EPA RE-Powering Mapper Region 2

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 6

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 8

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 7

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 5

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 3

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Solar on Landfills

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 9

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Utility Scale

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Screening Shapefile

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Center for Program Analysis (CPA) initiated the RE-Powering America??s Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

EPA RE-Powering Mapper Region 1

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Office of Land and Emergency Management (OLEM) Office of Communications, Partnerships and Analysis (OCPA) initiated the RE-Powering America's Land Initiative to demonstrate the enormous potential that contaminated lands, landfills, and mine sites provide for developing renewable energy in the United States. EPA developed national level site screening criteria in partnership with the U.S. Department of Energy (DOE) National Renewable Energy Laboratory (NREL) for wind, solar, biomass, and geothermal facilities. While the screening criteria demonstrate the potential to reuse contaminated land for renewable energy facilities, the criteria and data are neither designed to identify the best sites for developing renewable energy nor all-inclusive. Therefore, more detailed, site-specific analysis is necessary to identify or prioritize the best sites for developing renewable energy facilities based on the technical and economic potential. Please note that these sites were only pre-screened for renewable energy potential. The sites were not evaluated for land use constraints or current on the ground conditions. Additional research and site-specific analysis are needed to verify viability for renewable energy potential at a given site.

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

Unterberger, Claudia; Hanson, Steven; Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN

Little is known about determinants regulating expression of Mannan-binding lectin associated serine protease-2 (MASP-2), the effector component of the lectin pathway of complement activation. Comparative bioinformatic analysis of the MASP2 promoter regions in human, mouse, and rat, revealed conservation of two putative Stat binding sites, termed StatA and StatB. Site directed mutagenesis specific for these sites was performed. Transcription activity was decreased 5-fold when StatB site was mutated in the wildtype reporter gene construct. Gel retardation and competition assays demonstrated that proteins contained in the nuclear extract prepared from HepG2 specifically bound double-stranded StatB oligonucleotides. Supershift analysis revealed Stat3 tomore » be the major specific binding protein. We conclude that Stat3 binding is important for MASP2 promoter activity.« less

Exercise and Bone Density: Meta-Analysis

DTIC Science & Technology

2007-01-01

Statistically significant site-specific changes were also observed at the femur, lumbar , and os calcis sites. The results of this study suggest that site...specific exercise may help improve and maintain BMD at the femur, lumbar , and os calcis sites in older men. However, the biological importance of...examined the effects of progressive resistance training on BMD at the femur, lumbar spine, and radius in pre- and postmenopausal women.6 Twenty-nine

High-Affinity Quasi-Specific Sites in the Genome: How the DNA-Binding Proteins Cope with Them

PubMed Central

Chakrabarti, J.; Chandra, Navin; Raha, Paromita; Roy, Siddhartha

2011-01-01

Many prokaryotic transcription factors home in on one or a few target sites in the presence of a huge number of nonspecific sites. Our analysis of λ-repressor in the Escherichia coli genome based on single basepair substitution experiments shows the presence of hundreds of sites having binding energy within 3 Kcal/mole of the OR1 binding energy, and thousands of sites with binding energy above the nonspecific binding energy. The effect of such sites on DNA-based processes has not been fully explored. The presence of such sites dramatically lowers the occupation probability of the specific site far more than if the genome were composed of nonspecific sites only. Our Brownian dynamics studies show that the presence of quasi-specific sites results in very significant kinetic effects as well. In contrast to λ-repressor, the E. coli genome has orders of magnitude lower quasi-specific sites for GalR, an integral transcription factor, thus causing little competition for the specific site. We propose that GalR and perhaps repressors of the same family have evolved binding modes that lead to much smaller numbers of quasi-specific sites to remove the untoward effects of genomic DNA. PMID:21889449

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

PubMed

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

PubMed Central

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2016-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent. PMID:26779141

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

PubMed

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2015-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

Evaluation of site-specific tactics using bifenazate and Neoseiulus californicus for management of Tetranychus urticae (Acari: Tetranychidae) in strawberries.

PubMed

Liu, Ruohan; Nyoike, Teresia W; Liburd, Oscar E

2016-10-01

Greenhouse and field experiments were conducted to evaluate the effectiveness of site-specific tactics for management of the twospotted spider mite, Tetranychus urticae Koch, a major pest of greenhouse and field-grown strawberries (Fragaria x ananassa Duchesne). Two site-specific (spot) treatments, the miticide bifenazate (Acramite(®)) and the predatory mite Neoseiulus californicus McGregor, were compared with whole-plot treatments of bifenazate or N. californicus to determine whether T. urticae could be effectively managed in field-grown strawberry using only site-specific tactics. Additionally, the cost of site-specific tactics was compared with whole-plot treatments to determine the economic value of using site-specific management tactics for T. urticae in strawberries. In the greenhouse, all treatments equivalently reduced the number of T. urticae below control. In the field during the 2011-2012 season, more T. urticae eggs and motiles were in the whole-plot treatments of both N. californicus and bifenazate in the mid-season and late season, respectively, compared with the spot treatments. With the exception of site-specific N. californicus during the 2011-2012 field season, there were no differences in marketable yields between plots with site-specific treatments and whole-plot management. An economic analysis demonstrated a significant cost savings (75.3 %) with site-specific treatments of N. californicus compared with whole-plot application of N. californicus. Similarly, a 24.7 % reduction in cost was achieved in using site-specific bifenazate compared with whole-plot application of bifenazate. The findings indicate that site-specific treatments with N. californicus and bifenazate are competitive alternatives to whole-field application for T. urticae management in strawberries.

GREAT I Study of the Upper Mississippi River. Technical Appendixes. Volume 2. Floodplain Management, Dredged Material Uses, Dredging Requirements.

DTIC Science & Technology

1980-09-01

placement of dredged material is proposed, a quantitative analysis of the effects on the 1-percent chance flood be made. The analysis must include a...FPMWG will accept the site. b. Until a quantitative analysis is conducted, place- ment sites be selected following these guidelines. (1) Dredge4 material... Analysis of site-specific encroachments would continue to be made without considering the opposite bank impacts or the long-term cumulative effects. 5

Poster - Thur Eve - 54: A software solution for ongoing DVH quality assurance in radiation therapy.

PubMed

Annis, S-L; Zeng, G; Wu, X; Macpherson, M

2012-07-01

A program has been developed in MATLAB for use in quality assurance of treatment planning of radiation therapy. It analyzes patient DVH files and compiles dose volume data for review, trending, comparison and analysis. Patient DVH files are exported from the Eclipse treatment planning system and saved according to treatment sites and date. Currently analysis is available for 4 treatment sites; Prostate, Prostate Bed, Lung, and Upper GI, with two functions for data report and analysis: patient-specific and organ-specific. The patient-specific function loads one patient DVH file and reports the user-specified dose volume data of organs and targets. These data can be compiled to an external file for a third party analysis. The organ-specific function extracts a requested dose volume of an organ from the DVH files of a patient group and reports the statistics over this population. A graphical user interface is utilized to select clinical sites, function and structures, and input user's requests. We have implemented this program in planning quality assurance at our center. The program has tracked the dosimetric improvement in GU sites after VMAT was implemented clinically. It has generated dose volume statistics for different groups of patients associated with technique or time range. This program allows reporting and statistical analysis of DVH files. It is an efficient tool for the planning quality control in radiation therapy. © 2012 American Association of Physicists in Medicine.

Use of Order Sets in Inpatient Computerized Provider Order Entry Systems: A Comparative Analysis of Usage Patterns at Seven Sites

PubMed Central

Wright, Adam; Feblowitz, Joshua C.; Pang, Justine E.; Carpenter, James D.; Krall, Michael A.; Middleton, Blackford; Sittig, Dean F.

2012-01-01

Background Many computerized provider order entry (CPOE) systems include the ability to create electronic order sets: collections of clinically-related orders grouped by purpose. Order sets promise to make CPOE systems more efficient, improve care quality and increase adherence to evidence-based guidelines. However, the development and implementation of order sets can be expensive and time-consuming and limited literature exists about their utilization. Methods Based on analysis of order set usage logs from a diverse purposive sample of seven sites with commercially- and internally-developed inpatient CPOE systems, we developed an original order set classification system. Order sets were categorized across seven non-mutually exclusive axes: admission/discharge/transfer (ADT), perioperative, condition-specific, task-specific, service-specific, convenience, and personal. In addition, 731 unique subtypes were identified within five axes: four in ADT (S=4), three in perioperative, 144 in condition-specific, 513 in task-specific, and 67 in service-specific. Results Order sets (n=1,914) were used a total of 676,142 times at the participating sites during a one-year period. ADT and perioperative order sets accounted for 27.6% and 24.2% of usage respectively. Peripartum/labor, chest pain/Acute Coronary Syndrome/Myocardial Infarction and diabetes order sets accounted for 51.6% of condition-specific usage. Insulin, angiography/angioplasty and arthroplasty order sets accounted for 19.4% of task-specific usage. Emergency/trauma, Obstetrics/Gynecology/Labor Delivery and anesthesia accounted for 32.4% of service-specific usage. Overall, the top 20% of order sets accounted for 90.1% of all usage. Additional salient patterns are identified and described. Conclusion We observed recurrent patterns in order set usage across multiple sites as well as meaningful variations between sites. Vendors and institutional developers should identify high-value order set types through concrete data analysis in order to optimize the resources devoted to development and implementation. PMID:22819199

Life cycle based risk assessment of recycled materials in roadway construction.

PubMed

Carpenter, A C; Gardner, K H; Fopiano, J; Benson, C H; Edil, T B

2007-01-01

This paper uses a life-cycle assessment (LCA) framework to characterize comparative environmental impacts from the use of virgin aggregate and recycled materials in roadway construction. To evaluate site-specific human toxicity potential (HTP) in a more robust manner, metals release data from a demonstration site were combined with an unsaturated contaminant transport model to predict long-term impacts to groundwater. The LCA determined that there were reduced energy and water consumption, air emissions, Pb, Hg and hazardous waste generation and non-cancer HTP when bottom ash was used in lieu of virgin crushed rock. Conversely, using bottom ash instead of virgin crushed rock increased the cancer HTP risk due to potential leachate generation by the bottom ash. At this scale of analysis, the trade-offs are clearly between the cancer HTP (higher for bottom ash) and all of the other impacts listed above (lower for bottom ash). The site-specific analysis predicted that the contaminants (Cd, Cr, Se and Ag for this study) transported from the bottom ash to the groundwater resulted in very low unsaturated zone contaminant concentrations over a 200 year period due to retardation in the vadose zone. The level of contaminants predicted to reach the groundwater after 200 years was significantly less than groundwater maximum contaminant levels (MCL) set by the US Environmental Protection Agency for drinking water. Results of the site-specific contaminant release estimates vary depending on numerous site and material specific factors. However, the combination of the LCA and the site specific analysis can provide an appropriate context for decision making. Trade-offs are inherent in making decisions about recycled versus virgin material use, and regulatory frameworks should recognize and explicitly acknowledge these trade-offs in decision processes.

Analysis of the site-specific integration system of the Streptomyces aureofaciens phage μ1/6.

PubMed

Farkašovská, Jarmila; Godány, Andrej

2012-03-01

The bacteriophage μ1/6 integrates its DNA into the chromosome of tetracycline producing strains of Streptomyces aureofaciens by a site-specific recombination process. A bioinformatic analysis of the μ1/6 genome revealed that orf5 encodes a putative integrase, a basic protein of 416 amino acids. The μ1/6 integrase was found to belong to the integrase family of site-specific tyrosine recombinases. The phage attachment site (attP) was localized downstream of the int gene. The attachment junctions (attL and attR) were determined, allowing identification of the bacterial attachment site (attB). All attachment sites shared a 46-bp common core sequence within which a site-specific recombination occurs. This core sequence comprises the 3' end of a putative tRNA(Thr) gene (anticodon TGT) which is completely restored in attL after integration of the phage into the host genome. An integration vector containing μ1/6 int-attP region was inserted stably into the S. aureofaciens B96, S. lividans TK24, and S. coelicolor A3. The μ1/6 integrase was shown to be functional in vivo in heterologous Escherichia coli without any other factors encoded by Streptomyces. In vitro recombination assay using purified μ1/6 integrase demonstrated its ability to catalyze integrative recombination in the presence of a crude extract of E. coli cells.

Prognostic value of site-specific metastases in pancreatic adenocarcinoma: A Surveillance Epidemiology and End Results database analysis.

PubMed

Oweira, Hani; Petrausch, Ulf; Helbling, Daniel; Schmidt, Jan; Mannhart, Meinrad; Mehrabi, Arianeb; Schöb, Othmar; Giryes, Anwar; Decker, Michael; Abdel-Rahman, Omar

2017-03-14

To evaluate the prognostic value of site-specific metastases among patients with metastatic pancreatic carcinoma registered within the Surveillance, Epidemiology and End Results (SEER) database. SEER database (2010-2013) has been queried through SEER*Stat program to determine the presentation, treatment outcomes and prognostic outcomes of metastatic pancreatic adenocarcinoma according to the site of metastasis. In this study, metastatic pancreatic adenocarcinoma patients were classified according to the site of metastases (liver, lung, bone, brain and distant lymph nodes). We utilized chi-square test to compare the clinicopathological characteristics among different sites of metastases. We used Kaplan-Meier analysis and log-rank testing for survival comparisons. We employed Cox proportional model to perform multivariate analyses of the patient population; and accordingly hazard ratios with corresponding 95%CI were generated. Statistical significance was considered if a two-tailed P value < 0.05 was achieved. A total of 13233 patients with stage IV pancreatic cancer and known sites of distant metastases were identified in the period from 2010-2013 and they were included into the current analysis. Patients with isolated distant nodal involvement or lung metastases have better overall and pancreatic cancer-specific survival compared to patients with isolated liver metastases (for overall survival: lung vs liver metastases: P < 0.0001; distant nodal vs liver metastases: P < 0.0001) (for pancreatic cancer-specific survival: lung vs liver metastases: P < 0.0001; distant nodal vs liver metastases: P < 0.0001). Multivariate analysis revealed that age < 65 years, white race, being married, female gender; surgery to the primary tumor and surgery to the metastatic disease were associated with better overall survival and pancreatic cancer-specific survival. Pancreatic adenocarcinoma patients with isolated liver metastases have worse outcomes compared to patients with isolated lung or distant nodal metastases. Further research is needed to identify the highly selected subset of patients who may benefit from local treatment of the primary tumor and/or metastatic disease.

Integrated medical and behavioral laboratory measurement system engineering analysis and laboratory specification

NASA Technical Reports Server (NTRS)

Grave, C.; Margold, D. W.

1973-01-01

Site selection, program planning, cost and design studies for support of the IMBLMS program were investigated. Accomplishments are reported for the following areas: analysis of responses to site selection criteria, space-oriented biotechnology, life sciences payload definition, and program information transfer.

Vertical shear-wave velocity profiles generated from spectral analysis of surface waves : field examples

DOT National Transportation Integrated Search

2003-04-01

Surface wave (Rayleigh wave) seismic data were acquired at six separate bridge sites in southeast Missouri. Each acquired surface wave data set was processed (spectral analysis of surface waves; SASW) and transformed into a site-specific vertical she...

Efficient Site-Specific Labeling of Proteins via Cysteines

PubMed Central

Kim, Younggyu; Ho, Sam O.; Gassman, Natalie R.; Korlann, You; Landorf, Elizabeth V.; Collart, Frank R.; Weiss, Shimon

2011-01-01

Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70–90%, and specificities are better than ~95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis. PMID:18275130

Efficient site-specific labeling of proteins via cysteines.

PubMed

Kim, Younggyu; Ho, Sam O; Gassman, Natalie R; Korlann, You; Landorf, Elizabeth V; Collart, Frank R; Weiss, Shimon

2008-03-01

Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70-90%, and specificities are better than approximately 95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis.

Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

NASA Astrophysics Data System (ADS)

Zope, Rajendra R.; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

2015-08-01

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

Site specific atomic polarizabilities in endohedral fullerenes and carbon onions.

PubMed

Zope, Rajendra R; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

2015-08-28

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.

Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

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

Zope, Rajendra R., E-mail: rzope@utep.edu; Baruah, Tunna; Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79958

2015-08-28

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C{sub 60}@C{sub 240} and C{sub 60}@C{sub 180} onions shows that, compared to the polarizability of isolatedmore » C{sub 60} fullerene, the encapsulation of the C{sub 60} in C{sub 240} and C{sub 180} fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C{sub 60} in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.« less

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.

PubMed

Nguyen, Van-Nui; Huang, Kai-Yao; Huang, Chien-Hsun; Chang, Tzu-Hao; Bretaña, Neil; Lai, K; Weng, Julia; Lee, Tzong-Yi

2015-01-01

In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data. However, no development that focuses on the investigation of ubiquitinated substrate specificities has existed. Herein, we present an approach that exploits an iteratively statistical method to identify ubiquitin conjugation sites with substrate site specificities. In this investigation, totally 6259 experimentally validated ubiquitinated proteins were obtained from dbPTM. After having filtered out homologous fragments with 40% sequence identity, the training data set contained 2658 ubiquitination sites (positive data) and 5532 non-ubiquitinated sites (negative data). Due to the difficulty in characterizing the substrate site specificities of E3 ligases by conventional sequence logo analysis, a recursively statistical method has been applied to obtain significant conserved motifs. The profile hidden Markov model (profile HMM) was adopted to construct the predictive models learned from the identified substrate motifs. A five-fold cross validation was then used to evaluate the predictive model, achieving sensitivity, specificity, and accuracy of 73.07%, 65.46%, and 67.93%, respectively. Additionally, an independent testing set, completely blind to the training data of the predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (76.13%) and outperform other ubiquitination site prediction tool. A case study demonstrated the effectiveness of the characterized substrate motifs for identifying ubiquitination sites. The proposed method presents a practical means of preliminary analysis and greatly diminishes the total number of potential targets required for further experimental confirmation. This method may help unravel their mechanisms and roles in E3 recognition and ubiquitin-mediated protein degradation.

GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences.

PubMed

Deng, Wankun; Wang, Chenwei; Zhang, Ying; Xu, Yang; Zhang, Shuang; Liu, Zexian; Xue, Yu

2016-12-22

Protein acetylation catalyzed by specific histone acetyltransferases (HATs) is an essential post-translational modification (PTM) and involved in the regulation a broad spectrum of biological processes in eukaryotes. Although several ten thousands of acetylation sites have been experimentally identified, the upstream HATs for most of the sites are unclear. Thus, the identification of HAT-specific acetylation sites is fundamental for understanding the regulatory mechanisms of protein acetylation. In this work, we first collected 702 known HAT-specific acetylation sites of 205 proteins from the literature and public data resources, and a motif-based analysis demonstrated that different types of HATs exhibit similar but considerably distinct sequence preferences for substrate recognition. Using 544 human HAT-specific sites for training, we constructed a highly useful tool of GPS-PAIL for the prediction of HAT-specific sites for up to seven HATs, including CREBBP, EP300, HAT1, KAT2A, KAT2B, KAT5 and KAT8. The prediction accuracy of GPS-PAIL was critically evaluated, with a satisfying performance. Using GPS-PAIL, we also performed a large-scale prediction of potential HATs for known acetylation sites identified from high-throughput experiments in nine eukaryotes. Both online service and local packages were implemented, and GPS-PAIL is freely available at: http://pail.biocuckoo.org.

GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences

PubMed Central

Deng, Wankun; Wang, Chenwei; Zhang, Ying; Xu, Yang; Zhang, Shuang; Liu, Zexian; Xue, Yu

2016-01-01

Protein acetylation catalyzed by specific histone acetyltransferases (HATs) is an essential post-translational modification (PTM) and involved in the regulation a broad spectrum of biological processes in eukaryotes. Although several ten thousands of acetylation sites have been experimentally identified, the upstream HATs for most of the sites are unclear. Thus, the identification of HAT-specific acetylation sites is fundamental for understanding the regulatory mechanisms of protein acetylation. In this work, we first collected 702 known HAT-specific acetylation sites of 205 proteins from the literature and public data resources, and a motif-based analysis demonstrated that different types of HATs exhibit similar but considerably distinct sequence preferences for substrate recognition. Using 544 human HAT-specific sites for training, we constructed a highly useful tool of GPS-PAIL for the prediction of HAT-specific sites for up to seven HATs, including CREBBP, EP300, HAT1, KAT2A, KAT2B, KAT5 and KAT8. The prediction accuracy of GPS-PAIL was critically evaluated, with a satisfying performance. Using GPS-PAIL, we also performed a large-scale prediction of potential HATs for known acetylation sites identified from high-throughput experiments in nine eukaryotes. Both online service and local packages were implemented, and GPS-PAIL is freely available at: http://pail.biocuckoo.org. PMID:28004786

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

PubMed Central

2013-01-01

Background Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex. Results Phylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA. Conclusions Based on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia. PMID:24059783

Cleaning up contaminated wood-treating sites. Background paper

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

NONE

This report identifies technologies available for organic hazardous waste cleanup at woodtreating sites throughout the country. OTA has identified a range of such technologies that have been selected in the past and could be applied to other sites in the future. The applicability of a technology to a particular Superfund site has to be based on many site-specific factors. Nevertheless, it is clear that a number of the approaches identified by OTA may be appropriate and could prove useful if more detailed site-specific studies and tests were done. Although this study focused on the Texarkana site, decisionmakers and the publicmore » could benefit from this analysis in selecting future cleanup strategies for other sites.« less

40 CFR 60.57b - Siting requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... on ambient air quality, visibility, soils, and vegetation. (2) The analysis shall consider air pollution control alternatives that minimize, on a site-specific basis, to the maximum extent practicable...

33 CFR Appendix A to Part 279 - Sample Resource Use Objectives

Code of Federal Regulations, 2010 CFR

2010-07-01

... boating. (Discussion) The analysis of regional and site specific factors indicates that this project with...) The analysis of regional and site factors indicate that this project with its small water surface and... factors indicate that this project with its outstanding scenic qualities and its location, is suitable for...

Phenology satellite experiment

NASA Technical Reports Server (NTRS)

Dethier, B. E. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The detection of a phenological event (the Brown Wave-vegetation sensescence) for specific forest and crop types using ERTS-1 imagery is described. Data handling techniques including computer analysis and photointerpretation procedures are explained. Computer analysis of multspectral scanner digital tapes in all bands was used to give the relative changes of spectral reflectance with time of forests and specified crops. These data were obtained for a number of the twenty-four sites located within four north-south corridors across the United States. Analysis of ground observation photography and ERTS-1 imagery for sites in the Appalachian Corridor and Mississippi Valley Corridor indicates that the recession of vegetation development can be detected very well. Tentative conclusions are that specific phenological events such as crop maturity or leaf fall can be mapped for specific sites and possible for different regions. Preliminary analysis based on a number of samples in mixed deciduous hardwood stands indicates that as senescence proceeds both the rate of change and differences in color among species can be detected. The results to data show the feasibility of the development and refinement of phenoclimatic models.

Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins*

PubMed Central

Hoffmann, Marcus; Marx, Kristina; Reichl, Udo; Wuhrer, Manfred; Rapp, Erdmann

2016-01-01

Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from low-energy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono- and disialylated core-1 mucin-type O-glycans (T-antigen). The developed workflow allows the identification and characterization of the major population of the human blood plasma O-glycoproteome and our results provide new insights, which can help to unravel structure-function relationships. The data were deposited to ProteomeXchange PXD003270. PMID:26598643

Analysis of Phosphorylation of the Receptor-Like Protein Kinase HAESA during Arabidopsis Floral Abscission

PubMed Central

Taylor, Isaiah; Wang, Ying; Seitz, Kati; Baer, John; Bennewitz, Stefan; Mooney, Brian P.; Walker, John C.

2016-01-01

Receptor-like protein kinases (RLKs) are the largest family of plant transmembrane signaling proteins. Here we present functional analysis of HAESA, an RLK that regulates floral organ abscission in Arabidopsis. Through in vitro and in vivo analysis of HAE phosphorylation, we provide evidence that a conserved phosphorylation site on a region of the HAE protein kinase domain known as the activation segment positively regulates HAE activity. Additional analysis has identified another putative activation segment phosphorylation site common to multiple RLKs that potentially modulates HAE activity. Comparative analysis suggests that phosphorylation of this second activation segment residue is an RLK specific adaptation that may regulate protein kinase activity and substrate specificity. A growing number of RLKs have been shown to exhibit biologically relevant dual specificity toward serine/threonine and tyrosine residues, but the mechanisms underlying dual specificity of RLKs are not well understood. We show that a phospho-mimetic mutant of both HAE activation segment residues exhibits enhanced tyrosine auto-phosphorylation in vitro, indicating phosphorylation of this residue may contribute to dual specificity of HAE. These results add to an emerging framework for understanding the mechanisms and evolution of regulation of RLK activity and substrate specificity. PMID:26784444

Site-specific electronic structure analysis by channeling EELS and first-principles calculations.

PubMed

Tatsumi, Kazuyoshi; Muto, Shunsuke; Yamamoto, Yu; Ikeno, Hirokazu; Yoshioka, Satoru; Tanaka, Isao

2006-01-01

Site-specific electronic structures were investigated by electron energy loss spectroscopy (EELS) under electron channeling conditions. The Al-K and Mn-L(2,3) electron energy loss near-edge structure (ELNES) of, respectively, NiAl2O4 and Mn3O4 were measured. Deconvolution of the raw spectra with the instrumental resolution function restored the blunt and hidden fine features, which allowed us to interpret the experimental spectral features by comparing with theoretical spectra obtained by first-principles calculations. The present method successfully revealed the electronic structures specific to the differently coordinated cationic sites.

An evaluation of contaminated estuarine sites using sediment quality guidelines and ecological assessment methodologies.

PubMed

Fulton, M; Key, P; Wirth, E; Leight, A K; Daugomah, J; Bearden, D; Sivertsen, S; Scott, G

2006-10-01

Toxic contaminants may enter estuarine ecosystems through a variety of pathways. When sediment contaminant levels become sufficiently high, they may impact resident biota. One approach to predict sediment-associated toxicity in estuarine ecosystems involves the use of sediment quality guidelines (ERMs, ERLs) and site-specific contaminant chemistry while a second approach utilizes site-specific ecological sampling to assess impacts at the population or community level. The goal of this study was to utilize an integrated approach including chemical contaminant analysis, sediment quality guidelines and grass shrimp population monitoring to evaluate the impact of contaminants from industrial sources. Three impacted sites and one reference site were selected for study. Grass shrimp populations were sampled using a push-netting approach. Sediment samples were collected at each site and analyzed for metals, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and pesticides. Contaminant levels were then compared to sediment quality guidelines. In general, grass shrimp population densities at the sites decreased as the ERM quotients increased. Grass shrimp densities were significantly reduced at the impacted site that had an ERM exceedance for chromium and the highest Mean ERM quotient. Regression analysis indicated that sediment chromium concentrations were negatively correlated with grass shrimp density. Grass shrimp size was reduced at two sites with intermediate levels of contamination. These findings support the use of both sediment quality guidelines and site-specific population monitoring to evaluate the impacts of sediment-associated contaminants in estuarine systems.

