gene-tagged markers. Modern genomics has produced large amount of ESTs, which can be exploited to develop molecular markers based on comparative analysis with EST datasets of related crops and whole rice genome sequence, and accentuate their cross-technical functionality in orphan crops like tropical grasses. Utilising 246,180 Saccharum officinarum EST sequences vis-à-vis its comparative analysis with ESTs of sorghum and barley and the whole rice genome sequence, we have developed 3425 novel gene-tagged markers - namely, conserved-intron scanning primers (CISP) - using the web program GeMprospector. Rice orthologue annotation results indicated homology of 1096 sequences with expressed proteins, 491 with hypothetical proteins. The remaining 1838 were miscellaneous in nature. A total of 367 primer-pairs were tested in diverse panel of samples. The data indicate amplification of 41% polymorphic bands leading to 0.52 PIC and 3.50 MI with a set of sugarcane varieties and Saccharum species. In addition, a moderate technical functionality of a set of such markers with orphan tropical grasses (22%) and fodder cum cereal oat (33%) is observed. Developed gene-tagged CISP markers exhibited considerable technical functionality with varieties of sugarcane and unexplored species of tropical grasses. These markers would thus be particularly useful in identifying the economical traits in sugarcane and developing conservation strategies for orphan tropical grasses.

Promises, pitfalls and practicalities of prenatal whole exome sequencing.

PubMed

Best, Sunayna; Wou, Karen; Vora, Neeta; Van der Veyver, Ignatia B; Wapner, Ronald; Chitty, Lyn S

2018-01-01

Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd. © 2017 John Wiley & Sons, Ltd.

Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pakrasi, Himadri

The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N 2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O 2-limited intracellular environment during the night to perform O 2-sensitive processes such as N 2-fixation. Thus, Cyanothece cells are natural bioreactorsmore » for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genome sequences of many organisms.« less

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

PubMed Central

Nesvizhskii, Alexey I.

2013-01-01

Analysis of protein interaction networks and protein complexes using affinity purification and mass spectrometry (AP/MS) is among most commonly used and successful applications of proteomics technologies. One of the foremost challenges of AP/MS data is a large number of false positive protein interactions present in unfiltered datasets. Here we review computational and informatics strategies for detecting specific protein interaction partners in AP/MS experiments, with a focus on incomplete (as opposite to genome-wide) interactome mapping studies. These strategies range from standard statistical approaches, to empirical scoring schemes optimized for a particular type of data, to advanced computational frameworks. The common denominator among these methods is the use of label-free quantitative information such as spectral counts or integrated peptide intensities that can be extracted from AP/MS data. We also discuss related issues such as combining multiple biological or technical replicates, and dealing with data generated using different tagging strategies. Computational approaches for benchmarking of scoring methods are discussed, and the need for generation of reference AP/MS datasets is highlighted. Finally, we discuss the possibility of more extended modeling of experimental AP/MS data, including integration with external information such as protein interaction predictions based on functional genomics data. PMID:22611043

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

PubMed

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Recent Advances in Microbial Single Cell Genomics Technology and Applications

NASA Astrophysics Data System (ADS)

Stepanauskas, R.

2016-02-01

Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle.

PubMed

Mikheikin, Andrey; Olsen, Anita; Leslie, Kevin; Russell-Pavier, Freddie; Yacoot, Andrew; Picco, Loren; Payton, Oliver; Toor, Amir; Chesney, Alden; Gimzewski, James K; Mishra, Bud; Reed, Jason

2017-11-21

Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new "nanomapping" method to detect and map precisely BCL2-IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM "nanomapping" technique can be complementary to both sequencing and other physical mapping approaches.

76 FR 80226 - Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-23

... final rule, effective upon publication. Generally, the Administrative Procedure Act (APA) requires a.... Additionally, the APA requires that a final rule must have a delayed effective date of 30 days from the date of... delayed effective date requirement under the APA. 5 U.S.C. 553(d)(3). Again the technical change conforms...

"Type Ia Supernovae: Tools for Studying Dark Energy" Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woosley, Stan; Kasen, Dan

2017-05-10

Final technical report for project "Type Ia Supernovae: Tools for the Study of Dark Energy" awarded jointly to scientists at the University of California, Santa Cruz and Berkeley, for computer modeling, theory and data analysis relevant to the use of Type Ia supernovae as standard candles for cosmology.

76 FR 50202 - National Technical Assistance and Dissemination Center for Children Who Are Deaf-Blind; Final...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-12

... DEPARTMENT OF EDUCATION [CFDA No. 84.326T] National Technical Assistance and Dissemination Center for Children Who Are Deaf-Blind; Final Extension of Project Period and Waiver AGENCY: Office of Special Education Programs, Office of Special Education and Rehabilitative Services, Department of...

TADS Final Evaluation Report, 1980-81. Appendix S.

ERIC Educational Resources Information Center

Suarez, Tanya M.; And Others

The document contains the final report of the Technical Assistance Development System (TADS), a program which provided technical assistance (TA) services to 53 Handicapped Children's Early Education Program (HCEEP) demonstration projects and 13 State Implementation Grants (SIGs). The evaluation report is divided into five sections. Section 1…

Proteomics technique opens new frontiers in mobilome research

PubMed Central

Davidson, Andrew D.; Matthews, David A.

2017-01-01

ABSTRACT A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the “mobilome,” which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the “domestication” of transposon proteins for cellular functions. Although ‘omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons. In a recent paper, we overcame these technical hurdles using a technique called “proteomics informed by transcriptomics” (PIT), and thus published the first unbiased global mobilome-derived proteome for any organism (using cell lines derived from the mosquito Aedes aegypti). In this commentary, we describe our methods in more detail, and summarise our major findings. We also use new genome sequencing data to show that, in many cases, the specific genomic element expressing a given protein can be identified using PIT. This proteomic technique therefore represents an important technological advance that will open new avenues of research into the role that proteins derived from transposons and other repetitive and sequence diverse genetic elements, such as endogenous retroviruses, play in health and disease. PMID:28932623

Scanning the human genome at kilobase resolution.

PubMed

Chen, Jun; Kim, Yeong C; Jung, Yong-Chul; Xuan, Zhenyu; Dworkin, Geoff; Zhang, Yanming; Zhang, Michael Q; Wang, San Ming

2008-05-01

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.

Enhanced CRISPR/Cas9-mediated biallelic genome targeting with dual surrogate reporter-integrated donors.

PubMed

Wu, Yun; Xu, Kun; Ren, Chonghua; Li, Xinyi; Lv, Huijiao; Han, Furong; Wei, Zehui; Wang, Xin; Zhang, Zhiying

2017-03-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has recently emerged as a simple, yet powerful genome engineering tool, which has been widely used for genome modification in various organisms and cell types. However, screening biallelic genome-modified cells is often time-consuming and technically challenging. In this study, we incorporated two different surrogate reporter cassettes into paired donor plasmids, which were used as both the surrogate reporters and the knock-in donors. By applying our dual surrogate reporter-integrated donor system, we demonstrate high frequency of CRISPR/Cas9-mediated biallelic genome integration in both human HEK293T and porcine PK15 cells (34.09% and 18.18%, respectively). Our work provides a powerful genetic tool for assisting the selection and enrichment of cells with targeted biallelic genome modification. © 2017 Federation of European Biochemical Societies.

Microbial Genomes Multiply

NASA Technical Reports Server (NTRS)

Doolittle, Russell F.

2002-01-01

The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.).

PubMed

Liu, Pu; Zhang, Chao; Ma, Jin-Qi; Zhang, Li-Yuan; Yang, Bo; Tang, Xin-Yu; Huang, Ling; Zhou, Xin-Tong; Lu, Kun; Li, Jia-Na

2018-03-16

Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus , genome-wide identification and expression analysis of the BnCKX gene family has become technically feasible. In this study, we identified 23 BnCKX genes and analyzed their phylogenetic relationships, gene structures, conserved motifs, protein subcellular localizations, and other properties. We also analyzed the expression of the 23 BnCKX genes in the B. napus cultivar Zhong Shuang 11 ('ZS11') by quantitative reverse-transcription polymerase chain reaction (qRT-PCR), revealing their diverse expression patterns. We selected four BnCKX genes based on the results of RNA-sequencing and qRT-PCR and compared their expression in cultivated varieties with extremely long versus short siliques. The expression levels of BnCKX5-1 , 5-2 , 6-1 , and 7-1 significantly differed between the two lines and changed during pod development, suggesting they might play roles in determining silique length and in pod development. Finally, we investigated the effects of treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA) and the auxin indole-3-acetic acid (IAA) on the expression of the four selected BnCKX genes. Our results suggest that regulating BnCKX expression is a promising way to enhance the harvest index and stress resistance in plants.

Design of a Genomics Curriculum: Competencies for Practicing Pathologists.

PubMed

Laudadio, Jennifer; McNeal, Jeffrey L; Boyd, Scott D; Le, Long Phi; Lockwood, Christina; McCloskey, Cindy B; Sharma, Gaurav; Voelkerding, Karl V; Haspel, Richard L

2015-07-01

The field of genomics is rapidly impacting medical care across specialties. To help guide test utilization and interpretation, pathologists must be knowledgeable about genomic techniques and their clinical utility. The technology allowing timely generation of genomic data is relatively new to patient care and the clinical laboratory, and therefore, many currently practicing pathologists have been trained without any molecular or genomics exposure. Furthermore, the exposure that current and recent trainees receive in this field remains inconsistent. To assess pathologists' learning needs in genomics and to develop a curriculum to address these educational needs. A working group formed by the College of American Pathologists developed an initial list of genomics competencies (knowledge and skills statements) that a practicing pathologist needs to be successful. Experts in genomics were then surveyed to rate the importance of each competency. These data were used to create a final list of prioritized competencies. A subset of the working group defined subtopics and tasks for each competency. Appropriate delivery methods for the educational material were also proposed. A final list of 32 genomics competency statements was developed. A prioritized curriculum was created with designated subtopics and tasks associated with each competency. We present a genomics curriculum designed as a first step toward providing practicing pathologists with the competencies needed to practice successfully.

78 FR 57264 - Final Waiver and Extension of the Project Period for the Technical Assistance Coordination Center

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-18

...: 84.326Z.] Final Waiver and Extension of the Project Period for the Technical Assistance Coordination... project period. SUMMARY: The Secretary waives the requirements in the Education Department General Administrative Regulations that generally prohibit project periods exceeding five years and extensions of project...

77 FR 16923 - Agreements and Memoranda of Understanding Between the Food and Drug Administration and Other...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-23

...: Direct final rule. SUMMARY: This direct final rule makes technical changes that will update a requirement that many of our written agreements and memoranda of understanding (MOUs) with other departments..., accordingly, eliminates it. We are making these technical changes to conserve Agency time and resources...

1988 Underground Storage Tanks; Technical Requirements; Final Rule and Underground Storage Tanks Containing Petroleum-Financial Responsibility Requirements and State Program Approval Objective; Final Rule

EPA Pesticide Factsheets

EPA's 1988 regulations concerning USTs are contained in 40 CFR Part 280, 40 CFR Part 281 and 40 CFR Parts 282.50-282.105 and divided into three sections: technical requirements, financial responsibility requirements, and state program approval objectives.

PITTSBURGH TECHNICAL HEALTH TRAINING INSTITUTE DEMONSTRATION PROJECT. FINAL REPORT, VOLUME II.

ERIC Educational Resources Information Center

KISHKUNAS, LOUIS J.

APPENDIXES TO THE "FINAL REPORT," VOLUME I (VT 005 511), ARE INCLUDED--(1) A SCHEMATIC REPRESENTATION OF CURRICULUM DEVELOPMENT, (2) TECHNICAL BEHAVIOR CHECKLISTS, (3) PERFORMANCE INVENTORY FORMS USED IN ON-THE-JOB OBSERVATIONS, (4) REPORT FORM FOR TYPICAL JOB BEHAVIOR OF EMPLOYEE, (5) COOPERATING AREA HEALTH INSTITUTIONS, (6) TABLES OF Z SCORES…

Invention and Writing in Technical Work: Representing the Object.

ERIC Educational Resources Information Center

Winsor, Dorothy A.

1994-01-01

Describes the way invention is relevant to the practice of technical writing. Studies three engineering students engaged in a real-world project. Shows how the students' technical work and invention for the final report were simultaneous activities. Claims that invention for and through writing overlaps with technical invention. (HB)

Project T.E.A.M. (Technical Education Advancement Modules). Final Report.

ERIC Educational Resources Information Center

Greenville Technical Coll., SC.

Project TEAM (Technical Education Advancement Modules), a cooperative demonstration program for high technology training, created an introductory technical training program and a consumer education package emphasizing the benefits of technical training. The curriculum and training focus of the project began with an assessment of employee needs in…

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

PubMed

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

77 FR 39623 - Airworthiness Standards: Aircraft Engines; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-05

...] Airworthiness Standards: Aircraft Engines; Technical Amendment AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Final rule; technical amendment. SUMMARY: This amendment clarifies aircraft engine... from applicants requesting FAA engine type certifications and aftermarket certifications, such as...

The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains.

PubMed

Pfeiffer, Friedhelm; Zamora-Lagos, Maria-Antonia; Blettinger, Martin; Yeroslaviz, Assa; Dahl, Andreas; Gruber, Stephan; Habermann, Bianca H

2018-01-05

Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. Here we report the finalized genome sequence of the environmental strain Aeromonas salmonicida subsp. pectinolytica 34mel, for which only a draft genome with 253 contigs is currently available. Successful completion of the transposon-rich genome critically depended on the PacBio long read sequencing technology. Using finalized genome sequences of A. salmonicida subsp. pectinolytica and other Aeromonads, we report the detailed analysis of the transposon composition of these bacterial species. Mobilome evolution is exemplified by a complex transposon, which has shifted from pathogenicity-related to environmental-related gene content in A. salmonicida subsp. pectinolytica 34mel. Obtaining the complete, circular genome of A. salmonicida subsp. pectinolytica allowed us to perform an in-depth analysis of its mobilome. We demonstrate the mobilome-dependent evolution of this strain's genetic profile from pathogenic to environmental.

7 CFR 652.36 - Appeal of decertification decisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... technical service provider's written appeal, the Chief or his designee, will make a final determination, in... CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE SUPPORT ACTIVITIES TECHNICAL SERVICE PROVIDER ASSISTANCE... of the State Conservationist's decertification determination, the technical service provider may...

Capturing Cognitive Fingerprints for Active Authentication

DTIC Science & Technology

2014-10-01

CAPTURING COGNITIVE FINGERPRINTS FOR ACTIVE AUTHENTICATION IOWA STATE UNIVERSITY OF SCIENCE & TECHNOLOGY OCTOBER 2014 FINAL TECHNICAL REPORT...REPORT TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) SEP 2013 – APR 2014 4. TITLE AND SUBTITLE CAPTURING COGNITIVE FINGERPRINTS FOR ACTIVE...The project ended before the IRB application was approved. 15. SUBJECT TERMS Active Authentication, Cognitive Fingerprints , Biometric Modalities

Application of Communications Satellites to Educational Development. Final Technical Report, September 1, 1969-August 31, 1975.

ERIC Educational Resources Information Center

Morgan, Robert P.

Research is summarized in a brief final report built around a four-section bibliography. The first section lists periodic progress reports and articles which provide an overview of the program, including articles which pertain primarily to educational rather than technical aspects of satellite utilization. Theses carried out in the fields of…

Head Start Impact Study. Technical Report

ERIC Educational Resources Information Center

Puma, Michael; Bell, Stephen; Cook, Ronna; Heid, Camilla; Shapiro, Gary; Broene, Pam; Jenkins, Frank; Fletcher, Philip; Quinn, Liz; Friedman, Janet; Ciarico, Janet; Rohacek, Monica; Adams, Gina; Spier, Elizabeth

2010-01-01

This Technical Report is designed to provide technical detail to support the analysis and findings presented in the "Head Start Impact Study Final Report" (U.S. Department of Health and Human Services, January 2010). Chapter 1 provides an overview of the Head Start Impact Study and its findings. Chapter 2 provides technical information on the…

Matching Community and Technical College Professional/Technical Education Capacity to Employer Demand. Final Report.

ERIC Educational Resources Information Center

Sommers, Paul; Heg, Deena

A project was conducted to improve the state of Washington's community and technical college system by developing and using an improved occupational forecasting system to assess and respond to education and training needs. First, long-term occupational forecast data from Washington's Employment Security Department were matched with technical and…

75 FR 5784 - Guidance on Preparation of Market-Based Rate Filings and Electric Quarterly Reports by Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-04

... Preparation of Market-Based Rate Filings and Electric Quarterly Reports by Public Utilities; Notice of Technical Conference January 28, 2010. Take notice that Commission staff will convene a technical conference... final agenda of the technical conference. The March 3, 2010 technical conference will focus on the...

A Revision of Technical Mathematics Based on the NCTM Standards. Final Report.

ERIC Educational Resources Information Center

Near, Barbara

Between 1993 and 1996, Henry Ford Community College (Michigan) worked with business, industry, and technical instructors to revise their Technical Mathematics program in accordance with the National Council of Teachers of Mathematics (NCTM) Standards. The purpose of the project was to restructure the technical math curriculum and create a context…

76 FR 11327 - Technical Amendments to Rule 17a-8: Financial Recordkeeping and Reporting of Currency and Foreign...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... SECURITIES AND EXCHANGE COMMISSION 17 CFR Part 240 [Release No. 34-63949] Technical Amendments to...: Securities and Exchange Commission. ACTION: Final rule; technical amendments. SUMMARY: The Securities and Exchange Commission (``Commission'') is adopting technical amendments to Rule 17a-8 under the Securities...

Final priority; technical assistance to improve state data capacity--National Technical Assistance Center to improve state capacity to accurately collect and report IDEA data. Final priority.

PubMed

2013-05-20

The Assistant Secretary for Special Education and Rehabilitative Services announces a priority under the Technical Assistance to Improve State Data Capacity program. The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2013 and later years. We take this action to focus attention on an identified national need to provide technical assistance (TA) to States to improve their capacity to meet the data collection and reporting requirements of the Individuals with Disabilities Education Act (IDEA). We intend this priority to establish a TA center to improve State capacity to accurately collect and report IDEA data (Data Center).

Technical Evaluation Motor No. 10 (TEM-10)

NASA Technical Reports Server (NTRS)

1993-01-01

Technical Evaluation Motor No. 10 (TEM-10) was static fired on 27 Apr. 1993 at the Thiokol Corporation full-scale motor static test bay, T-24. This final test report documents the procedures, performance, and results of the static test firing of TEM-10. All observations, discussions, conclusions, and recommendations contained are final. Included is a presentation and discussion of TEM-10 performance, anomalies, and test results in concurrence with the objectives outlined in CTP-0110, Revision D, Space Shuttle Technical Evaluation Motor No. 10 (TEM-10) Static Fire Test Plan.

Final priority; Technical Assistance on State Data Collection--IDEA Data Management Center. Final priority.

PubMed

2014-08-05

The Assistant Secretary for the Office of Special Education and Rehabilitative Services (OSERS) announces a priority under the Technical Assistance on State Data Collection program. The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2014 and later years. We take this action to fund a cooperative agreement to establish and operate an IDEA Data Management Center (Center) that will provide technical assistance (TA) to improve the capacity of States to meet the data collection requirements of the Individuals with Disabilities Education Act (IDEA).

Technical Topic 3.2.2.d Bayesian and Non-Parametric Statistics: Integration of Neural Networks with Bayesian Networks for Data Fusion and Predictive Modeling

DTIC Science & Technology

2016-05-31

and included explosives such as TATP, HMTD, RDX, RDX, ammonium nitrate , potassium perchlorate, potassium nitrate , sugar, and TNT. The approach...Distribution Unlimited UU UU UU UU 31-05-2016 15-Apr-2014 14-Jan-2015 Final Report: Technical Topic 3.2.2. d Bayesian and Non- parametric Statistics...of Papers published in non peer-reviewed journals: Final Report: Technical Topic 3.2.2. d Bayesian and Non-parametric Statistics: Integration of Neural

Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD.

PubMed

Perelman, Polina L; Pichler, Rudolf; Gaggl, Anna; Larkin, Denis M; Raudsepp, Terje; Alshanbari, Fahad; Holl, Heather M; Brooks, Samantha A; Burger, Pamela A; Periasamy, Kathiravan

2018-01-31

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000 RAD and 15000 RAD ) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000 RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000 RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000 RAD panel is an important high-resolution complement to the main 5000 RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

PubMed

Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; van Sinderen, Douwe; Ventura, Marco

2016-04-01

Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding

PubMed Central

Wang, Wenqin; Le, Hien T. T.

2016-01-01

Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN) based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding. PMID:28097123

Breeding next generation tree fruits: technical and legal challenges

PubMed Central

Dalla Costa, Lorenza; Malnoy, Mickael; Gribaudo, Ivana

2017-01-01

The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of ‘green’ biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome. Grapevine, the most important fruit crop in the world from an economical point of view, is a peculiar case for NPBTs because of the load of cultural aspects, varietal traditions and consumer demands, which hinder the use of classical breeding techniques and, furthermore, the application of genetic engineering to wine grape cultivars. Here we explore the technical challenges which may hamper the application of cisgenesis and genome editing to this perennial plant, in particular focusing on the bottlenecks of the Agrobacterium-mediated gene transfer. In addition, strategies to eliminate undesired sequences from the genome and to choose proper target sites are discussed in light of peculiar features of this species. Furthermore is reported an update of the international legislative frameworks regulating NPBT products which shows conflicting positions and, in the case of the European Union, a prolonged lack of regulation. PMID:29238598

Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes.

PubMed

Zheng, Chunfang; Zhu, Qian; Adam, Zaky; Sankoff, David

2008-07-01

Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to 'halve' the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly nonunique. To resolve this problem, we take account of outgroups, external reference genomes, to guide and narrow down the search. We improve on a previous, computationally costly, 'brute force' method by adapting the genome halving algorithm of El-Mabrouk and Sankoff so that it rapidly and accurately constructs an ancestor close the outgroups, prior to a local optimization heuristic. We apply this to reconstruct the predoubling ancestor of Saccharomyces cerevisiae and Candida glabrata, guided by the genomes of three other yeasts that diverged before the genome doubling event. We analyze the results in terms (1) of the minimum evolution criterion, (2) how close the genome halving result is to the final (local) minimum and (3) how close the final result is to an ancestor manually constructed by an expert with access to additional information. We also visualize the set of reconstructed ancestors using classic multidimensional scaling to see what aspects of the two doubled and three unduplicated genomes influence the differences among the reconstructions. The experimental software is available on request.

Convergent functional genomics of psychiatric disorders.

PubMed

Niculescu, Alexander B

2013-10-01

Genetic and gene expression studies, in humans and animal models of psychiatric and other medical disorders, are becoming increasingly integrated. Particularly for genomics, the convergence and integration of data across species, experimental modalities and technical platforms is providing a fit-to-disease way of extracting reproducible and biologically important signal, in contrast to the fit-to-cohort effect and limited reproducibility of human genetic analyses alone. With the advent of whole-genome sequencing and the realization that a major portion of the non-coding genome may contain regulatory variants, Convergent Functional Genomics (CFG) approaches are going to be essential to identify disease-relevant signal from the tremendous polymorphic variation present in the general population. Such work in psychiatry can provide an example of how to address other genetically complex disorders, and in turn will benefit by incorporating concepts from other areas, such as cancer, cardiovascular diseases, and diabetes. © 2013 Wiley Periodicals, Inc.

Facilitating a culture of responsible and effective sharing of cancer genome data.

PubMed

Siu, Lillian L; Lawler, Mark; Haussler, David; Knoppers, Bartha Maria; Lewin, Jeremy; Vis, Daniel J; Liao, Rachel G; Andre, Fabrice; Banks, Ian; Barrett, J Carl; Caldas, Carlos; Camargo, Anamaria Aranha; Fitzgerald, Rebecca C; Mao, Mao; Mattison, John E; Pao, William; Sellers, William R; Sullivan, Patrick; Teh, Bin Tean; Ward, Robyn L; ZenKlusen, Jean Claude; Sawyers, Charles L; Voest, Emile E

2016-05-05

Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer care. Information systems must be harmonized to overcome the multiple technical and logistical barriers to data sharing. Against this backdrop, the Global Alliance for Genomic Health (GA4GH) was established in 2013 to create a common framework that enables responsible, voluntary and secure sharing of clinical and genomic data. This Perspective from the GA4GH Clinical Working Group Cancer Task Team highlights the data-aggregation challenges faced by the field, suggests potential collaborative solutions and describes how GA4GH can catalyze a harmonized data-sharing culture.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

PubMed Central

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. PMID:24454756

Measurement of locus copy number by hybridisation with amplifiable probes

PubMed Central

Armour, John A. L.; Sismani, Carolina; Patsalis, Philippos C.; Cross, Gareth

2000-01-01

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications. PMID:10606661

Measurement of locus copy number by hybridisation with amplifiable probes.

PubMed

Armour, J A; Sismani, C; Patsalis, P C; Cross, G

2000-01-15

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicro-scopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader-Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

Genomic Epidemiology of Tuberculosis.

PubMed

Comas, Iñaki

2017-01-01

The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still exploring the wider potential of this new technology. Whole genome sequencing in tuberculosis still requires bacterial cultures. Thus, although whole genome sequencing has revolutionized the interpretation of transmission patterns, it is not yet ready to be applied at the point-of-care. In this chapter, I will review the promises and challenges of genomic epidemiology, as well as some of the new questions that have arisen from the use of this new technology. In addition, I will examine the role of molecular epidemiology within the general frame of global tuberculosis control and how genomic epidemiology can contribute towards the elimination of the disease.

Genome Writing: Current Progress and Related Applications.

PubMed

Wang, Yueqiang; Shen, Yue; Gu, Ying; Zhu, Shida; Yin, Ye

2018-02-01

The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Copyright © 2018. Production and hosting by Elsevier B.V.

Final June Revisions Rule Significant Contribution Assessment TSD

EPA Pesticide Factsheets

This Technical Support Document (TSD) presents quantitative assessments of the relationship between the final February revisions to the Transport Rule, the final June revisions rule, and the original analysis conducted for the final Transport Rule.