Enhanced forensic discrimination of pollutants by position-specific isotope analysis using isotope ratio monitoring by (13)C nuclear magnetic resonance spectrometry.

PubMed

Julien, Maxime; Nun, Pierrick; Höhener, Patrick; Parinet, Julien; Robins, Richard J; Remaud, Gérald S

2016-01-15

In forensic environmental investigations the main issue concerns the inference of the original source of the pollutant for determining the liable party. Isotope measurements in geochemistry, combined with complimentary techniques for contaminant identification, have contributed significantly to source determination at polluted sites. In this work we have determined the intramolecular (13)C profiles of several molecules well-known as pollutants. By giving additional analytical parameters, position-specific isotope analysis performed by isotope ratio monitoring by (13)C nuclear magnetic resonance (irm-(13)C NMR) spectrometry gives new information to help in answering the major question: what is the origin of the detected contaminant? We have shown that isotope profiling of the core of a molecule reveals both the raw materials and the process used in its manufacture. It also can reveal processes occurring between the contamination site 'source' and the sampling site. Thus, irm-(13)C NMR is shown to be a very good complement to compound-specific isotope analysis currently performed by mass spectrometry for assessing polluted sites involving substantial spills of pollutant. Copyright © 2015 Elsevier B.V. All rights reserved.

The Determination and Analysis of Site-Specific Rates of Mitochondrial Reactive Oxygen Species Production

PubMed Central

Quinlan, Casey L.; Perevoschikova, Irina V.; Goncalves, Renata L.S.; Hey-Mogensen, Martin; Brand, Martin D.

2014-01-01

Mitochondrial reactive oxygen species (ROS) are widely implicated in physiological and pathological pathways. We propose that it is critical to understand the specific sites of mitochondrial ROS production and their mechanisms of action. Mitochondria possess at least eight distinct sites of ROS production in the electron transport chain and matrix compartment. In this chapter, we describe the nature of the mitochondrial ROS-producing machinery and the relative capacities of each site. We provide detailed methods for the measurement of H2O2 release and the conditions under which maximal rates from each site can be achieved in intact skeletal muscle mitochondria. PMID:23791102

Mannose-recognition mutant of the galactose/N-acetylgalactosamine-specific C-type lectin CEL-I engineered by site-directed mutagenesis.

PubMed

Moriuchi, Hiromi; Unno, Hideaki; Goda, Shuichiro; Tateno, Hiroaki; Hirabayashi, Jun; Hatakeyama, Tomomitsu

2015-07-01

CEL-I is a galactose/N-acetylgalactosamine-specific C-type lectin isolated from the sea cucumber Cucumaria echinata. Its carbohydrate-binding site contains a QPD (Gln-Pro-Asp) motif, which is generally recognized as the galactose specificity-determining motif in the C-type lectins. In our previous study, replacement of the QPD motif by an EPN (Glu-Pro-Asn) motif led to a weak binding affinity for mannose. Therefore, we examined the effects of an additional mutation in the carbohydrate-binding site on the specificity of the lectin. Trp105 of EPN-CEL-I was replaced by a histidine residue using site-directed mutagenesis, and the binding affinity of the resulting mutant, EPNH-CEL-I, was examined by sugar-polyamidoamine dendrimer assay, isothermal titration calorimetry, and glycoconjugate microarray analysis. Tertiary structure of the EPNH-CEL-I/mannose complex was determined by X-ray crystallographic analysis. Sugar-polyamidoamine dendrimer assay and glycoconjugate microarray analysis revealed a drastic change in the specificity of EPNH-CEL-I from galactose/N-acetylgalactosamine to mannose. The association constant of EPNH-CEL-I for mannose was determined to be 3.17×10(3) M(-1) at 25°C. Mannose specificity of EPNH-CEL-I was achieved by stabilization of the binding of mannose in a correct orientation, in which the EPN motif can form proper hydrogen bonds with 3- and 4-hydroxy groups of the bound mannose. Specificity of CEL-I can be engineered by mutating a limited number of amino acid residues in addition to the QPD/EPN motifs. Versatility of the C-type carbohydrate-recognition domain structure in the recognition of various carbohydrate chains could become a promising platform to develop novel molecular recognition proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe

PubMed Central

Hendrickson, Edwin R.; Payne, Jo Ann; Young, Roslyn M.; Starr, Mark G.; Perry, Michael P.; Fahnestock, Stephen; Ellis, David E.; Ebersole, Richard C.

2002-01-01

The environmental distribution of Dehalococcoides group organisms and their association with chloroethene-contaminated sites were examined. Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences. Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites. Full dechlorination of chloroethenes to ethene occurred at these sites. Dehalococcoides sequences were not detected in samples from three sites at which partial dechlorination of chloroethenes occurred, where dechlorination appeared to stop at 1,2-cis-dichloroethene. Phylogenetic analysis of the 16S rDNA amplicons confirmed that Dehalococcoides sequences formed a unique 16S rDNA group. These 16S rDNA sequences were divided into three subgroups based on specific base substitution patterns in variable regions 2 and 6 of the Dehalococcoides 16S rDNA sequence. Analyses also demonstrated that specific base substitution patterns were signature patterns. The specific base substitutions distinguished the three sequence subgroups phylogenetically. These results demonstrated that members of the Dehalococcoides group are widely distributed in nature and can be found in a variety of geological formations and in different climatic zones. Furthermore, the association of these organisms with full dechlorination of chloroethenes suggests that they are promising candidates for engineered bioremediation and may be important contributors to natural attenuation of chloroethenes. PMID:11823182

Decreased Surgical Site Infection Rate in Hysterectomy: Effect of a Gynecology-Specific Bundle.

PubMed

Andiman, Sarah E; Xu, Xiao; Boyce, John M; Ludwig, Elizabeth M; Rillstone, Heidi R W; Desai, Vrunda B; Fan, Linda L

2018-06-01

We implemented a hysterectomy-specific surgical site infection prevention bundle after a higher-than-expected surgical site infection rate was identified at our institution. We evaluate how this bundle affected the surgical site infection rate, length of hospital stay, and 30-day postoperative readmission rate. This is a quality improvement study featuring retrospective analysis of a prospectively implemented, multidisciplinary team-designed surgical site infection prevention bundle that consisted of chlorhexidine-impregnated preoperative wipes, standardized aseptic surgical preparation, standardized antibiotic dosing, perioperative normothermia, surgical dressing maintenance, and direct feedback to clinicians when the protocol was breached. There were 2,099 hysterectomies completed during the 33-month study period. There were 61 surgical site infections (4.51%) in the pre-full bundle implementation period and 14 (1.87%) in the post-full bundle implementation period; we found a sustained reduction in the proportion of patients experiencing surgical site infection during the last 8 months of the study period. After adjusting for clinical characteristics, patients who underwent surgery after full implementation were less likely to develop a surgical site infection (adjusted odds ratio [OR] 0.46, P=.01) than those undergoing surgery before full implementation. Multivariable regression analysis showed no statistically significant difference in postoperative days of hospital stay (adjusted mean ratio 0.95, P=.09) or rate of readmission for surgical site infection-specific indication (adjusted OR 2.65, P=.08) between the before and after full-bundle implementation periods. The multidisciplinary implementation of a gynecologic perioperative surgical site infection prevention bundle was associated with a significant reduction in surgical site infection rate in patients undergoing hysterectomy.

Site-Specific Phosphorylation of Ikaros Induced by Low-Dose Ionizing Radiation Regulates Cell Cycle Progression of B Lymphoblast Through CK2 and AKT Activation.

PubMed

Cho, Seong-Jun; Kang, Hana; Kim, Min Young; Lee, Jung Eun; Kim, Sung Jin; Nam, Seon Young; Kim, Ji Young; Kim, Hee Sun; Pyo, Suhkneung; Yang, Kwang Hee

2016-04-01

To determine how low-dose ionizing radiation (LDIR) regulates B lympho-proliferation and its molecular mechanism related with Ikaros, transcription factor. Splenocytes and IM-9 cells were uniformly irradiated with various doses of a (137)Cs γ-source, and cell proliferation was analyzed. To determine the LDIR-specific phosphorylation of Ikaros, immunoprecipitation and Western blot analysis were performed. To investigate the physiologic function of LDIR-mediatied Ikaros phosphorylation, Ikaros mutants at phosphorylation sites were generated, and cell cycle analysis was performed. First, we found that LDIR enhances B lymphoblast proliferation in an Ikaros-dependent manner. Moreover, we found that LDIR elevates the phosphorylation level of Ikaros protein. Interestingly, we showed that CK2 and AKT are involved in LDIR-induced Ikaros phosphorylation and capable of regulating DNA binding activity of Ikaros via specific phosphorylation. Finally, we identified LDIR-specific Ikaros phosphorylation sites at S391/S393 and showed that the Ikaros phosphorylations at these sites control Ikaros's ability to regulate G1/S cell cycle progression. Low-dose ionizing radiation specifically phosphorylates Ikaros protein at Ser 391/393 residues to regulate cell cycle progression in B lymphoblast. Copyright © 2016 Elsevier Inc. All rights reserved.

Position-specific 13C distributions within propane from experiments and natural gas samples

NASA Astrophysics Data System (ADS)

Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Santos Neto, E. V.; Ellis, Geoffrey S.; Lewan, Michael D.; Eiler, John M.

2018-01-01

Site-specific carbon isotope measurements of organic compounds potentially recover information that is lost in a conventional, 'bulk' isotopic analysis. Such measurements are useful because isotopically fractionating processes may have distinct effects at different molecular sites, and thermodynamically equilibrated populations of molecules tend to concentrate heavy isotopes in one molecular site versus another. Most recent studies of site-specific 13C in organics use specialized Nuclear Magnetic Resonance (NMR) techniques or complex chemical degradations prior to mass spectrometric measurements. Herein we present the first application of a new mass spectrometric technique that reconstructs the site-specific carbon isotope composition of propane based on measurements of the 13C/12C ratios of two or more fragment ions that sample different proportions of the terminal and central carbon sites. We apply this method to propane from laboratory experiments and natural gas samples to explore the relationships between site-specific carbon isotope composition, full-molecular δ13C, thermal maturity, and variation in organic matter precursors. Our goal is to advance the understanding of the sources and histories of short-chain alkanes within geologic systems. Our findings suggest that propane varies in its site-specific carbon isotope structure, which is correlated with increasing thermal maturity, first increasing in terminal position δ13C and then increasing in both center and terminal position δ13C. This pattern is observed in both experimental and natural samples, and is plausibly explained by a combination of site-specific, temperature-dependent isotope effects associated with conversion of different precursor molecules (kerogen, bitumen, and/or oil) to propane, differences in site-specific isotopic contents of those precursors, and possibly distillation of reactive components of those precursors with increasing maturity. We hypothesize that the largest changes in site-specific isotopic content of propane occur when bitumen and/or oil replace kerogen as the dominant precursors. If correct, this phenomenon could have significant utility for understanding gas generation in thermogenic petroleum systems.

Position-specific 13C distributions within propane from experiments and natural gas samples

USGS Publications Warehouse

Piasecki, Alison; Sessions, Alex L.; Lawson, Michael; Ferreira, A.A.; Santos Neto, E. V.; Ellis, Geoffrey S.; Lewan, Michael; Eilers, J.M.

2018-01-01

Site-specific carbon isotope measurements of organic compounds potentially recover information that is lost in a conventional, ‘bulk’ isotopic analysis. Such measurements are useful because isotopically fractionating processes may have distinct effects at different molecular sites, and thermodynamically equilibrated populations of molecules tend to concentrate heavy isotopes in one molecular site versus another. Most recent studies of site-specific 13C in organics use specialized Nuclear Magnetic Resonance (NMR) techniques or complex chemical degradations prior to mass spectrometric measurements. Herein we present the first application of a new mass spectrometric technique that reconstructs the site-specific carbon isotope composition of propane based on measurements of the 13C/12C ratios of two or more fragment ions that sample different proportions of the terminal and central carbon sites. We apply this method to propane from laboratory experiments and natural gas samples to explore the relationships between site-specific carbon isotope composition, full-molecular δ13C, thermal maturity, and variation in organic matter precursors. Our goal is to advance the understanding of the sources and histories of short-chain alkanes within geologic systems. Our findings suggest that propane varies in its site-specific carbon isotope structure, which is correlated with increasing thermal maturity, first increasing in terminal position δ13C and then increasing in both center and terminal position δ13C. This pattern is observed in both experimental and natural samples, and is plausibly explained by a combination of site-specific, temperature-dependent isotope effects associated with conversion of different precursor molecules (kerogen, bitumen, and/or oil) to propane, differences in site-specific isotopic contents of those precursors, and possibly distillation of reactive components of those precursors with increasing maturity. We hypothesize that the largest changes in site-specific isotopic content of propane occur when bitumen and/or oil replace kerogen as the dominant precursors. If correct, this phenomenon could have significant utility for understanding gas generation in thermogenic petroleum systems.

THE OHIO RIVER BASIN ENERGY FACILITY SITING MODEL. VOLUME II: SITES AND ON-LINE DATES

EPA Science Inventory

The report was prepared as part of the Ohio River Basin Energy Study (ORBES), a multidisciplinary policy research program. The siting model developed for ORBES is specifically designed for regional policy analysis. The region includes 423 counties in an area that consists of all ...

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

PubMed Central

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Švedas, Vytas

2014-01-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure–function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. PMID:24852248

Cogestion and recreation site demand: a model of demand-induced quality effects

USGS Publications Warehouse

Douglas, Aaron J.; Johnson, Richard L.

1993-01-01

This analysis focuses on problems of estimating site-specific dollar benefits conferred by outdoor recreation sites in the face of congestion costs. Encounters, crowding effects and congestion costs have often been treated by natural resource economists in a piecemeal fashion. In the current paper, encounters and crowding effects are treated systematically. We emphasize the quantitative impact of congestion costs on site-specific estimates of benefits conferred by improvements in outdoor recreation sites. The principal analytic conclusion is that techniques that streamline on data requirements produce biased estimates of benefits conferred by site improvements at facilities with significant crowding effects. The principal policy recommendation is that the Federal and state agencies should collect and store information on visitation rates, encounter levels and congestion costs at various outdoor recreation sites.

Development of a geophysical data fusion system for assessment and remediation studies of polluted groundwater aquifers. Scientific report No. 1

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

Murphy, J.R.; O`Neill, D.C.; Barker, B.W.

1994-10-01

The research described in this report is directed toward the development of a workstation-based data management, analysis and visualization system which can be used to improve the Air Force`s capability to evaluate site specific environmental hazards. The initial prototype system described in this report is directed toward a specific application to the Massachusetts Military Reservation (formerly Otis Air Force Base) on Cape Cod, Massachusetts. This system integrates a comprehensive, on-line environmental database for the site together with a map-based graphical user interface which facilitates analyst access to the databases and analysis tools needed to characterize the subsurface geologic and hydrologicmore » environments at the site.« less

Combined Analyses of Bacterial, Fungal and Nematode Communities in Andosolic Agricultural Soils in Japan

PubMed Central

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols. PMID:22223474

Combined analyses of bacterial, fungal and nematode communities in andosolic agricultural soils in Japan.

PubMed

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.

Concept analysis: wrong-site surgery.

PubMed

Watson, Donna S

2015-06-01

A concept analysis was conducted on the concept of wrong-site surgery (WSS) using the principle-based method by Penrod and Hupcey. It included analysis of WSS within the context of epistemological, pragmatic, linguistic, and logical principles. The analysis found that WSS is an important concept that is universally accepted, but the definition could be improved with inclusion of comprehensive labeling for types of WSS that may occur, such as wrong patient, wrong site, wrong level/part, wrong procedure, and wrong side. Wrong-site surgery falls into the domains of both nursing and medicine, and there is limited research on the topic specific to nursing interventions, perceptions, and contributions to prevent WSS. Copyright © 2015 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Prediction of earthquake ground motion at rock sites in Japan: evaluation of empirical and stochastic approaches for the PEGASOS Refinement Project

NASA Astrophysics Data System (ADS)

Edwards, Benjamin; Fäh, Donat

2017-11-01

Strong ground-motion databases used to develop ground-motion prediction equations (GMPEs) and calibrate stochastic simulation models generally include relatively few recordings on what can be considered as engineering rock or hard rock. Ground-motion predictions for such sites are therefore susceptible to uncertainty and bias, which can then propagate into site-specific hazard and risk estimates. In order to explore this issue we present a study investigating the prediction of ground motion at rock sites in Japan, where a wide range of recording-site types (from soil to very hard rock) are available for analysis. We employ two approaches: empirical GMPEs and stochastic simulations. The study is undertaken in the context of the PEGASOS Refinement Project (PRP), a Senior Seismic Hazard Analysis Committee (SSHAC) Level 4 probabilistic seismic hazard analysis of Swiss nuclear power plants, commissioned by swissnuclear and running from 2008 to 2013. In order to reduce the impact of site-to-site variability and expand the available data set for rock and hard-rock sites we adjusted Japanese ground-motion data (recorded at sites with 110 m s-1 < Vs30 < 2100 m s-1) to a common hard-rock reference. This was done through deconvolution of: (i) empirically derived amplification functions and (ii) the theoretical 1-D SH amplification between the bedrock and surface. Initial comparison of a Japanese GMPE's predictions with data recorded at rock and hard-rock sites showed systematic overestimation of ground motion. A further investigation of five global GMPEs' prediction residuals as a function of quarter-wavelength velocity showed that they all presented systematic misfit trends, leading to overestimation of median ground motions at rock and hard-rock sites in Japan. In an alternative approach, a stochastic simulation method was tested, allowing the direct incorporation of site-specific Fourier amplification information in forward simulations. We use an adjusted version of the model developed for Switzerland during the PRP. The median simulation prediction at true rock and hard-rock sites (Vs30 > 800 m s-1) was found to be comparable (within expected levels of epistemic uncertainty) to predictions using an empirical GMPE, with reduced residual misfit. As expected, due to including site-specific information in the simulations, the reduction in misfit could be isolated to a reduction in the site-related within-event uncertainty. The results of this study support the use of finite or pseudo-finite fault stochastic simulation methods in estimating strong ground motions in regions of weak and moderate seismicity, such as central and northern Europe. Furthermore, it indicates that weak-motion data has the potential to allow estimation of between- and within-site variability in ground motion, which is a critical issue in site-specific seismic hazard analysis, particularly for safety critical structures.

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

PubMed Central

Grey, Corinne; Clément, Julie A.J.; Buard, Jérôme; Leblanc, Benjamin; Gut, Ivo; Gut, Marta; Duret, Laurent

2017-01-01

In mouse and human meiosis, DNA double-strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence-specific DNA binding domain of the PRDM9 histone methyl transferase. Here, we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a noncanonical recruitment of PRDM9 to sites that lack recombination activity and the PRDM9 binding consensus motif. These sites include gene promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis. PMID:28336543

Environmental siting suitability analysis for commercial scale ocean renewable energy: A southeast Florida case study

NASA Astrophysics Data System (ADS)

Mulcan, Amanda

This thesis aims to facilitate the siting and implementation of Florida Atlantic University Southeast National Marine Renewable Energy Center (FAU SNMREC) ocean current energy (OCE) projects offshore southeastern Florida through the analysis of benthic anchoring conditions. Specifically, a suitability analysis considering all presently available biologic and geologic datasets within the legal framework of OCE policy and regulation was done. OCE related literature sources were consulted to assign suitability levels to each dataset, ArcGIS interpolations generated seafloor substrate maps, and existing submarine cable pathways were considered for OCE power cables. The finalized suitability map highlights the eastern study area as most suitable for OCE siting due to its abundance of sand/sediment substrate, existing underwater cable route access, and minimal biologic presence. Higher resolution datasets are necessary to locate specific OCE development locales, better understand their benthic conditions, and minimize potentially negative OCE environmental impacts.

Recombinase-Mediated Cassette Exchange Using Adenoviral Vectors.

PubMed

Kolb, Andreas F; Knowles, Christopher; Pultinevicius, Patrikas; Harbottle, Jennifer A; Petrie, Linda; Robinson, Claire; Sorrell, David A

2017-01-01

Site-specific recombinases are important tools for the modification of mammalian genomes. In conjunction with viral vectors, they can be utilized to mediate site-specific gene insertions in animals and in cell lines which are difficult to transfect. Here we describe a method for the generation and analysis of an adenovirus vector supporting a recombinase-mediated cassette exchange reaction and discuss the advantages and limitations of this approach.

Molecular cloning and analysis of Schizosaccharomyces pombe Reb1p: sequence-specific recognition of two sites in the far upstream rDNA intergenic spacer.

PubMed Central

Zhao, A; Guo, A; Liu, Z; Pape, L

1997-01-01

The coding sequences for a Schizosaccharomyces pombe sequence-specific DNA binding protein, Reb1p, have been cloned. The predicted S. pombe Reb1p is 24-29% identical to mouse TTF-1 (transcription termination factor-1) and Saccharomyces cerevisiae REB1 protein, both of which direct termination of RNA polymerase I catalyzed transcripts. The S.pombe Reb1 cDNA encodes a predicted polypeptide of 504 amino acids with a predicted molecular weight of 58.4 kDa. The S. pombe Reb1p is unusual in that the bipartite DNA binding motif identified originally in S.cerevisiae and Klyveromyces lactis REB1 proteins is uninterrupted and thus S.pombe Reb1p may contain the smallest natural REB1 homologous DNA binding domain. Its genomic coding sequences were shown to be interrupted by two introns. A recombinant histidine-tagged Reb1 protein bearing the rDNA binding domain has two homologous, sequence-specific binding sites in the S. pomber DNA intergenic spacer, located between 289 and 480 nt downstream of the end of the approximately 25S rRNA coding sequences. Each binding site is 13-14 bp downstream of two of the three proposed in vivo termination sites. The core of this 17 bp site, AGGTAAGGGTAATGCAC, is specifically protected by Reb1p in footprinting analysis. PMID:9016645

The Skeletal Site-Specific Role of Connective Tissue Growth Factor in Prenatal Osteogenesis

PubMed Central

Lambi, Alex G.; Pankratz, Talia L.; Mundy, Christina; Gannon, Maureen; Barbe, Mary F.; Richtsmeier, Joan T.; Popoff, Steven N.

2013-01-01

Background Connective tissue growth factor (CTGF/CCN2) is a matricellular protein that is highly expressed during bone development. Mice with global CTGF ablation (knockout, KO) have multiple skeletal dysmorphisms and perinatal lethality. A quantitative analysis of the bone phenotype has not been conducted. Results We demonstrated skeletal site-specific changes in growth plate organization, bone microarchitecture, and shape and gene expression levels in CTGF KO compared with wild-type mice. Growth plate malformations included reduced proliferation zone and increased hypertrophic zone lengths. Appendicular skeletal sites demonstrated decreased metaphyseal trabecular bone, while having increased mid-diaphyseal bone and osteogenic expression markers. Axial skeletal analysis showed decreased bone in caudal vertebral bodies, mandibles, and parietal bones in CTGF KO mice, with decreased expression of osteogenic markers. Analysis of skull phenotypes demonstrated global and regional differences in CTGF KO skull shape resulting from allometric (size-based) and nonallometric shape changes. Localized differences in skull morphology included increased skull width and decreased skull length. Dysregulation of the transforming growth factor-β-CTGF axis coupled with unique morphologic traits provides a potential mechanistic explanation for the skull phenotype. Conclusions We present novel data on a skeletal phenotype in CTGF KO mice, in which ablation of CTGF causes site-specific aberrations in bone formation. PMID:23073844

SPEER-SERVER: a web server for prediction of protein specificity determining sites

PubMed Central

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

2012-01-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

PubMed

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

2012-07-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

oPOSSUM: integrated tools for analysis of regulatory motif over-representation

PubMed Central

Ho Sui, Shannan J.; Fulton, Debra L.; Arenillas, David J.; Kwon, Andrew T.; Wasserman, Wyeth W.

2007-01-01

The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/ PMID:17576675

Usability and Gratifications--Towards a Website Analysis Model.

ERIC Educational Resources Information Center

Bunz, Ulla K.

This paper discusses Web site usability issues. Specifically, it assumes that the usability of a Web site depends more on the perception of the user than on the objectively assessable usability criteria of the Web site. Two pilot studies, based on theoretical notions of uses and gratifications theory and similar theories, are presented. In the…

Quantitative chemoproteomics for site-specific analysis of protein alkylation by 4-hydroxy-2-nonenal in cells.

PubMed

Yang, Jing; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C

2015-03-03

Protein alkylation by 4-hydroxy-2-nonenal (HNE), an endogenous lipid derived electrophile, contributes to stress signaling and cellular toxicity. Although previous work has identified protein targets for HNE alkylation, the sequence specificity of alkylation and dynamics in a cellular context remain largely unexplored. We developed a new quantitative chemoproteomic platform, which uses isotopically tagged, photocleavable azido-biotin reagents to selectively capture and quantify the cellular targets labeled by the alkynyl analogue of HNE (aHNE). Our analyses site-specifically identified and quantified 398 aHNE protein alkylation events (386 cysteine sites and 12 histidine sites) in intact cells. This data set expands by at least an order of magnitude the number of such modification sites previously reported. Although adducts formed by Michael addition are thought to be largely irreversible, we found that most aHNE modifications are lost rapidly in situ. Moreover, aHNE adduct turnover occurs only in intact cells and loss rates are site-selective. This quantitative chemoproteomics platform provides a versatile general approach to map bioorthogonal-chemically engineered post-translational modifications and their cellular dynamics in a site-specific and unbiased manner.

Toxicity risk assessment of mercury, DDT and arsenic legacy pollution in sediments: A triad approach under low concentration conditions.

PubMed

Marziali, L; Rosignoli, F; Drago, A; Pascariello, S; Valsecchi, L; Rossaro, B; Guzzella, L

2017-09-01

The determination of sediment toxicity is challenging due to site-specific factors affecting pollutants distribution and bioavailability, especially when contamination levels are close to expected non-effect concentrations. Different lines of evidence and sensitive tools are necessary for a proper toxicity risk assessment. We examined the case study of the Toce River (Northern Italy), where past industrial activities determined Hg, DDT and As enrichment in sediments. A triad approach comprising chemical, ecotoxicological and ecological analyses (benthic invertebrates) was carried out for risk assessment of residual contamination in river sediments. A "blank" site upstream from the industrial site was selected to compare the other sites downstream. Sediment, water and benthic invertebrate samplings were carried out following standard protocols. Results emphasized that despite the emissions of the industrial site ceased about 20years ago, sediments in the downstream section of the river remain contaminated by Hg, DDT and As with concentrations exceeding Threshold Effect Concentrations. A chronic whole-sediment test with Chironomus riparius showed decreased development rate and a lower number of eggs per mass in the contaminated sediments. Benthic community was analyzed with the calculation of integrated (STAR_ICMi) and stressor-specific metrics (SPEAR pesticide and mean sensitivity to Hg), but no significant differences were found between upstream and downstream sites. On the other hand, multivariate analysis (partial Redundancy Analysis and variation partitioning) emphasized a slight impact on invertebrate community, accounting for 5% variation in taxa composition. Results show that legacy contaminants in sediments, even at low concentrations, may be bioavailable and possibly toxic for benthic invertebrates. At low concentration levels, sensitive and site-specific tools need to be developed for a proper risk analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Milestones for Selection, Characterization, and Analysis of the Performance of a Repository for Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain.

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

Rechard, Robert P.

This report presents a concise history in tabular form of events leading up to site identification in 1978, site selection in 1987, subsequent characterization, and ongoing analysis through 2008 of the performance of a repository for spent nuclear fuel and high-level radioactive waste at Yucca Mountain in southern Nevada. The tabulated events generally occurred in five periods: (1) commitment to mined geologic disposal and identification of sites; (2) site selection and analysis, based on regional geologic characterization through literature and analogous data; (3) feasibility analysis demonstrating calculation procedures and importance of system components, based on rough measures of performance usingmore » surface exploration, waste process knowledge, and general laboratory experiments; (4) suitability analysis demonstrating viability of disposal system, based on environment-specific laboratory experiments, in-situ experiments, and underground disposal system characterization; and (5) compliance analysis, based on completed site-specific characterization. Because the relationship is important to understanding the evolution of the Yucca Mountain Project, the tabulation also shows the interaction between four broad categories of political bodies and government agencies/institutions: (a) technical milestones of the implementing institutions, (b) development of the regulatory requirements and related federal policy in laws and court decisions, (c) Presidential and agency directives and decisions, and (d) critiques of the Yucca Mountain Project and pertinent national and world events related to nuclear energy and radioactive waste.« less

Differential Sox10 Genomic Occupancy in Myelinating Glia

PubMed Central

Lopez-Anido, Camila; Sun, Guannan; Koenning, Matthias; Srinivasan, Rajini; Hung, Holly A.; Emery, Ben; Keles, Sunduz; Svaren, John

2015-01-01

Myelin is formed by specialized myelinating glia: oligodendrocytes and Schwann cells in the central and peripheral nervous systems, respectively. While there are distinct developmental aspects and regulatory pathways in these two cell types, myelination in both systems requires the transcriptional activator Sox10. Sox10 interacts with cell type-specific transcription factors at some loci to induce myelin gene expression, but it is largely unknown how Sox10 transcriptional networks globally compare between oligodendrocytes and Schwann cells. We used in vivo ChIP-Seq analysis of spinal cord and peripheral nerve (sciatic nerve) to identify unique and shared Sox10 binding sites and assess their correlation with active enhancers and transcriptional profiles in oligodendrocytes and Schwann cells. Sox10 binding sites overlap with active enhancers and critical cell type-specific regulators of myelination, such as Olig2 and Myrf in oligodendrocytes, and Egr2/Krox20 in Schwann cells. Sox10 sites also associate with genes critical for myelination in both oligodendrocytes and Schwann cells, and are found within super-enhancers previously defined in brain. In Schwann cells, Sox10 sites contain binding motifs of putative partners in the Sp/Klf, Tead, and nuclear receptor protein families. Specifically, siRNA analysis of nuclear receptors Nr2f1 and Nr2f2 revealed downregulation of myelin genes Mbp and Ndrg1 in primary Schwann cells. Our analysis highlights different mechanisms that establish cell type-specific genomic occupancy of Sox10, which reflects the unique characteristics of oligodendrocyte and Schwann cell differentiation. PMID:25974668

An analysis of wilderness water in Kings Canyon, Sequoia, and Yosemite national parks for coliform and pathologic bacteria.

PubMed

Derlet, Robert W; Carlson, James R

2004-01-01

To determine the prevalence of coliform and potentially pathogenic bacteria in remote backcountry alpine lakes and streams of national parks in the Sierra Nevada mountains. Water was sampled at 55 predetermined lakes and streams that would stratify the risk, based on sites used by backpackers, sites used by pack animals, and uncontaminated wild areas. Sites were distributed among Kings Canyon (15), Sequoia (17), and Yosemite (23). Water was collected using Millipore bacterial samplers, which provided specific counts of coliform and other bacteria in each water sample and also served as a transport media from the wilderness to the laboratory. On return to the laboratory, bacteria were harvested from the samplers and subjected to specific identification and qualitative analysis using standard microbiology techniques for the analysis of water. Coliform bacteria were detected in 22 of the 55 sites. All of these sites were below areas used by backpackers or pack animals. Thirty-three sites were free of coliforms. These sites included both those used lightly by backpackers and those with no human or domestic animal use. All samples contained expected amounts of normal aquatic bacteria including Pseudomonas, Rahnella aquatilis, Serratia spp, and nonpathogenic species of Yersinia. Most sampling sites in these national parks are free of coliform or pathogenic organisms. Low levels of coliform bacteria are found in some bodies of water where the watershed has been affected by human or pack animal travel.

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

2014-07-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cyclosporine a inhibits apoptosis of rat gingival epithelium.

PubMed

Ma, Su; Liu, Peihong; Li, Yanwu; Hou, Lin; Chen, Li; Qin, Chunlin

2014-08-01

The use of cyclosporine A (CsA) induces hyperplasia of the gingival epithelium in a site-specific response manner, but the molecular mechanism via which the lesion occurs is unclear. The present research aims to investigate the site-specific effect of CsA on the apoptosis of gingival epithelium associated with gingival hyperplasia. Forty Wistar rats were divided into CsA-treated and non-treated groups. Paraffin-embedded sections of mandibular first molars were selected for hematoxylin and eosin staining, immunohistochemistry analyses of bcl-2 and caspase-3, and the staining of terminal deoxynucleotidyl transfer-mediated dUTP nick-end labeling (TUNEL). The area of the whole gingival epithelium and the length of rete pegs were measured, and the number of bcl-2- and caspase-3-positive cells in the longest rete peg were counted. The analysis of variance for factorial designs and Fisher least significant difference test for post hoc analysis were used to determine the significance levels. In CsA-treated rats, bcl-2 expression was significantly upregulated, whereas caspase-3 expression was downregulated, along with a reduced number of TUNEL-positive cells. The site-specific distribution of bcl-2 was consistent with the site-specific hyperplasia of the gingival epithelium in CsA-treated rats. CsA inhibited gingival epithelial apoptosis via the mitochondrial pathway and common pathway. The antiapoptotic protein bcl-2 might play a critical role in the pathogenesis of the site-specific hyperplasia of gingival epithelium induced by CsA. There were mechanistic differences in the regulation of apoptosis for cells in the attached gingival epithelium, free gingival epithelium, and junctional epithelium.

The Ohio River Basin energy facility siting model. Volume 1: Methodology

NASA Astrophysics Data System (ADS)

Fowler, G. L.; Bailey, R. E.; Gordon, S. I.; Jansen, S. D.; Randolph, J. C.; Jones, W. W.

1981-04-01

The siting model developed for ORBES is specifically designed for regional policy analysis. The region includes 423 counties in an area that consists of all of Kentucky and substantial portions of Illinois, Indiana, Ohio, Pennsylvania, and West Virginia.

Comparison of screening-level and Monte Carlo approaches for wildlife food web exposure modeling

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

Pastorok, R.; Butcher, M.; LaTier, A.

1995-12-31

The implications of using quantitative uncertainty analysis (e.g., Monte Carlo) and site-specific tissue residue data for wildlife exposure modeling were examined with data on trace elements at the Clark Fork River Superfund Site. Exposure of white-tailed deer, red fox, and American kestrel was evaluated using three approaches. First, a screening-level exposure model was based on conservative estimates of exposure parameters, including estimates of dietary residues derived from bioconcentration factors (BCFs) and soil chemistry. A second model without Monte Carlo was based on site-specific data for tissue residues of trace elements (As, Cd, Cu, Pb, Zn) in key dietary species andmore » plausible assumptions for habitat spatial segmentation and other exposure parameters. Dietary species sampled included dominant grasses (tufted hairgrass and redtop), willows, alfalfa, barley, invertebrates (grasshoppers, spiders, and beetles), and deer mice. Third, the Monte Carlo analysis was based on the site-specific residue data and assumed or estimated distributions for exposure parameters. Substantial uncertainties are associated with several exposure parameters, especially BCFS, such that exposure and risk may be greatly overestimated in screening-level approaches. The results of the three approaches are compared with respect to realism, practicality, and data gaps. Collection of site-specific data on trace elements concentrations in plants and animals eaten by the target wildlife receptors is a cost-effective way to obtain realistic estimates of exposure. Implications of the results for exposure and risk estimates are discussed relative to use of wildlife exposure modeling and evaluation of remedial actions at Superfund sites.« less

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

A method for the quantitative site-specific study of the biochemistry within dental plaque biofilms formed in vivo.

PubMed

Robinson, C; Kirkham, J; Percival, R; Shore, R C; Bonass, W A; Brookes, S J; Kusa, L; Nakagaki, H; Kato, K; Nattress, B

1997-01-01

The study of plaque biofilms in the oral cavity is difficult as plaque removal inevitably disrupts biofilm integrity precluding kinetic studies involving the penetration of components and metabolism of substrates in situ. A method is described here in which plaque is formed in vivo under normal (or experimental) conditions using a collection device which can be removed from the mouth after a specified time without physical disturbance to the plaque biofilm, permitting site-specific analysis or exposure of the undisturbed plaque to experimental conditions in vitro. Microbiological analysis revealed plaque flora which was similar to that reported from many natural sources. Analytical data can be related to plaque volume rather than weight. Using this device, plaque fluoride concentrations have been shown to vary with plaque depth and in vitro short-term exposure to radiolabelled components may be carried out, permitting important conclusions to be drawn regarding the site-specific composition and dynamics of dental plaque.

Tolerance design of patient-specific range QA using the DMAIC framework in proton therapy.

PubMed

Rah, Jeong-Eun; Shin, Dongho; Manger, Ryan P; Kim, Tae Hyun; Oh, Do Hoon; Kim, Dae Yong; Kim, Gwe-Ya

2018-02-01

To implement the DMAIC (Define-Measure-Analyze-Improve-Control) can be used for customizing the patient-specific QA by designing site-specific range tolerances. The DMAIC framework (process flow diagram, cause and effect, Pareto chart, control chart, and capability analysis) were utilized to determine the steps that need focus for improving the patient-specific QA. The patient-specific range QA plans were selected according to seven treatment site groups, a total of 1437 cases. The process capability index, C pm was used to guide the tolerance design of patient site-specific range. For prostate field, our results suggested that the patient range measurements were capable at the current tolerance level of ±1 mm in clinical proton plans. For other site-specific ranges, we analyzed that the tolerance tends to be overdesigned to insufficient process capability calculated by the patient-specific QA data. The customized tolerances were calculated for treatment sites. Control charts were constructed to simulate the patient QA time before and after the new tolerances were implemented. It is found that the total simulation QA time was decreased on average of approximately 20% after establishing new site-specific range tolerances. We simulated the financial impact of this project. The QA failure for whole process in proton therapy would lead up to approximately 30% increase in total cost. DMAIC framework can be used to provide an effective QA by setting customized tolerances. When tolerance design is customized, the quality is reasonably balanced with time and cost demands. © 2017 American Association of Physicists in Medicine.

System description for DART (Decision Analysis for Remediation Technologies)

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

Nonte, J.; Bolander, T.; Nickelson, D.

1997-09-01

DART is a computer aided system populated with influence models to determine quantitative benefits derived by matching requirements and technologies. The DART database is populated with data from over 900 DOE sites from 10 Field Offices. These sites are either source terms, such as buried waste pits, or soil or groundwater contaminated plumes. The data, traceable to published documents, consists of site-specific data (contaminants, area, volume, depth, size, remedial action dates, site preferred remedial option), problems (e.g., offsite contaminant plume), and Site Technology Coordinating Group (STCG) need statements (also contained in the Ten-Year Plan). DART uses this data to calculatemore » and derive site priorities, risk rankings, and site specific technology requirements. DART is also populated with over 900 industry and DOE SCFA technologies. Technology capabilities can be used to match technologies to waste sites based on the technology`s capability to meet site requirements and constraints. Queries may be used to access, sort, roll-up, and rank site data. Data roll-ups may be graphically displayed.« less

Seneca Compressed Air Energy Storage (CAES) Project

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

None

2012-11-30

This document provides specifications for the process air compressor for a compressed air storage project, requests a budgetary quote, and provides supporting information, including compressor data, site specific data, water analysis, and Seneca CAES value drivers.

Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates

PubMed Central

Botzanowski, Thomas; Erb, Stéphane; Hernandez-Alba, Oscar; Ehkirch, Anthony; Colas, Olivier; Wagner-Rousset, Elsa; Rabuka, David; Beck, Alain; Drake, Penelope M.; Cianférani, Sarah

2017-01-01

ABSTRACT Antibody-drug conjugates (ADCs) have emerged as a family of compounds with promise as efficient immunotherapies. First-generation ADCs were generated mostly via reactions on either lysine side-chain amines or cysteine thiol groups after reduction of the interchain disulfide bonds, resulting in heterogeneous populations with a variable number of drug loads per antibody. To control the position and the number of drug loads, new conjugation strategies aiming at the generation of more homogeneous site-specific conjugates have been developed. We report here the first multi-level characterization of a site-specific ADC by state-of-the-art mass spectrometry (MS) methods, including native MS and its hyphenation to ion mobility (IM-MS). We demonstrate the versatility of native MS methodologies for site-specific ADC analysis, with the unique ability to provide several critical quality attributes within one single run, along with a direct snapshot of ADC homogeneity/heterogeneity without extensive data interpretation. The capabilities of native IM-MS to directly access site-specific ADC conformational information are also highlighted. Finally, the potential of these techniques for assessing an ADC's heterogeneity/homogeneity is illustrated by comparing the analytical characterization of a site-specific DAR4 ADC to that of first-generation ADCs. Altogether, our results highlight the compatibility, versatility, and benefits of native MS approaches for the analytical characterization of all types of ADCs, including site-specific conjugates. Thus, we envision integrating native MS and IM-MS approaches, even in their latest state-of-the-art forms, into workflows that benchmark bioconjugation strategies. PMID:28406343

Women with peritoneal carcinomatosis of unknown origin: Efficacy of image-guided biopsy to determine site-specific diagnosis.

PubMed

Hewitt, M J; Anderson, K; Hall, G D; Weston, M; Hutson, R; Wilkinson, N; Perren, T J; Lane, G; Spencer, J A

2007-01-01

To evaluate the use of image-guided biopsy (IGB) in routine clinical practice to obtain site-specific diagnoses in women presenting with peritoneal carcinomatosis (PC). Retrospective case study. Tertiary referral centre. A total of 149 consecutive women with PC who underwent IGB. Biopsy was performed in women considered unsuitable for primary surgery because of poor performance status or disease unlikely to be optimally debulked, with a prior history of malignancy or where there was clinicoradiological uncertainty about primary tumour site. Standard haematoxylin-eosin histological analysis was supplemented with immunohistochemistry. The rate of site-specific diagnosis. A total of 149 women underwent IGB using computed tomography or ultrasound over a 6-year period. The only complication was one rectus sheath haematoma. In 138 (93%) women, a site-specific cancer diagnosis was made on the IGB (including 111 müllerian tract, 8 gastrointestinal tract, 4 breast and 3 lymphoma); in ten women, a repeat biopsy was necessary, giving an overall failure rate of 7%. In a further six women, malignancy was confirmed but a site-specific diagnosis could not be made, and in four women, biopsy showed benign tissue. A site-specific diagnosis was obtained in 29 of the 32 women (94%) with previous malignancy, of which 18/32 (56%) showed a new primary cancer. IGB is a safe and accurate technique for providing site-specific diagnoses in women with PC in routine clinical practice, including those with a previous relevant malignancy. IGB can replace laparoscopic or open biopsy in defining primary therapeutic options. The data would suggest that the biopsy should be performed with ultrasound where feasible.

Integrating proximal and satellite optical data for the analysis of ecosystem carbon uptake and plant phenology at the European larch Specnet site

NASA Astrophysics Data System (ADS)

Galvagno, Marta; Gamon, John; Cremonese, Edoardo; Garrity, Steven; Huemmrich, K. Fred; Filippa, Gianluca; Morra di Cella, Umberto; Rossini, Micol

2017-04-01

Automated canopy-level optical sampling in tandem with ecosystem-atmosphere flux observations is continuously carried on at a variety of ecosystems through the Specnet network (http://specnet.info/). Specifically, 9 sites within US and Europe were selected since 2015, to investigate the use of novel NDVI and PRI low-cost sensors for the analysis of ecosystem functioning and phenology. Different plant functional types, such as grasslands, deciduous, and evergreen forests belong to the network, here we present specific data from the larch (Larix decidua Mill.) forest Italian site. Three automated NDVI and three automated PRI spectral reflectance sensors (Decagon Devices Inc.) were installed in 2015 on the top of the 20-meters eddy covariance tower, pointing toward the west, north, and east orientations. An additional system, composed by one NDVI and PRI system was installed to monitor the understory component. The objective of this analysis is the comparison between these in-situ inexpensive sensors, independent NDVI and PRI sensors (Skye Instruments) previously installed on the 20-meters tower and satellite-derived NDVI. Both MODIS and Sentinel NDVI data were used for the comparison. Moreover, the newly derived chlorophyll/carotenoid index (CCI, Gamon et al. 2016), computed as the normalized difference between the NDVI red band and PRI 532 nm band, was tested to estimate the seasonal pattern of daily Gross Primary Productivity (GPP) of the larch forest. Results showed that the seasonality of NDVI was comparable among in-situ sensors and satellite data, though orientation-specific differences were observed. Both NDVI and CCI tracked daily GPP, but with different sensitivity to its seasonality. Future analysis will be directed toward a comparison between this site-based results with the other sites within the Specnet network.

Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.

PubMed

Myette, James R; Soundararajan, Venkataramanan; Shriver, Zachary; Raman, Rahul; Sasisekharan, Ram

2009-12-11

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) comprise a chemically heterogeneous class of sulfated polysaccharides. The development of structure-activity relationships for this class of polysaccharides requires the identification and characterization of degrading enzymes with defined substrate specificity and enzymatic activity. Toward this end, we report here the molecular cloning and extensive structure-function analysis of a 6-O-sulfatase from the Gram-negative bacterium Flavobacterium heparinum. In addition, we report the recombinant expression of this enzyme in Escherichia coli in a soluble, active form and identify it as a specific HSGAG sulfatase. We further define the mechanism of action of the enzyme through biochemical and structural studies. Through the use of defined substrates, we investigate the kinetic properties of the enzyme. This analysis was complemented by homology-based molecular modeling studies that sought to rationalize the substrate specificity of the enzyme and mode of action through an analysis of the active-site topology of the enzyme including identifying key enzyme-substrate interactions and assigning key amino acids within the active site of the enzyme. Taken together, our structural and biochemical studies indicate that 6-O-sulfatase is a predominantly exolytic enzyme that specifically acts on N-sulfated or N-acetylated 6-O-sulfated glucosamines present at the non-reducing end of HSGAG oligosaccharide substrates. This requirement for the N-acetyl or N-sulfo groups on the glucosamine substrate can be explained through eliciting favorable interactions with key residues within the active site of the enzyme. These findings provide a framework that enables the use of 6-O-sulfatase as a tool for HSGAG structure-activity studies as well as expand our biochemical and structural understanding of this important class of enzymes.

Human cytosolic glutathione-S-transferases: quantitative analysis of expression, comparative analysis of structures and inhibition strategies of isozymes involved in drug resistance.

PubMed

Mohana, Krishnamoorthy; Achary, Anant

2017-08-01

Glutathione-S-transferase (GST) inhibition is a strategy to overcome drug resistance. Several isoforms of human GSTs are present and they are expressed in almost all the organs. Specific expression levels of GSTs in various organs are collected from the human transcriptome data and analysis of the organ-specific expression of GST isoforms is carried out. The variations in the level of expressions of GST isoforms are statistically significant. The GST expression differs in diseased conditions as reported by many investigators and some of the isoforms of GSTs are disease markers or drug targets. Structure analysis of various isoforms is carried out and literature mining has been performed to identify the differences in the active sites of the GSTs. The xenobiotic binding H site is classified into H1, H2, and H3 and the differences in the amino acid composition, the hydrophobicity and other structural features of H site of GSTs are discussed. The existing inhibition strategies are compared. The advent of rational drug design, mechanism-based inhibition strategies, availability of high-throughput screening, target specific, and selective inhibition of GST isoforms involved in drug resistance could be achieved for the reversal of drug resistance and aid in the treatment of diseases.

Cre recombinase-mediated site-specific recombination between plant chromosomes.

PubMed Central

Qin, M; Bayley, C; Stockton, T; Ow, D W

1994-01-01

We report the use of the bacteriophage P1 Cre-lox system for generating conservative site-specific recombination between tobacco chromosomes. Two constructs, one containing a promoterless hygromycin-resistance gene preceded by a lox site (lox-hpt) and the other containing a cauliflower mosaic virus 35S promoter linked to a lox sequence and the cre coding region (35S-lox-cre), were introduced separately into tobacco plants. Crosses between plants harboring either construct produced plants with the two constructs situated on different chromosomes. Plants with recombination events were identified by selecting for hygromycin resistance, a phenotype expressed upon recombination. Molecular analysis showed that these recombination events occurred specifically at the lox sites and resulted in the reciprocal exchange of flanking host DNA. Progenies of these plants showed 67-100% cotransmission of the new transgenes, 35S-lox-hpt and lox-cre, consistent with the preferential cosegregation of translocated chromosomes. These results illustrate that site-specific recombination systems can be useful tools for the large-scale manipulation of eukaryotic chromosomes in vivo. Images PMID:8127869

Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

PubMed

Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

2016-06-07

As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation and implementation of an improved methodology for earthquake ground response analysis : uniform treatment source, path and site effects.

DOT National Transportation Integrated Search

2008-12-01

Shortly after the 1994 Northridge Earthquake, Caltrans geotechnical engineers charged with developing site-specific : response spectra for high priority California bridges initiated a research project aimed at broadening their perspective : from simp...

Cape Blanco wind farm feasibility study

NASA Astrophysics Data System (ADS)

1987-11-01

The Cape Blanco Wind Farm (CBWF) Feasibility Study was undertaken as a prototype for determining the feasibility of proposals for wind energy projects at Northwest sites. It was intended to test for conditions under which wind generation of electricity could be commercially feasible, not by another abstract survey of alternative technologies, but rather through a site-specific, machine-specific analysis of one proposal. Some of the study findings would be most pertinent to the Cape Blanco site - local problems require local solutions. Other findings would be readily applicable to other sites and other machines, and study methodologies would be designed to be modified for appraisal of other proposals. This volume discusses environmental, economic, and technical issues of the Wind Farm.

Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites

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

None

2012-10-24

This plan incorporates U.S. Department of Energy (DOE) Office of Legacy Management (LM) standard operating procedures (SOPs) into environmental monitoring activities and will be implemented at all sites managed by LM. This document provides detailed procedures for the field sampling teams so that samples are collected in a consistent and technically defensible manner. Site-specific plans (e.g., long-term surveillance and maintenance plans, environmental monitoring plans) document background information and establish the basis for sampling and monitoring activities. Information will be included in site-specific tabbed sections to this plan, which identify sample locations, sample frequencies, types of samples, field measurements, and associatedmore » analytes for each site. Additionally, within each tabbed section, program directives will be included, when developed, to establish additional site-specific requirements to modify or clarify requirements in this plan as they apply to the corresponding site. A flowchart detailing project tasks required to accomplish routine sampling is displayed in Figure 1. LM environmental procedures are contained in the Environmental Procedures Catalog (LMS/PRO/S04325), which incorporates American Society for Testing and Materials (ASTM), DOE, and U.S. Environmental Protection Agency (EPA) guidance. Specific procedures used for groundwater and surface water monitoring are included in Appendix A. If other environmental media are monitored, SOPs used for air, soil/sediment, and biota monitoring can be found in the site-specific tabbed sections in Appendix D or in site-specific documents. The procedures in the Environmental Procedures Catalog are intended as general guidance and require additional detail from planning documents in order to be complete; the following sections fulfill that function and specify additional procedural requirements to form SOPs. Routine revision of this Sampling and Analysis Plan will be conducted annually at the beginning of each fiscal year when attachments in Appendix D, including program directives and sampling location/analytical tables, will be reviewed by project personnel and updated. The sampling location/analytical tables in Appendix D, however, may have interim updates according to project direction that are not reflected in this plan. Deviations from location/analytical tables in Appendix D prior to sampling will be documented in project correspondence (e.g., startup letters). If significant changes to other aspects of this plan are required before the annual update, then the plan will be revised as needed.« less

An integrated assessment of location-dependent scaling for microalgae biofuel production facilities

DOE PAGES

Coleman, André M.; Abodeely, Jared M.; Skaggs, Richard L.; ...

2014-06-19

Successful development of a large-scale microalgae-based biofuels industry requires comprehensive analysis and understanding of the feedstock supply chain—from facility siting and design through processing and upgrading of the feedstock to a fuel product. The evolution from pilot-scale production facilities to energy-scale operations presents many multi-disciplinary challenges, including a sustainable supply of water and nutrients, operational and infrastructure logistics, and economic competitiveness with petroleum-based fuels. These challenges are partially addressed by applying the Integrated Assessment Framework (IAF) – an integrated multi-scale modeling, analysis, and data management suite – to address key issues in developing and operating an open-pond microalgae production facility.more » This is done by analyzing how variability and uncertainty over space and through time affect feedstock production rates, and determining the site-specific “optimum” facility scale to minimize capital and operational expenses. This approach explicitly and systematically assesses the interdependence of biofuel production potential, associated resource requirements, and production system design trade-offs. To provide a baseline analysis, the IAF was applied in this paper to a set of sites in the southeastern U.S. with the potential to cumulatively produce 5 billion gallons per year. Finally, the results indicate costs can be reduced by scaling downstream processing capabilities to fit site-specific growing conditions, available and economically viable resources, and specific microalgal strains.« less

Collection, processing and dissemination of data for the national solar demonstration program

NASA Technical Reports Server (NTRS)

Day, R. E.; Murphy, L. J.; Smok, J. T.