Develop a Comprehensive Technical Training and Data Collection Program for Structural Welders and Fitters: Technical Proposal

DTIC Science & Technology

2006-05-30

implementation Final Report 4 TECHNICAL PLAN AND RESULTS Task 1: Initiate the Project Management System Two senior NGSS production management...1 Technical Plan and Results...Third the system is hosted on a handheld unit which provides the foremen with an efficient daily planning tool. The Pilot System which entails

Laser Technician Associate Degree Program. A Proposal Submitted to Wisconsin State Board of Vocational, Technical, and Adult Education. (Curriculum Development.) Final Report.

ERIC Educational Resources Information Center

North Central Technical Inst., Wausau, WI.

This final report contains the program proposal with supporting data for developing curriculum materials for and implementing an associate-degree laser technology program at the North Central Technical Institute. The proposal outline provides this information: (1) objectives for the program designed to prepare a technician to safely operate,…

California Deaf-Blind Services Final Report, October 1, 1995-September 30, 1999 [and] October 1, 1999-June 30, 2000 (No Cost Extension).

ERIC Educational Resources Information Center

Goertz, Lori; Franklin, Barbara

This final report describes the activities and outcomes of the California Deaf-Blind Services (CDBS) program, a regionally based, family focused technical assistance and training project designed to improve services to children with deaf-blindness. The project conducted the following activities: (1) provided technical assistance to families and…

New Jersey Technical Assistance Project (N.J. TAP): "Educational Resources and Support Services on Behalf of Children with Multiple Sensory Impairment." Final Report.

ERIC Educational Resources Information Center

New Jersey State Dept. of Education, Trenton.

This final report describes activities and accomplishments of the New Jersey Technical Assistance Project, a project to improve educational resources and support services for students with multiple sensory impairment (deaf-blindness). Activities and accomplishments are presented in a tabular format for each project goal and objective. The project…

Quantitative high-resolution genomic analysis of single cancer cells.

PubMed

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harwood, Caroline S.

Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied tomore » the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.« less

78 FR 77563 - Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-24

... NATIONAL CREDIT UNION ADMINISTRATION 12 CFR Parts 700, 701, and 704 RIN 3133-AE33 Technical Amendments AGENCY: National Credit Union Administration (NCUA). ACTION: Final rule. SUMMARY: The NCUA Board... credit unions. The technical amendments conform the regulations to a recent policy change adopted by the...

75 FR 33682 - Export Administration Regulations; Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-15

...-01] RIN 0694-AE93 Export Administration Regulations; Technical Amendments AGENCY: Bureau of Industry... Bureau of Industry and Security (BIS) makes a technical amendment to the Export Administration... review of final decisions and orders issued in BIS export control administrative enforcement proceedings...

78 FR 41331 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-10

... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System 48 CFR Part 225 Defense Federal Acquisition Regulation Supplement; Technical Amendments AGENCY: Defense Acquisition Regulations System, Department of Defense (DoD). ACTION: Final rule. SUMMARY: DoD is making technical amendment to the Defense...

Orthology prediction methods: A quality assessment using curated protein families

PubMed Central

Trachana, Kalliopi; Larsson, Tomas A; Powell, Sean; Chen, Wei-Hua; Doerks, Tobias; Muller, Jean; Bork, Peer

2011-01-01

The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community. PMID:21853451

Final Revisions Rule Significant Contribution Assessment TSD

EPA Pesticide Factsheets

This Technical Support Document (TSD) presents quantitative assessments of the relationship between final revisions to the Transport Rule and the original analysis conducted for the final Transport Rule.

A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH.

PubMed

Möhlendick, Birte; Bartenhagen, Christoph; Behrens, Bianca; Honisch, Ellen; Raba, Katharina; Knoefel, Wolfram T; Stoecklein, Nikolas H

2013-01-01

Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH) of single cells. The protocol is based on an established adapter-linker PCR (WGAM) and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS) could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost-) effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.

75 FR 15342 - Advisory Committees; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-29

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration 21 CFR Part 14 [Docket No. FDA-2010-N-0001] Advisory Committees; Technical Amendment Agency: Food and Drug Administration, HHS. ACTION: Final rule; technical amendment. SUMMARY: The Food and Drug Administration (FDA) is amending its...

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum

DOE PAGES

De León, Kara B.; Utturkar, Sagar M.; Camilleri, Laura B.; ...

2015-09-24

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Finally, nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.

Genome-Wide Association Identifies Multiple Genomic Regions Associated with Susceptibility to and Control of Ovine Lentivirus

DTIC Science & Technology

2012-10-17

may also be of great interest for further study in goats , which are host to the closely related caprine encephalitis arthritis virus. Materials and...the farm crews at Washington State University, ADRU, and USSES for technical assistance. The genotyping of TMEM154 diplotypes was performed at USMARC...of lentiviral species in sheep and goats with cumulative evidence of cross species transmission. Curr HIV Res 8: 94–100. 2. Blacklaws B, Harkiss GD

Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies.

PubMed

Ozsolak, Fatih

2016-01-01

With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's superior technical performance and cost advantages. By enabling genetic analysis capabilities that were not possible previously, NGS technologies have started to play an integral role in all areas of biomedical research. This chapter outlines the low-quantity DNA and cDNA sequencing capabilities and applications developed with the Helicos single molecule DNA sequencing technology.

2012 Technical Corrections Fact Sheet

EPA Pesticide Factsheets

Final Rule: 2012 Technical Corrections, Clarifying and Other Amendments to theGreenhouse Gas Reporting Rule, and Confidentiality Determinations for Certain DataElements of the Fluorinated Gas Source Category

Evaluation of Routine Atmospheric Sounding Measurements using Unmanned Systems (ERASMUS): Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Boer, Gijs; Lawrence, Dale; Palo, Scott

2017-03-29

This final technical report details activities undertaken as part of the referenced project. Included is information on the preparation of aircraft for deployment to Alaska, summaries of the three deployments covered under this project, and a brief description of the dataset and science directions pursued. Additionally, we provide information on lessons learned, publications, and presentations resulting from this work.

Vocational Curriculum Modification. Teaching Technical Language to Learning Handicapped Students. Project HIRE: A Curriculum Management System for Instructing the Handicapped. Final Report, Volume 1.

ERIC Educational Resources Information Center

Gardner, David C.; And Others

Volume 1 of the final report on Project HIRE reports the design, development, field-testing, and refining of self-instructional packages to teach entry level technical vocabulary to learning handicapped students mainstreamed in vocational programs. Volume 2, a management handbook, reports the methods and findings concerning development of…

Joint Technical Architecture for Robotic Systems (JTARS)-Final Report

NASA Technical Reports Server (NTRS)

Bradley, Arthur T.; Holloway, Sidney E., III

2006-01-01

This document represents the final report for the Joint Technical Architecture for Robotic Systems (JTARS) project, funded by the Office of Exploration as part of the Intramural Call for Proposals of 2005. The project was prematurely terminated, without review, as part of an agency-wide realignment towards the development of a Crew Exploration Vehicle (CEV) and meeting the near-term goals of lunar exploration.

Review of Final Year MSP Evaluations, Performance Period 2007. Analytic and Technical Support for Mathematics and Science Partnerships

ERIC Educational Resources Information Center

Bobronnikov, Ellen; Rhodes, Hilary; Bradley, Cay

2010-01-01

This final report culminates the evaluation and technical assistance provided for the U.S. Department of Education's Mathematics and Science Partnership (MSP) Program and its projects since 2005. As part of this support, Abt Associates looked across the portfolio of projects funded by the MSP program to draw lessons on best practices. This…

Genomics and breeding in food crops

USDA-ARS?s Scientific Manuscript database

Plant biology is in the midst of a revolution. The generation of tremendous volumes of sequence information introduce new technical challenges into plant biology and agriculture. The relatively new field of bioinformatics addresses these challenges by utilizing efficient data management strategies;...

Pacific Educational Computer Network Study. Final Report.

ERIC Educational Resources Information Center

Hawaii Univ., Honolulu. ALOHA System.

The Pacific Educational Computer Network Feasibility Study examined technical and non-technical aspects of the formation of an international Pacific Area computer network for higher education. The technical study covered the assessment of the feasibility of a packet-switched satellite and radio ground distribution network for data transmission…

Comparative biochemistry and physiology of iron-respiring bacteria from acidic and neutral-pH environments: Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magnuson, T S

2009-04-07

Acidophilic dissimilatory iron-reducing bacteria (DIRB) are now being detected in a variety of ‘extreme’ low-pH, radionuclide- and heavy-metal contaminated habitats where Fe(III) reduction is taking place, and may represent a significant proportion of metal-transforming organisms in these environments. Acidiphilium cryptum is our model organism, a facultative iron-respiring Alphaproteobacterium. Major findings of this project have been 1) Discovery of novel outer-membrane and periplasmic cytochromes c in acidophiles that are reactive with Fe and Cr, 2) Discovery of Cr(VI) reduction mechanisms in acidophiles, mediated by c-type cytochromes and other reductase activity, 3) Development of enzyme detection methods specific for Cr-reducing enzymes, 4)more » Characterization of biofilm formation in A. cryptum, and 5) Annotation of the Acidiphilium cryptum genome (Magnuson, Kusel, and Cummings, DOE-JGI 2005-2006). Two manuscripts and one book chapter have been published, and several more mauscripts are prepared for submission.« less

Crowdsourcing in biomedicine: challenges and opportunities.

PubMed

Khare, Ritu; Good, Benjamin M; Leaman, Robert; Su, Andrew I; Lu, Zhiyong

2016-01-01

The use of crowdsourcing to solve important but complex problems in biomedical and clinical sciences is growing and encompasses a wide variety of approaches. The crowd is diverse and includes online marketplace workers, health information seekers, science enthusiasts and domain experts. In this article, we review and highlight recent studies that use crowdsourcing to advance biomedicine. We classify these studies into two broad categories: (i) mining big data generated from a crowd (e.g. search logs) and (ii) active crowdsourcing via specific technical platforms, e.g. labor markets, wikis, scientific games and community challenges. Through describing each study in detail, we demonstrate the applicability of different methods in a variety of domains in biomedical research, including genomics, biocuration and clinical research. Furthermore, we discuss and highlight the strengths and limitations of different crowdsourcing platforms. Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Synthetic biology and the technicity of biofuels.

PubMed

Mackenzie, Adrian

2013-06-01

The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Community College Technical Mathematics Project. Final Report.

ERIC Educational Resources Information Center

Self, Samuel L.

The purpose of the research project was to develop an applied or technical mathematics curriculum which would meet the needs of vocational-technical students at the community college level. The research project was divided into three distinct phases: Identifying the mathematical concepts requisite for job-entry competencies in each of the…

7 CFR 614.10 - Appeals before the Farm Service Agency county committee.

Code of Federal Regulations, 2010 CFR

2010-01-01

... section are completed, provide the FSA county committee with a written technical determination in the form... part 780, a participant may appeal a final technical determination or a program decision to the FSA... appeal requests review of the technical determination by the applicable State Conservationist prior to...

77 FR 47495 - Final Priority; Technical Assistance on State Data Collection, Analysis, and Reporting-National...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-08

... intervention and preschool service providers with data on their qualifications, certification, and preparation... Priority; Technical Assistance on State Data Collection, Analysis, and Reporting--National IDEA Technical Assistance Center on Early Childhood Longitudinal Data Systems; Rule #0;#0;Federal Register / Vol. 77, No...

77 FR 18716 - Transportation Security Administration Postal Zip Code Change; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-28

... organizational changes and it has no substantive effect on the public. DATES: Effective March 28, 2012. FOR... No. 1572-9] Transportation Security Administration Postal Zip Code Change; Technical Amendment AGENCY: Transportation Security Administration, DHS. ACTION: Final rule. SUMMARY: This rule is a technical change to...

Microfluidics for genome-wide studies involving next generation sequencing

PubMed Central

Murphy, Travis W.; Lu, Chang

2017-01-01

Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine. PMID:28396707

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

PubMed Central

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A.; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. PMID:22140428

Known unknowns: building an ethics of uncertainty into genomic medicine.

PubMed

Newson, Ainsley J; Leonard, Samantha J; Hall, Alison; Gaff, Clara L

2016-09-01

Genomic testing has reached the point where, technically at least, it can be cheaper to undertake panel-, exome- or whole genome testing than it is to sequence a single gene. An attribute of these approaches is that information gleaned will often have uncertain significance. In addition to the challenges this presents for pre-test counseling and informed consent, a further consideration emerges over how - ethically - we should conceive of and respond to this uncertainty. To date, the ethical aspects of uncertainty in genomics have remained under-explored. In this paper, we draft a conceptual and ethical response to the question of how to conceive of and respond to uncertainty in genomic medicine. After introducing the problem, we articulate a concept of 'genomic uncertainty'. Drawing on this, together with exemplar clinical cases and related empirical literature, we then critique the presumption that uncertainty is always problematic and something to be avoided, or eradicated. We conclude by outlining an 'ethics of genomic uncertainty'; describing how we might handle uncertainty in genomic medicine. This involves fostering resilience, welfare, autonomy and solidarity. Uncertainty will be an inherent aspect of clinical practice in genomics for some time to come. Genomic testing should not be offered with the explicit aim to reduce uncertainty. Rather, uncertainty should be appraised, adapted to and communicated about as part of the process of offering and providing genomic information.

Studying the Cost and Value of Library Services: Final Report. Technical Report APLAB/94-3/1,2,3,4.

ERIC Educational Resources Information Center

Kantor, Paul B.; And Others

This is the final technical report (in three parts) of a 15-month long project to study the costs and value of library functions at five major research libraries. Twenty-one services or service aspects were studied, and numerous measures of the importance or benefit of the service to the users were made. These measures were studied together to lay…

An Inquiry into Testing of Information Retrieval Systems. Comparative Systems Laboratory Final Technical Report, Part III: CSL Related Studies.

ERIC Educational Resources Information Center

Zull, Carolyn Gifford, Ed.; And Others

This third volume of the Comparative Systems Laboratory (CSL) Final Technical Report is a collection of relatively independent studies performed on CSL materials. Covered in this document are studies on: (1) properties of files, including a study of the growth rate of a dictionary of index terms as influenced by number of documents in the file and…

Programs of Study as a State Policy Mandate: A Longitudinal Study of the South Carolina Personal Pathways to Success Initiative. Unabridged Final Technical Report (Years 1-5)

ERIC Educational Resources Information Center

Hammond, Cathy; Withington, Cairen; Sharp, Julia L.; Mobley, Catherine; Drew, Sam F.; Stringfield, Samuel C.; Stipanovic, Natalie; Swiger, Caroline M.; Daugherty, Lindsay; Griffith, Cathy

2014-01-01

This final report presents findings from data collection and analysis conducted during a five-year study by the National Dropout Prevention Center (NDPC) at Clemson University, in conjunction with colleagues from the National Research Center for Career and Technical Education (NRCCTE) at the University of Louisville. This project was one of three…

Ground-Based Radiometric Measurements of Slant Path Attenuation in the V/W Bands

DTIC Science & Technology

2016-04-01

GROUND-BASED RADIOMETRIC MEASUREMENTS OF SLANT PATH ATTENUATION IN THE V/W BANDS APRIL 2016 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE...2. REPORT TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) OCT 2012 – SEP 2015 4. TITLE AND SUBTITLE GROUND-BASED RADIOMETRIC MEASUREMENTS ...SUPPLEMENTARY NOTES 14. ABSTRACT Ground-based radiometric techniques were applied to measure the slant path attenuation cumulative distribution function to

Final Technical Progress Report: Development of Low-Cost Suspension Heliostat; December 7, 2011 - December 6, 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bender, W.

2013-01-01

Final technical progress report of SunShot Incubator Solaflect Energy. The project succeeded in demonstrating that the Solaflect Suspension Heliostat design is viable for large-scale CSP installations. Canting accuracy is acceptable and is continually improving as Solaflect improves its understanding of this design. Cost reduction initiatives were successful, and there are still many opportunities for further development and further cost reduction.

Sequencing and assembly of the 22-gb loblolly pine genome.

PubMed

Zimin, Aleksey; Stevens, Kristian A; Crepeau, Marc W; Holtz-Morris, Ann; Koriabine, Maxim; Marçais, Guillaume; Puiu, Daniela; Roberts, Michael; Wegrzyn, Jill L; de Jong, Pieter J; Neale, David B; Salzberg, Steven L; Yorke, James A; Langley, Charles H

2014-03-01

Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.

Advanced Transportation System Studies Technical Area 2 (TA-2) Heavy Lift Launch Vehicle Development Contract. Volume 2; Technical Results

NASA Technical Reports Server (NTRS)

1995-01-01

The purpose of the Advanced Transportation System Studies (ATSS) Technical Area 2 (TA-2) Heavy Lift Launch Vehicle Development contract was to provide advanced launch vehicle concept definition and analysis to assist NASA in the identification of future launch vehicle requirements. Contracted analysis activities included vehicle sizing and performance analysis, subsystem concept definition, propulsion subsystem definition (foreign and domestic), ground operations and facilities analysis, and life cycle cost estimation. This document is Volume 2 of the final report for the contract. It provides documentation of selected technical results from various TA-2 analysis activities, including a detailed narrative description of the SSTO concept assessment results, a user's guide for the associated SSTO sizing tools, an SSTO turnaround assessment report, an executive summary of the ground operations assessments performed during the first year of the contract, a configuration-independent vehicle health management system requirements report, a copy of all major TA-2 contract presentations, a copy of the FLO launch vehicle final report, and references to Pratt & Whitney's TA-2 sponsored final reports regarding the identification of Russian main propulsion technologies.

Technical Evaluation Motor No. 7 (TEM-7)

NASA Technical Reports Server (NTRS)

Hughes, Phil

1991-01-01

The Technical Evaluation Motor No. 7 (TEM-7) test was a full-scale, full duration static test firing of a high performance motor-configuration solid rocket motor with nozzle vectoring. The final test report documents the procedures, performance, and results of the static test firing of TEM-7. All observations, discussions, conclusions, and recommendations included in the report are complete and final except for the TEM-7 fixed housing unbond investigation. A presentation and discussion of TEM-7 performance, anomalies, and test result concurrence with the objectives outlined in CTP-0107, Rev A, Space Shuttle Technical Evaluation Motor No. 7 (TEM-7) Static Fire Test Plan are included.

Building Stronger State Energy Partnerships with the U.S. Department of Energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marks, Kate

2011-09-30

This final technical report details the results of total work efforts and progress made from October 2007 – September 2011 under the National Association of State Energy Officials (NASEO) cooperative agreement DE-FC26-07NT43264, Building Stronger State Energy Partnerships with the U.S. Department of Energy. Major topical project areas in this final report include work efforts in the following areas: Energy Assurance and Critical Infrastructure, State and Regional Technical Assistance, Regional Initiative, Regional Coordination and Technical Assistance, and International Activities in China. All required deliverables have been provided to the National Energy Technology Laboratory and DOE program officials.

Final Technical Report of Project DE-FG02-96ER14647

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundeen, Stephen R.

This is the final technical report of work completed under DOE support over the period Sept. 1, 1996 until May 31, 2015. The title of the project was "Ion/Excited Atom Collision Studies with a Rydberg Target and a CO2 Laser" from 9/1/96 to 10/31/06, and "Properties of Actinide Ions from Measurements of Rydberg Ion Fine Structure" from 11/1/06 until 5/31/15. The primary technical results were a detailed experimental study of resonant charge transfer between Rydberg atoms and highly-charged ions, and unique measurements of many properties of multiply-charged Thorium ions.

Implementation of a patient-facing genomic test report in the electronic health record using a web-application interface.

PubMed

Williams, Marc S; Kern, Melissa S; Lerch, Virginia R; Billet, Jonathan; Williams, Janet L; Moore, Gregory J

2018-05-30

Genomic medicine is emerging into clinical care. Communication of genetic laboratory results to patients and providers is hampered by the complex technical nature of the laboratory reports. This can lead to confusion and misinterpretation of the results resulting in inappropriate care. Patients usually do not receive a copy of the report leading to further opportunities for miscommunication. To address these problems, interpretive reports were created using input from the intended end users, patients and providers. This paper describes the technical development and deployment of the first patient-facing genomic test report (PGR) within an electronic health record (EHR) ecosystem using a locally developed standards-based web-application interface. A patient-facing genomic test report with a companion provider report was configured for implementation within the EHR using a locally developed software platform, COMPASS™. COMPASS™ is designed to manage secure data exchange, as well as patient and provider access to patient reported data capture and clinical display tools. COMPASS™ is built using a Software as a Service (SaaS) approach which exposes an API that apps can interact with. An authoring tool was developed that allowed creation of patient-specific PGRs and the accompanying provider reports. These were converted to a format that allowed them to be presented in the patient portal and EHR respectively using the existing COMPASS™ interface thus allowing patients, caregivers and providers access to individual reports designed for the intended end user. The PGR as developed was shown to enhance patient and provider communication around genomic results. It is built on current standards but is designed to support integration with other tools and be compatible with emerging opportunities such as SMART on FHIR. This approach could be used to support genomic return of results as the tool is scalable and generalizable.

Accelerated Genome Engineering through Multiplexing

PubMed Central

Zhao, Huimin

2015-01-01

Throughout the biological sciences, the past fifteen years have seen a push towards the analysis and engineering of biological systems at the organism level. Given the complexity of even the simplest organisms, though, to elicit a phenotype of interest often requires genotypic manipulation of several loci. By traditional means, sequential editing of genomic targets requires a significant investment of time and labor, as the desired editing event typically occurs at a very low frequency against an overwhelming unedited background. In recent years, the development of a suite of new techniques has greatly increased editing efficiency, opening up the possibility for multiple editing events to occur in parallel. Termed as multiplexed genome engineering, this approach to genome editing has greatly expanded the scope of possible genome manipulations in diverse hosts, ranging from bacteria to human cells. The enabling technologies for multiplexed genome engineering include oligonucleotide-based and nuclease-based methodologies, and their application has led to the great breadth of successful examples described in this review. While many technical challenges remain, there also exists a multiplicity of opportunities in this rapidly expanding field. PMID:26394307

Strategies used for genetically modifying bacterial genome: ite-directed mutagenesis, gene inactivation, and gene over-expression*

PubMed Central

Xu, Jian-zhong; Zhang, Wei-guo

2016-01-01

With the availability of the whole genome sequence of Escherichia coli or Corynebacterium glutamicum, strategies for directed DNA manipulation have developed rapidly. DNA manipulation plays an important role in understanding the function of genes and in constructing novel engineering bacteria according to requirement. DNA manipulation involves modifying the autologous genes and expressing the heterogenous genes. Two alternative approaches, using electroporation linear DNA or recombinant suicide plasmid, allow a wide variety of DNA manipulation. However, the over-expression of the desired gene is generally executed via plasmid-mediation. The current review summarizes the common strategies used for genetically modifying E. coli and C. glutamicum genomes, and discusses the technical problem of multi-layered DNA manipulation. Strategies for gene over-expression via integrating into genome are proposed. This review is intended to be an accessible introduction to DNA manipulation within the bacterial genome for novices and a source of the latest experimental information for experienced investigators. PMID:26834010

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

PubMed Central

Kumar, Rajendra; Sobhy, Haitham

2017-01-01

Abstract Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community. PMID:28973466

Improvement of industrially important microbial strains by genome shuffling: Current status and future prospects.

PubMed

Magocha, Tinashe Archbold; Zabed, H; Yang, Miaomiao; Yun, Junhua; Zhang, Huanhuan; Qi, Xianghui

2018-06-01

The growing demand for biotechnological products against limited metabolic capacity of industrially used microorganisms has led to an increased interest on strain-improvement over the last several decades, which aimed to enhance metabolite yield, substrate uptake and tolerance of the strains. Among a few techniques of strain-improvement, genome shuffling is the most recent and promising approach used for rapid strain-improvement that can yield a new strain by combining whole genomes of multi-parental microorganisms using the principles of protoplast fusion. Genome shuffling has brought a major breakthrough in the strain-improvement concept as it is found to be effective and reliable for expressing complex phenotypes. This review will discuss the technical aspects and applications of genome shuffling for various industrial strains to present its current status and recent progress. In the concluding remarks, a summary will be presented focusing on the major challenges and future outlooks of this technology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies.

PubMed

Zeitoun, Ramsey I; Pines, Gur; Grau, Willliam C; Gill, Ryan T

2017-04-21

Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory time scales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites. This approach works by assembling genome engineered sites with cell-specific barcodes into a format compatible with high-throughput sequencing technologies. This approach, called barcoded-TRACE (bTRACE) was applied to assess E. coli populations engineered by recursive multiplex recombineering across both 6-target sites and 31-target sites. The 31-target library was then tracked throughout growth selections in the presence and absence of isopentenol (a potential next-generation biofuel). We also use the resolution of bTRACE to compare the influence of technical and biological noise on genome engineering efforts.

78 FR 34392 - Guidance for Industry and Food and Drug Administration Staff: Technical Considerations for Pen...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-07

...] Guidance for Industry and Food and Drug Administration Staff: Technical Considerations for Pen, Jet, and... availability of a final guidance document entitled ``Technical Considerations for Pen, Jet, and Related... developing information to support a marketing application for a pen, jet, or related injector device intended...

Florida Study of Career and Technical Education. Final Report

ERIC Educational Resources Information Center

Jacobson, Louis; Mokher, Christine

2014-01-01

A key goal of the "Carl D. Perkins Career and Technical Education Act of 2006" ("Perkins IV") is to ensure career and technical education (CTE) programs are widely available for preparing high school and college students for "high skill, high wage, or high demand occupations in current or emerging professions"…

A Million Cancer Genome Warehouse

DTIC Science & Technology

2012-11-20

Software, Strawberry Canyon, 2012. 25 Units (GPUs) without any changes needed to the client applications. ● Service-level APIs are designed to... Strawberry Canyon, 2012. 62 Patterson, D. For better or worse, benchmarks shape a field: technical perspective, Communications of the ACM, v.55 n.7

How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study.