1978-01-01

A national solar data system developed for the DOE by IBM provides for automatic gathering, conversion, transfer, and analysis of demonstration site data. NASA requirements for this system include providing solar site hardware, engineering, data collection, and analysis. The specific tasks include: (1) solar energy system design/integration; (2) developing a site data acquisition subsystem; (3) developing a central data processing system; (4) operating the test facility at Marshall Space Flight Center; (5) collecting and analyzing data. The systematic analysis and evaluation of the data from the National Solar Data System is reflected in a monthly performance report and a solar energy system performance evaluation report.

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

PubMed

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

PubMed

Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

2014-04-08

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a "site-specific" homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional "non-site-specific" allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

Assessment of In-Situ Reductive Dechlorination Using Compound-Specific Stable Isotopes, Functional-Gene Pcr, and Geochemical Data

PubMed Central

Carreón-Diazconti, Concepción; Santamaría, Johanna; Berkompas, Justin; Field, James A.; Brusseau, Mark L.

2010-01-01

Isotopic analysis and molecular-based bioassay methods were used in conjunction with geochemical data to assess intrinsic reductive dechlorination processes for a chlorinated-solvent contaminated site in Tucson, Arizona. Groundwater samples were obtained from monitoring wells within a contaminant plume comprising tetrachloroethene and its metabolites trichloroethene, cis-1,2-dichloroethene, vinyl chloride, and ethene, as well as compounds associated with free-phase diesel present at the site. Compound specific isotope (CSI) analysis was performed to characterize biotransformation processes influencing the transport and fate of the chlorinated contaminants. PCR analysis was used to assess the presence of indigenous reductive dechlorinators. The target regions employed were the 16s rRNA gene sequences of Dehalococcoides sp. and Desulfuromonas sp., and DNA sequences of genes pceA, tceA, bvcA, and vcrA, which encode reductive dehalogenases. The results of the analyses indicate that relevant microbial populations are present and that reductive dechlorination is presently occurring at the site. The results further show that potential degrader populations as well as biotransformation activity is non-uniformly distributed within the site. The results of laboratory microcosm studies conducted using groundwater collected from the field site confirmed the reductive dechlorination of tetrachloroethene to dichloroethene. This study illustrates the use of an integrated, multiple-method approach for assessing natural attenuation at a complex chlorinated-solvent contaminated site. PMID:19603638

Mapping of epitopes and structural analysis of antigenic sites in the nucleoprotein of rabies virus.

PubMed

Goto, H; Minamoto, N; Ito, H; Ito, N; Sugiyama, M; Kinjo, T; Kawai, A

2000-01-01

Linear epitopes on the rabies virus nucleoprotein (N) recognized by six MAbs raised against antigenic sites I (MAbs 6-4, 12-2 and 13-27) and IV (MAbs 6-9, 7-12 and 8-1) were investigated. Based on our previous studies on sites I and IV, 24 consecutively overlapping octapeptides and N- and C-terminal-deleted mutant N proteins were prepared. Results showed that all three site I epitopes studied and two site IV epitopes (for MAbs 8-1 and 6-9) mapped to aa 358-367, and that the other site IV epitope of MAb 7-12 mapped to aa 375-383. Tests using chimeric and truncated proteins showed that MAb 8-1 also requires the N-terminal sequence of the N protein to recognize its binding region more efficiently. Immunofluorescence studies demonstrated that all three site I-specific MAbs and one site IV-specific MAb (7-12) stained the N antigen that was diffusely distributed in the whole cytoplasm; the other two site IV-specific MAbs (6-9 and 8-1) detected only the N antigen in the cytoplasmic inclusion bodies (CIB). An antigenic site II-specific MAb (6-17) also detected CIB-associated N antigen alone. Furthermore, the level of diffuse N antigens decreased after treatment of infected cells with cycloheximide. These results suggest that epitopes at site I are expressed on the immature form of the N protein, but epitope structures of site IV MAbs 6-9 and 8-1 are created and/or exposed only after maturation of the N protein.

[Groundwater organic pollution source identification technology system research and application].

PubMed

Wang, Xiao-Hong; Wei, Jia-Hua; Cheng, Zhi-Neng; Liu, Pei-Bin; Ji, Yi-Qun; Zhang, Gan

2013-02-01

Groundwater organic pollutions are found in large amount of locations, and the pollutions are widely spread once onset; which is hard to identify and control. The key process to control and govern groundwater pollution is how to control the sources of pollution and reduce the danger to groundwater. This paper introduced typical contaminated sites as an example; then carried out the source identification studies and established groundwater organic pollution source identification system, finally applied the system to the identification of typical contaminated sites. First, grasp the basis of the contaminated sites of geological and hydrogeological conditions; determine the contaminated sites characteristics of pollutants as carbon tetrachloride, from the large numbers of groundwater analysis and test data; then find the solute transport model of contaminated sites and compound-specific isotope techniques. At last, through groundwater solute transport model and compound-specific isotope technology, determine the distribution of the typical site of organic sources of pollution and pollution status; invest identified potential sources of pollution and sample the soil to analysis. It turns out that the results of two identified historical pollution sources and pollutant concentration distribution are reliable. The results provided the basis for treatment of groundwater pollution.

Inactivation by Phenylglyoxal of the Specific Binding of 1-Naphthyl Acetic Acid with Membrane-Bound Auxin Binding Sites from Maize Coleoptiles

PubMed Central

Navé, Jean-François; Benveniste, Pierre

1984-01-01

The specific binding of 1-[3H]naphthyl acetic acid (NAA) to membrane-bound binding sites from maize (Zea mays cv INRA 258) coleoptiles is inactivated by phenylglyoxal. The inactivation obeys pseudo first-order kinetics. The rate of inactivation is proportional to phenylglyoxal concentration. Under conditions at which significant binding occurs, NAA, R and S-1-naphthyl 2-propionic acids protect the auxin binding site against inactivation by phenylglyoxal. Scatchard analysis shows that the inhibition of binding corresponds to a decrease in the concentration of sites but not in the affinity. The results of the present chemical modification study indicate that at least one arginyl residue is involved in the positively charged recognition site of the carboxylate anion of NAA. PMID:16663499

Planning for Cost Effectiveness.

ERIC Educational Resources Information Center

Schlaebitz, William D.

1984-01-01

A heat pump life-cycle cost analysis is used to explain the technique. Items suggested for the life-cycle analysis approach include lighting, longer-life batteries, site maintenance, and retaining experts to inspect specific building components. (MLF)

Compound-specific carbon isotope analysis of a contaminant plume in Kingsford, Michigan, USA

USGS Publications Warehouse

Michel, R.L.; Silva, S.R.; Bemis, B.; Godsy, E.M.; Warren, E.

2001-01-01

Compound-specific isotope analysis was used to study a contaminated site near Kingsford, Michigan, USA. Organic compounds at three of the sites studied had similar ??13C values indicating that the contaminant source is the same for all sites. At a fourth site, chemical and ??13C values had evolved due to microbial degradation of organics, with the ??13C being much heavier than the starting materials. A microcosm experiment was run to observe isotopic changes with time in the methane evolved and in compounds remaining in the water during degradation. The ??13C values of the methane became heavier during the initial period of the run when volatile fatty acids were being consumed. There was an abrupt decrease in the ??13C values when fatty acids had been consumed and phenols began to be utilized. The ??13C value of the propionate remaining in solution also increased, similar to the results found in the field.

Columbia River Component Data Gap Analysis

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

L. C. Hulstrom

2007-10-23

This Data Gap Analysis report documents the results of a study conducted by Washington Closure Hanford (WCH) to compile and reivew the currently available surface water and sediment data for the Columbia River near and downstream of the Hanford Site. This Data Gap Analysis study was conducted to review the adequacy of the existing surface water and sediment data set from the Columbia River, with specific reference to the use of the data in future site characterization and screening level risk assessments.

Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum.

PubMed Central

Dupont, L; Boizet-Bonhoure, B; Coddeville, M; Auvray, F; Ritzenthaler, P

1995-01-01

Temperate phage mv4 integrates its DNA into the chromosome of Lactobacillus delbrueckii subsp. bulgaricus strains via site-specific recombination. Nucleotide sequencing of a 2.2-kb attP-containing phage fragment revealed the presence of four open reading frames. The larger open reading frame, close to the attP site, encoded a 427-amino-acid polypeptide with similarity in its C-terminal domain to site-specific recombinases of the integrase family. Comparison of the sequences of attP, bacterial attachment site attB, and host-phage junctions attL and attR identified a 17-bp common core sequence, where strand exchange occurs during recombination. Analysis of the attB sequence indicated that the core region overlaps the 3' end of a tRNA(Ser) gene. Phage mv4 DNA integration into the tRNA(Ser) gene preserved an intact tRNA(Ser) gene at the attL site. An integration vector based on the mv4 attP site and int gene was constructed. This vector transforms a heterologous host, L. plantarum, through site-specific integration into the tRNA(Ser) gene of the genome and will be useful for development of an efficient integration system for a number of additional bacterial species in which an identical tRNA gene is present. PMID:7836291

Text Mining Improves Prediction of Protein Functional Sites

PubMed Central

Cohn, Judith D.; Ravikumar, Komandur E.

2012-01-01

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

Formaldehyde activation of mitoxantrone yields CpG and CpA specific DNA adducts

PubMed Central

Parker, Belinda S.; Cutts, Suzanne M.; Cullinane, Carleen; Phillips, Don R.

2000-01-01

Recently we have found that mitoxantrone, like Adriamycin, can be activated by formaldehyde and subsequently form adducts which stabilise double-stranded DNA in vitro. This activation by formaldehyde may be biologically relevant since formaldehyde levels are elevated in those tumours in which mitoxantrone is most cytotoxic. In vitro transcription analysis revealed that these adducts block the progression of RNA polymerase during transcription and cause truncated RNA transcripts. There was an absolute requirement for both mitoxantrone and formaldehyde in transcriptional blockage formation and the activated complex was found to exhibit site specificity, with blockage occurring prior to CpG and CpA sites in the DNA (non-template strand). The stability of the adduct at 37°C was site dependent. The half-lives ranged from 45 min to ~5 h and this was dependent on both the central 2 bp blockage site as well as flanking sequences. The CpG specificity of mitoxantrone adduct sites was also confirmed independently by a λ exonuclease digestion assay. PMID:10648792

Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations.

PubMed

Centler, Florian; Heße, Falk; Thullner, Martin

2013-09-01

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways. © 2013.

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

NASA Astrophysics Data System (ADS)

Crittenden, Christopher M.; Parker, W. Ryan; Jenner, Zachary B.; Bruns, Kerry A.; Akin, Lucas D.; McGee, William M.; Ciccimaro, Eugene; Brodbelt, Jennifer S.

2016-05-01

A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules

PubMed Central

2013-01-01

Background Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription) family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. Results We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM), which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. Conclusions Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors. PMID:23324445

Automated Hazard Analysis

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

Riddle, F. J.

2003-06-26

The Automated Hazard Analysis (AHA) application is a software tool used to conduct job hazard screening and analysis of tasks to be performed in Savannah River Site facilities. The AHA application provides a systematic approach to the assessment of safety and environmental hazards associated with specific tasks, and the identification of controls regulations, and other requirements needed to perform those tasks safely. AHA is to be integrated into existing Savannah River site work control and job hazard analysis processes. Utilization of AHA will improve the consistency and completeness of hazard screening and analysis, and increase the effectiveness of the workmore » planning process.« less

Nuclear factors that bind to the enhancer region of nondefective Friend murine leukemia virus.

PubMed Central

Manley, N R; O'Connell, M A; Sharp, P A; Hopkins, N

1989-01-01

Nondefective Friend murine leukemia virus (MuLV) causes erythroleukemia when injected into newborn NFS mice, while Moloney MuLV causes T-cell lymphoma. Exchange of the Friend virus enhancer region, a sequence of about 180 nucleotides including the direct repeat and a short 3'-adjacent segment, for the corresponding region in Moloney MuLV confers the ability to cause erythroid disease on Moloney MuLV. We have used the electrophoretic mobility shift assay and methylation interference analysis to identify cellular factors which bind to the Friend virus enhancer region and compared these with factors, previously identified, that bind to the Moloney virus direct repeat (N. A. Speck and D. Baltimore, Mol. Cell. Biol. 7:1101-1110, 1987). We identified five binding sites for sequence-specific DNA-binding proteins in the Friend virus enhancer region. While some binding sites are present in both the Moloney and Friend virus enhancers, both viruses contain unique sites not present in the other. Although none of the factors identified in this report which bind to these unique sites are present exclusively in T cells or erythroid cells, they bind to three regions of the enhancer shown by genetic analysis to encode disease specificity and thus are candidates to mediate the tissue-specific expression and distinct disease specificities encoded by these virus enhancer elements. Images PMID:2778872

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

Cho, Seong-Jun; Kang, Hana; Kim, Min Young

Purpose: To determine how low-dose ionizing radiation (LDIR) regulates B lympho-proliferation and its molecular mechanism related with Ikaros, transcription factor. Methods and Materials: Splenocytes and IM-9 cells were uniformly irradiated with various doses of a {sup 137}Cs γ-source, and cell proliferation was analyzed. To determine the LDIR-specific phosphorylation of Ikaros, immunoprecipitation and Western blot analysis were performed. To investigate the physiologic function of LDIR-mediatied Ikaros phosphorylation, Ikaros mutants at phosphorylation sites were generated, and cell cycle analysis was performed. Results: First, we found that LDIR enhances B lymphoblast proliferation in an Ikaros-dependent manner. Moreover, we found that LDIR elevates the phosphorylationmore » level of Ikaros protein. Interestingly, we showed that CK2 and AKT are involved in LDIR-induced Ikaros phosphorylation and capable of regulating DNA binding activity of Ikaros via specific phosphorylation. Finally, we identified LDIR-specific Ikaros phosphorylation sites at S391/S393 and showed that the Ikaros phosphorylations at these sites control Ikaros's ability to regulate G1/S cell cycle progression. Conclusion: Low-dose ionizing radiation specifically phosphorylates Ikaros protein at Ser 391/393 residues to regulate cell cycle progression in B lymphoblast.« less

Mammalian Protein Arginine Methyltransferase 7 (PRMT7) Specifically Targets RXR Sites in Lysine- and Arginine-rich Regions*

PubMed Central

Feng, You; Maity, Ranjan; Whitelegge, Julian P.; Hadjikyriacou, Andrea; Li, Ziwei; Zurita-Lopez, Cecilia; Al-Hadid, Qais; Clark, Amander T.; Bedford, Mark T.; Masson, Jean-Yves; Clarke, Steven G.

2013-01-01

The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7. PMID:24247247

Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions.

PubMed

Feng, You; Maity, Ranjan; Whitelegge, Julian P; Hadjikyriacou, Andrea; Li, Ziwei; Zurita-Lopez, Cecilia; Al-Hadid, Qais; Clark, Amander T; Bedford, Mark T; Masson, Jean-Yves; Clarke, Steven G

2013-12-27

The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7.

Preliminary economic analysis of aquifer winter-chill storage at the John F. Kennedy airport

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

Fox, E.C.; Thomas, J.F.

A conceptual design was formulated in conjuction with a cost analysis to determine the feasibility of retrofitting the present John F. Kennedy (JFK) airport air-conditioning system with an aquifer cold water storage system. It appears technically feasible to chill and store aquifer water at the airport site during the winter months for later air-conditioning use. However, the economic analysis shows that although a significant energy savings is realized, the money saved from reduced energy costs would not be enough to recover the necessary capital investment over a 20-year period. JFK airport may be a poor economic choice for an aquifermore » cold water storage demonstration site due to site specific problems, and other sites may provide economic incentive.« less

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

PubMed

Arenillas, David J; Forrest, Alistair R R; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W; Mathelier, Anthony

2016-09-15

With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM CONTACTS: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

PubMed Central

Arenillas, David J.; Forrest, Alistair R. R.; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W.; Mathelier, Anthony

2016-01-01

With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. Availability and Implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM. Contacts: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27334471

Critical radionuclide/critical pathway analysis for the U.S. Department of Energy's Savannah River Site.

PubMed

Jannik, G T

1999-06-01

Many different radionuclides have been released to the environment from the Savannah River Site (SRS) during the facility's operational history. However, as shown by this analysis, only a small number of the released radionuclides have been significant contributors to potential doses and risks to off-site people. This article documents the radiological critical contaminant/critical pathway analysis performed for SRS. If site missions and operations remain constant over the next 30 years, only tritium oxide releases are projected to exceed a maximally exposed individual (MEI) risk of 1.0E-06 for either the airborne or liquid pathways. The critical exposure pathways associated with site airborne releases are inhalation and vegetation consumption, whereas the critical exposure pathways associated with liquid releases are drinking water and fish consumption. For the SRS-specific, nontypical exposure pathways (i.e., recreational fishing and deer and hog hunting), cesium-137 is the critical radionuclide.

Site-Specific Protein Adducts of 4-Hydroxy-2(E)-Nonenal in Human THP-1 Monocytic Cells: Protein Carbonylation Is Diminished by Ascorbic Acid

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

Chavez, Juan; Chung, Woon-Gye; Miranda, Cristobal L.

2010-01-18

The protein targets and sites of modification by 4-hydroxy-2(E)-nonenal (HNE) in human monocytic THP-1 cells after exogenous exposure to HNE were examined using a multipronged proteomic approach involving electrophoretic, immunoblotting, and mass spectrometric methods. Immunoblot analysis using monoclonal anti-HNE antibodies showed several proteins as targets of HNE adduction. Pretreatment of THP-1 cells with ascorbic acid resulted in reduced levels of HNE-protein adducts. Biotinylation of Michael-type HNE adducts using an aldehyde-reactive hydroxylamine-functionalized probe (aldehyde-reactive probe, ARP) and subsequent enrichment facilitated the identification and site-specific assignment of the modifications by LC-MS/MS analysis. Sixteen proteins were unequivocally identified as targets of HNE adduction,more » and eighteen sites of HNE modification at Cys and His residues were assigned. HNE exposure of THP-1 cells resulted in the modification of proteins involved in cytoskeleton organization and regulation, proteins associated with stress responses, and enzymes of the glycolytic and other metabolic pathways. Finally, this study yielded the first evidence of site-specific adduction of HNE to Cys-295 in tubulin α-1B chain, Cys-351 and Cys-499 in α-actinin-4, Cys-328 in vimentin, Cys-369 in d-3-phosphoglycerate dehydrogenase, and His-246 in aldolase A.« less

Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites.

PubMed

Fang, Chun; Noguchi, Tamotsu; Yamana, Hayato

2014-10-01

Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

The influence of sex and trauma impact on the rupture site of the ulnar collateral ligament of the thumb.

PubMed

Boesmueller, Sandra; Huf, Wolfgang; Rettl, Gregor; Dahm, Falko; Meznik, Alexander; Muschitz, Gabriela; Kitzinger, Hugo; Bukaty, Adam; Fialka, Christian; Vierhapper, Martin

2017-01-01

Although sex- and gender-specific analyses have been gaining more attention during the last years they have rarely been performed in orthopaedic literature. The primary purpose of this study was to investigate whether for injuries of the UCL the specific location of the rupture is influenced by sex. A secondary study question addressed the sex-independent effect of trauma intensity on the rupture site of the UCL. This study is a retrospective analysis of all patients with either a proximal or distal bony avulsion or with a mid-substance tear or ligament avulsion of the UCL treated surgically between 1992 and 2015 at two level-I trauma centres. Trauma mechanisms leading to the UCL injury were classified into the following categories: (1) blunt trauma (i.e., strains), (2) low-velocity injuries (e.g., fall from standing height, assaults), and (3) high-velocity injuries (e.g., sports injuries, motor vehicle accidents). After reviewing the surgical records, patients were divided into three groups, depending upon the ligament rupture site: (1) mid-substance tears, (2) proximal ligament or bony avulsions and (3) distal ligament or bony avulsions. Dependencies between the specific rupture site and the explanatory variables (sex, age, and trauma intensity) were evaluated using χ2 test and logistic regression analysis. In total, 1582 patients (1094 males, 488 females) met the inclusion criteria. Mean age was 41 years (range: 9-90 years). Taking into account the effects of sex on trauma intensity (p<0.001) and of trauma intensity on rupture site (p<0.001), mid-substance tears occurred more frequently in women, whereas men were more prone to distal ligament or bony avulsions (p<0.001). In other words, sex and rupture site correlated due to the effects of sex on trauma intensity and of trauma intensity on rupture site, but taking into account those effects there still was a significant effect of sex on rupture site. The results of this study demonstrate that with regression analysis both sex and trauma intensity allow to predict rupture site in UCL injuries.

The influence of sex and trauma impact on the rupture site of the ulnar collateral ligament of the thumb

PubMed Central

Huf, Wolfgang; Rettl, Gregor; Dahm, Falko; Meznik, Alexander; Muschitz, Gabriela; Kitzinger, Hugo; Bukaty, Adam; Fialka, Christian; Vierhapper, Martin

2017-01-01

Purpose and hypothesis Although sex- and gender-specific analyses have been gaining more attention during the last years they have rarely been performed in orthopaedic literature. The primary purpose of this study was to investigate whether for injuries of the UCL the specific location of the rupture is influenced by sex. A secondary study question addressed the sex-independent effect of trauma intensity on the rupture site of the UCL. Methods This study is a retrospective analysis of all patients with either a proximal or distal bony avulsion or with a mid-substance tear or ligament avulsion of the UCL treated surgically between 1992 and 2015 at two level-I trauma centres. Trauma mechanisms leading to the UCL injury were classified into the following categories: (1) blunt trauma (i.e., strains), (2) low-velocity injuries (e.g., fall from standing height, assaults), and (3) high-velocity injuries (e.g., sports injuries, motor vehicle accidents). After reviewing the surgical records, patients were divided into three groups, depending upon the ligament rupture site: (1) mid-substance tears, (2) proximal ligament or bony avulsions and (3) distal ligament or bony avulsions. Dependencies between the specific rupture site and the explanatory variables (sex, age, and trauma intensity) were evaluated using χ2 test and logistic regression analysis. Results In total, 1582 patients (1094 males, 488 females) met the inclusion criteria. Mean age was 41 years (range: 9–90 years). Taking into account the effects of sex on trauma intensity (p<0.001) and of trauma intensity on rupture site (p<0.001), mid-substance tears occurred more frequently in women, whereas men were more prone to distal ligament or bony avulsions (p<0.001). In other words, sex and rupture site correlated due to the effects of sex on trauma intensity and of trauma intensity on rupture site, but taking into account those effects there still was a significant effect of sex on rupture site. Conclusions The results of this study demonstrate that with regression analysis both sex and trauma intensity allow to predict rupture site in UCL injuries. PMID:28738083

AAVS1-Targeted Plasmid Integration in AAV Producer Cell Lines.

PubMed

Luo, Yuxia; Frederick, Amy; Martin, John M; Scaria, Abraham; Cheng, Seng H; Armentano, Donna; Wadsworth, Samuel C; Vincent, Karen A

2017-06-01

Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield. Plasmid integration sites within several independent cell lines were assessed via Southern, fluorescence in situ hybridization (FISH) and PCR analyses. In the Southern analyses, the presence of fragments detected by both rep- and AAVS1-specific probes suggested that for several mid- and high-producing lines, plasmid DNA had integrated into the AAVS1 locus. Analysis with puroR and AAVS1-specific probes suggested that integration in AAVS1 was a more widespread phenomenon. High-producing AAV2-secreted alkaline phosphatase (SEAP) lines (masterwell 82 [MW82] and MW278) were evaluated via FISH using probes specific for the plasmid, AAVS1, and a chr19 marker. FISH analysis detected two plasmid integration sites in MW278 (neither in AAVS1), while a total of three sites were identified in MW82 (two in AAVS1). An inverse PCR assay confirmed integration within AAVS1 for several mid- and high-producing lines. In summary, the FISH, Southern, and PCR data provide evidence of site-specific integration of the plasmid within AAVS1 in several AAV producer cell lines. The data also suggest that integration in AAVS1 is a general phenomenon that is not necessarily restricted to high producers. The results also suggest that plasmid integration within the AAVS1 locus is not an absolute requirement for a high vector yield.

Repeatable source, site, and path effects on the standard deviation for empirical ground-motion prediction models

USGS Publications Warehouse

Lin, P.-S.; Chiou, B.; Abrahamson, N.; Walling, M.; Lee, C.-T.; Cheng, C.-T.

2011-01-01

In this study, we quantify the reduction in the standard deviation for empirical ground-motion prediction models by removing ergodic assumption.We partition the modeling error (residual) into five components, three of which represent the repeatable source-location-specific, site-specific, and path-specific deviations from the population mean. A variance estimation procedure of these error components is developed for use with a set of recordings from earthquakes not heavily clustered in space.With most source locations and propagation paths sampled only once, we opt to exploit the spatial correlation of residuals to estimate the variances associated with the path-specific and the source-location-specific deviations. The estimation procedure is applied to ground-motion amplitudes from 64 shallow earthquakes in Taiwan recorded at 285 sites with at least 10 recordings per site. The estimated variance components are used to quantify the reduction in aleatory variability that can be used in hazard analysis for a single site and for a single path. For peak ground acceleration and spectral accelerations at periods of 0.1, 0.3, 0.5, 1.0, and 3.0 s, we find that the singlesite standard deviations are 9%-14% smaller than the total standard deviation, whereas the single-path standard deviations are 39%-47% smaller.

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Uncertainty analysis of the simulations of effects of discharging treated wastewater to the Red River of the North at Fargo, North Dakota, and Moorhead, Minnesota

USGS Publications Warehouse

Wesolowski, Edwin A.