PubMed

Sanderson, Saskia C; Linderman, Michael D; Zinberg, Randi; Bashir, Ali; Kasarskis, Andrew; Zweig, Micol; Suckiel, Sabrina; Shah, Hardik; Mahajan, Milind; Diaz, George A; Schadt, Eric E

2015-11-01

Health-care professionals need to be trained to work with whole-genome sequencing (WGS) in their practice. Our aim was to explore how students responded to a novel genome analysis course that included the option to analyze their own genomes. This was an observational cohort study. Questionnaires were administered before (T3) and after the genome analysis course (T4), as well as 6 months later (T5). In-depth interviews were conducted at T5. All students (n = 19) opted to analyze their own genomes. At T5, 12 of 15 students stated that analyzing their own genomes had been useful. Ten reported they had applied their knowledge in the workplace. Technical WGS knowledge increased (mean of 63.8% at T3, mean of 72.5% at T4; P = 0.005). In-depth interviews suggested that analyzing their own genomes may increase students' motivation to learn and their understanding of the patient experience. Most (but not all) of the students reported low levels of WGS results-related distress and low levels of regret about their decision to analyze their own genomes. Giving students the option of analyzing their own genomes may increase motivation to learn, but some students may experience personal WGS results-related distress and regret. Additional evidence is required before considering incorporating optional personal genome analysis into medical education on a large scale.

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

PubMed

Luan, Ming-Bao; Jian, Jian-Bo; Chen, Ping; Chen, Jun-Hui; Chen, Jian-Hua; Gao, Qiang; Gao, Gang; Zhou, Ju-Hong; Chen, Kun-Mei; Guang, Xuan-Min; Chen, Ji-Kang; Zhang, Qian-Qian; Wang, Xiao-Fei; Fang, Long; Sun, Zhi-Min; Bai, Ming-Zhou; Fang, Xiao-Dong; Zhao, Shan-Cen; Xiong, He-Ping; Yu, Chun-Ming; Zhu, Ai-Guo

2018-05-01

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae. © 2018 John Wiley & Sons Ltd.

Final Technical Report for Award DESC0011912, "Trimodal Tapping Mode Atomic Force Microscopy: Simultaneous 4D Mapping of Conservative and Dissipative Probe-Sample Interactions of Energy-Relevant Materials”

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solares, Santiago D.

The final project report covering the period 7/1/14-6/30/17 provides an overview of the technical accomplishments in the areas of (i) fundamental viscoelasticity, (ii) multifrequency atomic force microscopy, and (iii) characterization of energy-relevant materials with atomic force microscopy. A list of publications supported by the project is also provided.

Application of Knowledge-Based Techniques to Tracking Function

DTIC Science & Technology

2006-09-01

38394041 42434445 46474849 505152 53545556 57585960 616263 646566 676869 707172 737475 7677 7879 8081 8283 8485 8687 8889 9091 9293 9495 969798 99100...Knowledge-based applications to adaptive space-time processing. Volume I: Summary”, AFRL-SN-TR-2001-146 Vol. I (of Vol. VI ), Final Technical Report, July...2001-146 Vol. IV (of Vol. VI ), Final Technical Report, July 2001. [53] C. Morgan, L. Moyer, “Knowledge-based applications to adaptive space-time

Forecasting the Future Food Service World of Work. Final Report. Volume III. Technical Papers on the Future of the Food Service Industry. Service Management Reports.

ERIC Educational Resources Information Center

Powers, Thomas F., Ed.; Swinton, John R., Ed.

This third and final volume of a study on the future of the food service industry contains the technical papers on which the information in the previous two volumes was based. The papers were written by various members of the Pennsylvania State University departments of economics, food science, nutrition, social psychology, and engineering and by…

Final Technical Report for contract number DE-FG02-05ER15670

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glazebrook, Jane

This is the final technical report for contract number DE-FG02-05ER15670. The project is now complete, and results of the project have been published. Two papers were published based on work done in the last three-year funding period. The DOIs of these papers are included below. The abstracts of the papers, providing summaries of the work, are included in the body of the report.

Genomic sequencing of Pleistocene cave bears

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noonan, James P.; Hofreiter, Michael; Smith, Doug

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome,more » the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.« less

Astrobee Periodic Technical Review (PTR) Delta 3

NASA Technical Reports Server (NTRS)

Provencher, Christopher; Smith, Marion F.; Smith, Ernest Everett; Bualat, Maria Gabriele; Barlow, Jonathan Spencer

2017-01-01

Astrobee is a free flying robot for the inside of the International Space Station (ISS). The Periodic Technical Review (PTR) delta 3 is the final design review of the system presented to stakeholders.

Polar source analysis : technical memorandum

DOT National Transportation Integrated Search

2017-09-29

The following technical memorandum describes the development, testing and analysis of various polar source data sets. The memorandum also includes recommendation for potential inclusion in future releases of AEDT. This memorandum is the final deliver...

2005 v4.2 Technical Support Document

EPA Pesticide Factsheets

Technical Support Document for the Final Transport Rule describes how updated 2005 NEI, version 2 emissions and were processed for air quality modeling in support of the Cross-state Air Pollution Rule (CSAPR).

Direct Final Rule for Technical Amendments for Marine Spark-Ignition Engines and Vessels

EPA Pesticide Factsheets

Rule published September 16, 2010 to make technical amendments to the design standard for portable marine fuel tanks. This rule incorporates safe recommended practices, developed through industry consensus.

Novel multiregion hybridization assay for the identification of the most prevalent genetic forms of the human immunodeficiency virus type 1 circulating in Portugal.

PubMed

Freitas, Ferdinando B; Esteves, Aida; Piedade, João; Parreira, Ricardo

2013-02-01

The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). In this context, the aim of our study was the development of a technical variant of an MHA (vMHA(B/G/02)) for genotyping the most prevalent genetic forms of HIV-1 circulating in Portugal. Different sets of primers were designed for universal and clade-specific amplifications of several sections of the viral genome: gag, pol(Pr), pol(RT), vpu, env(gp120), and env(gp41). vMHA(B/G/02) was implemented using a real-time PCR-based approach, with detection dependent on the use of SYBR Green I. As an alternative, a technically less demanding strategy based on conventional PCR and agarose gel analysis of the reaction products was also developed. This method performed with overall good sensitivity and specificity (>91%) when a convenience sample of 45 plasma-derived HIV-1 strains was analyzed. Apart from the detection of subtype B, G, CRF02_AG, and CRF14_BG viruses, several unique B/G recombinant were also detected. Curiously, recombinant viruses including CRF02_AG sequences were not detected in the group of samples analyzed.

Understanding development and stem cells using single cell-based analyses of gene expression

PubMed Central

Kumar, Pavithra; Tan, Yuqi

2017-01-01

In recent years, genome-wide profiling approaches have begun to uncover the molecular programs that drive developmental processes. In particular, technical advances that enable genome-wide profiling of thousands of individual cells have provided the tantalizing prospect of cataloging cell type diversity and developmental dynamics in a quantitative and comprehensive manner. Here, we review how single-cell RNA sequencing has provided key insights into mammalian developmental and stem cell biology, emphasizing the analytical approaches that are specific to studying gene expression in single cells. PMID:28049689

Overview of hybridization and detection techniques.

PubMed

Hilario, Elena

2007-01-01

A misconception regarding the sensitivity of nonradioactive methods for screening genomic DNA libraries often hinders the establishment of these environmentally friendly techniques in molecular biology laboratories. Nonradioactive probes, properly prepared and quantified, can detect DNA target molecules to the femtomole range. However, appropriate hybridization techniques and detection methods should also be adopted for an efficient use of nonradioactive techniques. Detailed descriptions of genomic library handling before and during the nonradioactive hybridization and detection are often omitted from publications. This chapter aims to fill this void by providing a collection of technical tips on hybridization and detection techniques.

Sequencing technologies - the next generation.

PubMed

Metzker, Michael L

2010-01-01

Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

BlackOPs: increasing confidence in variant detection through mappability filtering.

PubMed

Cabanski, Christopher R; Wilkerson, Matthew D; Soloway, Matthew; Parker, Joel S; Liu, Jinze; Prins, Jan F; Marron, J S; Perou, Charles M; Hayes, D Neil

2013-10-01

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin ('mismapping') and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.

From prenatal genomic diagnosis to fetal personalized medicine: progress and challenges

PubMed Central

Bianchi, Diana W

2015-01-01

Thus far, the focus of personalized medicine has been the prevention and treatment of conditions that affect adults. Although advances in genetic technology have been applied more frequently to prenatal diagnosis than to fetal treatment, genetic and genomic information is beginning to influence pregnancy management. Recent developments in sequencing the fetal genome combined with progress in understanding fetal physiology using gene expression arrays indicate that we could have the technical capabilities to apply an individualized medicine approach to the fetus. Here I review recent advances in prenatal genetic diagnostics, the challenges associated with these new technologies and how the information derived from them can be used to advance fetal care. Historically, the goal of prenatal diagnosis has been to provide an informed choice to prospective parents. We are now at a point where that goal can and should be expanded to incorporate genetic, genomic and transcriptomic data to develop new approaches to fetal treatment. PMID:22772565

Sequencing-based diagnostics for pediatric genetic diseases: progress and potential

PubMed Central

Tayoun, Ahmad Abou; Krock, Bryan; Spinner, Nancy B.

2016-01-01

Introduction The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. Areas Covered We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert Commentary NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics. PMID:27388938

Drafting human ancestry: what does the Neanderthal genome tell us about hominid evolution? Commentary on Green et al. (2010).

PubMed

Hofreiter, Michael

2011-02-01

Ten years after the first draft versions of the human genome were announced, technical progress in both DNA sequencing and ancient DNA analyses has allowed a research team around Ed Green and Svante Pääbo to complete this task from infinitely more difficult hominid samples: a few pieces of bone originating from our closest, albeit extinct, relatives, the Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating environmental DNA impregnating the bones and at the same time avoiding the problems of contamination with modern human DNA is in itself a remarkable accomplishment. However, the crucial question in the long run is, what can we learn from such genomic data about hominid evolution?

A CRISPR toolbox to study virus–host interactions

PubMed Central

Puschnik, Andreas S.; Majzoub, Karim; Ooi, Yaw Shin; Carette, Jan E.

2018-01-01

Viruses depend on their hosts to complete their replication cycles; they exploit cellular receptors for entry and hijack cellular functions to replicate their genome, assemble progeny virions and spread. Recently, genome-scale CRISPR–Cas screens have been used to identify host factors that are required for virus replication, including the replication of clinically relevant viruses such as Zika virus, West Nile virus, dengue virus and hepatitis C virus. In this Review, we discuss the technical aspects of genome-scale knockout screens using CRISPR–Cas technology, and we compare these screens with alternative genetic screening technologies. The relative ease of use and reproducibility of CRISPR–Cas make it a powerful tool for probing virus–host interactions and for identifying new antiviral targets. PMID:28420884

Crop Science Applications

USDA-ARS?s Scientific Manuscript database

The final speaker, Paul Nakata from the USDA Children’s Nutrition Research Center in Houston, Texas, discussed manipulating the plant genome, with emphasis on CRISPR/Cas9-mediated genome editing. Dating back thousands of years ago, traditional and then mutational breeding was used to influence, for ...

Orthology prediction methods: a quality assessment using curated protein families.

PubMed

Trachana, Kalliopi; Larsson, Tomas A; Powell, Sean; Chen, Wei-Hua; Doerks, Tobias; Muller, Jean; Bork, Peer

2011-10-01

The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community. Copyright © 2011 WILEY Periodicals, Inc.

[Multilocus genotyping of polymorphous STR-loci of chromosomal DNA in individual cells: technical difficulties].

PubMed

Ivanov, P L; Leonov, S N; Zemskova, E Iu; Kobylianskiĭ, A G; Dziubenko, E V

2013-01-01

This study was designed to estimate the effectiveness of special technical procedures for the enhancement of sensitivity of multiplex analysis of DNA, such as the use of low-plexity PCR systems and the whole genome preamplification technology, and the possibility of their application for the purpose of forensic medical genotyping of polymorphous STR-loci of chromosomal DNA in individual cells. The authors refused to use the imitation model (equivalent DNA dilutions) for the sake of obtaining the maximally informative data and chose to work with real preparations of solitary buccal epithelial cells isolated by the laser microdissection technique. It was shown that neither the use of the low-plexity multilocus PCR systems nor the whole genome pre-amplification technology makes possible reliable genotyping of STR-loci of chromosomal DNA in individual cells. The proposed techniques allow for DNA genotyping in preparations consisting of 10 diploid cells whereas the methods for reliable genotyping of STR-loci of chromosomal DNA in individual cells remains to be developed.

Primer on Molecular Genetics; DOE Human Genome Program

DOE R&D Accomplishments Database

1992-04-01

This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

Seattle To Portland Inter-City ITS Corridor Study And Communications Plan, Final Report

DOT National Transportation Integrated Search

1996-03-01

THIS DOCUMENT IS THE FINAL REPORT PRESENTING THE SEATTLE TO PORTLAND INTELLIGENT TRANSPORTATION SYSTEM (ITS) EARLY DEPLOYMENT PLAN. THE FINAL REPORT SYNTHESIZES INFORMATION FROM TECHNICAL MEMORANDUMS 1 THROUGH 5; INCLUDING EXISTING AND FUTURE CONDITI...

Benchmark Analysis of Career and Technical Education in Lenawee County. Final Report.

ERIC Educational Resources Information Center

Hollenbeck, Kevin

The career and technical education (CTE) provided in grades K-12 in the county's vocational-technical center and 12 local public school districts of Lenawee County, Michigan, was benchmarked with respect to its attention to career development. Data were collected from the following sources: structured interviews with a number of key respondents…

International Project on Technical and Vocational Education (UNEVOC). International Advisory Committee (Third Session, Paris, France, October 2-4, 1995). Final Report = Projet International pour l'Enseignement Technique et Professionnel (UNEVOC). Comite Consultatif International (Troisieme Session, Paris, France, 2-4 octobre 1995). Rapport Final.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France).

The international advisory committee of the International Project on Technical and Vocational Education (UNEVOC) held its third session in Paris in October 1995. Advisory committee members and observers from the United Nations' specialized, intergovernmental, and nongovernmental organizations reviewed the major UNEVOC project activities undertaken…

International Project on Technical and Vocational Education (UNEVOC). International Advisory Committee (Second Session, Paris, France, December 12-14, 1994). Final Report = Projet International pour l'Enseignement Technique et Professionnel (UNEVOC). Comite Consultatif International (Deuxieme Session, Paris, France, 12-14 decembre 1994). Rapport Final.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France).

The international advisory committee of the International Project on Technical and Vocational Education (UNEVOC) held its second session in Paris in December 1994. Nine advisory committee members and observers from the United Nations' specialized, intergovernmental, and nongovernmental organizations reviewed the major UNEVOC project activities…

Final Technical Report for ARRA Funding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rusack, Roger; Mans, Jeremiah; Poling, Ronald

Final technical report of the University of Minnesota experimental high energy physics group for ARRA support. The Cryogenic Dark Matter Experiment (CDMS) used the funds received to construct a new passive shield to protect a high-purity germanium detector located in the Soudan mine in Northern Minnesota from cosmic rays. The BESIII and the CMS groups purchased computing hardware to assemble computer farms for data analysis and to generate large volumes of simulated data for comparison with the data collected.

Making a Difference in the Lives of Infants and Toddlers and Their Families: The Impacts of Early Head Start. Volumes I-III: Final Technical Report [and] Appendixes [and] Local Contributions to Understanding the Programs and Their Impacts.

ERIC Educational Resources Information Center

Love, John M.; Kisker, Ellen Eliason; Ross, Christine M.; Schochet, Peter Z.; Brooks-Gunn, Jeanne; Paulsell, Diane; Boller, Kimberly; Constantine, Jill; Vogel, Cheri; Fuligni, Alison Sidle; Brady-Smith, Christy

Early Head Start was designed in 1994 as a 2-generation program to enhance children's development and health, strengthen family and community partnerships, and support the staff delivering new services to low-income families with pregnant women, infants, or toddlers. This document contains the final technical report, appendixes, and local…

International Project on Technical and Vocational Education (UNEVOC). International Advisory Committee (First Session, Berlin, Germany, September 20-22, 1993). Final Report = Projet International pour l'Enseignement Technique et Professionnel (UNEVOC). Comite Consultatif International (Premiere Session, Berlin, Germany, 20-22 septembre 1993). Rapport Final.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France).

The international advisory committee of the International Project on Technical and Vocational Education (UNEVOC) held its first session in Berlin in September 1993. The advisory committee's 10 members and observers from the United Nations' specialized, intergovernmental, and nongovernmental organizations discussed educational policy, links between…

Efficient CRISPR/Cas9-Based Genome Engineering in Human Pluripotent Stem Cells.

PubMed

Kime, Cody; Mandegar, Mohammad A; Srivastava, Deepak; Yamanaka, Shinya; Conklin, Bruce R; Rand, Tim A

2016-01-01

Human pluripotent stem cells (hPS cells) are rapidly emerging as a powerful tool for biomedical discovery. The advent of human induced pluripotent stem cells (hiPS cells) with human embryonic stem (hES)-cell-like properties has led to hPS cells with disease-specific genetic backgrounds for in vitro disease modeling and drug discovery as well as mechanistic and developmental studies. To fully realize this potential, it will be necessary to modify the genome of hPS cells with precision and flexibility. Pioneering experiments utilizing site-specific double-strand break (DSB)-mediated genome engineering tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have paved the way to genome engineering in previously recalcitrant systems such as hPS cells. However, these methods are technically cumbersome and require significant expertise, which has limited adoption. A major recent advance involving the clustered regularly interspaced short palindromic repeats (CRISPR) endonuclease has dramatically simplified the effort required for genome engineering and will likely be adopted widely as the most rapid and flexible system for genome editing in hPS cells. In this unit, we describe commonly practiced methods for CRISPR endonuclease genomic editing of hPS cells into cell lines containing genomes altered by insertion/deletion (indel) mutagenesis or insertion of recombinant genomic DNA. Copyright © 2016 John Wiley & Sons, Inc.

Illinois Clean Coal Institute 2005 annual report. Final technical report for the period September 1st, 2004, through August 31, 2005 on projects funded by the Illinois Department of Commerce and Economic Opportunity

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2005-11-08

This final technical report contains the abstracts and executive summaries of projects funded through the Illinois Clean Coal Institute solicitation entitled 'Request for proposals No. 04-1(ICCI/RFP04-1)'. Support of these projects is by the Office of Coal Development and Department of Commerce and Economic Opportunity. The projects fall into the following categories: advanced coal mining technologies; coal preparation and coal production business practice; management of coal combustion byproducts; commercialization and technology transfer. Final project extensions are also recorded.

Renewable Fuel Standard (RFS2): Final Rule Additional Resources

EPA Pesticide Factsheets

The final rule of fuels and fuel additives: renewable fuel standard program is published on March 26, 2010 and is effective on July 1, 2010. You will find the links to this final rule and technical amendments supporting this rule.

Informational laws of genome structures

PubMed Central

Bonnici, Vincenzo; Manca, Vincenzo

2016-01-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

Informational laws of genome structures

NASA Astrophysics Data System (ADS)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

75 FR 48273 - Technical Service Provider Assistance

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-10

... DEPARTMENT OF AGRICULTURE Natural Resources Conservation Service 7 CFR Part 652 RIN 0578-AA48 Technical Service Provider Assistance AGENCY: Natural Resources Conservation Service, United States Department of Agriculture. ACTION: Final rule; Correcting amendment. SUMMARY: The Natural Resources...

Partial Withdrawal and Final Rule for Nonroad Technical Amendments

EPA Pesticide Factsheets

Amendments to the technical hardship provisions under the Transition Program for Equipment Manufacturers related to the Tier 4 standards for nonroad diesel engines, and to the replacement engine exemption generally applicable to new nonroad engines.

Final Report for LDRD Project 02-ERD-069: Discovering the Unknown Mechanism(s) of Virulence in a BW, Class A Select Agent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chain, P; Garcia, E

2003-02-06

The goal of this proposed effort was to assess the difficulty in identifying and characterizing virulence candidate genes in an organism for which very limited data exists. This was accomplished by first addressing the finishing phase of draft-sequenced F. tularensis genomes and conducting comparative analyses to determine the coding potential of each genome; to discover the differences in genome structure and content, and to identify potential genes whose products may be involved in the F. tularensis virulence process. The project was divided into three parts: (1) Genome finishing: This part involves determining the order and orientation of the consensus sequencesmore » of contigs obtained from Phrap assemblies of random draft genomic sequences. This tedious process consists of linking contig ends using information embedded in each sequence file that relates the sequence to the original cloned insert. Since inserts are sequenced from both ends, we can establish a link between these paired-ends in different contigs and thus order and orient contigs. Since these genomes carry numerous copies of insertion sequences, these repeated elements ''confuse'' the Phrap assembly program. It is thus necessary to break these contigs apart at the repeated sequences and individually join the proper flanking regions using paired-end information, or using results of comparisons against a similar genome. Larger repeated elements such as the small subunit ribosomal RNA operon require verification with PCR. Tandem repeats require manual intervention and typically rely on single nucleotide polymorphisms to be resolved. Remaining gaps require PCR reactions and sequencing. Once the genomes have been ''closed'', low quality regions are addressed by resequencing reactions. (2) Genome analysis: The final consensus sequences are processed by combining the results of three gene modelers: Glimmer, Critica and Generation. The final gene models are submitted to a battery of homology searches and domain prediction programs in order to annotate them (e.g. BLAST, Pfam, TIGRfam, COG, KEGG, InterPro, TMhmm, SignalP). The genome structure is also assessed in terms of G+C content, GC bias (GC skew), and locations of repeated regions (e.g. IS elements) and phage-like genes. (3) Comparative genomics: The results of the various genome analyses are compared between the finished (or almost finished) genomes. Here, we have compared the F. tularensis genomes from the extremely lethal strain Schu4 (subsp. tularensis), the vaccine strain LVS (subsp. holartica), and strain UT01-4992 of the less virulent, opportunistic subsp. novicida. Regions present in the highly virulent strain that are absent from the other less virulent strains may provide insight into what factors are required for the high level of virulence.« less

Generation and validation of PAX7 reporter lines from human iPS cells using CRISPR/Cas9 technology.

PubMed

Wu, Jianbo; Hunt, Samuel D; Xue, Haipeng; Liu, Ying; Darabi, Radbod

2016-03-01

Directed differentiation of iPS cells toward various tissue progenitors has been the focus of recent research. Therefore, generation of tissue-specific reporter iPS cell lines provides better understanding of developmental stages in iPS cells. This technical report describes an efficient strategy for generation and validation of knock-in reporter lines in human iPS cells using the Cas9-nickase system. Here, we have generated a knock-in human iPS cell line for the early myogenic lineage specification gene of PAX7. By introduction of site-specific double-stranded breaks (DSB) in the genomic locus of PAX7 using CRISPR/Cas9 nickase pairs, a 2A-GFP reporter with selection markers has been incorporated before the stop codon of the PAX7 gene at the last exon. After positive and negative selection, single cell-derived human iPS clones have been isolated and sequenced for in-frame positioning of the reporter construct. Finally, by using a nuclease-dead Cas9 activator (dCas9-VP160) system, the promoter region of PAX7 has been targeted for transient gene induction to validate the GFP reporter activity. This was confirmed by flow cytometry analysis and immunostaining for PAX7 and GFP. This technical report provides a practical guideline for generation and validation of knock-in reporters using CRISPR/Cas9 system. Published by Elsevier B.V.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

PubMed Central

Glusman, Gustavo; Severson, Alissa; Dhankani, Varsha; Robinson, Max; Farrah, Terry; Mauldin, Denise E.; Stittrich, Anna B.; Ament, Seth A.; Roach, Jared C.; Brunkow, Mary E.; Bodian, Dale L.; Vockley, Joseph G.; Shmulevich, Ilya; Niederhuber, John E.; Hood, Leroy

2015-01-01

The identification of DNA copy numbers from short-read sequencing data remains a challenge for both technical and algorithmic reasons. The raw data for these analyses are measured in tens to hundreds of gigabytes per genome; transmitting, storing, and analyzing such large files is cumbersome, particularly for methods that analyze several samples simultaneously. We developed a very efficient representation of depth of coverage (150–1000× compression) that enables such analyses. Current methods for analyzing variants in whole-genome sequencing (WGS) data frequently miss copy number variants (CNVs), particularly hemizygous deletions in the 1–100 kb range. To fill this gap, we developed a method to identify CNVs in individual genomes, based on comparison to joint profiles pre-computed from a large set of genomes. We analyzed depth of coverage in over 6000 high quality (>40×) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC. To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used. Normalization of the scaled coverage to the RCP followed by hidden Markov model (HMM) segmentation enables efficient detection of CNVs and large deletions in individual genomes. Use of pre-computed multi-genome coverage profiles improves our ability to analyze each individual genome. We make available RCPs and tools for performing these analyses on personal genomes. We expect the increased sensitivity and specificity for individual genome analysis to be critical for achieving clinical-grade genome interpretation. PMID:25741365

A Pilot Program to Provide Ownership Skills to Seniors in the Vocational Technical Schools and Other Educational Institutions, Year Two. Final Report.

ERIC Educational Resources Information Center

Norwich Regional Vocational Technical School, CT.

Responding to a Small Business Administration statement that technical school graduates lack knowledge of business principles, the Norwich (Connecticut) Regional Vocational Technical School conducted a course in small business ownership/management for all of its seniors. The required course, a fifty-four-hour module, replaced one English,…

A Case Study of Technical Assistance to Demonstration Programs for Young Handicapped Children. Part III.

ERIC Educational Resources Information Center

Behr, Shirley K.; And Others

The report describes the third and final year of a 3-year case study of the technical assistance process as implemented by the Technical Assistance Development System (TADS) for the staffs of two demonstration programs for preschool handicapped children and their families. Following a review of TADS and the two demonstration programs, the…

IMG 4 version of the integrated microbial genomes comparative analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts providemore » support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).« less

Chemical Durability Improvement and Static Fatigue of Glasses.

DTIC Science & Technology

1982-08-01

Afl-Alla 837 RENSSELAER POLYIECmfJ!C INST TRtOY NY DEPT OF MATERIAL--ETC F/6 ii/ CHEMICAL DURABILITY IMPROVEMENT AND STATIC FATIGUE OF GLASSESW AUC2...82 M TOMOZAWA NOGGIN 7A-C-0315 UNC LASS IF IED N ENEEEEEE FINAL TECHNICAL REPORT For the period April 1, 1978 "u March 31, 198200 CHEMICAL DURABILITY...REPORT A PERIOD COVERED Chemical Durability Improvement and Static Final Technical Report Fatiue o GlasesApril 1, 1978"’,March 31, 1982 S. PERFORMING ORG

Experimental Program Final Technical Progress Report: 15 February 2007 to 30 September 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kinney, Edward R.