1996-01-01

Two separate studies to simulate the effects of discharging treated wastewater to the Red River of the North at Fargo, North Dakota, and Moorhead, Minnesota, have been completed. In the first study, the Red River at Fargo Water-Quality Model was calibrated and verified for icefree conditions. In the second study, the Red River at Fargo Ice-Cover Water-Quality Model was verified for ice-cover conditions.To better understand and apply the Red River at Fargo Water-Quality Model and the Red River at Fargo Ice-Cover Water-Quality Model, the uncertainty associated with simulated constituent concentrations and property values was analyzed and quantified using the Enhanced Stream Water Quality Model-Uncertainty Analysis. The Monte Carlo simulation and first-order error analysis methods were used to analyze the uncertainty in simulated values for six constituents and properties at sites 5, 10, and 14 (upstream to downstream order). The constituents and properties analyzed for uncertainty are specific conductance, total organic nitrogen (reported as nitrogen), total ammonia (reported as nitrogen), total nitrite plus nitrate (reported as nitrogen), 5-day carbonaceous biochemical oxygen demand for ice-cover conditions and ultimate carbonaceous biochemical oxygen demand for ice-free conditions, and dissolved oxygen. Results are given in detail for both the ice-cover and ice-free conditions for specific conductance, total ammonia, and dissolved oxygen.The sensitivity and uncertainty of the simulated constituent concentrations and property values to input variables differ substantially between ice-cover and ice-free conditions. During ice-cover conditions, simulated specific-conductance values are most sensitive to the headwatersource specific-conductance values upstream of site 10 and the point-source specific-conductance values downstream of site 10. These headwater-source and point-source specific-conductance values also are the key sources of uncertainty. Simulated total ammonia concentrations are most sensitive to the point-source total ammonia concentrations at all three sites. Other input variables that contribute substantially to the variability of simulated total ammonia concentrations are the headwater-source total ammonia and the instream reaction coefficient for biological decay of total ammonia to total nitrite. Simulated dissolved-oxygen concentrations at all three sites are most sensitive to headwater-source dissolved-oxygen concentration. This input variable is the key source of variability for simulated dissolved-oxygen concentrations at sites 5 and 10. Headwatersource and point-source dissolved-oxygen concentrations are the key sources of variability for simulated dissolved-oxygen concentrations at site 14.During ice-free conditions, simulated specific-conductance values at all three sites are most sensitive to the headwater-source specific-conductance values. Headwater-source specificconductance values also are the key source of uncertainty. The input variables to which total ammonia and dissolved oxygen are most sensitive vary from site to site and may or may not correspond to the input variables that contribute the most to the variability. The input variables that contribute the most to the variability of simulated total ammonia concentrations are pointsource total ammonia, instream reaction coefficient for biological decay of total ammonia to total nitrite, and Manning's roughness coefficient. The input variables that contribute the most to the variability of simulated dissolved-oxygen concentrations are reaeration rate, sediment oxygen demand rate, and headwater-source algae as chlorophyll a.

Multi-Site Quality Assurance Project Plan for Wisconsin Public Service Corporation, Peoples Gas Light and Coke Company, and North Shore Gas

EPA Pesticide Factsheets

This Multi-Site QAPP presents the organization, data quality objectives (DQOs), a set of anticipated activities, sample analysis, data handling and specific Quality Assurance/Quality Control (QA/QC) procedures associated with Studies done in EPA Region 5

[Analysis of heat transfer in the biological tissue layer with distributed system of blood vessels].

PubMed

Bogatov, N M; Pelipenko, O N

2005-09-01

Processes of heat transfer in the skin layer with blood vessels were investigated using mathematical modeling. Analysis of influence of a pathological state of blood vessels on heterogeneity of thermal field of the skin surface was carried out. For each site of body surface, there is a certain difference of temperature between normal and pathological sites, being specific for differential diagnosis of diseases of dermal and hypodermic vessels.

Earthquake ground motion: Chapter 3

USGS Publications Warehouse

Luco, Nicolas; Kircher, Charles A.; Crouse, C. B.; Charney, Finley; Haselton, Curt B.; Baker, Jack W.; Zimmerman, Reid; Hooper, John D.; McVitty, William; Taylor, Andy

2016-01-01

Most of the effort in seismic design of buildings and other structures is focused on structural design. This chapter addresses another key aspect of the design process—characterization of earthquake ground motion into parameters for use in design. Section 3.1 describes the basis of the earthquake ground motion maps in the Provisions and in ASCE 7 (the Standard). Section 3.2 has examples for the determination of ground motion parameters and spectra for use in design. Section 3.3 describes site-specific ground motion requirements and provides example site-specific design and MCER response spectra and example values of site-specific ground motion parameters. Section 3.4 discusses and provides an example for the selection and scaling of ground motion records for use in various types of response history analysis permitted in the Standard.

Proteomic Analysis of Arginine Methylation Sites in Human Cells Reveals Dynamic Regulation During Transcriptional Arrest*

PubMed Central

Sylvestersen, Kathrine B.; Horn, Heiko; Jungmichel, Stephanie; Jensen, Lars J.; Nielsen, Michael L.

2014-01-01

The covalent attachment of methyl groups to the side-chain of arginine residues is known to play essential roles in regulation of transcription, protein function, and RNA metabolism. The specific N-methylation of arginine residues is catalyzed by a small family of gene products known as protein arginine methyltransferases; however, very little is known about which arginine residues become methylated on target substrates. Here we describe a proteomics methodology that combines single-step immunoenrichment of methylated peptides with high-resolution mass spectrometry to identify endogenous arginine mono-methylation (MMA) sites. We thereby identify 1027 site-specific MMA sites on 494 human proteins, discovering numerous novel mono-methylation targets and confirming the majority of currently known MMA substrates. Nuclear RNA-binding proteins involved in RNA processing, RNA localization, transcription, and chromatin remodeling are predominantly found modified with MMA. Despite this, MMA sites prominently are located outside RNA-binding domains as compared with the proteome-wide distribution of arginine residues. Quantification of arginine methylation in cells treated with Actinomycin D uncovers strong site-specific regulation of MMA sites during transcriptional arrest. Interestingly, several MMA sites are down-regulated after a few hours of transcriptional arrest. In contrast, the corresponding di-methylation or protein expression levels are not altered, confirming that MMA sites contain regulated functions on their own. Collectively, we present a site-specific MMA data set in human cells and demonstrate for the first time that MMA is a dynamic post-translational modification regulated during transcriptional arrest by a hitherto uncharacterized arginine demethylase. PMID:24563534

Streamflow, specific-conductance, and temperature data for Bayou and Little Bayou Creeks near Paducah, Kentucky, August 15 and 16, 1989

USGS Publications Warehouse

Evaldi, R.D.; McClain, D.L.

1989-01-01

Discharge, temperature, and specific conductance measurements were made August 15 and 16, 1989, at 74 main channel sites and seven flowing tributaries on Bayou and Little Bayou Creeks, Kentucky in the vicinity of the Paducah Gaseous Diffusion Plant. These measurements were made during base flow conditions to provide data for analysis of the interaction of surface and groundwater. The discharge of Bayou Creek was 0.30 cfs at the most upstream site, and 5.8 cfs at the most downstream site. Total measured tributary inflow of Bayou Creek was 5.7 cfs. Specific conductance values in the Bayou Creek watershed ranged from 208 to 489 microsiemens/cm, and water temperature ranged from 20.0 to 32.6 C. The discharge of Little Bayou Creek was 0.65 cfs at the most upstream site, and 1.8 cfs at the most downstream site. Total measured tributary inflow of Little Bayou Creek was 0.38 cfs. Specific conductance values in the Little Bayou Creek watershed ranged from 211 to 272 microsiemens/cm, and water temperature ranged from 14.5 to 24.9 C. (USGS)

Landsat-TM identification of Amblyomma variegatum (Acari: Ixodidae) habitats in Guadeloupe

NASA Technical Reports Server (NTRS)

Hugh-Jones, M.; Barre, N.; Nelson, G.; Wehnes, K.; Warner, J.; Garvin, J.; Garris, G.

1992-01-01

The feasibility of identifying specific habitats of the African bont tick, Amblyomma variegatum, from Landsat-TM images was investigated by comparing remotely sensed images of visible farms in Grande Terre (Guadeloupe) with field observations made in the same period of time (1986-1987). The different tick habitates could be separated using principal component analysis. The analysis clustered the sites by large and small variance of band values, and by vegetation and moisture indexes. It was found that herds in heterogeneous sites with large variances had more ticks than those in homogeneous or low variance sites. Within the heterogeneous sites, those with high vegetation and moisture indexes had more ticks than those with low values.

Hierarchy within the mammary STAT5-driven Wap super-enhancer.

PubMed

Shin, Ha Youn; Willi, Michaela; HyunYoo, Kyung; Zeng, Xianke; Wang, Chaochen; Metser, Gil; Hennighausen, Lothar

2016-08-01

Super-enhancers comprise dense transcription factor platforms highly enriched for active chromatin marks. A paucity of functional data led us to investigate the role of super-enhancers in the mammary gland, an organ characterized by exceptional gene regulatory dynamics during pregnancy. ChIP-seq analysis for the master regulator STAT5A, the glucocorticoid receptor, H3K27ac and MED1 identified 440 mammary-specific super-enhancers, half of which were associated with genes activated during pregnancy. We interrogated the Wap super-enhancer, generating mice carrying mutations in STAT5-binding sites within its constituent enhancers. Individually, the most distal site displayed the greatest enhancer activity. However, combinatorial mutation analysis showed that the 1,000-fold induction in gene expression during pregnancy relied on all enhancers. Disabling the binding sites of STAT5, NFIB and ELF5 in the proximal enhancer incapacitated the entire super-enhancer. Altogether, these data suggest a temporal and functional enhancer hierarchy. The identification of mammary-specific super-enhancers and the mechanistic exploration of the Wap locus provide insights into the regulation of cell-type-specific expression of hormone-sensing genes.

A content analysis of Web sites promoting smoking culture and lifestyle.

PubMed

Ribisl, Kurt M; Lee, Rebecca E; Henriksen, Lisa; Haladjian, Harry H

2003-02-01

The present study examined smoking culture and lifestyle Web sites listed on Yahoo!, a popular Internet search catalog, to determine whether the sites were easily accessible to youth, featured age or health warnings, and mentioned specific tobacco brands. A content analysis of photographs on these sites assessed the demographics of individuals depicted and the amount of smoking and nudity in the photographs. The sample included 30 Web sites, all of which were accessible to youth and did not require age verification services to enter them. Cigarette brand names were mentioned in writing on 35% of the sites, and brand images were present on 24% of the sites. Nearly all of the photographs (95%) depicted smoking, 92% featured women, and 7% contained partial or full nudity. These results underscore the need for greater research and monitoring of smoking-related Internet content by health educators and tobacco control advocates.

Systems analysis of singly and multiply O-glycosylated peptides in the human serum glycoproteome via EThcD and HCD mass spectrometry.

PubMed

Zhang, Yong; Xie, Xinfang; Zhao, Xinyuan; Tian, Fang; Lv, Jicheng; Ying, Wantao; Qian, Xiaohong

2018-01-06

Human serum has been intensively studied to identify biomarkers via global proteomic analysis. The altered O-glycoproteome is associated with human pathological state including cancer, inflammatory and degenerative diseases and is an attractive source of disease biomarkers. Because of the microheterogeneity and macroheterogeneity of O-glycosylation, site-specific O-glycosylation analysis in human serum is still challenging. Here, we developed a systematic strategy that combined multiple enzyme digestion, multidimensional separation for sample preparation and high-resolution tandem MS with Byonic software for intact O-glycopeptide characterization. We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD is not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Totally, with the strict scoring criteria, 499 non-redundant intact O-glycopeptides, 173 O-glycosylation sites and 6 types of O-glycans originating from 49 O-glycoprotein groups were identified in human serum, including 121 novel O-glycosylation sites. Currently, this is the largest data set of site-specific native O-glycoproteome from human serum samples. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and provide opportunities to understand the functional roles of protein O-glycosylation in human health and diseases. The altered O-glycoproteome is associated with human pathological state and is an attractive source of disease biomarkers. However, site-specific O-glycosylation analysis is challenging because of the microheterogeneity (different glycoforms attached to one glycosylation site) and macroheterogeneity (site occupancy) of O-glycosylation. In this work, we developed a systematic strategy for intact O-glycopeptide characterization. This study took advantage of the inherent properties of the new fragmentation method called EThcD, which provides more complete fragmentation information about O-glycosylated peptides and a more confident site localization of O-glycans than collision-induced dissociation (HCD). We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD was not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Finally, we got a largest data set of site-specific native O-glycoproteome from human serum samples. Furthermore, quantitative analysis of intact O-glycopeptides from the serum samples of IgA nephropathy (IgAN) patients and healthy donors was performed, and the results showed the potential of the strategy to discover O-glycosylation biomarkers. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and lead to exciting opportunities to understand the functional roles of protein O-glycosylation in human health and diseases. Copyright © 2017. Published by Elsevier B.V.

Analysis of polycyclic aromatic hydrocarbons in tree-rings of Masson pine (Pinus massoniana L.) from two industrial sites in the Pearl River Delta, south China.

PubMed

Kuang, Yuan-wen; Zhou, Guo-yi; Wen, Da-zhi; Li, Jiong; Sun, Fang-fang

2011-09-01

Concentrations of polycyclic aromatic hydrocarbons (PAHs) were examined and potential sources of PAHs were identified from the dated tree-rings of Masson pine (Pinus massoniana L.) near two industrial sites (Danshuikeng, DSK and Xiqiaoshan, XQS) in the Pearl River Delta of south China. Total concentrations of PAHs (∑PAHs) were revealed with similar patterns of temporal trends in the tree-rings at both sites, suggesting tree-rings recorded the historical variation in atmospheric PAHs. The differences of individual PAHs and of ∑PAHs detected in the tree-rings between the two sites reflected the historical differences of airborne PAHs. Regional changes in industrial activities might contribute to the site-specific and period-specific patterns of the tree-ring PAHs. The diagnostic PAH ratios of Ant/(Ant + PA), FL/(FL + Pyr), and BaA/(BaA + Chr)) revealed that PAHs in the tree-rings at both sites mainly stemmed from the combustion process (pyrogenic sources). Principal component analysis further confirmed that wood burning, coal combustion, diesel, and gasoline-powered vehicular emissions were the dominant contributors of PAHs sources at DSK, while diesel combustion, gasoline and natural gas combustion, and incomplete coal combustion were responsible for the main origins of PAHs at XQS. Tree-ring analysis of PAHs was indicative of PAHs from a mixture of sources of combustion, thus minimizing the bias of short-term active air sampling.

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

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

Solovyev, V.V.; Salamov, A.A.; Lawrence, C.B.

1994-12-31

Discriminant analysis is applied to the problem of recognition 5`-, internal and 3`-exons in human DNA sequences. Specific recognition functions were developed for revealing exons of particular types. The method based on a splice site prediction algorithm that uses the linear Fisher discriminant to combine the information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotide in protein coding and nation regions. The accuracy of our splice site recognition function is about 97%. A discriminant function for 5`-exon prediction includes hexanucleotide composition of upstream region, triplet composition around the ATG codon, ORF codingmore » potential, donor splice site potential and composition of downstream introit region. For internal exon prediction, we combine in a discriminant function the characteristics describing the 5`- intron region, donor splice site, coding region, acceptor splice site and Y-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79% and a level of pseudoexon ORF prediction of 99.96%. The recognition quality computed at the level of individual nucleotides is 89%, for exon sequences and 98% for intron sequences. A discriminant function for 3`-exon prediction includes octanucleolide composition of upstream nation region, triplet composition around the stop codon, ORF coding potential, acceptor splice site potential and hexanucleotide composition of downstream region. We unite these three discriminant functions in exon predicting program FEX (find exons). FEX exactly predicts 70% of 1016 exons from the test of 181 complete genes with specificity 73%, and 89% exons are exactly or partially predicted. On the average, 85% of nucleotides were predicted accurately with specificity 91%.« less

NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region.

PubMed Central

Stamatoyannopoulos, J A; Goodwin, A; Joyce, T; Lowrey, C H

1995-01-01

The beta-like globin genes require the upstream locus control region (LCR) for proper expression. The active elements of the LCR coincide with strong erythroid-specific DNase I-hypersensitive sites (HSs). We have used 5' HS4 as a model to study the formation of these HSs. Previously, we identified a 101 bp element that is required for the formation of this HS. This element binds six proteins in vitro. We now report a mutational analysis of the HS4 HS-forming element (HSFE). This analysis indicates that binding sites for the hematopoietic transcription factors NF-E2 and GATA-1 are required for the formation of the characteristic chromatin structure of the HS following stable transfection into murine erythroleukemia cells. Similarly arranged NF-E2 and GATA binding sites are present in the other HSs of the human LCR, as well as in the homologous mouse and goat sequences and the chicken beta-globin enhancer. A combination of DNase I and micrococcal nuclease sensitivity assays indicates that the characteristic erythroid-specific hypersensitivity of HS4 to DNase I is the result of tissue-specific alterations in both nucleosome positioning and tertiary DNA structure. Images PMID:7828582

Multi-element compound specific stable isotope analysis of chlorinated aliphatic contaminants derived from chlorinated pitches.

PubMed

Filippini, Maria; Nijenhuis, Ivonne; Kümmel, Steffen; Chiarini, Veronica; Crosta, Giovanni; Richnow, Hans H; Gargini, Alessandro

2018-05-30

Tetrachloroethene and trichloroethene are typical by-products of the industrial production of chloromethanes. These by-products are known as "chlorinated pitches" and were often dumped in un-contained waste disposal sites causing groundwater contaminations. Previous research showed that a strongly depleted stable carbon isotope signature characterizes chlorinated compounds associated with chlorinated pitches whereas manufactured commercial compounds have more enriched carbon isotope ratios. The findings were restricted to a single case study and one element (i.e. carbon). This paper presents a multi-element Compound-Specific Stable Isotope Analysis (CSIA, including carbon, chlorine and hydrogen) of chlorinated aliphatic contaminants originated from chlorinated pitches at two sites with different hydrogeology and different producers of chloromethanes. The results show strongly depleted carbon signatures at both sites whereas the chlorine and the hydrogen signatures are comparable to those presented in the literature for manufactured commercial compounds. Multi-element CSIA allowed the identification of sources and site-specific processes affecting chloroethene transformation in groundwater as a result of emergency remediation measures. CSIA turned out to be an effective forensic tool to address the liability for the contamination, leading to a conviction for the crimes of unintentional aggravated public water supply poisoning and environmental disaster. Copyright © 2018 Elsevier B.V. All rights reserved.

Cognitive and Affective Uses of a Thoracic Outlet Syndrome Facebook Support Group.

PubMed

Walker, Kimberly K

2014-09-01

There are currently many disease-specific groups on Facebook in which patients may take an active part (Greene, Choudhry, Kilabuk, & Shrank, 2011). Although uses and gratifications of patient-disease groups have begun to be identified for chronic diseases, rare diseases have been omitted, even though they collectively affect roughly 30 million people in the United States and 350 million people worldwide. This study is a content analysis of one Facebook rare disease patient group, the Thoracic Outlet Syndrome (TOS) Awareness group. All wall posts were recorded and content analyzed for cognitive and affective categories and subcategories between October 9, 2011 (date of site origin), and May 1, 2012. Analysis of cognitive needs indicated TOS patients used the site more to share information about their own TOS symptoms and journey with diagnosis than to seek information. Analysis of affective needs found patients were more likely to use the site to give support and encouragement to others than to express concerns and complaints. The complaints they did express were primarily related to their frustration with the general medical community's perceived inability to diagnose and understand their disease or to question a specific doctor's diagnosis/recommendation. Results point to needs specific to TOS patients that uses and gratifications research can help clarify.

Symmetry of Fv architecture is conducive to grafting a second antibody binding site in the Fv region.

PubMed Central

Keck, P C; Huston, J S

1996-01-01

Molecular modeling studies on antibody Fv regions have been pursued to design a second antigen-binding site (chi-site) in a chimeric single-chain Fv (chi sFv) species of about 30 kDa. This analysis has uncovered an architectural basis common to many Fv regions that permits grafting a chi-site onto the Fv surface that diametrically opposes the normal combining site. By using molecular graphics analysis, chimeric complementarity-determining regions (chi CDRs) were defined that comprised most of the CDRs from an antibody binding site of interest. The chain directionality of chi CDRs was consistent with that of specific bottom loops of the sFv, which allowed for grafting of chi CDRs with an overall geometry approximating CDRs in the parent combining site. Analysis of 10 different Fv crystal structures indicates that the positions for inserting chi CDRs are very highly conserved, as are the corresponding chi CDR boundaries in the parent binding site. The results of this investigation suggest that it should be possible to generally apply this approach to the development of chimeric bispecific antibody binding site (chi BABS) proteins. Images FIGURE 2 FIGURE 3 PMID:8889174

Radioimmunoassays and 2-site immunoradiometric "sandwich" assays: basic principles.

PubMed

Rodbard, D

1988-10-01

The "sandwich" or noncompetitive reagent-excess, 2-site immunoradiometric assay (2-site IRMA), ELISA, USERIA, and related techniques, have several advantages compared with the traditional or competitive radioimmunoassays. IRMAs can provide improved sensitivity and specificity. However, IRMAs present some practical problems with nonspecific binding, increased consumption of antibody, biphasic dose response curve, (high dose hook effect), and may require special techniques for dose response curve analysis. We anticipate considerable growth in the popularity and importance of 2-site IRMA.

Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

PubMed

Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

2015-03-01

Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed.

Use of on-site high performance liquid chromatography to evaluate the magnitude and extent of organic contaminants in aquifers

USGS Publications Warehouse

Goerlitz, D.F.; Franks, B.J.

1989-01-01

Appraisal of ground water contaminated by organic substances raises problems of difficult sample collection and timely chemical analysis. High-performance liquid chromatography was evaluated for on-site determination of specific organic contaminants in ground water samples and was used at three study sites. Organic solutes were determined directly in water samples, with little or no preparation, and usually in less than an hour after collection. This information improved sampling efficiency and was useful in screening for subsequent laboratory analysis. On two occasions, on-site analysis revealed that samples were undergoing rapid change, with major solutes being upgraded and alteration products being formed. In addition to sample stability, this technique proved valuable for monitoring other sampling factors such as compositional changes with respect to pumping, filtration, and cross contamination. -Authors

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

PubMed

Waszak, Sebastian M; Kilpinen, Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil T; Deplancke, Bart

2014-01-15

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. The R package abs filter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter

Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation

PubMed Central

Li, Ao; Wang, Minghui

2015-01-01

Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue. We found that proteins with in situ O-GlcNAc/Phos cross talk were significantly enriched in some specific gene ontology terms and no obvious evolutionary pressure was observed. Moreover, 3 functional motifs associated with O-GlcNAc/Phos sites were extracted. We further used sequence features and GO features to predict O-GlcNAc/Phos cross talk sites based on phosphorylated sites and O-GlcNAcylated sites separately by the use of SVM model. The AUC of classifier based on phosphorylated sites is 0.896 and the other classifier based on GlcNAcylated sites is 0.843. Both classifiers achieved a relatively better performance compared with other existing methods. PMID:26601103

Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation.

PubMed

Yao, Heming; Li, Ao; Wang, Minghui

2015-01-01

Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue. We found that proteins with in situ O-GlcNAc/Phos cross talk were significantly enriched in some specific gene ontology terms and no obvious evolutionary pressure was observed. Moreover, 3 functional motifs associated with O-GlcNAc/Phos sites were extracted. We further used sequence features and GO features to predict O-GlcNAc/Phos cross talk sites based on phosphorylated sites and O-GlcNAcylated sites separately by the use of SVM model. The AUC of classifier based on phosphorylated sites is 0.896 and the other classifier based on GlcNAcylated sites is 0.843. Both classifiers achieved a relatively better performance compared with other existing methods.

Comprehensive analysis of MGMT promoter methylation: correlation with MGMT expression and clinical response in GBM.

PubMed

Shah, Nameeta; Lin, Biaoyang; Sibenaller, Zita; Ryken, Timothy; Lee, Hwahyung; Yoon, Jae-Geun; Rostad, Steven; Foltz, Greg

2011-01-07

O⁶-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR  = 5.23, 95% CI [2.089-13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR  = 3.076, 95% CI [1.301-7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting.

Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM

PubMed Central

Shah, Nameeta; Lin, Biaoyang; Sibenaller, Zita; Ryken, Timothy; Lee, Hwahyung; Yoon, Jae-Geun; Rostad, Steven; Foltz, Greg

2011-01-01

O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR  = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR  = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting. PMID:21249131

A Gibbs sampler for Bayesian analysis of site-occupancy data

USGS Publications Warehouse

Dorazio, Robert M.; Rodriguez, Daniel Taylor

2012-01-01

1. A Bayesian analysis of site-occupancy data containing covariates of species occurrence and species detection probabilities is usually completed using Markov chain Monte Carlo methods in conjunction with software programs that can implement those methods for any statistical model, not just site-occupancy models. Although these software programs are quite flexible, considerable experience is often required to specify a model and to initialize the Markov chain so that summaries of the posterior distribution can be estimated efficiently and accurately. 2. As an alternative to these programs, we develop a Gibbs sampler for Bayesian analysis of site-occupancy data that include covariates of species occurrence and species detection probabilities. This Gibbs sampler is based on a class of site-occupancy models in which probabilities of species occurrence and detection are specified as probit-regression functions of site- and survey-specific covariate measurements. 3. To illustrate the Gibbs sampler, we analyse site-occupancy data of the blue hawker, Aeshna cyanea (Odonata, Aeshnidae), a common dragonfly species in Switzerland. Our analysis includes a comparison of results based on Bayesian and classical (non-Bayesian) methods of inference. We also provide code (based on the R software program) for conducting Bayesian and classical analyses of site-occupancy data.

An international ecological study of adult height in relation to cancer incidence for 24 anatomical sites.

PubMed

Jiang, Yannan; Marshall, Roger J; Walpole, Sarah C; Prieto-Merino, David; Liu, Dong-Xu; Perry, Jo K

2015-03-01

Anthropometric indices associated with childhood growth and height attained in adulthood, have been associated with an increased incidence of certain malignancies. To evaluate the cancer-height relationship, we carried out a study using international data, comparing various cancer rates with average adult height of women and men in different countries. An ecological analysis of the relationship between country-specific cancer incidence rates and average adult height was conducted for twenty-four anatomical cancer sites. Age-standardized rates were obtained from GLOBOCAN 2008. Average female (112 countries) and male (65 countries) heights were sourced and compiled primarily from national health surveys. Graphical and weighted regression analysis was conducted, taking into account BMI and controlling for the random effect of global regions. A significant positive association between a country's average adult height and the country's overall cancer rate was observed in both men and women. Site-specific cancer incidence for females was positively associated with height for most cancers: lung, kidney, colorectum, bladder, melanoma, brain and nervous system, breast, non-Hodgkin lymphoma, multiple myeloma, corpus uteri, ovary, and leukemia. A significant negative association was observed with cancer of the cervix uteri. In males, site-specific cancer incidence was positively associated with height for cancers of the brain and nervous system, kidney, colorectum, non-Hodgkin lymphoma, multiple myeloma, prostate, testicular, lip and oral cavity, and melanoma. Incidence of cancer was associated with tallness in the majority of anatomical/cancer sites investigated. The underlying biological mechanisms are unclear, but may include nutrition and early-life exposure to hormones, and may differ by anatomical site.

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

PubMed Central

Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

2016-01-01

Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

Application of the MIDAS approach for analysis of lysine acetylation sites.