2014-09-12

This is the final technical report of the grant DE-FG02-04ER41301 to the University of Colorado at Boulder entitled "Intermediate Energy Nuclear Physics" and describes the results of our funded activities during the period 15 February 2007 to 30 September 2012. These activities were primarily carried out at Fermilab, RHIC, and the German lab DESY. Significant advances in these experiments were carried out by members of the Colorado group and are described in detail.

Final Technical Report - Center for Technology for Advanced Scientific Component Software (TASCS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sussman, Alan

2014-10-21

This is a final technical report for the University of Maryland work in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS). The Maryland work focused on software tools for coupling parallel software components built using the Common Component Architecture (CCA) APIs. Those tools are based on the Maryland InterComm software framework that has been used in multiple computational science applications to build large-scale simulations of complex physical systems that employ multiple separately developed codes.

Iowa Hill Pumped Storage Project Investigations - Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, David

2016-07-01

This Final Technical Report is a summary of the activities and outcome of the Department of Energy (DOE) Assistance Agreement DE-EE0005414 with the Sacramento Municipal Utility District (SMUD). The Assistance Agreement was created in 2012 to support investigations into the Iowa Hill Pumped-storage Project (Project), a new development that would add an additional 400 MW of capacity to SMUD’s existing 688MW Upper American River Hydroelectric Project (UARP) in the Sierra Nevada mountains east of Sacramento, California.

Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements.

PubMed

Nunes, Luiz R; Rosato, Yoko B; Muto, Nair H; Yanai, Giane M; da Silva, Vivian S; Leite, Daniela B; Gonçalves, Edmilson R; de Souza, Alessandra A; Coletta-Filho, Helvécio D; Machado, Marcos A; Lopes, Silvio A; de Oliveira, Regina Costa

2003-04-01

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.

Renewable Fuel Standard Program (RFS1): Final Rule Additional Resources

EPA Pesticide Factsheets

The final rule of fuels and fuel additives: renewable fuel standard program is published on May 1, 2007 and is effective on September 1, 2007. You will find the links to this final rule and technical amendments supporting this rule.

Assurance Penalty Level Analysis Final Rule TSD

EPA Pesticide Factsheets

This Technical Support Document (TSD) supports EPA’s determination that the final Transport Rule’s assurance provision penalty requirement provides sufficient deterrence against a state exceeding its assurance level.

Final Rule for Technical Amendments to the Highway and Nonroad Diesel Regulations

EPA Pesticide Factsheets

This action corrects errors and omissions from the previous rules, makes minor changes to the regulations to assist entities with regulatory compliance, and makes technical amendments that resulted from discussions with various diesel stakeholders.

LINE-1 Elements in Structural Variation and Disease

PubMed Central

Beck, Christine R.; Garcia-Perez, José Luis; Badge, Richard M.; Moran, John V.

2014-01-01

The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes. PMID:21801021

Ethical, legal, and social implications of incorporating genomic information into electronic health records.

PubMed

Hazin, Ribhi; Brothers, Kyle B; Malin, Bradley A; Koenig, Barbara A; Sanderson, Saskia C; Rothstein, Mark A; Williams, Marc S; Clayton, Ellen W; Kullo, Iftikhar J

2013-10-01

The inclusion of genomic data in the electronic health record raises important ethical, legal, and social issues. In this article, we highlight these challenges and discuss potential solutions. We provide a brief background on the current state of electronic health records in the context of genomic medicine, discuss the importance of equitable access to genome-enabled electronic health records, and consider the potential use of electronic health records for improving genomic literacy in patients and providers. We highlight the importance of privacy, access, and security, and of determining which genomic information is included in the electronic health record. Finally, we discuss the challenges of reporting incidental findings, storing and reinterpreting genomic data, and nondocumentation and duty to warn family members at potential genetic risk.

Transposable elements in cancer.

PubMed

Burns, Kathleen H

2017-07-01

Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.

Genome Editing and Its Applications in Model Organisms.

PubMed

Ma, Dongyuan; Liu, Feng

2015-12-01

Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, DA; Li, T; Yang, B

Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleasesmore » to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges, and future prospects of this quickly evolving area of study and application.« less

The Global Genome Biodiversity Network (GGBN) Data Standard specification

PubMed Central

Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

Toward mapping the biology of the genome.

PubMed

Chanock, Stephen

2012-09-01

This issue of Genome Research presents new results, methods, and tools from The ENCODE Project (ENCyclopedia of DNA Elements), which collectively represents an important step in moving beyond a parts list of the genome and promises to shape the future of genomic research. This collection sheds light on basic biological questions and frames the current debate over the optimization of tools and methodological challenges necessary to compare and interpret large complex data sets focused on how the genome is organized and regulated. In a number of instances, the authors have highlighted the strengths and limitations of current computational and technical approaches, providing the community with useful standards, which should stimulate development of new tools. In many ways, these papers will ripple through the scientific community, as those in pursuit of understanding the "regulatory genome" will heavily traverse the maps and tools. Similarly, the work should have a substantive impact on how genetic variation contributes to specific diseases and traits by providing a compendium of functional elements for follow-up study. The success of these papers should not only be measured by the scope of the scientific insights and tools but also by their ability to attract new talent to mine existing and future data.

Efficient CRISPR/Cas9-based gene knockout in watermelon.

PubMed

Tian, Shouwei; Jiang, Linjian; Gao, Qiang; Zhang, Jie; Zong, Mei; Zhang, Haiying; Ren, Yi; Guo, Shaogui; Gong, Guoyi; Liu, Fan; Xu, Yong

2017-03-01

CRISPR/Cas9 system can precisely edit genomic sequence and effectively create knockout mutations in T0 generation watermelon plants. Genome editing offers great advantage to reveal gene function and generate agronomically important mutations to crops. Recently, RNA-guided genome editing system using the type II clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) has been applied to several plant species, achieving successful targeted mutagenesis. Here, we report the genome of watermelon, an important fruit crop, can also be precisely edited by CRISPR/Cas9 system. ClPDS, phytoene desaturase in watermelon, was selected as the target gene because its mutant bears evident albino phenotype. CRISPR/Cas9 system performed genome editing, such as insertions or deletions at the expected position, in transfected watermelon protoplast cells. More importantly, all transgenic watermelon plants harbored ClPDS mutations and showed clear or mosaic albino phenotype, indicating that CRISPR/Cas9 system has technically 100% of genome editing efficiency in transgenic watermelon lines. Furthermore, there were very likely no off-target mutations, indicated by examining regions that were highly homologous to sgRNA sequences. Our results show that CRISPR/Cas9 system is a powerful tool to effectively create knockout mutations in watermelon.

Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

EPA Science Inventory

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

Final priority. Rehabilitation Training: Job-Driven Vocational Rehabilitation Technical Assistance Center. Final priority.

PubMed

2014-08-19

The Assistant Secretary for Special Education and Rehabilitative Services announces a priority under the Rehabilitation Training program to establish a Job-Driven Vocational Rehabilitation Technical Assistance Center (JDVRTAC). The Assistant Secretary may use this priority for competitions in fiscal year (FY) 2014 and later years. We take this action to focus on training in an area of national need. Specifically, this priority responds to the Presidential Memorandum to Federal agencies directing them to take action to address job-driven training for the Nation's workers. The JDVRTAC will provide technical assistance (TA) to State vocational rehabilitation (VR) agencies to help them develop for individuals with disabilities training and employment opportunities that meet the needs of today's employers.

Understanding development and stem cells using single cell-based analyses of gene expression.

PubMed

Kumar, Pavithra; Tan, Yuqi; Cahan, Patrick

2017-01-01

In recent years, genome-wide profiling approaches have begun to uncover the molecular programs that drive developmental processes. In particular, technical advances that enable genome-wide profiling of thousands of individual cells have provided the tantalizing prospect of cataloging cell type diversity and developmental dynamics in a quantitative and comprehensive manner. Here, we review how single-cell RNA sequencing has provided key insights into mammalian developmental and stem cell biology, emphasizing the analytical approaches that are specific to studying gene expression in single cells. © 2017. Published by The Company of Biologists Ltd.

The Tolypocladium inflatum CPA element encodes a RecQ helicase-like gene.

PubMed

Kempken, Frank

2008-12-01

Previously, a repetitive CPA element was discovered in the genome of the filamentous fungus Tolypocladium inflatum; however, no further characterization was technically possible at that time. In this study, PCR amplification was used to detect a 4 kb conserved portion of the CPA element that appeared to be present in most, if not all, genomic CPA elements. The amplicons included a large open reading frame that was most similar to a RecQ helicase-like gene from Metarhizium anisopliae. The repetitive nature of the CPA element suggests that it is related to the eukaryotic Helitron class of transposable elements.

NASA's Pursuit of Low-Noise Propulsion for Low-Boom Commercial Supersonic Vehicles

NASA Technical Reports Server (NTRS)

Bridges, James; Brown, Clifford A.; Seidel, Jonathan A.

2018-01-01

Since 2006, when the Fundamental Aeronautics Program was instituted within NASA's Aeronautics Mission Directorate, there has been a Project looking at the technical barriers to commercial supersonic flight. Among the barriers is the noise produced by aircraft during landing and takeoff. Over the years that followed, research was carried out at NASA aeronautics research centers, often in collaboration with academia and industry, addressing the problem. In 2013, a high-level milestone was established, described as a Technical Challenge, with the objective of demonstrating the feasibility of a low-boom supersonic airliner that could meet current airport noise regulations. The Technical Challenge was formally called "Low Noise Propulsion for Low Boom Aircraft", and was completed in late 2016. This paper reports the technical findings from this Technical Challenge, reaching back almost 10 years to review the technologies and tools that were developed along the way. It also discusses the final aircraft configuration and propulsion systems required for a supersonic civilian aircraft to meet noise regulations using the technologies available today. Finally, the paper documents the model-scale tests that validated the acoustic performance of the study aircraft.

NASA's Pursuit of Low-Noise Propulsion for Low-Boom Commercial Supersonic Vehicles

NASA Technical Reports Server (NTRS)

Bridges, James; Brown, Clifford A.; Seidel, Jonathan

2018-01-01

Since 2006, when the Fundamental Aeronautics Program was instituted within NASA's Aeronautics Mission Directorate, there has been a Project looking at the technical barriers to commercial supersonic flight. Among the barriers is the noise produced by aircraft during landing and takeoff. Over the years that followed, research was carried out at NASA aeronautics research centers, often in collaboration with academia and industry, addressing the problem. In 2013, a high-level milestone was established, described as a Technical Challenge, with the objective of demonstrating the feasibility of a low-boom supersonic airliner that could meet current airport noise regulations. The Technical Challenge was formally called a Low Noise Propulsion for Low Boom Aircraft and was completed in late 2016. This paper reports the technical findings from this Technical Challenge, reaching back almost 10 years to review the technologies and tools that were developed along the way. It also discusses the final aircraft configuration and propulsion systems required for a supersonic civilian aircraft to meet noise regulations using the technologies available today. Finally, the paper documents the model-scale tests that validated the acoustic performance of the study aircraft.

Final Revisions Rule State Budgets and New Unit Set-Asides TSD

EPA Pesticide Factsheets

This technical support document shows the underlying data and calculations used to quantify the state budget revisions and new unit set-aside revisions made in the final revisions rule, as well as those revisions included in the direct final revisions rule

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

PubMed Central

Wörheide, Gert

2017-01-01

Abstract One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. PMID:28633296

77 FR 37284 - Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-21

... DEPARTMENT OF LABOR Office of Workers' Compensation Programs 20 CFR Parts 701, 702, 703, 725, and 726 RIN 1240-AA05 Technical Amendments AGENCY: Office of Workers' Compensation Programs, Labor. ACTION: Final rule. SUMMARY: The Office of Workers' Compensation Programs is making [[Page 37285

Vehicle infrastructure integration proof of concept : technical description--vehicle : final report

DOT National Transportation Integrated Search

2009-05-19

This report provides the technical description of the VII system developed for the Cooperative Agreement VII Program between the USDOT and the VII Consortium. The basic architectural elements are summarized and detailed descriptions of the hardware a...

Alteration in oligonucleotide fingerprint patterns of the viral genome in poliovirus type 2 isolated from paralytic patients.

PubMed Central

Yoneyama, T; Hagiwara, A; Hara, M; Shimojo, H

1982-01-01

A close relationship was demonstrated by oligonucleotide fingerprinting between genomes of the poliovirus type 2 Sabin vaccine strain and recent isolates from paralytic cases associated with vaccination in Japan. The oligonucleotide maps of isolates from an agammaglobulinemic patient, who continued to excrete poliovirus type 2 for 3.5 years after the administration of oral vaccine, showed that the genomic alteration proceeded gradually, retaining the majority of the oligonucleotides characteristic of the vaccine strain for a long period, indicating vaccine origin for the isolates. The final isolate at month 41, however, lost the majority of these oligonucleotides. The heterologous antigenic relationship between the final isolate and the previous isolates was also observed. The serial alteration in electrophoretic mobility of the major structural proteins (VP1, VP2, and VP3) was observed throughout the excreting period. These results indicate that the population of the virus in this individual changed markedly during the last short period (about 3 months), in which the treatment with secretory immunoglobulin A was carried out. Genome comparisons in oligonucleotide maps show that some oligonucleotides in the genome of the vaccine strain are highly mutable after passage in humans. Images PMID:6179881

Genomic Approaches to Zebrafish Cancer

PubMed Central

2017-01-01

The zebrafish has emerged as an important model for studying cancer biology. Identification of DNA, RNA and chromatin abnormalities can give profound insight into the mechanisms of tumorigenesis and the there are many techniques for analyzing the genomes of these tumors. Here, I present an overview of the available technologies for analyzing tumor genomes in the zebrafish, including array based methods as well as next-generation sequencing technologies. I also discuss the ways in which zebrafish tumor genomes can be compared to human genomes using cross-species oncogenomics, which act to filter genomic noise and ultimately uncover central drivers of malignancy. Finally, I discuss downstream analytic tools, including network analysis, that can help to organize the alterations into coherent biological frameworks that can then be investigated further. PMID:27165352

A field ornithologist’s guide to genomics: Practical considerations for ecology and conservation

USGS Publications Warehouse

Oyler-McCance, Sara J.; Oh, Kevin; Langin, Kathryn; Aldridge, Cameron L.

2016-01-01

Vast improvements in sequencing technology have made it practical to simultaneously sequence millions of nucleotides distributed across the genome, opening the door for genomic studies in virtually any species. Ornithological research stands to benefit in three substantial ways. First, genomic methods enhance our ability to parse and simultaneously analyze both neutral and non-neutral genomic regions, thus providing insight into adaptive evolution and divergence. Second, the sheer quantity of sequence data generated by current sequencing platforms allows increased precision and resolution in analyses. Third, high-throughput sequencing can benefit applications that focus on a small number of loci that are otherwise prohibitively expensive, time-consuming, and technically difficult using traditional sequencing methods. These advances have improved our ability to understand evolutionary processes like speciation and local adaptation, but they also offer many practical applications in the fields of population ecology, migration tracking, conservation planning, diet analyses, and disease ecology. This review provides a guide for field ornithologists interested in incorporating genomic approaches into their research program, with an emphasis on techniques related to ecology and conservation. We present a general overview of contemporary genomic approaches and methods, as well as important considerations when selecting a genomic technique. We also discuss research questions that are likely to benefit from utilizing high-throughput sequencing instruments, highlighting select examples from recent avian studies.

NetView technical research

NASA Technical Reports Server (NTRS)

1993-01-01

This is the Final Technical Report for the NetView Technical Research task. This report is prepared in accordance with Contract Data Requirements List (CDRL) item A002. NetView assistance was provided and details are presented under the following headings: NetView Management Systems (NMS) project tasks; WBAFB IBM 3090; WPAFB AMDAHL; WPAFB IBM 3084; Hill AFB; McClellan AFB AMDAHL; McClellan AFB IBM 3090; and Warner-Robins AFB.

Inventory of greenhouse gas emissions from on-road vehicles in Midwestern USA States and integrated approach to achieving environmental sustainability in transportation : USDOT Region V Regional University Transportation Center final report : technical su

DOT National Transportation Integrated Search

2016-12-29

Two project objectives one technical and one educational- were laid out in this project. The technical objective was to assess current inventory of greenhouse gases (GHG) in the six Midwestern states of the nation and to estimate improvements as ...

Emissions Inventory Final Rule TSD

EPA Pesticide Factsheets

This technical support document (TSD) provides the details of emissions data processing done in support of EPA's final rulemaking effort for the Federal Transport Rule, now known as the Cross-State Air Pollution Rule.

Multiple Myeloma Genomics: A Systematic Review.

PubMed

Weaver, Casey J; Tariman, Joseph D

2017-08-01

This integrative review describes the genomic variants that have been found to be associated with poor prognosis in patients diagnosed with multiple myeloma (MM). Second, it identifies MM genetic and genomic changes using next-generation sequencing, specifically whole-genome sequencing or exome sequencing. A search for peer-reviewed articles through PubMed, EBSCOhost, and DePaul WorldCat Libraries Worldwide yielded 33 articles that were included in the final analysis. The most commonly reported genetic changes were KRAS, NRAS, TP53, FAM46C, BRAF, DIS3, ATM, and CCND1. These genetic changes play a role in the pathogenesis of MM, prognostication, and therapeutic targets for novel therapies. MM genetics and genomics are expanding rapidly; oncology nurse clinicians must have basic competencies in genetics and genomics to help patients understand the complexities of genetic and genomic alterations and be able to refer patients to appropriate genomic professionals if needed. Copyright © 2017 Elsevier Inc. All rights reserved.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michael Laub

2008-12-29

Our team of investigators from MIT (Michael Laub) and Stanford (Harley McAdams and Lucy Shapiro) conducted a multi-faceted, systematic experimental analysis of the 106 Caulobacter two-component signal transduction system proteins (62 histidine kinases and 44 response regulators) to understand how they coordinate cell cycle progression, metabolism, and response to environmental changes. These two-component signaling proteins were characterized at the genetic, biochemical, and genomic levels. The results generated by our laboratories have provided numerous insights into how Caulobacter cells sense and respond to a myriad of signals. As nearly all bacteria use two-component signaling for cell regulation, the results from thismore » project help to deepen our general understanding of bacterial signal transduction. The tools and approaches developed can be applied to other bacteria. In particular, work from the Laub laboratory now enables the systematic, rational rewiring of two-component signaling proteins, a major advance that stands to impact synthetic biology and the development of biosensors and other designer molecular circuits. Results are summarized from our work. Each section lists publications and publicly-available resources which result from the work described.« less

Quantifying heterogeneity in human tumours using MRI and PET.

PubMed

Asselin, Marie-Claude; O'Connor, James P B; Boellaard, Ronald; Thacker, Neil A; Jackson, Alan

2012-03-01

Most tumours, even those of the same histological type and grade, demonstrate considerable biological heterogeneity. Variations in genomic subtype, growth factor expression and local microenvironmental factors can result in regional variations within individual tumours. For example, localised variations in tumour cell proliferation, cell death, metabolic activity and vascular structure will be accompanied by variations in oxygenation status, pH and drug delivery that may directly affect therapeutic response. Documenting and quantifying regional heterogeneity within the tumour requires histological or imaging techniques. There is increasing evidence that quantitative imaging biomarkers can be used in vivo to provide important, reproducible and repeatable estimates of tumoural heterogeneity. In this article we review the imaging methods available to provide appropriate biomarkers of tumour structure and function. We also discuss the significant technical issues involved in the quantitative estimation of heterogeneity and the range of descriptive metrics that can be derived. Finally, we have reviewed the existing clinical evidence that heterogeneity metrics provide additional useful information in drug discovery and development and in clinical practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004.

PubMed

Wiechers, Ilse R; Perin, Noah C; Cook-Deegan, Robert

2013-01-01

Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004.

Transportation Network Data Requirements for Assessing Criticality for Resiliency and Adaptation Planning

DOT National Transportation Integrated Search

2017-11-01

This report is one of two NCST Research Report documents produced as part of a project to advance the technical modeling tools for resiliency and adaptation planning, especially those used for criticality rankings. The official final technical report...

Comment Deadlines Established Regarding the LightSquared Technical Working Group Report

DOT National Transportation Integrated Search

2011-06-30

On June 30, 2011, LightSquared Subsidiary LLC (LightSquared) submitted a final report of the : technical working group co-chaired by LightSquared and the United States Global Positioning System : (GPS) Industry Council (USGIC)1 and organized in respo...

Technical report on prototype intelligent network flow optimization (INFLO) dynamic speed harmonization and queue warning.

DOT National Transportation Integrated Search

2015-06-01

This Technical Report on Prototype Intelligent Network Flow Optimization (INFLO) Dynamic Speed Harmonization and Queue Warning is the final report for the project. It describes the prototyping, acceptance testing and small-scale demonstration of the ...

NUSC Technical Publications Guide.

DTIC Science & Technology

1985-05-01

Facility personnel especially that of A. Castelluzzo, E. Deland, J. Gesel , and E. Szlosek (all of Code 4343). Reviewed and Approved: 14 July 1980 D...their technical content and format. Review and approve the manual outline, the review manuscript, and the final camera - reproducible copy. Conduct in

Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes.

PubMed

Fu, Yong-Bi; Peterson, Gregory W; Dong, Yibo

2016-04-07

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications. Copyright © 2016 Fu et al.

Cross-State Air Pollution Rule Update Allowance Allocation Final Rule TSD

EPA Pesticide Factsheets

This Technical Support Document (TSD) provides information that supports EPA’s determination of unit-level allocations for existing and new units under the final Cross-State Air Pollution Rule Update.

Origins of the Human Genome Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook-Deegan, Robert

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information ismore » embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.« less

Origins of the Human Genome Project

DOE R&D Accomplishments Database

Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

Guidelines for producing training films and videos.

PubMed

Harper, P B

1991-01-01

Drawing from experience in producing a film on the surgical procedure of female sterilization, 4 guidelines to technical film production for training purposes are presented and discussed in this paper. In order of presentation in the text, the paper 1st encourages identifying and securing a technical expert, then clearly identifying steps of the technical procedure, involving trainees and trainers in the production process, and working with experienced producers, scriptwriters, and crew members. Returning to the 1st guideline, the technical advisor will have a central presence during all photography and editing, and ideally should not have any personal investment in the procedure being shown. Prior to script finalization and sorting, research is urged to ensure concrete procedural steps. Printed materials, slides, interviews of experienced clinicians, procedure observation, and test videotape shooting may be called upon and employed as parts of the research phase. Trainees should participate during preliminary research, script development, and pretesting of early film versions, their suggestions for change incorporated where appropriate in the final version. On the final point of securing experienced workers, country nationals sensitive to relevant cultural and background dynamics should be included in the team. The special concerns of airport security regulation and customs requirements knowledge are essential, as well as their attention to assuring adequate on-site electricity for camera equipment.

Lessons learned from the dog genome.

PubMed

Wayne, Robert K; Ostrander, Elaine A

2007-11-01

Extensive genetic resources and a high-quality genome sequence position the dog as an important model species for understanding genome evolution, population genetics and genes underlying complex phenotypic traits. Newly developed genomic resources have expanded our understanding of canine evolutionary history and dog origins. Domestication involved genetic contributions from multiple populations of gray wolves probably through backcrossing. More recently, the advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess specific phenotypic traits. Consequently, genome-wide association and selective sweep scans now allow the discovery of genes underlying breed-specific characteristics. The dog is finally emerging as a novel resource for studying the genetic basis of complex traits, including behavior.

Quantitative proteomics in Giardia duodenalis-Achievements and challenges.

PubMed

Emery, Samantha J; Lacey, Ernest; Haynes, Paul A

2016-08-01

Giardia duodenalis (syn. G. lamblia and G. intestinalis) is a protozoan parasite of vertebrates and a major contributor to the global burden of diarrheal diseases and gastroenteritis. The publication of multiple genome sequences in the G. duodenalis species complex has provided important insights into parasite biology, and made post-genomic technologies, including proteomics, significantly more accessible. The aims of proteomics are to identify and quantify proteins present in a cell, and assign functions to them within the context of dynamic biological systems. In Giardia, proteomics in the post-genomic era has transitioned from reliance on gel-based systems to utilisation of a diverse array of techniques based on bottom-up LC-MS/MS technologies. Together, these have generated crucial foundations for subcellular proteomes, elucidated intra- and inter-assemblage isolate variation, and identified pathways and markers in differentiation, host-parasite interactions and drug resistance. However, in Giardia, proteomics remains an emerging field, with considerable shortcomings evident from the published research. These include a bias towards assemblage A, a lack of emphasis on quantitative analytical techniques, and limited information on post-translational protein modifications. Additionally, there are multiple areas of research for which proteomic data is not available to add value to published transcriptomic data. The challenge of amalgamating data in the systems biology paradigm necessitates the further generation of large, high-quality quantitative datasets to accurately model parasite biology. This review surveys the current proteomic research available for Giardia and evaluates their technical and quantitative approaches, while contextualising their biological insights into parasite pathology, isolate variation and eukaryotic evolution. Finally, we propose areas of priority for the generation of future proteomic data to explore fundamental questions in Giardia, including the analysis of post-translational modifications, and the design of MS-based assays for validation of differentially expressed proteins in large datasets. Copyright © 2016 Elsevier B.V. All rights reserved.

Genomic Features That Predict Allelic Imbalance in Humans Suggest Patterns of Constraint on Gene Expression Variation

PubMed Central

Fédrigo, Olivier; Haygood, Ralph; Mukherjee, Sayan; Wray, Gregory A.

2009-01-01

Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In particular, measurements of gene expression usually do not reveal whether the genetic basis for any observed variation lies in cis or in trans to the gene, a distinction that has direct relevance to the physical location of the underlying genetic variant, and which may also impact its evolutionary trajectory. Allelic imbalance measurements identify cis-acting genetic effects by assaying the relative contribution of the two alleles of a cis-regulatory region to gene expression within individuals. Identification of patterns that predict commonly imbalanced genes could therefore serve as a useful tool and also shed light on the evolution of cis-regulatory variation itself. Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set. Reduction of this feature set to four factors revealed that only one factor significantly differentiated between commonly imbalanced and nonimbalanced genes. We demonstrate that these results are consistent between the original data set and a second published data set in humans obtained using different technical and statistical methods. Finally, we show that variation in the single allelic imbalance-associated factor is partially explained by the density of genes in the region of a target gene (allelic imbalance is less probable for genes in gene-dense regions), and, to a lesser extent, the evenness of expression of the gene across tissues and the magnitude of negative selection on putative regulatory regions of the gene. These results suggest that the genomic distribution of functional cis-regulatory variants in the human genome is nonrandom, perhaps due to local differences in evolutionary constraint. PMID:19506001

Genome Annotation and Transcriptomics of Oil-Producing Algae

DTIC Science & Technology

2015-03-16

AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

Northeast Corridor Improvement Project Electrification - New Haven, CT to Boston, MA : Final Environmental Statement/Report : v. 2. Technical Studies

DOT National Transportation Integrated Search

1994-10-31

This document is the final environmental impact statement and final environmental impact report (FEIS/R) on the proposal by the National Railroad Passenger Corporation (Amtrak) to complete the electrification of the Northeast Corridor main line by ex...