PubMed

Evans, Caroline A; Griffiths, John R; Unwin, Richard D; Whetton, Anthony D; Corfe, Bernard M

2013-01-01

Multiple Reaction Monitoring Initiated Detection and Sequencing (MIDAS™) is a mass spectrometry-based technique for the detection and characterization of specific post-translational modifications (Unwin et al. 4:1134-1144, 2005), for example acetylated lysine residues (Griffiths et al. 18:1423-1428, 2007). The MIDAS™ technique has application for discovery and analysis of acetylation sites. It is a hypothesis-driven approach that requires a priori knowledge of the primary sequence of the target protein and a proteolytic digest of this protein. MIDAS essentially performs a targeted search for the presence of modified, for example acetylated, peptides. The detection is based on the combination of the predicted molecular weight (measured as mass-charge ratio) of the acetylated proteolytic peptide and a diagnostic fragment (product ion of m/z 126.1), which is generated by specific fragmentation of acetylated peptides during collision induced dissociation performed in tandem mass spectrometry (MS) analysis. Sequence information is subsequently obtained which enables acetylation site assignment. The technique of MIDAS was later trademarked by ABSciex for targeted protein analysis where an MRM scan is combined with full MS/MS product ion scan to enable sequence confirmation.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

PubMed Central

Finak, Greg; Langweiler, Marc; Jaimes, Maria; Malek, Mehrnoush; Taghiyar, Jafar; Korin, Yael; Raddassi, Khadir; Devine, Lesley; Obermoser, Gerlinde; Pekalski, Marcin L.; Pontikos, Nikolas; Diaz, Alain; Heck, Susanne; Villanova, Federica; Terrazzini, Nadia; Kern, Florian; Qian, Yu; Stanton, Rick; Wang, Kui; Brandes, Aaron; Ramey, John; Aghaeepour, Nima; Mosmann, Tim; Scheuermann, Richard H.; Reed, Elaine; Palucka, Karolina; Pascual, Virginia; Blomberg, Bonnie B.; Nestle, Frank; Nussenblatt, Robert B.; Brinkman, Ryan Remy; Gottardo, Raphael; Maecker, Holden; McCoy, J Philip

2016-01-01

Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping. PMID:26861911

Characterization and analysis of temporal and spatial variations in habitat and macroinvertebrate community structure, Fountain Creek basin, Colorado Springs and vicinity, Colorado, 1998-2001

USGS Publications Warehouse

Bruce, James F.

2002-01-01

The Fountain Creek Basin in and around Colorado Springs, Colorado, is affected by various land- and water-use activities. Biological, hydrological, water-quality, and land-use data were collected at 10 sites in the Fountain Creek Basin from April 1998 through April 2001 to provide a baseline characterization of macroinvertebrate communities and habitat conditions for comparison in subsequent studies; and to assess variation in macroinvertebrate community structure relative to habitat quality. Analysis of variance results indicated that instream and riparian variables were not affected by season, but significant differences were found among sites. Nine metrics were used to describe and evaluate macroinvertebrate community structure. Statistical analysis indicated that for six of the nine metrics, significant variability occurred between spring and fall seasons for 60 percent of the sites. Cluster analysis (unweighted pair group method average) using macroinvertebrate presence-absence data showed a well-defined separation between spring and fall samples. Six of the nine metrics had significant spatial variation. Cluster analysis using Sorenson?s Coefficient of Community values computed from macroinvertebrate density (number of organisms per square meter) data showed that macroinvertebrate community structure was more similar among tributary sites than main-stem sites. Canonical correspondence analysis identified a substrate particle-size gradient from site-specific species-abundance data and environmental correlates that decreased the 10 sites to 5 site clusters and their associated taxa.

A summary of selected chemical-quality conditions in 66 California streams 1950-72

USGS Publications Warehouse

Irwin, George A.; Lemons, Michael

1975-01-01

Water from California streams has been analyzed for concentrations of selected chemical constituents since the early 1950's. This summary includes about 1,200 water years of data from 88 sampling sites on 66 streams. Results of this summary show that about 80 percent of the sites had a mean dissolved-solids concentration of 400 milligrams per litre or less. All the sites that had mean concentrations ranging from 601 to 800 milligrams per litre were in either the South Coastal or Central Coastal subregions. Results of regression analysis between specific conductance and calcium, magnesium, sodium, bicarbonate, dissolved solids, and hardness usually indicated a high percentage of explained variance. Other constituents, such as potassium, sulfate, chloride, and particularly nitrate, were not as frequently highly associated with specific conductance. At sites where the water discharge was highly regulated, the variation in specific conductance that was explained as a function of discharge ranged from 0 to more than 90 percent. Whereas at the unregulated sites, the explained variance ranged from 50 to more than 90 percent.

Probabilistic analysis of tsunami hazards

USGS Publications Warehouse

Geist, E.L.; Parsons, T.

2006-01-01

Determining the likelihood of a disaster is a key component of any comprehensive hazard assessment. This is particularly true for tsunamis, even though most tsunami hazard assessments have in the past relied on scenario or deterministic type models. We discuss probabilistic tsunami hazard analysis (PTHA) from the standpoint of integrating computational methods with empirical analysis of past tsunami runup. PTHA is derived from probabilistic seismic hazard analysis (PSHA), with the main difference being that PTHA must account for far-field sources. The computational methods rely on numerical tsunami propagation models rather than empirical attenuation relationships as in PSHA in determining ground motions. Because a number of source parameters affect local tsunami runup height, PTHA can become complex and computationally intensive. Empirical analysis can function in one of two ways, depending on the length and completeness of the tsunami catalog. For site-specific studies where there is sufficient tsunami runup data available, hazard curves can primarily be derived from empirical analysis, with computational methods used to highlight deficiencies in the tsunami catalog. For region-wide analyses and sites where there are little to no tsunami data, a computationally based method such as Monte Carlo simulation is the primary method to establish tsunami hazards. Two case studies that describe how computational and empirical methods can be integrated are presented for Acapulco, Mexico (site-specific) and the U.S. Pacific Northwest coastline (region-wide analysis).

The Information Professional's Profile: An Analysis of Brazilian Job Vacancies on the Internet

ERIC Educational Resources Information Center

da Cunha, Miriam Vieira

2009-01-01

Introduction: Report of a study to discover and describe job vacancies for information professionals available online at specific sites and discussion lists between January 2005 and February 2008. Method: The study uses Bardin's content analysis technique and the following analysis criteria: information source, institutional type, professional…

Acquisition of background and technical information and class trip planning

NASA Technical Reports Server (NTRS)

Mackinnon, R. M.; Wake, W. H.

1981-01-01

Instructors who are very familiar with a study area, as well as those who are not, find the field trip information acquisition and planning process speeded and made more effective by organizing it in stages. The stage follow a deductive progression: from the associated context region, to the study area, to the specific sample window sites, and from generalized background information on the study region to specific technical data on the environmental and human use systems to be interpreted at each site. On the class trip and in the follow up laboratory, the learning/interpretive process are at first deductive in applying previously learned information and skills to analysis of the study site, then inductive in reading and interpreting the landscape, imagery, and maps of the site, correlating them with information of other samples sites and building valid generalizations about the larger study area, its context region, and other (similar and/or contrasting) regions.

Source apportionment of particulate organic matter using infrared spectra at multiple IMPROVE sites

NASA Astrophysics Data System (ADS)

Kuzmiakova, A.; Dillner, A. M.; Takahama, S.

2016-12-01

As organic aerosol is a dominant contributor to air pollution and radiative forcing in many regions in the United States, characterizing its composition and apportioning the organic mass to its major sources provides insight into atmospheric processes and guidance for decreasing its abundance. National networks, such as Interagency Monitoring of Protected Visual Environment (IMPROVE), provide multi-site and multi-year particulate matter samples useful for evaluating sources over all four seasons. To this end, our study focuses on apportioning the particulate organic matter (OM) to specific anthropogenic and biological processes from year-long infrared aerosol measurements collected at six IMPROVE sites (five national park sites and one urban site) during 2011. Pooling these organic aerosol samples into one dataset, we apply factor and cluster analyses to extract four chemical factors (two dominated by processed emissions, one dominated by hydroxyl groups, and one by hydrocarbons) and ascribe each factor to a specific source depending on the site and season. We also present a method to characterize measurement uncertainty in infrared instrumental analysis and investigate sensitivity analysis in generated factors. In Phoenix (the urban site) we find the majority (80-95%) of the OM consisted of anthropogenic activities, such as traffic emissions, fossil fuel combustion (both all year long), and residential wood burning (fall to winter). Mineral dust emissions accounted for the rest of OM (5-20%). At the National Park sites the OM concentration was lower on average and consisted of marine and dust aerosols, summertime biomass burning and biogenic aerosols, processed fossil fuel combustion, and emissions from ships and oil refineries. Our study highlights the potential for further site-specific or multi-year aerosol characterization in the context of a long-term atmospheric sampling program to quantify sources of organic particles impacting air quality, aid in policy-making, and assess which (trans)formation mechanisms proposed in laboratory studies are consistent with observations.

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes

PubMed Central

Lee, Moon Young; Park, Chanjae; Berent, Robyn M.; Park, Paul J.; Fuchs, Robert; Syn, Hannah; Chin, Albert; Townsend, Jared; Benson, Craig C.; Redelman, Doug; Shen, Tsai-wei; Park, Jong Kun; Miano, Joseph M.; Sanders, Kenton M.; Ro, Seungil

2015-01-01

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies. PMID:26241044

DNA methylation profile distinguishes clear cell sarcoma of the kidney from other pediatric renal tumors.

PubMed

Ueno, Hitomi; Okita, Hajime; Akimoto, Shingo; Kobayashi, Kenichiro; Nakabayashi, Kazuhiko; Hata, Kenichiro; Fujimoto, Junichiro; Hata, Jun-Ichi; Fukuzawa, Masahiro; Kiyokawa, Nobutaka

2013-01-01

A number of specific, distinct neoplastic entities occur in the pediatric kidney, including Wilms' tumor, clear cell sarcoma of the kidney (CCSK), congenital mesoblastic nephroma (CMN), rhabdoid tumor of the kidney (RTK), and the Ewing's sarcoma family of tumors (ESFT). By employing DNA methylation profiling using Illumina Infinium HumanMethylation27, we analyzed the epigenetic characteristics of the sarcomas including CCSK, RTK, and ESFT in comparison with those of the non-neoplastic kidney (NK), and these tumors exhibited distinct DNA methylation profiles in a tumor-type-specific manner. CCSK is the most frequently hypermethylated, but least frequently hypomethylated, at CpG sites among these sarcomas, and exhibited 490 hypermethylated and 46 hypomethylated CpG sites in compared with NK. We further validated the results by MassARRAY, and revealed that a combination of four genes was sufficient for the DNA methylation profile-based differentiation of these tumors by clustering analysis. Furthermore, THBS1 CpG sites were found to be specifically hypermethylated in CCSK and, thus, the DNA methylation status of these THBS1 sites alone was sufficient for the distinction of CCSK from other pediatric renal tumors, including Wilms' tumor and CMN. Moreover, combined bisulfite restriction analysis could be applied for the detection of hypermethylation of a THBS1 CpG site. Besides the biological significance in the pathogenesis, the DNA methylation profile should be useful for the differential diagnosis of pediatric renal tumors.

A new spatial multi-criteria decision support tool for site selection for implementation of managed aquifer recharge.

PubMed

Rahman, M Azizur; Rusteberg, Bernd; Gogu, R C; Lobo Ferreira, J P; Sauter, Martin

2012-05-30

This study reports the development of a new spatial multi-criteria decision analysis (SMCDA) software tool for selecting suitable sites for Managed Aquifer Recharge (MAR) systems. The new SMCDA software tool functions based on the combination of existing multi-criteria evaluation methods with modern decision analysis techniques. More specifically, non-compensatory screening, criteria standardization and weighting, and Analytical Hierarchy Process (AHP) have been combined with Weighted Linear Combination (WLC) and Ordered Weighted Averaging (OWA). This SMCDA tool may be implemented with a wide range of decision maker's preferences. The tool's user-friendly interface helps guide the decision maker through the sequential steps for site selection, those steps namely being constraint mapping, criteria hierarchy, criteria standardization and weighting, and criteria overlay. The tool offers some predetermined default criteria and standard methods to increase the trade-off between ease-of-use and efficiency. Integrated into ArcGIS, the tool has the advantage of using GIS tools for spatial analysis, and herein data may be processed and displayed. The tool is non-site specific, adaptive, and comprehensive, and may be applied to any type of site-selection problem. For demonstrating the robustness of the new tool, a case study was planned and executed at Algarve Region, Portugal. The efficiency of the SMCDA tool in the decision making process for selecting suitable sites for MAR was also demonstrated. Specific aspects of the tool such as built-in default criteria, explicit decision steps, and flexibility in choosing different options were key features, which benefited the study. The new SMCDA tool can be augmented by groundwater flow and transport modeling so as to achieve a more comprehensive approach to the selection process for the best locations of the MAR infiltration basins, as well as the locations of recovery wells and areas of groundwater protection. The new spatial multicriteria analysis tool has already been implemented within the GIS based Gabardine decision support system as an innovative MAR planning tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

On Equivalence between Critical Probabilities of Dynamic Gossip Protocol and Static Site Percolation

NASA Astrophysics Data System (ADS)

Ishikawa, Tetsuya; Hayakawa, Tomohisa

The relationship between the critical probability of gossip protocol on the square lattice and the critical probability of site percolation on the square lattice is discussed. Specifically, these two critical probabilities are analytically shown to be equal to each other. Furthermore, we present a way of evaluating the critical probability of site percolation by approximating the saturation of gossip protocol. Finally, we provide numerical results which support the theoretical analysis.

Biological role of site-specific O-glycosylation in cell adhesion activity and phosphorylation of osteopontin.

PubMed

Oyama, Midori; Kariya, Yoshinobu; Kariya, Yukiko; Matsumoto, Kana; Kanno, Mayumi; Yamaguchi, Yoshiki; Hashimoto, Yasuhiro

2018-05-09

Osteopontin (OPN) is an extracellular glycosylated phosphoprotein that promotes cell adhesion by interacting with several integrin receptors. We previously reported that an OPN mutant lacking five O-glycosylation sites (Thr 134 /Thr 138 /Thr 143 /Thr 147 /Thr 152 ) in the threonine/proline-rich region increased cell adhesion activity and phosphorylation compared with the wild type. However, the role of O-glycosylation in cell adhesion activity and phosphorylation of OPN remains to be clarified. Here, we show that site-specific O-glycosylation in the threonine/proline-rich region of OPN affects its cell adhesion activity and phosphorylation independently and/or synergistically. Using site-directed mutagenesis, we found that OPN mutants with substitution sets of Thr 134 /Thr 138 or Thr 143 /Thr 147 /Thr 152 had decreased and increased cell adhesion activity, respectively. In contrast, the introduction of a single mutation into the O-glycosylation sites had no effect on OPN cell adhesion activity. An adhesion assay using function-blocking antibodies against αvβ3 and β1 integrins, as well as αvβ3 integrin-overexpressing A549 cells, revealed that site-specific O-glycosylation affected the association of OPN with the two integrins. Phosphorylation analyses using phos-tag and LC-MS/MS indicated that phosphorylation levels and sites were influenced by the O-glycosylation status, although the number of O-glycosylation sites was not correlated with the phosphorylation level in OPN. Furthermore, a correlation analysis between phosphorylation level and cell adhesion activity in OPN mutants with the site-specific O-glycosylation showed that they were not always correlated. These results provide conclusive evidence of a novel regulatory mechanism of cell adhesion activity and phosphorylation of OPN by site-specific O-glycosylation. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Application of Microtremor Horizontal-to-Vertical Spectral Ratio (MHVSR) Analysis for Site Characterization: State of the Art

NASA Astrophysics Data System (ADS)

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sánchez-Sesma, F. J.; Yong, A.

2018-03-01

Nakamura (Q Rep Railway Tech Res Inst 30:25-33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site's MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

Application of Microtremor Horizontal-to-Vertical Spectral Ratio (MHVSR) Analysis for Site Characterization: State of the Art

NASA Astrophysics Data System (ADS)

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sánchez-Sesma, F. J.; Yong, A.

2018-07-01

Nakamura (Q Rep Railway Tech Res Inst 30:25-33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site's MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (ray-finned fish).

PubMed

Yan, Jun; Cai, Zhonghua

2010-12-10

The cytochrome P450 (CYP) superfamily is a multifunctional hemethiolate enzyme that is widely distributed from Bacteria to Eukarya. The CYP3 family contains mainly the four subfamilies CYP3A, CYP3B, CYP3C and CYP3D in vertebrates; however, only the Actinopterygii (ray-finned fish) have all four subfamilies and detailed understanding of the evolutionary relationship of Actinopterygii CYP3 family members would be valuable. Phylogenetic relationships were constructed to trace the evolutionary history of the Actinopterygii CYP3 family genes. Selection analysis, relative rate tests and functional divergence analysis were combined to interpret the relationship of the site-specific evolution and functional divergence in the Actinopterygii CYP3 family. The results showed that the four CYP3 subfamilies in Actinopterygii might be formed by gene duplication. The first gene duplication event was responsible for divergence of the CYP3B/C clusters from ancient CYP3 before the origin of the Actinopterygii, which corresponded to the fish-specific whole genome duplication (WGD). Tandem repeat duplication in each of the homologue clusters produced stable CYP3B, CYP3C, CYP3A and CYP3D subfamilies. Acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of new subfamilies and functional divergence in the new subset after gene duplication, whereas positive selection was detected only in the retained CYP3A subfamily. Furthermore, nearly half of the functional divergence sites appear to be related to substrate recognition, which suggests that site-specific evolution is closely related with functional divergence in the Actinopterygii CYP3 family. The split of fish-specific CYP3 subfamilies was related to the fish-specific WGD, and site-specific acceleration of asymmetric evolutionary rates and purifying selection was the main force for the origin of the new subfamilies and functional divergence in the new subset after gene duplication. Site-specific evolution in substrate recognition was related to functional divergence in the Actinopterygii CYP3 family.

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

PubMed

Joshi, Rohit; Passner, Jonathan M; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A; Jacob, Vinitha; Aggarwal, Aneel K; Honig, Barry; Mann, Richard S

2007-11-02

The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells.

PubMed

Murray, Vincent; Chen, Jon K; Tanaka, Mark M

2016-07-01

The cancer chemotherapeutic agent, bleomycin, cleaves DNA at specific sites. For the first time, the genome-wide DNA sequence specificity of bleomycin breakage was determined in human cells. Utilising Illumina next-generation DNA sequencing techniques, over 200 million bleomycin cleavage sites were examined to elucidate the bleomycin genome-wide DNA selectivity. The genome-wide bleomycin cleavage data were analysed by four different methods to determine the cellular DNA sequence specificity of bleomycin strand breakage. For the most highly cleaved DNA sequences, the preferred site of bleomycin breakage was at 5'-GT* dinucleotide sequences (where the asterisk indicates the bleomycin cleavage site), with lesser cleavage at 5'-GC* dinucleotides. This investigation also determined longer bleomycin cleavage sequences, with preferred cleavage at 5'-GT*A and 5'- TGT* trinucleotide sequences, and 5'-TGT*A tetranucleotides. For cellular DNA, the hexanucleotide DNA sequence 5'-RTGT*AY (where R is a purine and Y is a pyrimidine) was the most highly cleaved DNA sequence. It was striking that alternating purine-pyrimidine sequences were highly cleaved by bleomycin. The highest intensity cleavage sites in cellular and purified DNA were very similar although there were some minor differences. Statistical nucleotide frequency analysis indicated a G nucleotide was present at the -3 position (relative to the cleavage site) in cellular DNA but was absent in purified DNA.

Cleavage-site specificity of prolyl endopeptidase FAP investigated with a full-length protein substrate.

PubMed

Huang, Chih-Hsiang; Suen, Ching-Shu; Lin, Ching-Ting; Chien, Chia-Hui; Lee, Hsin-Ying; Chung, Kuei-Min; Tsai, Ting-Yueh; Jiaang, Weir-Tong; Hwang, Ming-Jing; Chen, Xin

2011-06-01

Fibroblast activation protein (FAP) is a prolyl-cleaving endopeptidase proposed as an anti-cancer drug target. It is necessary to define its cleavage-site specificity to facilitate the identification of its in vivo substrates and to understand its biological functions. We found that the previously identified substrate of FAP, α(2)-anti-plasmin, is not a robust substrate in vitro. Instead, an intracellular protein, SPRY2, is cleavable by FAP and more suitable for investigation of its substrate specificity in the context of the full-length globular protein. FAP prefers uncharged residues, including small or bulky hydrophobic amino acids, but not charged amino acids, especially acidic residue at P1', P3 and P4 sites. Molecular modelling analysis shows that the substrate-binding site of FAP is surrounded by multiple tyrosine residues and some negatively charged residues, which may exert least preference for substrates with acidic residues. This provides an explanation why FAP cannot cleave interleukins, which have a glutamate at either P4 or P2', despite their P3-P2-P1 sites being identical to SPRY2 or α-AP. Our study provided new information on FAP cleavage-site specificity, which differs from the data obtained by profiling with a peptide library or with the denatured protein, gelatin, as the substrate. Furthermore, our study suggests that negatively charged residues should be avoided when designing FAP inhibitors.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens

PubMed Central

Glinsky, Gennadi V.

2016-01-01

Abstract Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8–10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. PMID:27503290

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

Faulds, James

We conducted a comprehensive analysis of the structural controls of geothermal systems within the Great Basin and adjacent regions. Our main objectives were to: 1) Produce a catalogue of favorable structural environments and models for geothermal systems. 2) Improve site-specific targeting of geothermal resources through detailed studies of representative sites, which included innovative techniques of slip tendency analysis of faults and 3D modeling. 3) Compare and contrast the structural controls and models in different tectonic settings. 4) Synthesize data and develop methodologies for enhancement of exploration strategies for conventional and EGS systems, reduction in the risk of drilling non-productive wells,more » and selecting the best EGS sites.« less

Semantics-based distributed I/O with the ParaMEDIC framework.

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

Balaji, P.; Feng, W.; Lin, H.

2008-01-01

Many large-scale applications simultaneously rely on multiple resources for efficient execution. For example, such applications may require both large compute and storage resources; however, very few supercomputing centers can provide large quantities of both. Thus, data generated at the compute site oftentimes has to be moved to a remote storage site for either storage or visualization and analysis. Clearly, this is not an efficient model, especially when the two sites are distributed over a wide-area network. Thus, we present a framework called 'ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing' which uses application-specific semantic information to convert the generatedmore » data to orders-of-magnitude smaller metadata at the compute site, transfer the metadata to the storage site, and re-process the metadata at the storage site to regenerate the output. Specifically, ParaMEDIC trades a small amount of additional computation (in the form of data post-processing) for a potentially significant reduction in data that needs to be transferred in distributed environments.« less

Nest success, cause-specific nest failure, and hatchability of aquatic birds at selenium-contaminated Kesterson Reservoir and a reference site

USGS Publications Warehouse

Ohlendorf, Harry M.; Hothem, Roger L.; Welsh, Daniel

1989-01-01

During 1983-1985, we studied the reproductive success of several species of aquatic birds (coots, ducks, shorebirds, and grebes) nesting at two sites in Merced County, California: a selenium-contaminated site (Kesterson Reservoir) and a nearby reference site (Volta Wildlife Area). We used a computer program (MICROMORT) developed for the analysis of radiotelemetry data (Heisey and Fuller 1985) to estimate nest success and cause-specific failure rates, and then compared these parameters and hatchability between sites and among years. Nest success and causes of failure varied by species, site, and year. The most important causes of nest failure were usually predation, desertion, and water-level changes. However, embryotoxicosis (mortality, deformity, and lack of embryonic development) was the most important cause of nest failure in Eared Grebes (Podiceps nigricollis) at Kesterson Reservoir. Embryotoxicosis also reduced the hatchability of eggs of all other species at Kesterson in one or more years; embryonic mortality occurred rarely at Volta, and abnormalities were not observed.

AFB/open cycle gas turbine conceptual design study

NASA Technical Reports Server (NTRS)

Dickinson, T. W.; Tashjian, R.

1983-01-01

Applications of coal fired atmospheric fluidized bed gas turbine systems in industrial cogeneration are identified. Based on site-specific conceptual designs, the potential benefits of the AFB/gas turbine system were compared with an atmospheric fluidized design steam boiler/steam turbine system. The application of these cogeneration systems at four industrial plant sites is reviewed. A performance and benefit analysis was made along with a study of the representativeness of the sites both in regard to their own industry and compared to industry as a whole. A site was selected for the conceptual design, which included detailed site definition, AFB/gas turbine and AFB/steam turbine cogeneration system designs, detailed cost estimates, and comparative performance and benefit analysis. Market and benefit analyses identified the potential market penetration for the cogeneration technologies and quantified the potential benefits.

AFB/open cycle gas turbine conceptual design study

NASA Astrophysics Data System (ADS)

Dickinson, T. W.; Tashjian, R.

1983-09-01

Applications of coal fired atmospheric fluidized bed gas turbine systems in industrial cogeneration are identified. Based on site-specific conceptual designs, the potential benefits of the AFB/gas turbine system were compared with an atmospheric fluidized design steam boiler/steam turbine system. The application of these cogeneration systems at four industrial plant sites is reviewed. A performance and benefit analysis was made along with a study of the representativeness of the sites both in regard to their own industry and compared to industry as a whole. A site was selected for the conceptual design, which included detailed site definition, AFB/gas turbine and AFB/steam turbine cogeneration system designs, detailed cost estimates, and comparative performance and benefit analysis. Market and benefit analyses identified the potential market penetration for the cogeneration technologies and quantified the potential benefits.

An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction.

PubMed Central

Shan, S O; Herschlag, D

2000-01-01

The presence of catalytic metal ions in RNA active sites has often been inferred from metal-ion rescue of modified substrates and sometimes from inhibitory effects of alternative metal ions. Herein we report that, in the Tetrahymena group I ribozyme reaction, the deleterious effect of a thio substitution at the pro-Sp position of the reactive phosphoryl group is rescued by Mn2+. However, analysis of the reaction of this thio substrate and of substrates with other modifications strongly suggest that this rescue does not stem from a direct Mn2+ interaction with the Sp sulfur. Instead, the apparent rescue arises from a Mn2+ ion interacting with the residue immediately 3' of the cleavage site, A(+1), that stabilizes the tertiary interactions between the oligonucleotide substrate (S) and the active site. This metal site is referred to as site D herein. We also present evidence that a previously observed Ca2+ ion that inhibits the chemical step binds to metal site D. These and other observations suggest that, whereas the interactions of Mn2+ at site D are favorable for the chemical reaction, the Ca2+ at site D exerts its inhibitory effect by disrupting the alignment of the substrates within the active site. These results emphasize the vigilance necessary in the design and interpretation of metal-ion rescue and inhibition experiments. Conversely, in-depth mechanistic analysis of the effects of site-specific substrate modifications can allow the effects of specific metal ion-RNA interactions to be revealed and the properties of individual metal-ion sites to be probed, even within the sea of metal ions bound to RNA. PMID:10864040

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

PubMed Central

Xie, Gary; Lo, Chien-Chi; Scholz, Matthew; Chain, Patrick S. G.

2014-01-01

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome. PMID:24454771

Theory on the mechanism of site-specific DNA-protein interactions in the presence of traps

NASA Astrophysics Data System (ADS)

Niranjani, G.; Murugan, R.

2016-08-01

The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA.

Plasma 25-hydroxyvitamin D concentration and subsequent risk of total and site specific cancers in Japanese population: large case-cohort study within Japan Public Health Center-based Prospective Study cohort

PubMed Central

Budhathoki, Sanjeev; Hidaka, Akihisa; Sawada, Norie; Tanaka-Mizuno, Sachiko; Kuchiba, Aya; Charvat, Hadrien; Goto, Atsushi; Kojima, Satoshi; Sudo, Natsuki; Shimazu, Taichi; Sasazuki, Shizuka; Inoue, Manami; Tsugane, Shoichiro; Iwasaki, Motoki

2018-01-01

Abstract Objective To evaluate the association between pre-diagnostic circulating vitamin D concentration and the subsequent risk of overall and site specific cancer in a large cohort study. Design Nested case-cohort study within the Japan Public Health Center-based Prospective Study cohort. Setting Nine public health centre areas across Japan. Participants 3301 incident cases of cancer and 4044 randomly selected subcohort participants. Exposure Plasma concentration of 25-hydroxyvitamin D measured by enzyme immunoassay. Participants were divided into quarters based on the sex and season specific distribution of 25-hydroxyvitamin D among subcohorts. Weighted Cox proportional hazard models were used to calculate the multivariable adjusted hazard ratios for overall and site specific cancer across categories of 25-hydroxyvitamin D concentration, with the lowest quarter as the reference. Main outcome measure Incidence of overall or site specific cancer. Results Plasma 25-hydroxyvitamin D concentration was inversely associated with the risk of total cancer, with multivariable adjusted hazard ratios for the second to fourth quarters compared with the lowest quarter of 0.81 (95% confidence interval 0.70 to 0.94), 0.75 (0.65 to 0.87), and 0.78 (0.67 to 0.91), respectively (P for trend=0.001). Among the findings for cancers at specific sites, an inverse association was found for liver cancer, with corresponding hazard ratios of 0.70 (0.44 to 1.13), 0.65 (0.40 to 1.06), and 0.45 (0.26 to 0.79) (P for trend=0.006). A sensitivity analysis showed that alternately removing cases of cancer at one specific site from total cancer cases did not substantially change the overall hazard ratios. Conclusions In this large prospective study, higher vitamin D concentration was associated with lower risk of total cancer. These findings support the hypothesis that vitamin D has protective effects against cancers at many sites. PMID:29514781

Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain

NASA Astrophysics Data System (ADS)

Hernández-Ceballos, M. A.; García-Mozo, H.; Galán, C.

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak ( Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.

Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain.

PubMed

Hernández-Ceballos, M A; García-Mozo, H; Galán, C

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak (Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

PubMed Central

Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R

1997-01-01

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

Prediction of Protein Modification Sites of Pyrrolidone Carboxylic Acid Using mRMR Feature Selection and Analysis

PubMed Central

Zheng, Lu-Lu; Niu, Shen; Hao, Pei; Feng, KaiYan; Cai, Yu-Dong; Li, Yixue

2011-01-01

Pyrrolidone carboxylic acid (PCA) is formed during a common post-translational modification (PTM) of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR) and incremental feature selection (IFS). We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations. PMID:22174779

Mental Constructions and Constructions of Web Sites: Learner and Teacher Points of View

ERIC Educational Resources Information Center

Hazzan, Orit

2004-01-01

This research focuses on knowledge and ways in which knowledge may be constructed in the learner's mind. Specifically, it addresses the Web as a cognitive supporter for learning, organising and constructing a new domain of knowledge. In particular, the research analyses student reflection on constructing web sites. The analysis is based on an…

Site of maxima of conductivity, temperatures, density of the current and specific capacity of the thermal emission in the HFI-discharge

NASA Astrophysics Data System (ADS)

Gerasimov, A.; Kirpichnikov, A.; Sabirova, F.; Gainullin, R.

2017-11-01

On the basis of theoretical analysis of distributions of the conductivity, current density and specific power of heat release in the high-frequency induction discharge, a law of crowding of maxima of these values has been established.

United States Air Force 611th Civil Engineer Squadron, Elmendorf AFB, Alaska. Final engineering evaluation/cost analysis: Petroleum, oil, and lubricants area, Galena Airport, Alaska

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

NONE

1996-02-05

This decision document presents the selected removal action for the Installation Restoration Program (IRP) site ST005, otherwise known as the POL Tank Farm, at Galena Airport, Alaska. This decision is based on the administrative record for this site, specifically the draft Remedial Investigation Report (March 1995) and the Treatability Study Report (January 1995) (PB95-225314). The information from these documents is summarized, along with an analysis of potential removal action alternatives in the Engineering Evaluation/Cost Analysis (EE/CA).

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling.

PubMed

Singec, Ilyas; Crain, Andrew M; Hou, Junjie; Tobe, Brian T D; Talantova, Maria; Winquist, Alicia A; Doctor, Kutbuddin S; Choy, Jennifer; Huang, Xiayu; La Monaca, Esther; Horn, David M; Wolf, Dieter A; Lipton, Stuart A; Gutierrez, Gustavo J; Brill, Laurence M; Snyder, Evan Y

2016-09-13

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt. Published by Elsevier Inc.

Analysis of laparoscopic port site complications: A descriptive study

PubMed Central

Karthik, Somu; Augustine, Alfred Joseph; Shibumon, Mundunadackal Madhavan; Pai, Manohar Varadaraya

2013-01-01

CONTEXT: The rate of port site complications following conventional laparoscopic surgery is about 21 per 100,000 cases. It has shown a proportional rise with increase in the size of the port site incision and trocar. Although rare, complications that occur at the port site include infection, bleeding, and port site hernia. AIMS: To determine the morbidity associated with ports at the site of their insertion in laparoscopic surgery and to identify risk factors for complications. SETTINGS AND DESIGN: Prospective descriptive study. MATERIALS AND METHODS: In the present descriptive study, a total of 570 patients who underwent laparoscopic surgeries for various ailments between August 2009 and July 2011 at our institute were observed for port site complications prospectively and the complications were reviewed. STATISTICAL ANALYSIS USED: Descriptive statistical analysis was carried out in the present study. The statistical software, namely, SPSS 15.0 was used for the analysis of the data. RESULTS: Of the 570 patients undergoing laparoscopic surgery, 17 (3%) had developed complications specifically related to the port site during a minimum follow-up of three months; port site infection (PSI) was the most frequent (n = 10, 1.8%), followed by port site bleeding (n = 4, 0.7%), omentum-related complications (n = 2; 0.35%), and port site metastasis (n = 1, 0.175%). CONCLUSIONS: Laparoscopic surgeries are associated with minimal port site complications. Complications are related to the increased number of ports. Umbilical port involvement is the commonest. Most complications are manageable with minimal morbidity, and can be further minimized with meticulous surgical technique during entry and exit. PMID:23741110

Development of a molecular approach to describe the composition of Trichoderma communities.

PubMed

Meincke, Remo; Weinert, Nicole; Radl, Viviane; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele

2010-01-01

Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites. Copyright 2009 Elsevier B.V. All rights reserved.

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

PubMed

Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

2016-08-31

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Colder environments are associated with a greater cancer incidence in the female population of the United States.

PubMed

Sharma, Ankit; Sharma, Tanu; Panwar, Mahaveer S; Sharma, Devesh; Bundel, Rashmi; Hamilton, Ryan T; Radosevich, James A; Mandal, Chandi C

2017-10-01

Cancer incidence and/or mortality among individuals varies with diet, socio-culture, ethnicity, race, gender, and age. Similarly, environmental temperature modulates many biological functions. To study the effect of environment temperature on cancer incidence, the US population was selected. Because, county-wise cancer incidence rate data of various anatomical site-specific cancers and different races/ethnicities for both males and females are available. Moreover, the differences amongst the aforementioned factors among individuals are much less, as compared to the world population. Statistical analysis showed a negative correlation between the average annual temperature and cancer incidence rate at all anatomical sites and individually for 13 types (out of 16 types) of anatomical site-specific cancer incidence rates (e.g. uterine, bladder, thyroid, breast, esophagus, ovary, melanoma, non-Hodgkin lymphoma, leukemia, brain, pancreas, etc.) for females. Further analysis found a similar inverse trend in all races/ethnicities of the female population but not in all male races/ethnicities or anatomical site-specific cancers. Moreover, the majority of the counties having the top-most cancer incidence rate in females are located above the latitude 36.5°N. These findings indicate that living in a cold county in the United States might have a higher risk of cancer irrespective of cancer type (except cervical and liver) and races/ethnicities for females but not in all such cases for the male population.

Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 2, Geology report. Revised final report

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

Not Available

1991-12-01

Detailed investigations of geologic, geomorphic, and seismic conditions at the Bodo Canyon disposal site were conducted. The purpose of these investigations was basic site characterization and identification of potential geologic hazards that could affect long-term site stability. Subsequent engineering studies, such as analyses of hydrologic and liquefaction hazards, used the data developed in these studies. The geomorphic analysis was employed in the design of effective erosion protection. Studies of the regional and local seismotectonic setting, which included a detailed search for possible capable faults within a 65 kilometer radius of the site, provided the basis for seismic design parameters. Themore » scope of work performed included the following: Compilation and analysis of previous published and unpublished geologic literature and maps; Review of historical and instrumental earthquake data; Review of site-specific subsurface geologic data, including lithologic and geophysical logs of exploratory boreholes advanced in the site area; Photogeologic interpretations of existing conventional aerial photographs; and, Ground reconnaissance and mapping of the site region.« less

Analysis of Thousands of Prehistoric Mediterranean Obsidian Artifacts Using a Nondestructive Portable X-Ray Fluorescence Spectrometer

NASA Astrophysics Data System (ADS)

Tykot, Robert

A portable, hand-held X-ray fluorescence spectrometer has been used for a decade to elementally analyze prehistoric obsidian artifacts in the Mediterranean. Nearly 400 geological obsidian samples and 7500 obsidian artifacts have been analyzed. The pXRF can distinguish all individual sources, as well as assign artifacts specifically to most subsources. For the island sources of Lipari, Pantelleria, Sardinia, and Melos, it is important to address the usage of obsidian from specific subsources due to human selection based on physical properties of the raw material and their production practices, which may have changed over time from the Early Neolithic to the Bronze Age. The analysis of 50 or more artifacts from 60 different archaeological sites allows for statistical comparison between sites, and their contexts, geographic areas (e.g. coastal/inland, highland/lowland) and distance from geological sources. The frequency of transport between island sources and mainland sites is suggestive of maritime capabilities also for the transport of domesticated animals, ceramics, and other materials. This presentation will specifically address potential limitations of the portable XRF, including non-destructive surface analysis of potentially heterogeneous materials, and limited trace element detection compared to other analytical methods, versus its highly beneficial ``package'' of analyzing great numbers of artifacts non-destructively and rapidly without needing to export them from museums and facilities in many countries.

Color vision: "OH-site" rule for seeing red and green.

PubMed

Sekharan, Sivakumar; Katayama, Kota; Kandori, Hideki; Morokuma, Keiji

2012-06-27

Eyes gather information, and color forms an extremely important component of the information, more so in the case of animals to forage and navigate within their immediate environment. By using the ONIOM (QM/MM) (ONIOM = our own N-layer integrated molecular orbital plus molecular mechanics) method, we report a comprehensive theoretical analysis of the structure and molecular mechanism of spectral tuning of monkey red- and green-sensitive visual pigments. We show that interaction of retinal with three hydroxyl-bearing amino acids near the β-ionone ring part of the retinal in opsin, A164S, F261Y, and A269T, increases the electron delocalization, decreases the bond length alternation, and leads to variation in the wavelength of maximal absorbance of the retinal in the red- and green-sensitive visual pigments. On the basis of the analysis, we propose the "OH-site" rule for seeing red and green. This rule is also shown to account for the spectral shifts obtained from hydroxyl-bearing amino acids near the Schiff base in different visual pigments: at site 292 (A292S, A292Y, and A292T) in bovine and at site 111 (Y111) in squid opsins. Therefore, the OH-site rule is shown to be site-specific and not pigment-specific and thus can be used for tracking spectral shifts in any visual pigment.

Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle

PubMed Central

Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

2012-01-01

As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

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

Brauchler, R.; Doetsch, J.; Dietrich, P.

2012-01-10

In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. Themore » experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.« less

RAS mutations affect pattern of metastatic spread and increase propensity for brain metastasis in colorectal cancer.

PubMed

Yaeger, Rona; Cowell, Elizabeth; Chou, Joanne F; Gewirtz, Alexandra N; Borsu, Laetitia; Vakiani, Efsevia; Solit, David B; Rosen, Neal; Capanu, Marinela; Ladanyi, Marc; Kemeny, Nancy

2015-04-15

RAS and PIK3CA mutations in metastatic colorectal cancer (mCRC) have been associated with worse survival. We sought to evaluate the impact of RAS and PIK3CA mutations on cumulative incidence of metastasis to potentially curable sites of liver and lung and other sites such as bone and brain. We performed a computerized search of the electronic medical record of our institution for mCRC cases genotyped for RAS or PIK3CA mutations from 2008 to 2012. Cases were reviewed for patient characteristics, survival, and site-specific metastasis. Among the 918 patients identified, 477 cases were RAS wild type, and 441 cases had a RAS mutation (394 at KRAS exon 2, 29 at KRAS exon 3 or 4, and 18 in NRAS). RAS mutation was significantly associated with shorter median overall survival (OS) and on multivariate analysis independently predicted worse OS (HR, 1.6; P < .01). RAS mutant mCRC exhibited a significantly higher cumulative incidence of lung, bone, and brain metastasis and on multivariate analysis was an independent predictor of involvement of these sites (HR, 1.5, 1.6, and 3.7, respectively). PIK3CA mutations occurred in 10% of the 786 cases genotyped, did not predict for worse survival, and did not exhibit a site-specific pattern of metastatic spread. The metastatic potential of CRC varies with the presence of RAS mutation. RAS mutation is associated with worse OS and increased incidence of lung, bone, and brain metastasis. An understanding of this site-specific pattern of spread may help to inform physicians' assessment of symptoms in patients with mCRC. © 2014 American Cancer Society.

Heavy metals bioaccumulation in selected tissues of red swamp crayfish: An easy tool for monitoring environmental contamination levels.

PubMed

Goretti, E; Pallottini, M; Ricciarini, M I; Selvaggi, R; Cappelletti, D

2016-07-15

In this paper we explored the heavy metal bioaccumulation (Cd, Cu, Pb and Zn) in Procambarus clarkii, a crayfish recently suggested as a potential bioindicator for metals pollution in freshwater systems. The present study is focused on crayfishes populations caught in a heavily polluted industrial and in a reference sites (Central Italy), though the results are generalized with a thorough analysis of literature metadata. In agreement with the literature, the hepatopancreas (Hep, detoxification tissues) of the red swamp crayfish showed a higher concentration of heavy metals in comparison to the abdominal muscle (AbM, not detoxification tissues) in the sites under scrutiny. Hep/AbM concentration ratio was dependent on the specific metal investigated and on its sediment contamination level. Specifically we found that Hep/AbM ratio decreases as follows: Cd (11.7)>Cu (5.5)>Pb (3.6)>Zn (1.0) and Pb (4.34)>Cd (3.66)>Zn (1.69)>Cu (0.87) for the industrial and reference sites, respectively. The analysis of our bioaccumulation data as well as of literature metadata allowed to elaborate a specific contamination index (Toxic Contamination Index, TCI), dependent only on the bioaccumulation data of hepatopancreas and abdominal muscle. In the industrial site, TCI expressed values much higher than the unit for Cd and Cu, confirming that these metals were the main contaminants; in contrast for lower levels of heavy metals, as those observed in the reference site for Cu, Zn and Pb, the index provided values below unit. TCI is proposed as a useful and easy tool to assess the toxicity level of contaminated sites by heavy metals in the environmental management. Copyright © 2016. Published by Elsevier B.V.

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets.

PubMed

Nelson, Christopher S; Fuller, Chris K; Fordyce, Polly M; Greninger, Alexander L; Li, Hao; DeRisi, Joseph L

2013-07-01

The transcription factor forkhead box P2 (FOXP2) is believed to be important in the evolution of human speech. A mutation in its DNA-binding domain causes severe speech impairment. Humans have acquired two coding changes relative to the conserved mammalian sequence. Despite intense interest in FOXP2, it has remained an open question whether the human protein's DNA-binding specificity and chromatin localization are conserved. Previous in vitro and ChIP-chip studies have provided conflicting consensus sequences for the FOXP2-binding site. Using MITOMI 2.0 microfluidic affinity assays, we describe the binding site of FOXP2 and its affinity profile in base-specific detail for all substitutions of the strongest binding site. We find that human and chimp FOXP2 have similar binding sites that are distinct from previously suggested consensus binding sites. Additionally, through analysis of FOXP2 ChIP-seq data from cultured neurons, we find strong overrepresentation of a motif that matches our in vitro results and identifies a set of genes with FOXP2 binding sites. The FOXP2-binding sites tend to be conserved, yet we identified 38 instances of evolutionarily novel sites in humans. Combined, these data present a comprehensive portrait of FOXP2's-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved.

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets

PubMed Central

Nelson, Christopher S.; Fuller, Chris K.; Fordyce, Polly M.; Greninger, Alexander L.; Li, Hao; DeRisi, Joseph L.

2013-01-01

The transcription factor forkhead box P2 (FOXP2) is believed to be important in the evolution of human speech. A mutation in its DNA-binding domain causes severe speech impairment. Humans have acquired two coding changes relative to the conserved mammalian sequence. Despite intense interest in FOXP2, it has remained an open question whether the human protein’s DNA-binding specificity and chromatin localization are conserved. Previous in vitro and ChIP-chip studies have provided conflicting consensus sequences for the FOXP2-binding site. Using MITOMI 2.0 microfluidic affinity assays, we describe the binding site of FOXP2 and its affinity profile in base-specific detail for all substitutions of the strongest binding site. We find that human and chimp FOXP2 have similar binding sites that are distinct from previously suggested consensus binding sites. Additionally, through analysis of FOXP2 ChIP-seq data from cultured neurons, we find strong overrepresentation of a motif that matches our in vitro results and identifies a set of genes with FOXP2 binding sites. The FOXP2-binding sites tend to be conserved, yet we identified 38 instances of evolutionarily novel sites in humans. Combined, these data present a comprehensive portrait of FOXP2’s-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved. PMID:23625967

Analysis of stream quality in the Yampa River Basin, Colorado and Wyoming

USGS Publications Warehouse

Wentz, Dennis A.; Steele, Timothy Doak

1980-01-01

Historic data show no significant water-temperature changes since 1951 for the Little Snake or Yampa Rivers, the two major streams of the Yampa River basin in Colorado and Wyoming. Regional analyses indicate that harmonic-mean temperature is negatively correlated with altitude. No change in specific conductance since 1951 was noted for the Little Snake River; however, specific conductance in the Yampa River has increaed 14 % since that time and is attributed to increased agricultural and municipal use of water. Site-specific relationships between major inorganic constituents and specific conductance for the Little Snake and Yampa Rivers were similar to regional relationships developed from both historic and recent (1975) data. These relationships provide a means for estimating concentrations of major inorganic constituents from specific conductance, which is easily measured. Trace-element and nutrient data collected from August 1975 through September 1976 at 92 sites in the Yampa River basin indicate that water-quality degradation occurred upstream from 3 sites. The degradation resulted from underground drainage from pyritic materials that probably are associated with coal at one site, discharge from powerplant cooling-tower blowdown water at a second site, and runoff from a small watershed containing a gas field at the third site. Ambient concentrations of dissolved and total iron and manganese frequently exceeded proposed Colorado water-quality standards. The concentrations of many dissolved and total trace elements and nutrients were greatest during March 1976. These were associated with larger suspended-sediment concentrations and smaller pH values than at other times of the year. (USGS)

Project X: competitive intelligence data mining and analysis

NASA Astrophysics Data System (ADS)

Gilmore, John F.; Pagels, Michael A.; Palk, Justin

2001-03-01

Competitive Intelligence (CI) is a systematic and ethical program for gathering and analyzing information about your competitors' activities and general business trends to further your own company's goals. CI allows companies to gather extensive information on their competitors and to analyze what the competition is doing in order to maintain or gain a competitive edge. In commercial business this potentially translates into millions of dollars in annual savings or losses. The Internet provides an overwhelming portal of information for CI analysis. The problem is how a company can automate the translation of voluminous information into valuable and actionable knowledge. This paper describes Project X, an agent-based data mining system specifically developed for extracting and analyzing competitive information from the Internet. Project X gathers CI information from a variety of sources including online newspapers, corporate websites, industry sector reporting sites, speech archiving sites, video news casts, stock news sites, weather sites, and rumor sites. It uses individual industry specific (e.g., pharmaceutical, financial, aerospace, etc.) commercial sector ontologies to form the knowledge filtering and discovery structures/content required to filter and identify valuable competitive knowledge. Project X is described in detail and an example competitive intelligence case is shown demonstrating the system's performance and utility for business intelligence.

Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE

NASA Astrophysics Data System (ADS)

Togayachi, Akira; Tomioka, Azusa; Fujita, Mika; Sukegawa, Masako; Noro, Erika; Takakura, Daisuke; Miyazaki, Michiyo; Shikanai, Toshihide; Narimatsu, Hisashi; Kaji, Hiroyuki

2018-04-01

To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. [Figure not available: see fulltext.

An analysis of current source density profiles activated by local stimulation in the mouse auditory cortex in vitro.

PubMed

Yamamura, Daiki; Sano, Ayaka; Tateno, Takashi

2017-03-15

To examine local network properties of the mouse auditory cortex in vitro, we recorded extracellular spatiotemporal laminar profiles driven by short electric local stimulation on a planar multielectrode array substrate. The recorded local field potentials were subsequently evaluated using current source density (CSD) analysis to identify sources and sinks. Current sinks are thought to be an indicator of net synaptic current in the small volume of cortex surrounding the recording site. Thus, CSD analysis combined with multielectrode arrays enabled us to compare mean synaptic activity in response to small current stimuli on a layer-by-layer basis. We also used senescence-accelerated mice (SAM), some strains of which show earlier onset of age-related hearing loss, to examine the characteristic spatiotemporal CSD profiles stimulated by electrodes in specific cortical layers. Thus, the CSD patterns were classified into several clusters based on stimulation sites in the cortical layers. We also found some differences in CSD patterns between the two SAM strains in terms of aging according to principle component analysis with dimension reduction. For simultaneous two-site stimulation, we modeled the obtained CSD profiles as a linear superposition of the CSD profiles to individual single-site stimulation. The model analysis indicated the nonlinearity of spatiotemporal integration over stimulus-driven activity in a layer-specific manner. Finally, on the basis of these results, we discuss the auditory cortex local network properties and the effects of aging on these mouse strains. Copyright © 2017 Elsevier B.V. All rights reserved.

Probabilistic seismic hazard analysis for a nuclear power plant site in southeast Brazil

NASA Astrophysics Data System (ADS)

de Almeida, Andréia Abreu Diniz; Assumpção, Marcelo; Bommer, Julian J.; Drouet, Stéphane; Riccomini, Claudio; Prates, Carlos L. M.

2018-05-01

A site-specific probabilistic seismic hazard analysis (PSHA) has been performed for the only nuclear power plant site in Brazil, located 130 km southwest of Rio de Janeiro at Angra dos Reis. Logic trees were developed for both the seismic source characterisation and ground-motion characterisation models, in both cases seeking to capture the appreciable ranges of epistemic uncertainty with relatively few branches. This logic-tree structure allowed the hazard calculations to be performed efficiently while obtaining results that reflect the inevitable uncertainty in long-term seismic hazard assessment in this tectonically stable region. An innovative feature of the study is an additional seismic source zone added to capture the potential contributions of characteristics earthquake associated with geological faults in the region surrounding the coastal site.

A needs analysis method for land-use planning of illegal dumping sites: a case study in Aomori-Iwate, Japan.

PubMed

Ishii, Kazuei; Furuichi, Toru; Nagao, Yukari

2013-02-01

Land use at contaminated sites, following remediation, is often needed for regional redevelopment. However, there exist few methods of developing economically and socially feasible land-use plans based on regional needs because of the wide variety of land-use requirements. This study proposes a new needs analysis method for the conceptual land-use planning of contaminated sites and illustrates this method with a case study of an illegal dumping site for hazardous waste. In this method, planning factors consisting of the land-use attributes and related facilities are extracted from the potential needs of the residents through a preliminary questionnaire. Using the extracted attributes of land use and the related facilities, land-use cases are designed for selection-based conjoint analysis. A second questionnaire for respondents to the first one who indicated an interest in participating in the second questionnaire is conducted for the conjoint analysis to determine the utility function and marginal cost of each attribute in order to prioritize the planning factors to develop a quantitative and economically and socially feasible land-use plan. Based on the results, site-specific land-use alternatives are developed and evaluated by the utility function obtained from the conjoint analysis. In this case study of an illegal dumping site for hazardous waste, the uses preferred as part of a conceptual land-use plan following remediation of the site were (1) agricultural land and a biogas plant designed to recover energy from biomass or (2) a park with a welfare facility and an athletic field. Our needs analysis method with conjoint analysis is applicable to the development of conceptual land-use planning for similar sites following remediation, particularly when added value is considered. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Method to Recognize Anatomical Site and Image Acquisition View in X-ray Images.

PubMed

Chang, Xiao; Mazur, Thomas; Li, H Harold; Yang, Deshan

2017-12-01

A method was developed to recognize anatomical site and image acquisition view automatically in 2D X-ray images that are used in image-guided radiation therapy. The purpose is to enable site and view dependent automation and optimization in the image processing tasks including 2D-2D image registration, 2D image contrast enhancement, and independent treatment site confirmation. The X-ray images for 180 patients of six disease sites (the brain, head-neck, breast, lung, abdomen, and pelvis) were included in this study with 30 patients each site and two images of orthogonal views each patient. A hierarchical multiclass recognition model was developed to recognize general site first and then specific site. Each node of the hierarchical model recognized the images using a feature extraction step based on principal component analysis followed by a binary classification step based on support vector machine. Given two images in known orthogonal views, the site recognition model achieved a 99% average F1 score across the six sites. If the views were unknown in the images, the average F1 score was 97%. If only one image was taken either with or without view information, the average F1 score was 94%. The accuracy of the site-specific view recognition models was 100%.

The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.

PubMed

González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred; Llosa, Matxalen

2017-06-15

Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery. IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site-specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination. Copyright © 2017 American Society for Microbiology.