A New Framework and Prototype Solution for Clinical Decision Support and Research in Genomics and Other Data-intensive Fields of Medicine.

PubMed

Evans, James P; Wilhelmsen, Kirk C; Berg, Jonathan; Schmitt, Charles P; Krishnamurthy, Ashok; Fecho, Karamarie; Ahalt, Stanley C

2016-01-01

In genomics and other fields, it is now possible to capture and store large amounts of data in electronic medical records (EMRs). However, it is not clear if the routine accumulation of massive amounts of (largely uninterpretable) data will yield any health benefits to patients. Nevertheless, the use of large-scale medical data is likely to grow. To meet emerging challenges and facilitate optimal use of genomic data, our institution initiated a comprehensive planning process that addresses the needs of all stakeholders (e.g., patients, families, healthcare providers, researchers, technical staff, administrators). Our experience with this process and a key genomics research project contributed to the proposed framework. We propose a two-pronged Genomic Clinical Decision Support System (CDSS) that encompasses the concept of the "Clinical Mendeliome" as a patient-centric list of genomic variants that are clinically actionable and introduces the concept of the "Archival Value Criterion" as a decision-making formalism that approximates the cost-effectiveness of capturing, storing, and curating genome-scale sequencing data. We describe a prototype Genomic CDSS that we developed as a first step toward implementation of the framework. The proposed framework and prototype solution are designed to address the perspectives of stakeholders, stimulate effective clinical use of genomic data, drive genomic research, and meet current and future needs. The framework also can be broadly applied to additional fields, including other '-omics' fields. We advocate for the creation of a Task Force on the Clinical Mendeliome, charged with defining Clinical Mendeliomes and drafting clinical guidelines for their use.

Whole-exome/genome sequencing and genomics.

PubMed

Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

2013-12-01

As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells.

PubMed

Han, Kyung Yeon; Kim, Kyu-Tae; Joung, Je-Gun; Son, Dae-Soon; Kim, Yeon Jeong; Jo, Areum; Jeon, Hyo-Jeong; Moon, Hui-Sung; Yoo, Chang Eun; Chung, Woosung; Eum, Hye Hyeon; Kim, Sangmin; Kim, Hong Kwan; Lee, Jeong Eon; Ahn, Myung-Ju; Lee, Hae-Ock; Park, Donghyun; Park, Woong-Yang

2018-01-01

Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level. © 2018 Han et al.; Published by Cold Spring Harbor Laboratory Press.

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

PubMed Central

Han, Kyung Yeon; Kim, Kyu-Tae; Joung, Je-Gun; Son, Dae-Soon; Kim, Yeon Jeong; Jo, Areum; Jeon, Hyo-Jeong; Moon, Hui-Sung; Yoo, Chang Eun; Chung, Woosung; Eum, Hye Hyeon; Kim, Sangmin; Kim, Hong Kwan; Lee, Jeong Eon; Ahn, Myung-Ju; Lee, Hae-Ock; Park, Donghyun; Park, Woong-Yang

2018-01-01

Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level. PMID:29208629

Health care fraud and abuse data collection program: technical revisions to Healthcare Integrity and Protection Data Bank data collection activities. Final rule.

PubMed

2004-09-21

The rule finalizes technical changes to the Healthcare Integrity and Protection Data Bank (HIPDB) data collection reporting requirements by clarifying the types of personal numeric identifiers that may be reported to the data bank in connection with adverse actions. The rule clarifies that in lieu of a Social Security Number (SSN), an individual taxpayer identification number (ITIN) may be reported to the data bank when, in those limited situations, an individual does not have an SSN.

Recovery Act-SmartGrid regional demonstration transmission and distribution (T&D) Infrastructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hedges, Edward T.

This document represents the Final Technical Report for the Kansas City Power & Light Company (KCP&L) Green Impact Zone SmartGrid Demonstration Project (SGDP). The KCP&L project is partially funded by Department of Energy (DOE) Regional Smart Grid Demonstration Project cooperative agreement DE-OE0000221 in the Transmission and Distribution Infrastructure application area. This Final Technical Report summarizes the KCP&L SGDP as of April 30, 2015 and includes summaries of the project design, implementation, operations, and analysis performed as of that date.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A; Taillefert, Martial

This final technical report describes results and findings from a research project to examine the role of microbial phosphohydrolase enzymes in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of the radionuclide uranium through the production of insoluble uranium phosphate minerals. The research project investigated the microbial mechanisms and the physical and chemical processes promoting uranium biomineralization and sequestration in oxygenated subsurface soils. Uranium biomineralization under aerobic conditions can provide a secondary biobarrier strategy to immobilize radionuclides should the metal precipitates formed by microbial dissimilatory mechanisms remobilize due to a change in redox state.

Waveguide Studies for Fiber Optics and Optical Signal Processing Applications.

DTIC Science & Technology

1980-04-01

AO-A086 115 UNI!VERtSIT? OF SOUTIUR CALEPCRNA LOS AMUSS / 5 WAVGUIDE STUIES15 FOR FEB53 OpTECS AND OpTICAL SEOSA.o P /0Ksu-y "/6 UNLSIIDAPR N0 E...SAMUE Flola-??-c-sa UNCASZFIORAC-M-8042 U Final Technical Report (1 1April 1950 L V ~ WAVEGUIDE STUDIES FOR FIBER OPTICS AND OPTICAL SIGNAL PROCESSING...and Subtitle) 081 6&4𔃾JODO )EI YAVECUIDESTUDIES FOR JIBER OPTICS ANDL 7 Final ,T/echnical epoErt, OPTICAL SI’tNAL PROCESSING APPLICATIONS.4 11 Se 77

SELECTIVE DISSEMINATION OF INFORMATION (SDI). VOLUME I, PILOT TEST AT U.S. ARMY NATICK LABORATORIES. FINAL REPORT. ARMY TECHNICAL LIBRARY IMPROVEMENT STUDIES (ATLIS), REPORT NO. 15.

ERIC Educational Resources Information Center

BIVONA, WILLIAM A.

THIS VOLUME PRESENTS THE RESULTS OF A NINE-MONTH TEST OF A PROTOTYPE SELECTIVE DISSEMINATION OF INFORMATION (SDI) SYSTEM DEVELOPED FOR THE ARMY TECHNICAL LIBRARIES. DURING THE PILOT TEST ONE THOUSAND DOCUMENTS WERE CATALOGED, INDEXED, AND DISSEMINATED TO TWENTY-FIVE SCIENTIFIC AND TECHNICAL PERSONNEL. MATCHING OF THE INTEREST PROFILES OF THESE…

Ceramic High Efficiency Particulate Air (HEPA) Filter Final Report CRADA No. TC02160.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, M.; Bergman, W.

2017-08-25

The technical objective of this project was to develop a ceramic HEPA filter technology, by initially producing and testing coupon ceramics, small scale prototypes, and full scale prototype HEPA filters, and to address relevant manufacturing and commercialization technical issues.

7 CFR 614.6 - Agency records and decision notices.

Code of Federal Regulations, 2010 CFR

2010-01-01

... notifies participants of the agency's preliminary and final technical determinations and program decisions... decision notice within 10 working days of rendering a technical determination or program decision. In lieu of certified mail, NRCS may hand deliver notices to participants with written acknowledgment of...

ECOS E-MATRIX Methane and Volatile Organic Carbon (VOC) Emissions Best Practices Database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parisien, Lia

2016-01-31

This final scientific/technical report on the ECOS e-MATRIX Methane and Volatile Organic Carbon (VOC) Emissions Best Practices Database provides a disclaimer and acknowledgement, table of contents, executive summary, description of project activities, and briefing/technical presentation link.

77 FR 18914 - National Motor Vehicle Title Information System (NMVTIS): Technical Corrections

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-29

... 1121-AA79 National Motor Vehicle Title Information System (NMVTIS): Technical Corrections AGENCY... (OJP) is promulgating this direct final rule for its National Motor Vehicle Title Information System... INFORMATION CONTACT paragraph. II. Background The National Motor Vehicle Title Information System was...

Intelligent transportation system (ITS) study for the Buffalo and Niagara Falls metropolitan area, Erie and Niagara Counties, New York : final report, technical summary

DOT National Transportation Integrated Search

1997-06-18

This document provides a technical summary for the seven working papers prepared for the New York State Department of Transportation (NYSDOT) Buffalo and Niagara Falls Intelligent Transportation System (ITS) Study.

77 FR 8095 - Technical Corrections to Commission Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-14

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission 18 CFR Part 2 [Docket No. RM11-30-000; Order No. 756] Technical Corrections to Commission Regulations Issued February 8, 2012. AGENCY: Federal Energy Regulatory Commission, DOE. ACTION: Final rule: correcting amendment. SUMMARY: This document adds...

78 FR 13543 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-28

... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System 48 CFR Parts 201, 204, 215, 225, 227, 242, 245, and 252 Defense Federal Acquisition Regulation Supplement; Technical Amendments AGENCY: Defense Acquisition Regulations System, Department of Defense (DoD). ACTION: Final rule. SUMMARY: DoD is...

MOLECULAR METHODS (E.G., MICROARRAYS) APPLIED TO PLANT GENOMES FOR ASSESSING GENETIC CHANGE AND ENVIRONMENTAL STRESS

EPA Science Inventory

This is a technical document that presents a detailed sample standard operating procedure (S.O.P.) for preparing plant nucleic acid samples for microarray analyses using commercial ¿chips¿ such as those sold by Affymetrix. It also presents the application of a commercially availa...

Bringing Next-Generation Sequencing into the Classroom through a Comparison of Molecular Biology Techniques

ERIC Educational Resources Information Center

Bowling, Bethany; Zimmer, Erin; Pyatt, Robert E.

2014-01-01

Although the development of next-generation (NextGen) sequencing technologies has revolutionized genomic research and medicine, the incorporation of these topics into the classroom is challenging, given an implied high degree of technical complexity. We developed an easy-to-implement, interactive classroom activity investigating the similarities…

Calibrating genomic and allelic coverage bias in single-cell sequencing.

PubMed

Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

2015-04-16

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

Calibrating genomic and allelic coverage bias in single-cell sequencing

PubMed Central

Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

2016-01-01

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

Evolution and Diversity of Transposable Elements in Vertebrate Genomes.

PubMed

Sotero-Caio, Cibele G; Platt, Roy N; Suh, Alexander; Ray, David A

2017-01-01

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.

PubMed

Schrijver, Iris; Aziz, Nazneen; Farkas, Daniel H; Furtado, Manohar; Gonzalez, Andrea Ferreira; Greiner, Timothy C; Grody, Wayne W; Hambuch, Tina; Kalman, Lisa; Kant, Jeffrey A; Klein, Roger D; Leonard, Debra G B; Lubin, Ira M; Mao, Rong; Nagan, Narasimhan; Pratt, Victoria M; Sobel, Mark E; Voelkerding, Karl V; Gibson, Jane S

2012-11-01

This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Although this testing is a next logical step for molecular pathology laboratories, the potential impact on the diagnostic process and clinical correlations is extraordinary and clinical interpretation will be challenging. We review the rapidly evolving technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent; and address the analytic, postanalytic, and professional implications. Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLoughlin, K.

2016-01-11

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from itsmore » nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.« less

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

PubMed

Munro, Sarah A; Lund, Steven P; Pine, P Scott; Binder, Hans; Clevert, Djork-Arné; Conesa, Ana; Dopazo, Joaquin; Fasold, Mario; Hochreiter, Sepp; Hong, Huixiao; Jafari, Nadereh; Kreil, David P; Łabaj, Paweł P; Li, Sheng; Liao, Yang; Lin, Simon M; Meehan, Joseph; Mason, Christopher E; Santoyo-Lopez, Javier; Setterquist, Robert A; Shi, Leming; Shi, Wei; Smyth, Gordon K; Stralis-Pavese, Nancy; Su, Zhenqiang; Tong, Weida; Wang, Charles; Wang, Jian; Xu, Joshua; Ye, Zhan; Yang, Yong; Yu, Ying; Salit, Marc

2014-09-25

There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here we assess technical performance with a proposed standard 'dashboard' of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared among 12 laboratories with three different measurement processes demonstrates generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias are also comparable among laboratories for the same measurement process. We observe different biases for measurement processes using different mRNA-enrichment protocols.

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.

PubMed

Francis, Warren R; Wörheide, Gert

2017-06-01

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Alternatives for Jet Engine Control. Volume 1: Modelling and Control Design with Jet Engine Data

NASA Technical Reports Server (NTRS)

Sain, M. K.

1985-01-01

This document compiles a comprehensive list of publications supported by, or related to, National Aeronautics and Space Administration Grant NSG-3048, entitled "Alternatives for Jet Engine Control". Dr. Kurt Seldner was the original Technical Officer for the grant, at Lewis Research Center. Dr. Bruce Lehtinen was the final Technical Officer. At the University of Notre Dame, Drs. Michael K. Sain and R. Jeffrey Leake were the original Project Directors, with Dr. Sain becoming the final Project Director. Publications cover work over a ten-year period. The Final Report is divided into two parts. Volume i, "Modelling and Control Design with Jet Engine Data", follows in this report. Volume 2, "Modelling and Control Design with Tensors", has been bound separately.

Germs, genomics and global public health: How can advances in genomic sciences be integrated into public health in the developing world to deal with infectious diseases?

PubMed

Pang, T

2009-12-01

Scientific and technological advances derived from the genomics revolution have a central role to play in dealing with continuing infectious disease threats in the developing world caused by emerging and re-emerging pathogens. These techniques, coupled with increasing knowledge of host-pathogen interactions, can assist in the early identification and containment of outbreaks as well as in the development of preventive vaccination and therapeutic interventions, including the urgent need for new antibiotics. However, the effective application of genomics technologies faces key barriers and challenges which occur at three stages: from the research to the products, from the products to individual patients, and, finally, from patients to entire populations. There needs to be an emphasis on research in areas of greatest need, in facilitating the translation of research into interventions and, finally, the effective delivery of such interventions to those in greatest need. Ultimate success will depend on bringing together science, society and policy to develop effective public health implementation strategies to provide health security and health equity for all peoples.

48 CFR 252.235-7011 - Final scientific or technical report.

Code of Federal Regulations, 2014 CFR

2014-10-01

... technical report. 252.235-7011 Section 252.235-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT... of the report; and (c) For submission of reports in other than paper copy, contact the Defense...

48 CFR 252.235-7011 - Final scientific or technical report.

Code of Federal Regulations, 2012 CFR

2012-10-01

... technical report. 252.235-7011 Section 252.235-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT... of the report; and (c) For submission of reports in other than paper copy, contact the Defense...

48 CFR 252.235-7011 - Final scientific or technical report.

Code of Federal Regulations, 2010 CFR

2010-10-01

... technical report. 252.235-7011 Section 252.235-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT... of the report; and (c) For submission of reports in other than paper copy, contact the Defense...

48 CFR 252.235-7011 - Final scientific or technical report.

Code of Federal Regulations, 2011 CFR

2011-10-01

... technical report. 252.235-7011 Section 252.235-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT... of the report; and (c) For submission of reports in other than paper copy, contact the Defense...

48 CFR 252.235-7011 - Final scientific or technical report.

Code of Federal Regulations, 2013 CFR

2013-10-01

... technical report. 252.235-7011 Section 252.235-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT... of the report; and (c) For submission of reports in other than paper copy, contact the Defense...

Vocational Outreach Involving Community Exchange (VOICE). Final Report.

ERIC Educational Resources Information Center

Huckabee, Johnni

A Jonesboro, Arkansas project was designed and implemented to increase the awareness of vocational education, increase community support and involvement in vocational education, and establish improved communication in the vocational-technical education field. Interaction between the vocational-technical school and the local school community was a…

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.

PubMed

Quétier, Francis

2016-01-01

The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

PubMed

Droege, G; Barker, K; Seberg, O; Coddington, J; Benson, E; Berendsohn, W G; Bunk, B; Butler, C; Cawsey, E M; Deck, J; Döring, M; Flemons, P; Gemeinholzer, B; Güntsch, A; Hollowell, T; Kelbert, P; Kostadinov, I; Kottmann, R; Lawlor, R T; Lyal, C; Mackenzie-Dodds, J; Meyer, C; Mulcahy, D; Nussbeck, S Y; O'Tuama, É; Orrell, T; Petersen, G; Robertson, T; Söhngen, C; Whitacre, J; Wieczorek, J; Yilmaz, P; Zetzsche, H; Zhang, Y; Zhou, X

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard. © The Author(s) 2016. Published by Oxford University Press.

The Impact of CRISPR/Cas9 Technology on Cardiac Research: From Disease Modelling to Therapeutic Approaches

PubMed Central

Pramstaller, Peter P.; Hicks, Andrew A.; Rossini, Alessandra

2017-01-01

Genome-editing technology has emerged as a powerful method that enables the generation of genetically modified cells and organisms necessary to elucidate gene function and mechanisms of human diseases. The clustered regularly interspaced short palindromic repeats- (CRISPR-) associated 9 (Cas9) system has rapidly become one of the most popular approaches for genome editing in basic biomedical research over recent years because of its simplicity and adaptability. CRISPR/Cas9 genome editing has been used to correct DNA mutations ranging from a single base pair to large deletions in both in vitro and in vivo model systems. CRISPR/Cas9 has been used to increase the understanding of many aspects of cardiovascular disorders, including lipid metabolism, electrophysiology and genetic inheritance. The CRISPR/Cas9 technology has been proven to be effective in creating gene knockout (KO) or knockin in human cells and is particularly useful for editing induced pluripotent stem cells (iPSCs). Despite these progresses, some biological, technical, and ethical issues are limiting the therapeutic potential of genome editing in cardiovascular diseases. This review will focus on various applications of CRISPR/Cas9 genome editing in the cardiovascular field, for both disease research and the prospect of in vivo genome-editing therapies in the future. PMID:29434642

King County Metro Transit Hybrid Articulated Buses: Final Evaluation Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandler, K.; Walkowicz, K.

2006-12-01

Final technical report compares and evaluates new diesel and diesel hybrid-electric articulated buses operated as part of the King County Metro Transit (KC Metro) fleet in Seattle, Washington. The evaluation lasted 12 months.

78 FR 1143 - Explosive Siting Requirements; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-08

... launch site operators in site planning for the storage and handling of energetic liquids and explosives...: For technical questions concerning this final rule, contact Yvonne Tran, Commercial Space... this final rule, contact Laura Montgomery, AGC 200, [[Page 1144

Final June Revisions Rule State Budgets and New Unit Set-Asides TSD

EPA Pesticide Factsheets

This technical support document (TSD) for the final revisions to the Transport Rule shows the underlying data and calculations used to quantify the state budget revisions and new unit set-aside revisions.

Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health

PubMed Central

Martin, William F.

2017-01-01

Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health. PMID:28444372

Using Genome-Wide Expression Profiling to Define Gene Networks Relevant to the Study of Complex Traits: From RNA Integrity to Network Topology

PubMed Central

O'Brien, M.A.; Costin, B.N.; Miles, M.F.

2014-01-01

Postgenomic studies of the function of genes and their role in disease have now become an area of intense study since efforts to define the raw sequence material of the genome have largely been completed. The use of whole-genome approaches such as microarray expression profiling and, more recently, RNA-sequence analysis of transcript abundance has allowed an unprecedented look at the workings of the genome. However, the accurate derivation of such high-throughput data and their analysis in terms of biological function has been critical to truly leveraging the postgenomic revolution. This chapter will describe an approach that focuses on the use of gene networks to both organize and interpret genomic expression data. Such networks, derived from statistical analysis of large genomic datasets and the application of multiple bioinformatics data resources, poten-tially allow the identification of key control elements for networks associated with human disease, and thus may lead to derivation of novel therapeutic approaches. However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression data. Thus, while the catch phrase may be “it's the network … stupid,” the understanding of factors extending from RNA isolation to genomic profiling technique, multivariate statistics, and bioinformatics are all critical to defining fully useful gene networks for study of complex biology. PMID:23195313

Genetic testing and genomic analysis: a debate on ethical, social and legal issues in the Arab world with a focus on Qatar.

PubMed

El Shanti, Hatem; Chouchane, Lotfi; Badii, Ramin; Gallouzi, Imed Eddine; Gasparini, Paolo

2015-11-14

In 2013 both Saudi Arabia and Qatar launched genome projects with the aim of providing information for better diagnosis, treatment and prevention of diseases and, ultimately to realize personalized medicine by sequencing hundred thousands samples. These population based genome activities raise a series of relevant ethical, legal and social issues general, related to the specific population structure as well as to the Islamic perspective on genomic analysis and genetic testing. To contribute to the debate, the Authors after reviewing the existing literature and taking advantage of their professional experience in the field and in the geographic area, discuss and provide their opinions. In particular, the Authors focus on the impact of consanguinity on population structure and disease frequency in the Arab world, on genetic testing and genomic analysis (i.e. technical aspects, impact, etc.) and on their regulations. A comparison between the Islamic perspective and the ethical, social and legal issues raised in other population contexts is also carried. In conclusion, this opinion article with an up-to-date contribution to the discussion on the relevance and impact of genomic analysis and genetic testing in the Arab world, might help in producing specific national guidelines on genetic testing and genomic analysis and help accelerate the implementation and roll out of genome projects in Muslim countries and more specifically in Qatar, and other countries of the Gulf.

Department of Defense Access to Intellectual Property for Weapon Systems Sustainment

DTIC Science & Technology

2017-05-01

and acquiring technical data rights …  The cost benefit analysis of including a priced contract option for the future delivery of technical data...entail in terms of cost and benefits , while one of the activities to be finalized is the contract-specific technical data elements.66...Virginia 22311-1882 May 2017 Approved for public release; distribution is unlimited. IDA Paper P-8266 Log: H 17-000030 About This Publication This

10 CFR 51.92 - Supplement to the final environmental impact statement.

Code of Federal Regulations, 2011 CFR

2011-01-01

... changes in the proposed action that are relevant to environmental concerns; or (2) There are new and..., technical, and other benefits and costs of the proposed action, to the extent that the final environmental... costs; (5) Include an analysis of other energy alternatives, to the extent that the final environmental...

Dissemination of Continuing Education Materials Via Television Delivery Systems. Final Technical Report and Final Report.

ERIC Educational Resources Information Center

Munushian, Jack

In 1972, the University of Southern California School of Engineering established a 4-channel interactive instructional television network. It was designed to allow employees of participating industries to take regular university science and engineering courses and special continuing education courses at or near their work locations. Final progress…

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

PubMed

Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

2017-07-01

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

The role of non-technical skills in surgery

PubMed Central

Agha, Riaz A.; Fowler, Alexander J.; Sevdalis, Nick

2015-01-01

Non-technical skills are of increasing importance in surgery and surgical training. A traditional focus on technical skills acquisition and competence is no longer enough for the delivery of a modern, safe surgical practice. This review discusses the importance of non-technical skills and the values that underpin successful modern surgical practice. This narrative review used a number of sources including written and online, there was no specific search strategy of defined databases. Modern surgical practice requires; technical and non-technical skills, evidence-based practice, an emphasis on lifelong learning, monitoring of outcomes and a supportive institutional and health service framework. Finally these requirements need to be combined with a number of personal and professional values including integrity, professionalism and compassionate, patient-centred care. PMID:26904193

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004

PubMed Central

2013-01-01

Background Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. Methods A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. Results A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. Conclusions These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004. PMID:24050173

75 FR 16345 - Administrative Practices and Procedures; Good Guidance Practices; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-01

.... FDA-1999-N-3539] (formerly Docket No. 1999N-4783) Administrative Practices and Procedures; Good Guidance Practices; Technical Amendment AGENCY: Food and Drug Administration, HHS. ACTION: Final rule... Subjects in 21 CFR Part 10 Administrative practice and procedure, News media. 0 Therefore, under the...

Final report : for the period of December 1999 through November 30, 2000 : Florida Transit Training Program (1999/2000) : Florida Technical Assistance Program (1999/2000)

DOT National Transportation Integrated Search

2000-01-01

The following progress report is intended to highlight the significant activities of the Florida Transit Training Program and Florida Technical Assistant Program. The following progress report is intended to highlight the significant activities of th...

78 FR 34264 - Technical Corrections to the HIPAA Privacy, Security, and Enforcement Rules

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-07

...-AA03 Technical Corrections to the HIPAA Privacy, Security, and Enforcement Rules AGENCY: Office for... corrections address certain inadvertent errors and omissions in the HIPAA Privacy, Security, and Enforcement... (HHS or ``the Department'') published a final rule to implement changes to the HIPAA Privacy, Security...

76 FR 11414 - Defense Federal Acquisition Regulation Supplement; Independent Research and Development Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... Acquisition Regulation Supplement; Independent Research and Development Technical Descriptions (DFARS Case... (DFARS) to require contractors to report independent research and development (IR&D) projects generating... the address shown below on or before May 2, 2011, to be considered in the formation of the final rule...

Professional Personnel Evaluation System: 1983-84 Final Technical Report.

ERIC Educational Resources Information Center

Doss, David A.

This technical report summarizes the evaluation ratings given to professionals on probation or up for contract renewal in the Austin Independent School District. Graphs, tables, and rankings are presented for each specified population: all district teachers combined; teachers by school level (elementary, junior high, senior high); teachers by…

High School Graduation Minimum Competency Requirements. Final Technical Report.

ERIC Educational Resources Information Center

Austin Independent School District, TX. Office of Research and Evaluation.

This technical report details the testing results and analyses supporting the evaluation findings related to the Austin (Texas) Independent School District (AISD) minimum competency graduation requirements. The graduation competency status of all AISD students in grades 8 to 12 are documented. The report provides additional information on the data…

76 FR 16531 - Technical Correction for Neurological Listing Cross-Reference

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-24

... 1-800-325-0778, or visit our Internet site, Social Security Online, at http://www.socialsecurity.gov... SOCIAL SECURITY ADMINISTRATION 20 CFR Part 404 [Docket No. SSA-2011-0019] RIN 0960-AH33 Technical Correction for Neurological Listing Cross-Reference AGENCY: Social Security Administration. ACTION: Final...

Improving Vocational Education in Post-High School Institutions. Final Report.

ERIC Educational Resources Information Center

MacArthur, Earl W.

Four ongoing programs in postsecondary vocational-technical education were examined in a national institute attended by 59 representatives from 31 states. Institutions reporting programs were: (1) Los Angeles Trade and Technical College, California, (2) Washtenaw Community College, Ann Arbor, Michigan, (3) Rockingham Community College, Wentworth,…

Chicago Manufacturing Tech Prep. Fiscal Year 1991 Final Report.

ERIC Educational Resources Information Center

Chicago City Colleges, IL.

During its first year of development in 1991, the Chicago Manufacturing Technical Preparation (Tech Prep) Program established a plan for implementing an industry-driven, articulated 4-year manufacturing technology course of study that integrates applied academic courses with technical courses and meets industry hiring standards. The project…

78 FR 29239 - Final Priority; Technical Assistance To Improve State Data Capacity-National Technical Assistance...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-20

... reporting requirements. Changes: None. Focus TA on Assessment and Discipline Data Comment: Three commenters agreed with the importance of focusing on assessment and discipline data, and two commenters agreed with... decisions and actions associated with data collection and reporting. One commenter stated that assessment...

Modular Radioisotope Thermoelectric Generator (RTG) Program. Final technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-12-31

Section 2.0 of this report summarizes the MOD-RTG reference flight design, and Section 3.0 discusses the Ground Demonstration System design. Multicouple technology development is discussed in Section 4.0, and Section 5.0 lists all published technical papers prepared during the course of the contract.

Methodology in Seeking Stakeholder Perceptions of Effective Technical Oral Presentations: An Exploratory Pilot Study

ERIC Educational Resources Information Center

Bhattacharyya, Ena; Patil, Arun; Sargunan, Rajeswary Appacutty

2010-01-01

Engineering communication studies indicate the importance of oral presentations as an indispensable component of workplace oral communication activities; however, since there is limited literature regarding stakeholder perceptions of effective presentation skills and attributes in technical oral presentations or final year engineering project…

Additional Final Area Designations and Technical Amendment for the 2012 Annual Fine Particle Standard Established in 2012 - Mar 2015

EPA Pesticide Factsheets

EPA is establishing or revising initial area designations and a technical amendment to correct an inadvertent error in the initial designation for one area for the 2012 annual national ambient air quality standards for fine particle pollution.

75 FR 41404 - List of Approved Spent Fuel Storage Casks: NUHOMS®

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-16

.... The NRC is taking this action because the applicant identified that a certain Technical Specification (TS) for Boral characterization was not written precisely. Specifically, the requirements for meeting... changes to the technical specifications. The NRC also published a direct final rule on May 6, 2010 (75 FR...

Research in Automatic Russian-English Scientific and Technical Lexicography. Final Report.

ERIC Educational Resources Information Center

Wayne State Univ., Detroit, MI.

Techniques of reversing English-Russian scientific and technical dictionaries into Russian-English versions through semi-automated compilation are described. Sections on manual and automatic processing discuss pre- and post-editing, the task program, updater (correction of errors and revision by specialist in a given field), the system employed…

National Data Program for the Marine Environment Technical Development Plan. Final Report, Volume Two.

ERIC Educational Resources Information Center

System Development Corp., Santa Monica, CA.

A national data program for the marine environment is recommended. Volume 2 includes: (1) objectives, scope, and methodology; (2) summary of the technical development plan; (3) agency development plans - Great Lakes and coastal development and (4) marine data network development plans. (Author)

Course of Study Project. Final Report. Vocational-Technical Education Departmental Report, Vol. 17, No. 18.

ERIC Educational Resources Information Center

Pennsylvania State Univ., University Park. Div. of Occupational and Vocational Studies.

Designed for use by area vocational-technical schools and other vocational programs, this project developed courses of study in eight occupational areas: commercial art, appliance repair, automotive mechanics, graphic arts, building trades maintenance, building construction trades, diesel mechanics, and welding. Course-of-study development…

Seminar for Preparation of Professional Personnel for Vocational-Technical Education. Final Report.

ERIC Educational Resources Information Center

Dillon, Roy D.; Horner, James T.

Seminar participants included college administrative officers, state vocational education directors, vocational-technical teacher educators, and Office of Education staff. The purpose of the June, 1968 seminar was to consider strategies for resolving critical vocational education personnel supply and demand problems. Presentations included in the…

75 FR 33167 - Technical Amendment Language Change From “Wholly” to “Fully”

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-11

... SOCIAL SECURITY ADMINISTRATION 20 CFR Parts 404, 405, 408, 416, and 418 [Docket No. SSA-2009-0062] RIN 0960-AH16 Technical Amendment Language Change From ``Wholly'' to ``Fully'' AGENCY: Social Security... these final rules, call Brian J. Rudick, Office of Regulations, Social Security Administration, 6401...

76 FR 58144 - Defense Federal Acquisition Regulation Supplement; Presumption of Development Exclusively at...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-20

... technical data package, in cases where the Government may have funded only a small portion of the... subcontractor's asserted restrictions on technical data and computer software. DATES: Effective date: September... data and computer software. More specifically, the final rule affects these validation procedures in...

75 FR 49408 - Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments, Bridges

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-13

... Conforming Amendments, Bridges AGENCY: Coast Guard, DHS. ACTION: Final rule. SUMMARY: This rule makes non... technical corrections to Coast Guard bridge and navigable waters regulations. This rule will have no... announces or gathers public opinion or other information regarding bridge matters, nor will it change the...

Research in network management techniques for tactical data communications networks

NASA Astrophysics Data System (ADS)

Boorstyn, R.; Kershenbaum, A.; Maglaris, B.; Sarachik, P.

1982-09-01

This is the final technical report for work performed on network management techniques for tactical data networks. It includes all technical papers that have been published during the control period. Research areas include Packet Network modelling, adaptive network routing, network design algorithms, network design techniques, and local area networks.

A System for Evaluating Microcomputer Courseware for Vocational and Technical Education. Final Report.

ERIC Educational Resources Information Center

Chase, Shirley A.; And Others

A project was conducted to design a system for evaluating microcomputer courseware for vocational and technical education. Through a literature review and contacts with organizations and individuals involved in courseware evaluation and use, project staff identified and acquired for review documents pertaining to courseware evaulation, vocational…

Genomic futures of prenatal screening: ethical reflection.

PubMed

Dondorp, W J; Page-Christiaens, G C M L; de Wert, G M W R

2016-05-01

The practice of prenatal screening is undergoing important changes as a result of the introduction of genomic testing technologies at different stages of the screening trajectory. It is expected that eventually it will become possible to routinely obtain a comprehensive 'genome scan' of all fetuses. Although this will still take several years, there are clear continuities between present developments and this future scenario. As this review shows, behind the still limited scope of screening for common aneuploidies, a rapid widening of the range of conditions tested for is already taking shape at the invasive testing stage. But the continuities are not just technical; they are also ethical. If screening for Down's syndrome is a matter of providing autonomous reproductive choice, then why would providing the choice to have a full fetal genome scan be something entirely different? There is a clear need for a sustainable normative framework that will have to answer three challenges: the indeterminateness of the autonomy paradigm, the need to acknowledge the future child as an interested stakeholder, and the prospect of broad-scope genomic prenatal screening with a double purpose: autonomy and prevention. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.

PubMed

Shipman, Seth L; Nivala, Jeff; Macklis, Jeffrey D; Church, George M

2017-07-20

DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome. Here we use the CRISPR-Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of the CRISPR-Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.

Explaining human uniqueness: genome interactions with environment, behaviour and culture.

PubMed

Varki, Ajit; Geschwind, Daniel H; Eichler, Evan E

2008-10-01

What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, 'anthropogeny' (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any 'genes versus environment' dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture - perhaps relaxing allowable thresholds for large-scale genomic diversity.

Explaining human uniqueness: genome interactions with environment, behaviour and culture

PubMed Central

Varki, Ajit; Geschwind, Daniel H.; Eichler, Evan E.

2009-01-01

What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, ‘anthropogeny’ (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any ‘genes versus environment’ dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture — perhaps relaxing allowable thresholds for large-scale genomic diversity. PMID:18802414

Primer in Genetics and Genomics, Article 2-Advancing Nursing Research With Genomic Approaches.

PubMed

Lee, Hyunhwa; Gill, Jessica; Barr, Taura; Yun, Sijung; Kim, Hyungsuk

2017-03-01

Nurses investigate reasons for variable patient symptoms and responses to treatments to inform how best to improve outcomes. Genomics has the potential to guide nursing research exploring contributions to individual variability. This article is meant to serve as an introduction to the novel methods available through genomics for addressing this critical issue and includes a review of methodological considerations for selected genomic approaches. This review presents essential concepts in genetics and genomics that will allow readers to identify upcoming trends in genomics nursing research and improve research practice. It introduces general principles of genomic research and provides an overview of the research process. It also highlights selected nursing studies that serve as clinical examples of the use of genomic technologies. Finally, the authors provide suggestions about how to apply genomic technology in nursing research along with directions for future research. Using genomic approaches in nursing research can advance the understanding of the complex pathophysiology of disease susceptibility and different patient responses to interventions. Nurses should be incorporating genomics into education, clinical practice, and research as the influence of genomics in health-care research and practice continues to grow. Nurses are also well placed to translate genomic discoveries into improved methods for patient assessment and intervention.

Mapping Our Genes--The Genome Projects: How Big, How Fast?

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Office of Technology Assessment.

Scientific and technical journals in biology and medicine in recent years have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part…

A New Framework and Prototype Solution for Clinical Decision Support and Research in Genomics and Other Data-intensive Fields of Medicine

PubMed Central

Evans, James P.; Wilhelmsen, Kirk C.; Berg, Jonathan; Schmitt, Charles P.; Krishnamurthy, Ashok; Fecho, Karamarie; Ahalt, Stanley C.

2016-01-01

Introduction: In genomics and other fields, it is now possible to capture and store large amounts of data in electronic medical records (EMRs). However, it is not clear if the routine accumulation of massive amounts of (largely uninterpretable) data will yield any health benefits to patients. Nevertheless, the use of large-scale medical data is likely to grow. To meet emerging challenges and facilitate optimal use of genomic data, our institution initiated a comprehensive planning process that addresses the needs of all stakeholders (e.g., patients, families, healthcare providers, researchers, technical staff, administrators). Our experience with this process and a key genomics research project contributed to the proposed framework. Framework: We propose a two-pronged Genomic Clinical Decision Support System (CDSS) that encompasses the concept of the “Clinical Mendeliome” as a patient-centric list of genomic variants that are clinically actionable and introduces the concept of the “Archival Value Criterion” as a decision-making formalism that approximates the cost-effectiveness of capturing, storing, and curating genome-scale sequencing data. We describe a prototype Genomic CDSS that we developed as a first step toward implementation of the framework. Conclusion: The proposed framework and prototype solution are designed to address the perspectives of stakeholders, stimulate effective clinical use of genomic data, drive genomic research, and meet current and future needs. The framework also can be broadly applied to additional fields, including other ‘-omics’ fields. We advocate for the creation of a Task Force on the Clinical Mendeliome, charged with defining Clinical Mendeliomes and drafting clinical guidelines for their use. PMID:27195307

Draft Genome Sequence of an Isolate of Colletotrichum fructicola, a Causal Agent of Mango Anthracnose.

PubMed

Li, Qili; Bu, Junyan; Yu, Zhihe; Tang, Lihua; Huang, Suiping; Guo, Tangxun; Mo, Jianyou; Hsiang, Tom

2018-02-22

Here, we present a draft genome sequence of isolate 15060 of Colletotrichum fructicola , a causal agent of mango anthracnose. The final assembly consists of 1,048 scaffolds totaling 56,493,063 bp (G+C content, 53.38%) and 15,180 predicted genes. Copyright © 2018 Li et al.

Final Technical Report, Wind Generator Project (Ann Arbor)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geisler, Nathan

A Final Technical Report (57 pages) describing educational exhibits and devices focused on wind energy, and related outreach activities and programs. Project partnership includes the City of Ann Arbor, MI and the Ann Arbor Hands-on Museum, along with additional sub-recipients, and U.S. Department of Energy/Office of Energy Efficiency and Renewable Energy (EERE). Report relays key milestones and sub-tasks as well as numerous graphics and images of five (5) transportable wind energy demonstration devices and five (5) wind energy exhibits designed and constructed between 2014 and 2016 for transport and use by the Ann Arbor Hands-on Museum.

Final Technical Report- Virginia Solar Pathways Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bond, Katharine; Cosby, Sarah

This Report provides a technical review of the final results of a funding award to Virginia Electric and Power Company (Dominion Energy Virginia (DEV) or the Company) for a project under the U.S. Department of Energy’s Solar Energy Technologies Office. The three-year project was formally known as the Virginia Solar Pathways Project (VSPP or the Project). The purpose of the VSPP was to develop a collaborative utility-administered solar strategy (Solar Strategy) for DEV’s service territory in the Commonwealth that could serve as a replicable model for other states with similar policy environments.

Examining the process of de novo gene birth: an educational primer on "integration of new genes into cellular networks, and their structural maturation".

PubMed

Frietze, Seth; Leatherman, Judith

2014-03-01

New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.

Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes.

PubMed

Vad-Nielsen, Johan; Lin, Lin; Bolund, Lars; Nielsen, Anders Lade; Luo, Yonglun

2016-11-01

The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that simultaneously targeting 10 genomic loci or simultaneously inhibition of multiple endogenous genes could be achieved using the multiplexed gRNA expression array vector in human cells. The complete set of plasmids is available through the non-profit plasmid repository Addgene.

M-X Environmental Technical Report. Socioeconomic Impact Estimates for White Pine County, Nevada. Detailed Tables.

DTIC Science & Technology

1980-12-22

8217AP0A095 772 HENNINGSON DURHAM AND RICHARDSON SANTA BARBARA CA F/G 16/1 B-B ENVIRONMENTAL TECHNICAL REPORT. SOCIOECONOMIC IMPACT ESTIMA--ETC(U) DEC... Environmental Technical Reports,. 53ocioeconctnic’ Final r1eport Impact . Estimates for White Pine County, Nevada. ____________ Detailed Tables 6. PERFORMING...background information for the analysis contained in the M-X Deploment Area Selection and Land Withirawal/Acquisition Draft Environmental Impact Statement

Optical fiber sensors for materials and structures characterization

NASA Technical Reports Server (NTRS)

Lindner, D. K.; Claus, R. O.

1991-01-01

The final technical report on Optical Fiber Sensors for Materials and Structures Characterization, covering the period August 1990 through August 1991 is presented. Research programs in the following technical areas are described; sapphire optical fiber sensors; vibration analysis using two-mode elliptical core fibers and sensors; extrinsic Fabry-Perot interferometer development; and coatings for fluorescent-based sensor. Research progress in each of these areas was substantial, as evidenced by the technical publications which are included as appendices.

A joint university-government technical editing program

NASA Technical Reports Server (NTRS)

Stohrer, Freda F.; Pinelli, Thomas E.

1978-01-01

The NASA Langley Research Center (LaRC) and Old Dominion University have designed a mutually useful technical editing program. A university team made up of an English instructor and two graduate students - one from English, one from engineering - works with a senior editor from LaRC to prepare technical reports for publication. A round-robin technique gives the university team editorial commentary from both language and technical specialists; the senior editor from LaRC supervises reports through final publication. To date, the system has provided LaRC with a respectable product and university students with valuable on-the-job training.

Minimal Absent Words in Four Human Genome Assemblies

PubMed Central

Garcia, Sara P.; Pinho, Armando J.

2011-01-01

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species. PMID:22220210

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

PubMed

Grayson, Phil; Sin, Simon Y W; Sackton, Timothy B; Edwards, Scott V

2017-01-01

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

Mature Programs of Study: Examining Policy Implementation at the Local Level. Final Report

ERIC Educational Resources Information Center

Alfeld, Corinne; Bhattacharya, Sharika

2013-01-01

The 2006 Carl D. Perkins Career and Technical Education Act required that all career technical education (CTE) programs offer secondary to postsecondary programs of study (POS), which integrate rigorous academics, offer dual enrollment options, and lead to an industry-recognized degree or credential. Focused on improving students' transition to…

75 FR 37722 - OMB Approvals Under the Paperwork Reduction Act; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-30

... since its last update. B. Why is this Technical Amendment Issued as a Final Rule? The information... provisions since the last update of this table. The paperwork burden associated with these new provisions was... amendment updates the table that lists the Office of Management and Budget (OMB) control numbers issued...

United States Air Force Training Line Simulator. Final Report.

ERIC Educational Resources Information Center

Nauta, Franz; Pierce, Michael B.

This report describes the technical aspects and potential applications of a computer-based model simulating the flow of airmen through basic training and entry-level technical training. The objective of the simulation is to assess the impacts of alternative recruit classification and training policies under a wide variety of assumptions regarding…

Final recovery plan of the southwestern willow flycatcher (Empidonax traillii extimus)

Treesearch

Deborah M. Finch; Stephen I. Rothstein; Jon C. Boren; William L. Graf; Jerry L. Holechek; Barbara E. Kus; Robert M. Marshall; Molly M. Pohl; Susan J. Sferra; Mark K. Sogge; Julie C. Stromberg; Bradley A. Valentine; Mary J. Whitfield; Sartor O. Williams

2002-01-01

The Southwestern Willow Flycatcher Recovery Team is composed of a Technical Subgroup (pg. ii), six Implementation Subgroups (Appendix A), and a Tribal Working Group. The Technical Subgroup consists of 14 academic scientists, researchers, and resource managers with a wide range of expertise in avian biology and ecology, southwestern willow flycatcher ecology, cowbird...

Local/State Bilingual Project. 1981-82 Final Technical Report. Appendixes.

ERIC Educational Resources Information Center

Austin Independent School District, TX. Office of Research and Evaluation.

The 1981-82 Local/State Bilingual Program Technical Report addresses the evaluation questions of the Local/State Bilingual Program Evaluation Design. It is organized into six appendixes. Each appendix reports the information collected by a specific measure. Each appendix consists of (1) an instrument description, (2) purpose of the measure, (3)…

77 FR 26444 - Revisions to Final Response To Petition From New Jersey Regarding SO2

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-04

... modeling or other technical analyses and no new analyses were necessary to make the revisions. III. Public... this modeling approach. Therefore, no new technical analyses or any changes to the modeling are...) modeling analysis submitted with the September 2010 petition identified NAAQS violations at receptors in...

77 FR 45282 - NRC Position on the Relationship Between General Design Criteria and Technical Specification...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-31

..., are described in the final safety analysis report (FSAR). The staff safety evaluation documents the acceptability of these analyses, and it is the combination of the FSAR analyses and the staff safety evaluation... analysis, maintain their capability to perform their safety functions. Technical Specification Operability...

A Dissemination Model for New Technical Education Programs. Final Report.

ERIC Educational Resources Information Center

Hull, Daniel M.

The Technical Education Research Center-SW has conceived, tested, and refined a model for disseminating newly developed programs and materials throughout the nation. The model performed successfully in the dissemination of more than 50,000 educational units (modules) of Laser/Electro-Optics Technician (LEOT) materials during a four-year period…

75 FR 28499 - Medical Certification Requirements as Part of the Commercial Driver's License (CDL); Technical...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-21

... Driver's License (CDL); Technical, Organizational, and Conforming Amendments AGENCY: Federal Motor... ``medical examiner's license or certificate number'' to refer to the number on a medical examiner's license... examiner qualifies him or her to drive. This inconsistency has been clarified in today's final rule so that...

A Simulation of DNA Sequencing Utilizing 3M Post-It[R] Notes

ERIC Educational Resources Information Center

Christensen, Doug

2009-01-01

An inexpensive and equipment free approach to teaching the technical aspects of DNA sequencing. The activity described requires an instructor with a familiarity of DNA sequencing technology but provides a straight forward method of teaching the technical aspects of sequencing in the absence of expensive sequencing equipment. The final sequence…

Installation and Assimilation of Educational Innovations in Vocational/Technical Programs in Post-Secondary Institutions. Final Report.

ERIC Educational Resources Information Center

Appel, Victor H.; Roueche, John E.

The factors which contribute to the successful installation and assimilation of educational innovations were examined in relation to vocational/technical programs in eight post-secondary institutions. About 555 instructors, administrators, and non-teaching professional staff were surveyed regarding the level and extent of use of individualized…

Final Technical Report on the Institute for Advanced Study in Student Personnel Work.

ERIC Educational Resources Information Center

Callis, Robert

This document reports the planning, implementation, and evaluation of a 9-month institute held at the University of Missouri-Columbia to prepare participants (approximately 20) for leadership positions in student personnel work at junior colleges and technical institutes. The following aspects of the instructional program are discussed and…

Demonstration and Research Program for Teaching Young String Players. Final Report.

ERIC Educational Resources Information Center

Yarborough, William

This report explains a system for rapidly training beginning students in the technical aspects of playing a stringed instrument. The program also affords them a well-rounded, basic knowledge of music. A "numerical" method of notation and concentrated muscular exercises greatly speeded the technical learning process. The daily coordination of ear…

Troubleshooting Instruction in Vocational-Technical Education Via Dynamic Simulation. Final Report.

ERIC Educational Resources Information Center

Finch, Curtis R.

This study was designed to examine the feasibility of using simulation as a means of teaching vocational-technical students to detect and identify malfunctions in selected electrical and mechanical systems. A dynamic simulator was employed which features interchangeable panels and logic that permits the simulation of electrical or mechanical…

Special Project for Research Training in Vocational Education: Research Training Series. Final Report.

ERIC Educational Resources Information Center

Vivian, Neal E.

To upgrade research and research utilization competence of vocational educators, The Center for Vocational and Technical Education and The American Vocational Association planned four 1-week research training programs on: (1) Planning Vocational/Technical Education Programs Based on Manpower Research, (2) Patterns of Career Development as Applied…

78 FR 4030 - Designation of Low-Income Status; Acceptance of Secondary Capital Accounts by Low-Income...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-18

... writing that it wishes to accept the designation. The final rule extends an FCU's response time from 30..., nonsubstantive technical amendments to NCUA's requirements for insurance regulation to reflect current agency... requirements for insurance regulation. These technical corrections are necessary to reflect current agency...

SURVEY OF INFORMATION ON VOCATIONAL AND TECHNICAL EDUCATION IN THE STATE OF ILLINOIS. FINAL REPORT.

ERIC Educational Resources Information Center

Corplan Associates, Chicago, IL. Technology Center.

THE BASIC OBJECTIVE OF THE SURVEY WAS TO GATHER INFORMATION HELPFUL IN PLANNING AND DEVELOPING VOCATIONAL AND TECHNICAL EDUCATION PRIMARILY WITHIN THE PUBLIC SCHOOL SYSTEM. OCCUPATIONAL NEEDS WERE IDENTIFIED FROM FORECASTS OF CHANGES IN CURRENT OCCUPATIONS, AN ANALYSIS OF THE IMPLICATIONS OF SCIENTIFIC AND TECHNOLOGICAL DEVELOPMENTS, AND…

75 FR 47211 - Navigation and Navigable Waters; Technical, Organizational, and Conforming Amendments, Sector...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-05

... Puget Sound, WA AGENCY: Coast Guard, DHS. ACTION: Final rule. SUMMARY: This rule makes non-substantive... technical corrections to reflect the renaming of Sector Seattle to Sector Puget Sound as part of the Coast... organizational structure. Sector Seattle has been disestablished and Sector Puget Sound has been established in...

Statewide Curriculum Articulation Project for Vocational-Technical Education in Minnesota. Final Report.

ERIC Educational Resources Information Center

Burger, Laura J.; And Others

The goal of this project was to develop, validate, and utilize a process for vertically articulating curriculum between secondary and post secondary levels of vocational technical education throughout the state of Minnesota. Procedures involved the identification of two areas of staff responsibility: research and development, and service to local…

Delivery of Instruction via Television. Final Report.

ERIC Educational Resources Information Center

Wisconsin State Board of Vocational, Technical, and Adult Education, Madison.

During 1985, the Wisconsin Board of Vocational, Technical, and Adult Education (VTAE) expanded its delivery of instruction via television. Approximately 3,000 persons at 170 sites throughout the United States and Canada participated in the VTAE's Technical School of the Air. In addition to delivering six to eight courses per semester, the network…

O*NET Final Technical Report. Volume I [and] Volume II [and] Volume III.

ERIC Educational Resources Information Center

Peterson, Norman G.; Mumford, Michael D.; Borman, Walter C.; Jeanneret, P. Richard; Fleishman, Edwin A.; Levin, Kerry Y.

This document contains the three volumes of the technical report for development of the prototype of the Occupational Information Network (O*NET), which is intended to replace the "Dictionary of Occupational Titles.""General Introduction" (Norman G. Peterson) presents an overview of O*NET's purpose, content, and structure.…

78 FR 34920 - Technical Amendments To Reflect the Authorizing Legislation of the Institute of Museum and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-11

... NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES Institute of Museum and Library Services 45 CFR... Museum and Library Services AGENCY: Institute of Museum and Library Services (IMLS), NFAH. ACTION: Technical amendment; final rule. SUMMARY: The Institute of Museum and Library amends its grants regulations...

Final report on technical work accomplished under contract NASw-2953

NASA Technical Reports Server (NTRS)

Fredricks, R. W.

1977-01-01

A report is given on the technical work accomplished in the area of plasma physics. The subjects covered are: (1) oblique whistler instabilities, (2) current-limited electron beam injection, (3) three-dimensional ion sound turbulence, (4) theoretical aspects of sounder antenna operation and (5) whistler modes in bow shock structures.

Development of German-English Machine Translation System. Final Technical Report.

ERIC Educational Resources Information Center

Lehmann, Winfred P.; Stachowitz, Rolf A.

This report describes work on a pilot system for a fully automatic, high-quality translation of German scientific and technical text into English and gives the results of an experiment designed to show the system's capability to produce quality mechanical translation. The areas considered were: (1) grammar formalism, mainly involving the addition…

Insights From Genomics Into Spatial and Temporal Variation in Batrachochytrium dendrobatidis.

PubMed

Byrne, A Q; Voyles, J; Rios-Sotelo, G; Rosenblum, E B

2016-01-01

Advances in genetics and genomics have provided new tools for the study of emerging infectious diseases. Researchers can now move quickly from simple hypotheses to complex explanations for pathogen origin, spread, and mechanisms of virulence. Here we focus on the application of genomics to understanding the biology of the fungal pathogen Batrachochytrium dendrobatidis (Bd), a novel and deadly pathogen of amphibians. We provide a brief history of the system, then focus on key insights into Bd variation garnered from genomics approaches, and finally, highlight new frontiers for future discoveries. Genomic tools have revealed unexpected complexity and variation in the Bd system suggesting that the history and biology of emerging pathogens may not be as simple as they initially seem. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic screens and functional genomics using CRISPR/Cas9 technology.

PubMed

Hartenian, Ella; Doench, John G

2015-04-01

Functional genomics attempts to understand the genome by perturbing the flow of information from DNA to RNA to protein, in order to learn how gene dysfunction leads to disease. CRISPR/Cas9 technology is the newest tool in the geneticist's toolbox, allowing researchers to edit DNA with unprecedented ease, speed and accuracy, and representing a novel means to perform genome-wide genetic screens to discover gene function. In this review, we first summarize the discovery and characterization of CRISPR/Cas9, and then compare it to other genome engineering technologies. We discuss its initial use in screening applications, with a focus on optimizing on-target activity and minimizing off-target effects. Finally, we comment on future challenges and opportunities afforded by this technology. © 2015 FEBS.

CRISPR/Cas9 in Genome Editing and Beyond.

PubMed

Wang, Haifeng; La Russa, Marie; Qi, Lei S

2016-06-02

The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.

The Role of Constitutional Copy Number Variants in Breast Cancer

PubMed Central

Walker, Logan C.; Wiggins, George A.R.; Pearson, John F.

2015-01-01

Constitutional copy number variants (CNVs) include inherited and de novo deviations from a diploid state at a defined genomic region. These variants contribute significantly to genetic variation and disease in humans, including breast cancer susceptibility. Identification of genetic risk factors for breast cancer in recent years has been dominated by the use of genome-wide technologies, such as single nucleotide polymorphism (SNP)-arrays, with a significant focus on single nucleotide variants. To date, these large datasets have been underutilised for generating genome-wide CNV profiles despite offering a massive resource for assessing the contribution of these structural variants to breast cancer risk. Technical challenges remain in determining the location and distribution of CNVs across the human genome due to the accuracy of computational prediction algorithms and resolution of the array data. Moreover, better methods are required for interpreting the functional effect of newly discovered CNVs. In this review, we explore current and future application of SNP array technology to assess rare and common CNVs in association with breast cancer risk in humans. PMID:27600231

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

PubMed

Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

2016-09-19

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C.

PubMed

Nagano, Takashi; Wingett, Steven W; Fraser, Peter

2017-01-01

Hi-C is a powerful method to investigate genome-wide, higher-order chromatin and chromosome conformations averaged from a population of cells. To expand the potential of Hi-C for single-cell analysis, we developed single-cell Hi-C. Similar to the existing "ensemble" Hi-C method, single-cell Hi-C detects proximity-dependent ligation events between cross-linked and restriction-digested chromatin fragments in cells. A major difference between the single-cell Hi-C and ensemble Hi-C protocol is that the proximity-dependent ligation is carried out in the nucleus. This allows the isolation of individual cells in which nearly the entire Hi-C procedure has been carried out, enabling the production of a Hi-C library and data from individual cells. With this new method, we studied genome conformations and found evidence for conserved topological domain organization from cell to cell, but highly variable interdomain contacts and chromosome folding genome wide. In addition, we found that the single-cell Hi-C protocol provided cleaner results with less technical noise suggesting it could be used to improve the ensemble Hi-C technique.

Integrating Genetics and Social Science: Genetic Risk Scores

PubMed Central

Belsky, Daniel W.; Israel, Salomon

2014-01-01

The sequencing of the human genome and the advent of low-cost genome-wide assays that generate millions of observations of individual genomes in a matter of hours constitute a disruptive innovation for social science. Many public-use social science datasets have or will soon add genome-wide genetic data. With these new data come technical challenges, but also new possibilities. Among these, the lowest hanging fruit and the most potentially disruptive to existing research programs is the ability to measure previously invisible contours of health and disease risk within populations. In this article, we outline why now is the time for social scientists to bring genetics into their research programs. We discuss how to select genetic variants to study. We explain how the polygenic architecture of complex traits and the low penetrance of individual genetic loci pose challenges to research integrating genetics and social science. We introduce genetic risk scores as a method of addressing these challenges and provide guidance on how genetic risk scores can be constructed. We conclude by outlining research questions that are ripe for social science inquiry. PMID:25343363

Mapping Challenging Mutations by Whole-Genome Sequencing

PubMed Central

Smith, Harold E.; Fabritius, Amy S.; Jaramillo-Lambert, Aimee; Golden, Andy

2016-01-01

Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semidominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping in Caenorhabditis elegans as our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means. PMID:26945029

Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9.

PubMed

Ren, Xingjie; Sun, Jin; Housden, Benjamin E; Hu, Yanhui; Roesel, Charles; Lin, Shuailiang; Liu, Lu-Ping; Yang, Zhihao; Mao, Decai; Sun, Lingzhu; Wu, Qujie; Ji, Jun-Yuan; Xi, Jianzhong; Mohr, Stephanie E; Xu, Jiang; Perrimon, Norbert; Ni, Jian-Quan

2013-11-19

The ability to engineer genomes in a specific, systematic, and cost-effective way is critical for functional genomic studies. Recent advances using the CRISPR-associated single-guide RNA system (Cas9/sgRNA) illustrate the potential of this simple system for genome engineering in a number of organisms. Here we report an effective and inexpensive method for genome DNA editing in Drosophila melanogaster whereby plasmid DNAs encoding short sgRNAs under the control of the U6b promoter are injected into transgenic flies in which Cas9 is specifically expressed in the germ line via the nanos promoter. We evaluate the off-targets associated with the method and establish a Web-based resource, along with a searchable, genome-wide database of predicted sgRNAs appropriate for genome engineering in flies. Finally, we discuss the advantages of our method in comparison with other recently published approaches.

Chemical biology on the genome.

PubMed

Balasubramanian, Shankar

2014-08-15

In this article I discuss studies towards understanding the structure and function of DNA in the context of genomes from the perspective of a chemist. The first area I describe concerns the studies that led to the invention and subsequent development of a method for sequencing DNA on a genome scale at high speed and low cost, now known as Solexa/Illumina sequencing. The second theme will feature the four-stranded DNA structure known as a G-quadruplex with a focus on its fundamental properties, its presence in cellular genomic DNA and the prospects for targeting such a structure in cels with small molecules. The final topic for discussion is naturally occurring chemically modified DNA bases with an emphasis on chemistry for decoding (or sequencing) such modifications in genomic DNA. The genome is a fruitful topic to be further elucidated by the creation and application of chemical approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recovering complete and draft population genomes from metagenome datasets

DOE PAGES

Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

2016-03-08

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem ofmore » chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.« less

Genome Editing Redefines Precision Medicine in the Cardiovascular Field

PubMed Central

Lahm, Harald; Dreßen, Martina; Lange, Rüdiger; Wu, Sean M.; Krane, Markus

2018-01-01

Genome editing is a powerful tool to study the function of specific genes and proteins important for development or disease. Recent technologies, especially CRISPR/Cas9 which is characterized by convenient handling and high precision, revolutionized the field of genome editing. Such tools have enormous potential for basic science as well as for regenerative medicine. Nevertheless, there are still several hurdles that have to be overcome, but patient-tailored therapies, termed precision medicine, seem to be within reach. In this review, we focus on the achievements and limitations of genome editing in the cardiovascular field. We explore different areas of cardiac research and highlight the most important developments: (1) the potential of genome editing in human pluripotent stem cells in basic research for disease modelling, drug screening, or reprogramming approaches and (2) the potential and remaining challenges of genome editing for regenerative therapies. Finally, we discuss social and ethical implications of these new technologies. PMID:29731778

Recovering complete and draft population genomes from metagenome datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem ofmore » chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.« less

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

PubMed

Gel, Bernat; Díez-Villanueva, Anna; Serra, Eduard; Buschbeck, Marcus; Peinado, Miguel A; Malinverni, Roberto

2016-01-15

Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). rmalinverni@carrerasresearch.org. © The Author 2015. Published by Oxford University Press.

The Independent Technical Analysis Process Final Report 2006-2007.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duberstein, Corey; Ham, Kenneth; Dauble, Dennis

2007-03-01

The Bonneville Power Administration (BPA) contracted with the Pacific Northwest National Laboratory (PNNL) to provide technical analytical support for system-wide fish passage information (BPA Project No. 2006-010-00). The goal of this project was to produce rigorous technical analysis products using independent analysts and anonymous peer reviewers. This project provided an independent technical source for non-routine fish passage analyses while allowing routine support functions to be performed by other well-qualified entities. The Independent Technical Analysis Process (ITAP) was created to provide non-routine analysis for fish and wildlife agencies and tribes in particular and the public in general on matters related tomore » juvenile and adult salmon and steelhead passage through the mainstem hydrosystem. The process was designed to maintain the independence of analysts and reviewers from parties requesting analyses, to avoid potential bias in technical products. The objectives identified for this project were to administer a rigorous, transparent process to deliver unbiased technical assistance necessary to coordinate recommendations for storage reservoir and river operations that avoid potential conflicts between anadromous and resident fish. Seven work elements, designated by numbered categories in the Pisces project tracking system, were created to define and accomplish project goals as follows: (1) 118 Coordination - Coordinate technical analysis and review process: (a) Retain expertise for analyst/reviewer roles. (b) Draft research directives. (c) Send directive to the analyst. (d) Coordinate two independent reviews of the draft report. (e) Ensure reviewer comments are addressed within the final report. (2) 162 Analyze/Interpret Data - Implement the independent aspects of the project. (3) 122 Provide Technical Review - Implement the review process for the analysts. (4) 132 Produce Annual Report - FY06 annual progress report with Pisces Disseminate (5) 161 Disseminate Raw/Summary Data and Results - Post technical products on the ITAP web site. (6) 185-Produce Pisces Status Report - Provide periodic status reports to BPA. (7) 119 Manage and Administer Projects - project/contract administration.« less

The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

PubMed

Smith, Adam Alexander Thil; Belda, Eugeni; Viari, Alain; Medigue, Claudine; Vallenet, David

2012-05-01

Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes), a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short). The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

Site Operator technical report. Final report (1992--1996)

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-12-01

The Southern California Edison Company (SCE) and the US Department of Energy (DOE) entered into cooperative agreement No. DE-FC07-91ID13077 on August 23, 1991, which expired on August 3, 1996. This cooperative agreement provided SCE with DOE cofunding for participation in the DOE`s Electric and Hybrid Vehicle Site Operator Program. In return, SCE provided the DOE with quarterly progress reports which include operating and maintenance data for the electric (EVs) vehicles in SCE`s fleet. Herein is SCE`s final report for the 1992 to 1996 agreement period. As of September 1, 1996 the SCE fleet had 65 electric vehicles in service. Amore » total of 578,200 miles had been logged. During the agreement period, SCE sent the DOE a total of 19 technical reports (Appendix B). This report summarizes the technical achievements which took place during a long, productive and rewarding, relationship with the DOE.« less

7 CFR 1944.419 - Final grantee evaluation.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) PROGRAM REGULATIONS (CONTINUED) HOUSING Self-Help Technical Assistance Grants § 1944.419 Final grantee... Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS..., application, this regulation, and any amendments. (a) This is a quantitative evaluation of the grantee to...

ECLSS medical support activities

NASA Technical Reports Server (NTRS)

Crump, William J.; Kilgore, Melvin V., Jr.

1991-01-01

During the period from April 10, 1990 to April 9, 1991, the Consortium for the Space Life Sciences provided technical assistance to the NASA/MSFC water recovery efforts. This assistance was in the form of literature reviews, technical recommendations, and presentations. This final report summarizes the activities completed during this period and identifies those areas requiring additional efforts. The tasks which the University of Alabama in Huntsville (UAH) water recovery team addressed were either identified by MSFC technical representatives or chosen from those outlined in the subject statement of work.

Switching gears and changing lanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammock, Earlene C.

2002-01-01

From musing over Shakespeare's fine lines and metaphors to teaching technical writing and editing, and finally, to cranking out scientific and technical documents, writing articles, and editing publications-how'd a nice girl like me end up in a place like this? Twice, after having prepared for an academic career of teaching and research, I found myself in a technical communications position-first, at the University of Texas at El Paso College of Engineering and later, at Los Alamos National Laboratory. What happened?

Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health.

PubMed

Hazkani-Covo, Einat; Martin, William F

2017-05-01

Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

NASA/DOD Aerospace Knowledge Diffusion Research Project. Paper 32: A new era in international technical communication: American-Russian collaboration

NASA Technical Reports Server (NTRS)

Flammia, Madelyn; Barclay, Rebecca O.; Pinelli, Thomas E.; Keene, Michael L.; Burger, Robert H.; Kennedy, John M.

1993-01-01

Until the recent dissolution of the Soviet Union, the Communist Party exerted a strict control of access to and dissemination of scientific and technical information (STI). This article presents models of the Soviet-style information society and the Western-style information society and discusses the effects of centralized governmental control of information on Russian technical communication practices. The effects of political control on technical communication are then used to interpret the results of a survey of Russian and U.S. aerospace engineers and scientists concerning the time devoted to technical communication, their collaborative writing practices and their attitudes toward collaboration, the kinds of technical documents they produce and use, their views regarding the appropriate content for an undergraduate technical communication course, and their use of computer technology. Finally, the implications of these findings for future collaboration between Russian and U.S. engineers and scientists are examined.

NASA/DoD Aerospace Knowledge Diffusion Research Project. XXXII - A new era in international technical communication: American-Russian collaboration

NASA Technical Reports Server (NTRS)

Flammia, Madelyn; Barclay, Rebecca O.; Pinelli, Thomas E.; Keene, Michael L.; Burger, Robert H.; Kennedy, John M.

1993-01-01

Until the recent dissolution of the Soviet Union, the Communist Party exerted a strict control of access to and dissemination of scientific and technical information. This article presents models of the Soviet-style information society and the Western-style information society and discusses the effects of centralized governmental control of information on Russian technical communication practices. The effects of political control on technical communication are then used to interpret the results of a survey of Russian and U.S. aerospace engineers and scientists concerning the time devoted to technical communication, their collaborative writing practices and their attitudes toward collaboration, the kinds of technical documents they produce and use, their views regarding the appropriate content for an undergraduate technical communication course, and their use of computer technology. Finally, the implications of these findings for future collaboration between Russian and U.S. engineers and scientists are examined.

Genetic correction using engineered nucleases for gene therapy applications.

PubMed

Li, Hongmei Lisa; Nakano, Takao; Hotta, Akitsu

2014-01-01

Genetic mutations in humans are associated with congenital disorders and phenotypic traits. Gene therapy holds the promise to cure such genetic disorders, although it has suffered from several technical limitations for decades. Recent progress in gene editing technology using tailor-made nucleases, such as meganucleases (MNs), zinc finger nucleases (ZFNs), TAL effector nucleases (TALENs) and, more recently, CRISPR/Cas9, has significantly broadened our ability to precisely modify target sites in the human genome. In this review, we summarize recent progress in gene correction approaches of the human genome, with a particular emphasis on the clinical applications of gene therapy. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'.

PubMed

Saito, Kazuki; Hirai, Masami Y; Yonekura-Sakakibara, Keiko

2008-01-01

Following the sequencing of whole genomes of model plants, high-throughput decoding of gene function is a major challenge in modern plant biology. In view of remarkable technical advances in transcriptomics and metabolomics, integrated analysis of these 'omics' by data-mining informatics is an excellent tool for prediction and identification of gene function, particularly for genes involved in complicated metabolic pathways. The availability of Arabidopsis public transcriptome datasets containing data of >1000 microarrays reinforces the potential for prediction of gene function by transcriptome coexpression analysis. Here, we review the strategy of combining transcriptome and metabolome as a powerful technology for studying the functional genomics of model plants and also crop and medicinal plants.

Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

DOE Office of Scientific and Technical Information (OSTI.GOV)

John, Vogel P.

Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge.more » Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/) and through the Phytozome genome browser (http://phytozome.jgi.doe.gov/pz/portal.html). The collection has been heavily utilized by the research community and, as of October 23, 2015, 223 orders for 12,069 seeds packets have been filled. In addition to creating this resource, we also optimized methods for transformation and sequencing DNA flanking insertion sites.« less

The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods

PubMed Central

Dermauw, Wannes; Van Leeuwen, Thomas; Vanholme, Bartel; Tirry, Luc

2009-01-01

Background The apparent scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). This subclass encompasses over 48,000 species and forms the largest group within the Arachnida. Although mitochondrial genomes are widely utilised for phylogenetic and population genetic studies, only 20 mitochondrial genomes of Acari have been determined, of which only one belongs to the diverse order of the Sarcoptiformes. In this study, we describe the mitochondrial genome of the European house dust mite Dermatophagoides pteronyssinus, the most important member of this largely neglected group. Results The mitochondrial genome of D. pteronyssinus is a circular DNA molecule of 14,203 bp. It contains the complete set of 37 genes (13 protein coding genes, 2 rRNA genes and 22 tRNA genes), usually present in metazoan mitochondrial genomes. The mitochondrial gene order differs considerably from that of other Acari mitochondrial genomes. Compared to the mitochondrial genome of Limulus polyphemus, considered as the ancestral arthropod pattern, only 11 of the 38 gene boundaries are conserved. The majority strand has a 72.6% AT-content but a GC-skew of 0.194. This skew is the reverse of that normally observed for typical animal mitochondrial genomes. A microsatellite was detected in a large non-coding region (286 bp), which probably functions as the control region. Almost all tRNA genes lack a T-arm, provoking the formation of canonical cloverleaf tRNA-structures, and both rRNA genes are considerably reduced in size. Finally, the genomic sequence was used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analysis clustered D. pteronyssinus with Steganacarus magnus, forming a sistergroup of the Trombidiformes. Conclusion Although the mitochondrial genome of D. pteronyssinus shares different features with previously characterised Acari mitochondrial genomes, it is unique in many ways. Gene order is extremely rearranged and represents a new pattern within the Acari. Both tRNAs and rRNAs are truncated, corroborating the theory of the functional co-evolution of these molecules. Furthermore, the strong and reversed GC- and AT-skews suggest the inversion of the control region as an evolutionary event. Finally, phylogenetic analysis using concatenated mt gene sequences succeeded in recovering Acari relationships concordant with traditional views of phylogeny of Acari. PMID:19284646

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savic, Vesna; Hector, Louis G.; Ezzat, Hesham

This paper presents an overview of a four-year project focused on development of an integrated computational materials engineering (ICME) toolset for third generation advanced high-strength steels (3GAHSS). Following a brief look at ICME as an emerging discipline within the Materials Genome Initiative, technical tasks in the ICME project will be discussed. Specific aims of the individual tasks are multi-scale, microstructure-based material model development using state-of-the-art computational and experimental techniques, forming, toolset assembly, design optimization, integration and technical cost modeling. The integrated approach is initially illustrated using a 980 grade transformation induced plasticity (TRIP) steel, subject to a two-step quenching andmore » partitioning (Q&P) heat treatment, as an example.« less

Communication Platform Payload Definition (CPPD) study. Volume 2: Technical report

NASA Technical Reports Server (NTRS)

Hunter, E. M.; Driggers, T.; Jorasch, R.

1986-01-01

This is Volume 2 (Technical Report) of the Ford Aerospace & Communications Corporation Final Report for the Communication Platform Payload Definition (CPPD) Study program conducted for NASA Lewis Research Center under contract No. NAS3-24235. This report presents the results of the study effort leading to five potential platform payloads to service CONUS and WARC Region 2 traffic demand as projected to the year 2008. The report addresses establishing the data bases, developing service aggregation scenarios, selecting and developing 5 payload concepts, performing detailed definition of the 5 payloads, costing them, identifying critical technology, and finally comparing the payloads with each other and also with non-aggregated equivalent services.

Best Practices for Continuous Monitoring of Temperature and Flow in Wadeable Streams (Final Report)

EPA Science Inventory

This final report is a technical "best practices" document describing sensor deployment for and collection of continuous temperature and flow data at ungaged sites in wadeable streams. This document addresses questions related to equipment needs; configuration, placement, and ins...

Hazardous Waste Management System - Identification and Listing of Hazardous Waste - Recycled Used Oil Management Standards - Federal Register Notice, May 3, 1993

EPA Pesticide Factsheets

This action corrects several technical errors and provides clarifying amendments to the final recycled used oil management standards rule. The final rule was published on September 10, 1992 (57 FR 41566).

75 FR 6839 - Technical Service Provider Assistance

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-12

... Executive Order 12866, the Office of Management and Budget determined that this final rule is not a... or are eligible to participate in conservation programs to help them make land management decisions...: Covered Programs. The interim final rule incorporated reference to the Agricultural Management Assistance...

Charlotte Circle Outreach. Final Report.

ERIC Educational Resources Information Center

Calhoun, Mary Lynne; Rose, Terry L.; Prendergast, Donna

This final report details the activities of the Charlotte Circle Outreach, a program designed to provide technical assistance and training to early intervention programs offering services to infants and young children with substantial disabilities, ages birth through two years. This mission was accomplished through cooperative planning with…

Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments (Final Report)

EPA Science Inventory

The Ecological Risk Assessment Support Center (ERASC) announced the release of the final report, Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments. This technical paper provides defensible approximations fo...

Using Full Genomic Information to Predict Disease: Breaking Down the Barriers Between Complex and Mendelian Diseases.

PubMed

Jordan, Daniel M; Do, Ron

2018-04-11

While sequence-based genetic tests have long been available for specific loci, especially for Mendelian disease, the rapidly falling costs of genome-wide genotyping arrays, whole-exome sequencing, and whole-genome sequencing are moving us toward a future where full genomic information might inform the prognosis and treatment of a variety of diseases, including complex disease. Similarly, the availability of large populations with full genomic information has enabled new insights about the etiology and genetic architecture of complex disease. Insights from the latest generation of genomic studies suggest that our categorization of diseases as complex may conceal a wide spectrum of genetic architectures and causal mechanisms that ranges from Mendelian forms of complex disease to complex regulatory structures underlying Mendelian disease. Here, we review these insights, along with advances in the prediction of disease risk and outcomes from full genomic information. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 19 is August 31, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Functional genomics of lactic acid bacteria: from food to health

PubMed Central

2014-01-01

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health. PMID:25186768

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

PubMed

Zimin, Aleksey V; Puiu, Daniela; Hall, Richard; Kingan, Sarah; Clavijo, Bernardo J; Salzberg, Steven L

2017-11-01

Common bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall haploid size of more than 15 billion bases. Multiple past attempts to assemble the genome have produced assemblies that were well short of the estimated genome size. Here we report the first near-complete assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15 344 693 583 bases and has a weighted average (N50) contig size of 232 659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome of Aegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4 179 762 575 bp of T. aestivum that correspond to its D genome components. © The Author 2017. Published by Oxford University Press.

Functional genomics of lactic acid bacteria: from food to health.

PubMed

Douillard, François P; de Vos, Willem M

2014-08-29

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

A Program of Technical Assistance to Industry in Twenty-Six Mississippi Counties and the Choctaw Indian Reservation. Final Report.

ERIC Educational Resources Information Center

Phillips, Jane; Sewell, Charles

A broad technical assistance program has been established in 25 EDA (Economic Development Administration) contract counties and on the Choctaw Indian Reservation Nashoba County) to stimulate new job opportunities by solving operational problems which limit the expansion and diversification of existing industry; professional services in evaluating…

For Work-Force Training, a Plan to Give College Credit Where It's Due

ERIC Educational Resources Information Center

Sander, Libby

2008-01-01

After nearly three years of planning, Ohio's higher-education officials are finalizing an ambitious program to grant college credit for some technical courses offered at the state's adult-education centers. The program, called the Career-Technical Credit Transfer, is the latest in a string of state efforts to more closely link work-force training…

Improving the Dissemination of Scientific and Technical Information: A Practitioner's Guide to Innovation. (Final Report).

ERIC Educational Resources Information Center

Capital Systems Group, Inc., Rockville, MD.

The aim of this guide is to alert persons with an operational interest in scientific communication to new ideas, techniques, and equipment in the field of communication media and publications. The focus is on the dissemination of scientific information via the technical journal or its equivalent. Secondary dissemination of information such as…

Unified Technical Concepts--Phase II. Expand Application to Industrial Technologies and Adult Education. Final Report.

ERIC Educational Resources Information Center

Technical Education Research Center, Waco, TX.

A project was conducted to develop a laboratory-based instructional system in physics for two-year technician programs that emphasizes both the analogies between basic physical principles and the applications of the principles in modern technology. The Unified Technical Concepts (UTC) system that was developed is (1) a reorganization of physics…

THE DEVELOPMENT OF ACHIEVEMENT MEASURES FOR TRADE AND TECHNICAL EDUCATION. PROGRESS REPORT NUMBER THREE.

ERIC Educational Resources Information Center

BALDWIN, THOMAS S.

DURING THIS PERIOD FROM SEPTEMBER 1 THROUGH NOVEMBER 30, 1966, 35 FIELD CONSULTANTS COMPLETED ANALYSIS OF THEIR INDIVIDUAL TRADE AND TECHNICAL CURRICULUMS. THESE ANALYSES WERE DEVELOPED INTO AN OUTLINE TO SERVE AS A GUIDE FOR DEVELOPING ACHIEVEMENT TESTS. THE FINAL OUTLINE WAS DIVIDED INTO AS MANY DIFFERENT AREAS AS THE CONSULTANTS FELT NECESSARY…

Word Lists to Simplify Vocabulary of Technical Information. Final Report.

ERIC Educational Resources Information Center

Kincaid, J. Peter; And Others

This report describes eight word lists developed for use as part of the computer readability editing system (CRES), which was developed to serve as an author's aid in improving the ease of comprehending Navy technical manuals and training materials. The system has features which flag uncommon and misspelled words and long sentences, suggest simple…

77 FR 1889 - Drivers of CMVs: Restricting the Use of Cellular Phones; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-12

... DEPARTMENT OF TRANSPORTATION Federal Motor Carrier Safety Administration 49 CFR Part 391 [Docket No. FMCSA-2010-0096] RIN 2126-AB29 Drivers of CMVs: Restricting the Use of Cellular Phones; Technical... Cellular Phones final rule (76 FR 75470) had a clerical error in Sec. 391.15(f)(1) that stated ``paragraph...

27 Years of Impact: Vocational-Technical Education in Ohio. Final Annual Report under Federal Law.

ERIC Educational Resources Information Center

Ohio State Council on Vocational Education, Westerville.

The Ohio Council on Vocational Education (OCOVE) was created to strengthen the career, vocational, and technical education services provided for Ohioans as a practical, efficient, and sure way to enhance the competitiveness of individual workers and the state and national economy. Some of the accomplishments of OCOVE during its 27 years of…

Vocational-Technical Education Interface with Ohio's High Technology Business and Industrial Sector. Final Report.

ERIC Educational Resources Information Center

McCormick, Robert W.

This study explored the relationship of vocational-technical educational institutions in Ohio with business and industry using high-technology applications. The study attempted to determine what high-technology applications will be adopted by Ohio's business and industry in the next 5 years, what experience the schools have had in working with…

National Institute of Statistical Sciences Data Confidentiality Technical Panel: Final Report. NCES 2011-608

ERIC Educational Resources Information Center

Karr, Alan

2011-01-01

NCES asked the National Institute of Statistical Sciences (NISS) to convene a technical panel of survey and policy experts to examine the NCES current and planned data dissemination strategies for confidential data with respect to: mandates and directives that NCES make data available; current and prospective technologies for protecting and…

[Municipalities as a Model for New Careers and Redirection of Vocational-Technical Education Programs.] Final Report.

ERIC Educational Resources Information Center

Institute for Local Self Government, Berkeley, CA.

To meet the manpower needs of local governments, the model developed for this project redirects national and technical education toward new careers programs. Designed by task forces of professional personnel, the model utilizes existing local government resources, including funds for new career activities. Accomplishments of the project include:…

Social Science Research Institutes in the Quality American University. Final Technical Report.

ERIC Educational Resources Information Center

Totman, Theodore L.

The technical report presents a chapter outline and thesis summary of an investigation of social science research institutes in American universities. The bulk of the report presents the thesis in four sections. Section I proposes a typology of organized social research units (OSRUs) in the 11 universities studied. Dimensions used to classify the…

Expanding Horizons: A Program for Students Entering Nontraditional Technical Occupations. PY95 Final Detailed Report.

ERIC Educational Resources Information Center

Austin Community Coll., TX.

The Expanding Horizons Project at Austin Community College successfully achieved its goals for Project Year 1994-95. During the year, the project accomplished the following: raised public awareness of the need to overcome gender bias, promoted career opportunities in nontraditional technical occupations to more than 1,200 prospective students,…

Technical Assistance and Training from the Document Design Project. Final Report.

ERIC Educational Resources Information Center

American Institutes for Research, Washington, DC.

Contained in this report is a description of the technical assistance and training phase of the Document Design Project, a program funded by the National Institute of Education and intended to address and correct the readability problems posed by public documents. The first section of the report provides background material on the assistance and…

Determining and Validating Barriers to Post-Secondary Vocational, Technical and Adult Education Programs in Wisconsin. Final Report.

ERIC Educational Resources Information Center

Farning, Max; Borden, Sally

A consortium of five Wisconsin Vocational, Technical, and Adult Education (VTAE) Districts (Gateway, Indianhead, Mid-State, Milwaukee, and Southwest) were utilized to identify, verify, and alleviate barriers to enrollment. A VTAE survey in 1976 identified six major reasons for individuals' failing to attend school after indicating an interest in…

Sociometric Clique Identification. Final Report.

ERIC Educational Resources Information Center

Kadushin, Charles

This report consists of four parts. The first part is a non-technical summary of the basic problem and an attempted solution. The second part is a technical review of the literature and a description of the basic algorithm used in the solution. The third part describes the use of the Sociogram System. The fourth part describes the use of CHAIN, a…

An Assessment of Workplace Skills Acquired by Students of Vocational and Technical Education Institutions

ERIC Educational Resources Information Center

Bakar, Ab Rahim; Mohamed, Shamsiah; Hamzah, Ramlah

2013-01-01

This study was performed to identify the employability skills of technical students from the Industrial Training Institutes (ITI) and Indigenous People's Trust Council (MARA) Skills Training Institutes (IKM) in Malaysia. The study sample consisted of 850 final year trainees of IKM and ITI. The sample was chosen by a random sampling procedure from…

Wisconsin Technical College System Board Equity Staff Development Workshops and Services--Phase IV. Final Report.

ERIC Educational Resources Information Center

Baldus, Lorayne

A staff development program on gender equity was conducted for personnel in Wisconsin's technical colleges using the train-the-trainer method. The training took two approaches: a class for college personnel and career challenge training for project directors of single parent and displaced homemaker grants. The inservice class resulted in increased…

A Technical, User and Cost Comparison Study of Microfiche Duplicate Film Material. Final Report.

ERIC Educational Resources Information Center

Prevel, James J.

A technical, user and cost comparison study was undertaken to provide the Educational Resources Information Clearinghouse (ERIC) staff with data on silver halide, diazo, and vesicular type films for microfiche duplication. This information will allow ERIC to determine if diazo and/or vesicular films should be considered in producing ERIC duplicate…

Project 1: Microbial Genomes: A Genomic Approach to Understanding the Evolution of Virulence. Project 2: From Genomes to Life: Drosophilia Development in Space and Time

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robert DeSalle

2004-09-10

This project seeks to use the genomes of two close relatives, A. actinomycetemcomitans and H. aphrophilus, to understand the evolutionary changes that take place in a genome to make it more or less virulent. Our primary specific aim of this project was to sequence, annotate, and analyze the genomes of Actinobacillus actinomycetemcomitans (CU1000, serotype f) and Haemophilus aphrophilus. With these genome sequences we have then compared the whole genome sequences to each other and to the current Aa (HK1651 www.genome.ou.edu) genome project sequence along with other fully sequenced Pasteurellaceae to determine inter and intra species differences that may account formore » the differences and similarities in disease. We also propose to create and curate a comprehensive database where sequence information and analysis for the Pasteurellaceae (family that includes the genera Actinobacillus and Haemophilus) are readily accessible. And finally we have proposed to develop phylogenetic techniques that can be used to efficiently and accurately examine the evolution of genomes. Below we report on progress we have made on these major specific aims. Progress on the specific aims is reported below under two major headings--experimental approaches and bioinformatics and systematic biology approaches.« less

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magnuson, Timothy S.

2013-09-10

The biochemistry of bacterial proteins involved in redox transformations of metals and minerals is, without dispute, an important area of research. Nevertheless, most studies on bacterial metal transformation have focused not on biochemistry but on genetics and genomics. The objective of this research is to better understand the role of conformation change in electron transfer from cytochromes to minerals, a process that underpins respiratory metal reduction by bacteria in nature and in bioremediation strategies, including reductive immobilization of radioactive contaminants. Our DOE-funded work is specifically focused on answering long-standing questions about the biochemical behavior of these very interesting proteins, andmore » our findings thus far have already made impacts in the fields of environmental microbiology and biogeochemistry. Among the key findings from the project are 1) Successful large-scale production of biomass for protein isolation; 2) Purification of several c-type cytochromes for biochemical study; 3) Characterization of these proteins using spectrophotometric and electrochemical techniques; 4) Examination of protein conformational change and redox activity towards metal oxides using a small mass cytochrome c from Acidiphilium cryptum; 5) Proteomic characterization of A. cryptum biofilms; 6) Training of 2 undergraduate research assistants; 7) Publications and several meeting presentations.« less

Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes

PubMed Central

Greenough, Lucia; Schermerhorn, Kelly M.; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Slatko, Barton E.; Gardner, Andrew F.

2016-01-01

Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner. PMID:26365239

Metaproteomics of complex microbial communities in biogas plants

PubMed Central

Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

2015-01-01

Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID:25874383

Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

PubMed

Wang, Daxi; Korhonen, Pasi K; Gasser, Robin B; Young, Neil D

Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. Copyright © 2018 Elsevier Inc. All rights reserved.

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

PubMed

Li, Gang; Hillier, LaDeana W; Grahn, Robert A; Zimin, Aleksey V; David, Victor A; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O'Brien, Stephen J; Minx, Pat; Wilson, Richard K; Lyons, Leslie A; Warren, Wesley C; Murphy, William J

2016-06-01

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location. Copyright © 2016 Li et al.

Marine Protists Are Not Just Big Bacteria.

PubMed

Keeling, Patrick J; Campo, Javier Del

2017-06-05

The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

Homoeologous chromosome pairing between the A and B genomes of Musa spp. revealed by genomic in situ hybridization

PubMed Central

Jeridi, Mouna; Bakry, Frédéric; Escoute, Jacques; Fondi, Emmanuel; Carreel, Françoise; Ferchichi, Ali; D'Hont, Angélique; Rodier-Goud, Marguerite

2011-01-01

Background and Aims Most cooking banana and several desert bananas are interspecific triploid hybrids between Musa acuminata (A genome) and Musa balbisiana (B genome). In addition, M. balbisiana has agronomical characteristics such as resistance to biotic and abiotic stresses that could be useful to improve monospecific acuminata cultivars. To develop efficient breeding strategies for improving Musa cultivars, it is therefore important to understand the possibility of chromosome exchange between these two species. Methods A protocol was developed to prepare chromosome at meiosis metaphase I suitable for genomic in situ hybridization. A series of technical challenges were encountered, the main ones being the hardness of the cell wall and the density of the microsporocyte's cytoplasm, which hampers accessibility of the probes to the chromosomes. Key parameters in solving these problems were addition of macerozyme in the enzyme mix, the duration of digestion and temperature during the spreading phase. Results and Conclusions This method was applied to analyse chromosome pairing in metaphase from triploid interspecific cultivars, and it was clearly demonstrated that interspecific recombinations between M. acuminata and M. balbisiana chromosomes do occur and may be frequent in triploid hybrids. These results provide new insight into Musa cultivar evolution and have important implications for breeding. PMID:21835815

Universal and idiosyncratic characteristic lengths in bacterial genomes

NASA Astrophysics Data System (ADS)

Junier, Ivan; Frémont, Paul; Rivoire, Olivier

2018-05-01

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10–20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.

Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees.

PubMed

Trapp, Judith; McAfee, Alison; Foster, Leonard J

2017-02-01

Globally, there are over 20 000 bee species (Hymenoptera: Apoidea: Anthophila) with a host of biologically fascinating characteristics. Although they have long been studied as models for social evolution, recent challenges to bee health (mainly diseases and pesticides) have gathered the attention of both public and research communities. Genome sequences of twelve bee species are now complete or under progress, facilitating the application of additional 'omic technologies. Here, we review recent developments in honey bee and native bee research in the genomic era. We discuss the progress in genome sequencing and functional annotation, followed by the enabled comparative genomics, proteomics and transcriptomics applications regarding social evolution and health. Finally, we end with comments on future challenges in the postgenomic era. © 2016 John Wiley & Sons Ltd.

De novo genome assembly of the red silk cotton tree (Bombax ceiba).

PubMed

Gao, Yong; Wang, Haibo; Liu, Chao; Chu, Honglong; Dai, Dongqin; Song, Shengnan; Yu, Long; Han, Lihong; Fu, Yi; Tian, Bin; Tang, Lizhou

2018-05-01

Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia as well as northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. We assembled a relatively intact genome of B. ceiba by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively. The high-quality draft genome assembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this tree species.

Contribution of radiation hybrids to genome mapping in domestic animals.

PubMed

Faraut, T; de Givry, S; Hitte, C; Lahbib-Mansais, Y; Morisson, M; Milan, D; Schiex, T; Servin, B; Vignal, A; Galibert, F; Yerle, M

2009-01-01

Radiation hybrid mapping has emerged in the end of the 1990 s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative mapping approaches, between 'gene-rich' and 'gene-poor' maps. Since its early development in human, radiation hybrid mapping played a pivotal role in the process of mapping animal genomes, especially mammalian ones. We review here all the different steps involved in radiation hybrid mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described. (c) 2009 S. Karger AG, Basel.

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback

PubMed Central

Sánchez-Rangel, Diana; Hernández-Domínguez, Eric; Pérez-Torres, Claudia-Anahí; Ortiz-Castro, Randy; Villafán, Emanuel; Alonso-Sánchez, Alexandro; Rodríguez-Haas, Benjamín; López-Buenfil, Abel; García-Avila, Clemente; Ramírez-Pool, José-Abrahán

2017-01-01

ABSTRACT Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes. PMID:28860245

Toolboxes for cyanobacteria: Recent advances and future direction.

PubMed

Sun, Tao; Li, Shubin; Song, Xinyu; Diao, Jinjin; Chen, Lei; Zhang, Weiwen

2018-05-03

Photosynthetic cyanobacteria are important primary producers and model organisms for studying photosynthesis and elements cycling on earth. Due to the ability to absorb sunlight and utilize carbon dioxide, cyanobacteria have also been proposed as renewable chassis for carbon-neutral "microbial cell factories". Recent progresses on cyanobacterial synthetic biology have led to the successful production of more than two dozen of fuels and fine chemicals directly from CO 2 , demonstrating their potential for scale-up application in the future. However, compared with popular heterotrophic chassis like Escherichia coli and Saccharomyces cerevisiae, where abundant genetic tools are available for manipulations at levels from single gene, pathway to whole genome, limited genetic tools are accessible to cyanobacteria. Consequently, this significant technical hurdle restricts both the basic biological researches and further development and application of these renewable systems. Though still lagging the heterotrophic chassis, the vital roles of genetic tools in tuning of gene expression, carbon flux re-direction as well as genome-wide manipulations have been increasingly recognized in cyanobacteria. In recent years, significant progresses on developing and introducing new and efficient genetic tools have been made for cyanobacteria, including promoters, riboswitches, ribosome binding site engineering, clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease (CRISPR/Cas) systems, small RNA regulatory tools and genome-scale modeling strategies. In this review, we critically summarize recent advances on development and applications as well as technical limitations and future directions of the genetic tools in cyanobacteria. In addition, toolboxes feasible for using in large-scale cultivation are also briefly discussed. Copyright © 2018 Elsevier Inc. All rights reserved.

Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test.

PubMed

Shum, Bennett O V; Henner, Ilya; Belluoccio, Daniele; Hinchcliffe, Marcus J

2017-07-01

The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations. Methods-focused validations do not use disease-specific controls but use benchmark reference DNA that contains known variants (benign, variants of unknown significance, and pathogenic) to assess variant calling accuracy of a next-generation sequencing workflow. Recently, four whole-genome reference materials (RMs) from the National Institute of Standards and Technology (NIST) were released to standardize methods-based validations of next-generation sequencing panels across laboratories. We provide a practical method for using NIST RMs to validate multigene panels. We analyzed the utility of RMs in validating a novel newborn screening test that targets 70 genes, called NEO1. Despite the NIST RM variant truth set originating from multiple sequencing platforms, replicates, and library types, we discovered a 5.2% false-negative variant detection rate in the RM truth set genes that were assessed in our validation. We developed a strategy using complementary non-RM controls to demonstrate 99.6% sensitivity of the NEO1 test in detecting variants. Our findings have implications for laboratories or proficiency testing organizations using whole-genome NIST RMs for testing. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Draft genome sequence of Halomonas lutea strain YIM 91125 T (DSM 23508 T) isolated from the alkaline Lake Ebinur in Northwest China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125 T was isolated from a hypersaline lake in China. The genome of strain YIM 91125 T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125 T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIMmore » 91125 T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.« less

Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets.

PubMed

Ali, Amjad; Naz, Anam; Soares, Siomar C; Bakhtiar, Marriam; Tiwari, Sandeep; Hassan, Syed S; Hanan, Fazal; Ramos, Rommel; Pereira, Ulisses; Barh, Debmalya; Figueiredo, Henrique César Pereira; Ussery, David W; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

2015-01-01

Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.

Draft genome sequence of Halomonas lutea strain YIM 91125 T (DSM 23508 T) isolated from the alkaline Lake Ebinur in Northwest China

DOE PAGES

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; ...

2015-01-20

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125 T was isolated from a hypersaline lake in China. The genome of strain YIM 91125 T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125 T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIMmore » 91125 T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.« less

Genomics-assisted breeding in fruit trees.

PubMed

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Genomics-assisted breeding in fruit trees

PubMed Central

Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

Chemical Frustration. A Design Principle for the Discovery of New Complex Alloy and Intermetallic Phases, Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, Daniel C

2015-06-23

Final technical report for "Chemical Frustration: A Design Principle for the Discovery of New Complex Alloy and Intermetallic Phases" funded by the Office of Science through the Materials Chemistry Program of the Office of Basic Energy Sciences.

Technical support for geopressured-geothermal activities in Louisiana. Final geological report, 1 November 1981-31 October 1982

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilger, R.H.

1984-06-25

This report contains the component Site-Specific Studies-Geophysics, Diagenesis, Geochemistry. Work for Site-Specific Studies is finished, and the results presented in this report are final. Individual studies have been entered separately into the data base. (ACR)

78 FR 54566 - Energy Labeling Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-05

... FEDERAL TRADE COMMISSION 16 CFR Part 305 RIN 3084-AB03 Energy Labeling Rule AGENCY: Federal Trade Commission. ACTION: Final rule; correction. SUMMARY: The Federal Trade Commission published a final rule on July 23, 2013 revising its Energy Labeling Rule. This document makes a technical correction to the...

Wyoming Deaf/Blind Grant. Final Report.

ERIC Educational Resources Information Center

Whitson, Joanne B.

This final report describes activities and accomplishments of the Wyoming Deaf-Blind Grant, a 3-year federally supported project to identify children who have deaf-blindness and to provide technical assistance in the development of educational services for these children. Major accomplishments of the project included: identification of more…

A new whole mitochondrial genome qPCR (WMG-qPCR) with SYBR Green® to identify phlebotomine sand fly blood meals.

PubMed

Rodrigues, Ana Caroline Moura; Magalhães, Rafaela Damasceno; Romcy, Kalil Andrade Mubarac; Freitas, Jeferson Lucas Sousa; Melo, Ana Carolina Fonseca Lindoso; Rodon, Fernanda Cristina Macedo; Bevilaqua, Claudia Maria Leal; Melo, Luciana Magalhães

2017-04-30

Phlebotomine sand flies are blood-feeding insects of marked medical and veterinary significance. Investigations on the biology of these insects hold great importance for both ecological and epidemiological purposes. The present work describes a new approach for real-time PCR (qPCR) with SYBR Green ® , named WMG-qPCR, to identify phlebotomine blood meals. The novelty of the assay was to design primers based on the Whole Mitochondrial Genome (WMG) of the potential hosts (human, dog, cat, brown rat and chicken) aiming to amplify through qPCR the regions of mitochondrial DNA (mtDNA) which are less conserved among all species. Initially, the best method for mtDNA extraction to be applied in WMG-qPCR was determined. Afterwards, amplification specificities were accessed by cross-reaction assays with mtDNA samples from all animal species, besides phlebotomine DNA. Finally, the selected primers were also tested for their limit of DNA detection through standard curves constructed by serial dilution of blood DNA obtained for each target animal species. The WMG-qPCR was able to detect as low as 10pL of blood, equivalent to 26, 84, 130, and 320fg DNA of cat, human, dog and rat, respectively. The assay was also capable to amplify as low as 5pL of chicken blood (5pg DNA). In conclusion, WMG-qPCR seems to be a promising tool to identify phlebotomine blood meals, with high species-specificity and sensitivity. Furthermore, as no supplementary techniques are required, this new approach presents minimized costs and simplified technical-training requirements for execution. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional Analysis of the Aspergillus nidulans Kinome

PubMed Central

De Souza, Colin P.; Hashmi, Shahr B.; Osmani, Aysha H.; Andrews, Peter; Ringelberg, Carol S.; Dunlap, Jay C.; Osmani, Stephen A.

2013-01-01

The filamentous fungi are an ecologically important group of organisms which also have important industrial applications but devastating effects as pathogens and agents of food spoilage. Protein kinases have been implicated in the regulation of virtually all biological processes but how they regulate filamentous fungal specific processes is not understood. The filamentous fungus Aspergillus nidulans has long been utilized as a powerful molecular genetic system and recent technical advances have made systematic approaches to study large gene sets possible. To enhance A. nidulans functional genomics we have created gene deletion constructs for 9851 genes representing 93.3% of the encoding genome. To illustrate the utility of these constructs, and advance the understanding of fungal kinases, we have systematically generated deletion strains for 128 A. nidulans kinases including expanded groups of 15 histidine kinases, 7 SRPK (serine-arginine protein kinases) kinases and an interesting group of 11 filamentous fungal specific kinases. We defined the terminal phenotype of 23 of the 25 essential kinases by heterokaryon rescue and identified phenotypes for 43 of the 103 non-essential kinases. Uncovered phenotypes ranged from almost no growth for a small number of essential kinases implicated in processes such as ribosomal biosynthesis, to conditional defects in response to cellular stresses. The data provide experimental evidence that previously uncharacterized kinases function in the septation initiation network, the cell wall integrity and the morphogenesis Orb6 kinase signaling pathways, as well as in pathways regulating vesicular trafficking, sexual development and secondary metabolism. Finally, we identify ChkC as a third effector kinase functioning in the cellular response to genotoxic stress. The identification of many previously unknown functions for kinases through the functional analysis of the A. nidulans kinome illustrates the utility of the A. nidulans gene deletion constructs. PMID:23505451

Surviving an Identity Crisis: A Revised View of Chromatin Insulators in the Genomics Era

PubMed Central

Matzat, Leah H.; Lei, Elissa P.

2013-01-01

The control of complex, developmentally regulated loci and partitioning of the genome into active and silent domains is in part accomplished through the activity of DNA-protein complexes termed chromatin insulators. Together, the multiple, well-studied classes of insulators in Drosophila melanogaster appear to be generally functionally conserved. In this review, we discuss recent genomic-scale experiments and attempt to reconcile these newer findings in the context of previously defined insulator characteristics based on classical genetic analyses and transgenic approaches. Finally, we discuss the emerging understanding of mechanisms of chromatin insulator regulation. PMID:24189492

The Human Genome Project: Information access, management, and regulation. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

McInerney, J.D.; Micikas, L.B.

The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

Translational Genomics in Low and Middle Income Countries: Opportunities and Challenges

PubMed Central

Tekola-Ayele, Fasil; Rotimi, Charles N.

2015-01-01

Translation of genomic discoveries into patient care is slowly becoming a reality in developed economies around the world. In contrast, low and middle income countries (LMIC) have participated minimally in genomic research for several reasons including lack of coherent national policies, limited number of well-trained genomic scientists, poor research infrastructure, and local economic and cultural challenges. Recent initiatives such as the Human Heredity and Health in Africa (H3Africa), the Qatar Genome Project and the Mexico National Institute of Genomic Medicine (INMEGEN) that aim to address these problems through capacity building and empowerment of local researchers have sparked a paradigm shift. In this short communication, we describe experiences of small-scale medical genetics and translational genomics research programs in LMIC. The lessons drawn from these programs drive home the importance of addressing resource, policy, and socio-cultural dynamics to realize the promise of precision medicine driven by genomic science globally. By echoing lessons from a bench-to-community translational genomics research, we advocate that large-scale genomics research projects can be successfully linked with health care programs. To harness the benefits of genomics-led health care, LMIC governments should begin to develop national genomics policies that will address human and technology capacity development within the context of their national economic and socio-cultural uniqueness. These policies should encourage international collaboration and promote link between the public health program and genomics researchers. Finally, we highlight the potential catalytic roles of the global community to foster translational genomics in LMIC. PMID:26138992

The Genetics Revolution: Programs and Issues for the Community College. A Monograph Highlighting the Winners of the Exxon Education Foundation Innovation Awards.

ERIC Educational Resources Information Center

Mays, Marilyn Elaine, Ed.

Presented at a 1996 conference on the implications of the Human Genome Project for community and technical colleges, the 30 papers included in this monograph describe methods for incorporating genetics studies into the two-year college curriculum. Among the papers provided are: (1) "Facing the Unknown: The Ethical Challenges of…

Age and Diet: Major interacting factors that drive sporadic intestinal cancer | Division of Cancer Prevention

Cancer.gov

Age and diet are the two most clearly recognized risk factors for common sporadic colon cancer, responsible for >90% of cases in developed countries. We will make use of an important technical advance for whole genome sequencing of single cells recently reported by co-investigator Vijg that can uniquely detect rare mutational events to define the mutational load and spectrum

Control technology appendices for pollution control technical manuals. Final report, June 1982-February 1983

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1983-04-01

The document is one of six technical handbooks prepared by EPA to help government officials granting permits to build synfuels facilities, synfuels process developers, and other interested parties. They provide technical data on waste streams from synfuels facilities and technologies capable of controlling them. Process technologies covered in the manuals include coal gasification, coal liquefaction by direct and idirect processing, and the extraction of oil from shale. The manuals offer no regulatory guidance, allowing the industry flexibility in deciding how best to comply with environmental regulations.

NATO Scientific and Technical Information Service (NSTIS): functional description. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molholm, K.N.; Blados, W.N.; Bulca, C.

1987-08-01

This report provides a functional description of the requirements for a NATO Scientific and Technical Information Service (NSTIS). The user requirements and much of the background information in this report were derived primarily from interviews with more than 60 NATO Headquarters staff members between 2 March and 25 March 1987. In addition, representatives of the Supreme Headquarters Applied Powers Europe (SHAPE) Technical Centre (STC), the Supreme Allied Commander Atlantic (Anti-Submarine Warfare Research) Centre (SACLANTCEN), the NATO Communications and Information Systems Agency (NACISA), The Advisory Group for Aerospace Research and Development (AGARD), the U.S. Defense Technical Information Center (DTIC), and themore » Technical Documentation Center for the Armed Forces in the Netherlands (TDCK), were interviewed, either in person or by telephone.« less