The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome

PubMed Central

González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred

2017-01-01

ABSTRACT Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery. IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site-specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination. PMID:28411218

Characterization of Epitope-Specific Anti-Respiratory Syncytial Virus (Anti-RSV) Antibody Responses after Natural Infection and after Vaccination with Formalin-Inactivated RSV

PubMed Central

Luytjes, Willem; Leenhouts, Kees; Rottier, Peter J. M.; van Kuppeveld, Frank J. M.; Haijema, Bert Jan

2016-01-01

ABSTRACT Antibodies against the fusion (F) protein of respiratory syncytial virus (RSV) play an important role in the protective immune response to this important respiratory virus. Little is known, however, about antibody levels against multiple F-specific epitopes induced by infection or after vaccination against RSV, while this is important to guide the evaluation of (novel) vaccines. In this study, we analyzed antibody levels against RSV proteins and F-specific epitopes in human sera and in sera of vaccinated and experimentally infected cotton rats and the correlation thereof with virus neutralization. Analysis of human sera revealed substantial diversity in antibody levels against F-, G (attachment)-, and F-specific epitopes between individuals. The highest correlation with virus neutralization was observed for antibodies recognizing prefusion-specific antigenic site Ø. Nevertheless, our results indicate that high levels of antibodies targeting other parts of the F protein can also mediate a potent antiviral antibody response. In agreement, sera of experimentally infected cotton rats contained high neutralizing activity despite lacking antigenic site Ø-specific antibodies. Strikingly, vaccination with formalin-inactivated RSV (FI-RSV) exclusively resulted in the induction of poorly neutralizing antibodies against postfusion-specific antigenic site I, although antigenic sites I, II, and IV were efficiently displayed in FI-RSV. The apparent immunodominance of antigenic site I in FI-RSV likely explains the low levels of neutralizing antibodies upon vaccination and challenge and may play a role in the vaccination-induced enhancement of disease observed with such preparations. IMPORTANCE RSV is an importance cause of hospitalization of infants. The development of a vaccine against RSV has been hampered by the disastrous results obtained with FI-RSV vaccine preparations in the 1960s that resulted in vaccination-induced enhancement of disease. To get a better understanding of the antibody repertoire induced after infection or after vaccination against RSV, we investigated antibody levels against fusion (F) protein, attachment (G) protein, and F-specific epitopes in human and animal sera. The results indicate the importance of prefusion-specific antigenic site Ø antibodies as well as of antibodies targeting other epitopes in virus neutralization. However, vaccination of cotton rats with FI-RSV specifically resulted in the induction of weakly neutralizing, antigenic site I-specific antibodies, which may play a role in the enhancement of disease observed after vaccination with such preparations. PMID:27099320

Analysis of Material Handling Safety in Construction Sites and Countermeasures for Effective Enhancement

PubMed Central

Anil Kumar, C. N.; Sakthivel, M.; Elangovan, R. K.; Arularasu, M.

2015-01-01

One of many hazardous workplaces includes the construction sites as they involve several dangerous tasks. Many studies have revealed that material handling equipment is a major cause of accidents at these sites. Though safety measures are being followed and monitored continuously, accident rates are still high as either workers are unaware of hazards or the safety regulations are not being strictly followed. This paper analyses the safety management systems at construction sites through means of questionnaire surveys with employees, specifically referring to safety of material handling equipment. Based on results of the questionnaire surveys, two construction sites were selected for a safety education program targeting worker safety related to material handling equipment. Knowledge levels of the workers were gathered before and after the program and results obtained were subjected to a t-test analysis to mark significance level of the conducted safety education program. PMID:26446572

Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

PubMed Central

Wang, Mengxing; Liu, Hui; Ge, Lingqiao; Xing, Guangwei; Wang, Meng; Weining, Song; Nie, Xiaojun

2016-01-01

RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 5′-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations. PMID:28042823

Transcript Isoform Variation Associated with Cytosine Modification in Human Lymphoblastoid Cell Lines.

PubMed

Zhang, Xu; Zhang, Wei

2016-06-01

Cytosine modification on DNA is variable among individuals, which could correlate with gene expression variation. The effect of cytosine modification on interindividual transcript isoform variation (TIV), however, remains unclear. In this study, we assessed the extent of cytosine modification-specific TIV in lymphoblastoid cell lines (LCLs) derived from unrelated individuals of European and African descent. Our study detected cytosine modification-specific TIVs for 17% of the analyzed genes at a 5% false discovery rate. Forty-five percent of the TIV-associated cytosine modifications correlated with the overall gene expression levels as well, with the corresponding CpG sites overrepresented in transcript initiation sites, transcription factor binding sites, and distinct histone modification peaks, suggesting that alternative isoform transcription underlies the TIVs. Our analysis also revealed 33% of the TIV-associated cytosine modifications that affected specific exons, with the corresponding CpG sites overrepresented in exon/intron junctions, splicing branching points, and transcript termination sites, implying that the TIVs are attributable to alternative splicing or transcription termination. Genetic and epigenetic regulation of TIV shared target preference but exerted independent effects on 61% of the common exon targets. Cytosine modification-specific TIVs detected from LCLs were differentially enriched in those detected from various tissues in The Cancer Genome Atlas, indicating their developmental dependency. Genes containing cytosine modification-specific TIVs were enriched in pathways of cancers and metabolic disorders. Our study demonstrated a prominent effect of cytosine modification variation on the transcript isoform spectrum over gross transcript abundance and revealed epigenetic contributions to diseases that were mediated through cytosine modification-specific TIV. Copyright © 2016 by the Genetics Society of America.

New Substrate-Guided Method of Predicting Slow Conducting Isthmuses of Ventricular Tachycardia: Preliminary Analysis to the Combined Use of Voltage Limit Adjustment and Fast-Fourier Transform Analysis.

PubMed

Kuroki, Kenji; Nogami, Akihiko; Igarashi, Miyako; Masuda, Keita; Kowase, Shinya; Kurosaki, Kenji; Komatsu, Yuki; Naruse, Yoshihisa; Machino, Takeshi; Yamasaki, Hiro; Xu, Dongzhu; Murakoshi, Nobuyuki; Sekiguchi, Yukio; Aonuma, Kazutaka

2018-04-01

Several conducting channels of ventricular tachycardia (VT) can be identified using voltage limit adjustment (VLA) of substrate mapping. However, the sensitivity or specificity to predict a VT isthmus is not high by using VLA alone. This study aimed to evaluate the efficacy of the combined use of VLA and fast-Fourier transform analysis to predict VT isthmuses. VLA and fast-Fourier transform analyses of local ventricular bipolar electrograms during sinus rhythm were performed in 9 postinfarction patients who underwent catheter ablation for a total of 13 monomorphic VTs. Relatively higher voltage areas on an electroanatomical map were defined as high voltage channels (HVCs), and relatively higher fast-Fourier transform areas were defined as high-frequency channels (HFCs). HVCs were classified into full or partial HVCs (the entire or >30% of HVC can be detectable, respectively). Twelve full HVCs were identified in 7 of 9 patients. HFCs were located on 7 of 12 full HVCs. Five VT isthmuses (71%) were included in the 7 full HVC+/HFC+ sites, whereas no VT isthmus was found in the 5 full HVC+/HFC- sites. HFCs were identical to 9 of 16 partial HVCs. Eight VT isthmuses (89%) were included in the 9 partial HVC+/HFC+ sites, whereas no VT isthmus was found in the 7 partial HVC+/HFC- sites. All HVC+/HFC+ sites predicted VT isthmus with a sensitivity of 100% and a specificity of 80%. Combined use of VLA and fast-Fourier transform analysis may be a useful method to detect VT isthmuses. © 2018 American Heart Association, Inc.

Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method.

PubMed

Gao, JianZhao; Tao, Xue-Wen; Zhao, Jia; Feng, Yuan-Ming; Cai, Yu-Dong; Zhang, Ning

2017-01-01

Lysine acetylation, as one type of post-translational modifications (PTM), plays key roles in cellular regulations and can be involved in a variety of human diseases. However, it is often high-cost and time-consuming to use traditional experimental approaches to identify the lysine acetylation sites. Therefore, effective computational methods should be developed to predict the acetylation sites. In this study, we developed a position-specific method for epsilon lysine acetylation site prediction. Sequences of acetylated proteins were retrieved from the UniProt database. Various kinds of features such as position specific scoring matrix (PSSM), amino acid factors (AAF), and disorders were incorporated. A feature selection method based on mRMR (Maximum Relevance Minimum Redundancy) and IFS (Incremental Feature Selection) was employed. Finally, 319 optimal features were selected from total 541 features. Using the 319 optimal features to encode peptides, a predictor was constructed based on dagging. As a result, an accuracy of 69.56% with MCC of 0.2792 was achieved. We analyzed the optimal features, which suggested some important factors determining the lysine acetylation sites. We developed a position-specific method for epsilon lysine acetylation site prediction. A set of optimal features was selected. Analysis of the optimal features provided insights into the mechanism of lysine acetylation sites, providing guidance of experimental validation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Medical Treatment Facility Workload Documentation Guide.

DTIC Science & Technology

1980-04-15

to the system implementation should be presented. This document is intended as a guidebook for determining the site specific characteristics of an...wide volume analysis of a communications system. Prior to collecting any data, objectives and initial operating characteristics of the system(s...unique characteristics involved. An on-site inspection of all spaces to be impacted by NIS implementation is required initially. During this inspection

Probabilistic Assessment of Above Zone Pressure Predictions at a Geologic Carbon Storage Site

PubMed Central

Namhata, Argha; Oladyshkin, Sergey; Dilmore, Robert M.; Zhang, Liwei; Nakles, David V.

2016-01-01

Carbon dioxide (CO2) storage into geological formations is regarded as an important mitigation strategy for anthropogenic CO2 emissions to the atmosphere. This study first simulates the leakage of CO2 and brine from a storage reservoir through the caprock. Then, we estimate the resulting pressure changes at the zone overlying the caprock also known as Above Zone Monitoring Interval (AZMI). A data-driven approach of arbitrary Polynomial Chaos (aPC) Expansion is then used to quantify the uncertainty in the above zone pressure prediction based on the uncertainties in different geologic parameters. Finally, a global sensitivity analysis is performed with Sobol indices based on the aPC technique to determine the relative importance of different parameters on pressure prediction. The results indicate that there can be uncertainty in pressure prediction locally around the leakage zones. The degree of such uncertainty in prediction depends on the quality of site specific information available for analysis. The scientific results from this study provide substantial insight that there is a need for site-specific data for efficient predictions of risks associated with storage activities. The presented approach can provide a basis of optimized pressure based monitoring network design at carbon storage sites. PMID:27996043

Probabilistic Assessment of Above Zone Pressure Predictions at a Geologic Carbon Storage Site

NASA Astrophysics Data System (ADS)

Namhata, Argha; Oladyshkin, Sergey; Dilmore, Robert M.; Zhang, Liwei; Nakles, David V.

2016-12-01

Carbon dioxide (CO2) storage into geological formations is regarded as an important mitigation strategy for anthropogenic CO2 emissions to the atmosphere. This study first simulates the leakage of CO2 and brine from a storage reservoir through the caprock. Then, we estimate the resulting pressure changes at the zone overlying the caprock also known as Above Zone Monitoring Interval (AZMI). A data-driven approach of arbitrary Polynomial Chaos (aPC) Expansion is then used to quantify the uncertainty in the above zone pressure prediction based on the uncertainties in different geologic parameters. Finally, a global sensitivity analysis is performed with Sobol indices based on the aPC technique to determine the relative importance of different parameters on pressure prediction. The results indicate that there can be uncertainty in pressure prediction locally around the leakage zones. The degree of such uncertainty in prediction depends on the quality of site specific information available for analysis. The scientific results from this study provide substantial insight that there is a need for site-specific data for efficient predictions of risks associated with storage activities. The presented approach can provide a basis of optimized pressure based monitoring network design at carbon storage sites.

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

NONE

The study was conducted to determine the pollutants of concern in the Istanbul metropolitan area, monitoring equipment specifications and monitoring and data analysis procedures for an air quality and meteorological monitoring program. This volume consists of: (1) Introduction; (2) Selection of Pollutants of Concern; (3) Selection of Monitoring Locations; (4) Equipment Specifications; (5) Site Preparation and Security; (6) Standard Operating Procedures; (7) Data Reduction and Analysis; (8) Future Phases; (9) References. Also included are Attachments A through G and List of Tables and List of Figures.

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection.

PubMed

Gao, Yu-Fei; Li, Bi-Qing; Cai, Yu-Dong; Feng, Kai-Yan; Li, Zhan-Dong; Jiang, Yang

2013-01-27

Identification of catalytic residues plays a key role in understanding how enzymes work. Although numerous computational methods have been developed to predict catalytic residues and active sites, the prediction accuracy remains relatively low with high false positives. In this work, we developed a novel predictor based on the Random Forest algorithm (RF) aided by the maximum relevance minimum redundancy (mRMR) method and incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility to predict active sites of enzymes and achieved an overall accuracy of 0.885687 and MCC of 0.689226 on an independent test dataset. Feature analysis showed that every category of the features except disorder contributed to the identification of active sites. It was also shown via the site-specific feature analysis that the features derived from the active site itself contributed most to the active site determination. Our prediction method may become a useful tool for identifying the active sites and the key features identified by the paper may provide valuable insights into the mechanism of catalysis.

Persistent foot-and-mouth disease virus infection in the nasopharynx of cattle: tissue-specific distribution and local cytokine expression

USDA-ARS?s Scientific Manuscript database

Tissues obtained post-mortem from cattle persistently infected with foot-and-mouth disease virus (FMDV) were analyzed to characterize the tissue-specific localization of FMDV and partial transcriptome profiles for selected immunoregulatory cytokines. Analysis of 28 distinct anatomic sites from 21 st...

Water quality of Rhode Island streams

USGS Publications Warehouse

Briggs, J.C.; Feiffer, J.S.

1986-01-01

Water quality data collected from November 1979 through September 1983 at five stream stations within Rhode Island and one in Massachusetts show that concentrations of the common constituents were low. Mean water hardness at all sites was in the ' soft ' category. Sodium concentrations were less than 20 mg/L at two sites and less than 35 mg/L at the other sites. Mean nitrogen values for the two Blackstone River sites were in the range that could cause undesirable growths of aquatic plants. Mean phosphorus values exceeded the recommended limits for protection of aquatic life at four sites. Trace-element concentrations in the water were generally low. Those trace elements which were found in concentrations near or exceeding any standard or criterion include cadmium, chromium, lead, iron, and manganese. High concentrations of several trace elements were found in the bottom materials at several sites. The bottom materials also contained pesticides and organic chemicals including aldrin, chlordane, DDD, DDE, DDT, dieldren, endosulfan , endrin, heptachlor, Mirex, and PCB. Results of trend analysis of total phosphorus, total nitrogen, and specific conductance show a downward trend in phosphorus at two sites; an upward trend in nitrogen at one site; and one downward trend and one upward trend in specific conductance. (USGS)

Bromide, Chloride, and Sulfate Concentrations, and Specific Conductance, Lake Texoma, Texas and Oklahoma, 2007-08

USGS Publications Warehouse

Baldys, Stanley

2009-01-01

The U.S. Geological Survey, in cooperation with the City of Dallas Water Utilities Division, collected water-quality data from 11 sites on Lake Texoma, a reservoir on the Texas-Oklahoma border, during April 2007-September 2008. At 10 of the sites, physical properties (depth, specific conductance, pH, temperature, dissolved oxygen, and alkalinity) were measured and samples were collected for analysis of selected dissolved constituents (bromide, calcium, magnesium, potassium, sodium, carbonate, bicarbonate, chloride, and sulfate); at one site, only physical properties were measured. The primary constituent of interest was bromide. Bromate can form when ozone is used to disinfect raw water containing bromide, and bromate is a suspected human carcinogen. Chloride and sulfate were of secondary interest. Only the analytical results for bromide, chloride, sulfate, and measured specific conductance are discussed in this report. Median dissolved bromide concentrations ranged from 0.28 to 0.60 milligrams per liter. The largest median dissolved bromide concentration (0.60 milligram per liter at site 11) was from the Red River arm of Lake Texoma. Dissolved bromide concentrations generally were larger in the Red River arm of Lake Texoma than in the Washita arm of the lake. Median dissolved chloride concentrations were largest in the Red River arm of Lake Texoma at site 11 (431 milligrams per liter) and smallest at site 8 (122 milligrams per liter) in the Washita arm. At site 11 in the Red River arm, the mean and median chloride concentrations exceeded the secondary maximum contaminant level of 300 milligrams per liter for chloride established by the 'Texas Surface Water Quality Standards' for surface-water bodies designated for the public water supply use. Median dissolved sulfate concentrations ranged from 182 milligrams per liter at site 4 in the Big Mineral arm to 246 milligrams per liter at site 11 in the Red River arm. None of the mean or median sulfate concentrations exceeded the secondary maximum contaminant level of 300 milligrams per liter. Median specific conductance measurements at sites ranged from 1,120 microsiemens per centimeter at site 8 in the Washita arm to 2,100 microsiemens per centimeter in the Red River arm. The spatial distribution of specific conductance in Lake Texoma was similar to that of bromide and chloride, with larger specific conductance values in the Red River arm compared to those in the Washita arm.

LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals.

PubMed

Liu, Haihua; Shang, Xiaoxiao; Zhu, Hao

2017-05-15

Genomic imprinting is regulated by lncRNAs and is important for embryogenesis, physiology and behaviour in mammals. Aberrant imprinting causes diseases and disorders. Experimental studies have examined genomic imprinting primarily in humans and mice, thus leaving some fundamental issues poorly addressed. The cost of experimentally examining imprinted genes in many tissues in diverse species makes computational analysis of lncRNAs' DNA binding sites valuable. We performed lncRNA/DNA binding analysis in imprinting clusters from multiple mammalian clades and discovered the following: (i) lncRNAs and imprinting sites show significant losses and gains and distinct lineage-specificity; (ii) binding of lncRNAs to promoters of imprinted genes may occur widely throughout the genome; (iii) a considerable number of imprinting sites occur in only evolutionarily more derived species; and (iv) multiple lncRNAs may bind to the same imprinting sites, and some lncRNAs have multiple DNA binding motifs. These results suggest that the occurrence of abundant lncRNAs in mammalian genomes makes genomic imprinting a mechanism of adaptive evolution at the epigenome level. The data and program are available at the database LongMan at lncRNA.smu.edu.cn. zhuhao@smu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC.

PubMed

Totten, Sarah M; Feasley, Christa L; Bermudez, Abel; Pitteri, Sharon J

2017-03-03

Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.

SU-E-T-420: Failure Effects Mode Analysis for Trigeminal Neuralgia Frameless Radiosurgery

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

Howe, J

2015-06-15

Purpose: Functional radiosurgery has been used successfully in the treatment of trigeminal neuralgia but presents significant challenges to ensuring the high prescription dose is delivered accurately. A review of existing practice should help direct the focus of quality improvement for this treatment regime. Method: Failure modes and effects analysis was used to identify the processes in preparing radiosurgery treatment for TN. The map was developed by a multidisciplinary team including: neurosurgeon, radiation oncology, physicist and therapist. Potential failure modes were identified for each step in the process map as well as potential causes and end effect. A risk priority numbermore » was assigned to each cause. Results: The process map identified 66 individual steps (see attached supporting document). Corrective actions were developed for areas of high risk priority number. Wrong site treatment is at higher risk for trigeminal neuralgia treatment due to the lack of site specific pathologic imaging on MR and CT – additional site specific checks were implemented to minimize the risk of wrong site treatment. Failed collision checks resulted from an insufficient collision model in the treatment planning system and a plan template was developed to address this problem. Conclusion: Failure modes and effects analysis is an effective tool for developing quality improvement in high risk radiotherapy procedures such as functional radiosurgery.« less

Immunoaffinity Enrichment and Mass Spectrometry Analysis of Protein Methylation

PubMed Central

Guo, Ailan; Gu, Hongbo; Zhou, Jing; Mulhern, Daniel; Wang, Yi; Lee, Kimberly A.; Yang, Vicky; Aguiar, Mike; Kornhauser, Jon; Jia, Xiaoying; Ren, Jianmin; Beausoleil, Sean A.; Silva, Jeffrey C.; Vemulapalli, Vidyasiri; Bedford, Mark T.; Comb, Michael J.

2014-01-01

Protein methylation is a common posttranslational modification that mostly occurs on arginine and lysine residues. Arginine methylation has been reported to regulate RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction. Lysine methylation is best known to regulate histone function and is involved in epigenetic regulation of gene transcription. To better study protein methylation, we have developed highly specific antibodies against monomethyl arginine; asymmetric dimethyl arginine; and monomethyl, dimethyl, and trimethyl lysine motifs. These antibodies were used to perform immunoaffinity purification of methyl peptides followed by LC-MS/MS analysis to identify and quantify arginine and lysine methylation sites in several model studies. Overall, we identified over 1000 arginine methylation sites in human cell line and mouse tissues, and ∼160 lysine methylation sites in human cell line HCT116. The number of methylation sites identified in this study exceeds those found in the literature to date. Detailed analysis of arginine-methylated proteins observed in mouse brain compared with those found in mouse embryo shows a tissue-specific distribution of arginine methylation, and extends the types of proteins that are known to be arginine methylated to include many new protein types. Many arginine-methylated proteins that we identified from the brain, including receptors, ion channels, transporters, and vesicle proteins, are involved in synaptic transmission, whereas the most abundant methylated proteins identified from mouse embryo are transcriptional regulators and RNA processing proteins. PMID:24129315

Analysis of free online physician advice services.

PubMed

Cohen, Raphael; Elhadad, Michael; Birk, Ohad

2013-01-01

Online Consumer Health websites are a major source of information for patients worldwide. We focus on another modality, online physician advice. We aim to evaluate and compare the freely available online expert physicians' advice in different countries, its scope and the type of content provided. Using automated methods for information retrieval and analysis, we compared consumer health portals from the US, Canada, the UK and Israel (WebMD,NetDoctor,AskTheDoctor and BeOK). The evaluated content was generated between 2002 and 2011. We analyzed the different sites, looking at the distribution of questions in the various health topics, answer lengths and content type. Answers could be categorized into longer broad-educational answers versus shorter patient-specific ones, with different physicians having personal preferences as to answer type. The Israeli website BeOK, providing 10 times the number of answers than in the other three health portals, supplied answers that are shorter on average than in the other websites. Response times in these sites may be rapid with 32% of the WebMD answers and 64% of the BeOK answers provided in less than 24 hours. The voluntary contribution model used by BeOK and WebMD enables generation of large numbers of physician expert answers at low cost, providing 50,000 and 3,500 answers per year, respectively. Unlike health information in online databases or advice and support in patient-forums, online physician advice provides qualified specialists' responses directly relevant to the questions asked. Our analysis showed that high numbers of expert answers could be generated in a timely fashion using a voluntary model. The length of answers varied significantly between the internet sites. Longer answers were associated with educational content while short answers were associated with patient-specific content. Standard site-specific guidelines for expert answers will allow for more desirable content (educational content) or better throughput (patient-specific content).

Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.

PubMed

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

PubMed

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

Isolation of the human chromosomal band Xq28 within somatic cell hybrids by fragile X site breakage.

PubMed Central

Warren, S T; Knight, S J; Peters, J F; Stayton, C L; Consalez, G G; Zhang, F P

1990-01-01

The chromosomal fragile-site mapping to Xq27.3 is associated with a frequent form of mental retardation and is prone to breakage after induced deoxyribonucleotide pool perturbation. The human hypoxanthine phosphoribosyltransferase (HPRT) and glucose-6-phosphate dehydrogenase (G6PD) genes flank the fragile X chromosome site and can be used to monitor integrity of the site in human-hamster somatic cell hybrids deficient in the rodent forms of these activities. After induction of the fragile X site, negative selection for HPRT and positive enrichment for G6PD resulted in 31 independent colonies of HPRT-,G6PD+ phenotype. Southern blot analysis demonstrated the loss of all tested markers proximal to the fragile X site with retention of all tested human Xq28 loci in a majority of the hybrids. In situ hybridization with a human-specific probe demonstrated the translocation of a small amount of human DNA to rodent chromosomes in these hybrids, suggesting chromosome breakage at the fragile X site and the subsequent translocation of Xq28. Southern blot hybridization of hybrid-cell DNA, resolved by pulsed-field gel electrophoresis, for human-specific repetitive sequences revealed abundant CpG-islands within Xq28, consistent with its known gene density. The electrophoretic banding patterns of human DNA among the hybrids were remarkably consistent, suggesting that fragile X site breakage is limited to a relatively small region in Xq27-28. These somatic cell hybrids, containing Xq27.3-qter as the sole human DNA, will aid the search for DNA associated with the fragile X site and will augment the high resolution genomic analysis of Xq28, including the identification of candidate genes for genetic-disease loci mapping to this region. Images PMID:2339126

Proceedings of the workshop for exchange of technology for CWC inspections

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

McGuire, R.R.

1993-04-01

With the signing of the Chemical Weapons Convention (CWC), the work of the Preparatory Commission in defining the modalities of on-site verification inspections will begin early in 1993. One of the methods for increasing the effectiveness of inspections is the collection of samples for chemical analysis. The CWC allows for this analysis to be performed either at the site of the inspection or in a dedicated off-site laboratory. The decision as to where samples are to be analyzed in any specific instance may involve a consideration of the threat, real or perceived, to the compromise of legitimate sensitive host-party information.more » The ability to perform efficient chemical analysis at the inspection site, where samples remain in joint (host-inspector) custody and the analytical procedures can be observed by the host, can alleviate much of the concern over possible loss of confidential information in both government and industry. This workshop was designed to encourage the exchange of information among participants with experience in the use of analytical equipment for on-site sample collection and analysis. Individual projects are processed separately for the databases.« less

Data Integration Tool: Permafrost Data Debugging

NASA Astrophysics Data System (ADS)

Wilcox, H.; Schaefer, K. M.; Jafarov, E. E.; Pulsifer, P. L.; Strawhacker, C.; Yarmey, L.; Basak, R.

2017-12-01

We developed a Data Integration Tool (DIT) to significantly speed up the time of manual processing needed to translate inconsistent, scattered historical permafrost data into files ready to ingest directly into the Global Terrestrial Network-Permafrost (GTN-P). The United States National Science Foundation funded this project through the National Snow and Ice Data Center (NSIDC) with the GTN-P to improve permafrost data access and discovery. We leverage this data to support science research and policy decisions. DIT is a workflow manager that divides data preparation and analysis into a series of steps or operations called widgets (https://github.com/PermaData/DIT). Each widget does a specific operation, such as read, multiply by a constant, sort, plot, and write data. DIT allows the user to select and order the widgets as desired to meet their specific needs, incrementally interact with and evolve the widget workflows, and save those workflows for reproducibility. Taking ideas from visual programming found in the art and design domain, debugging and iterative design principles from software engineering, and the scientific data processing and analysis power of Fortran and Python it was written for interactive, iterative data manipulation, quality control, processing, and analysis of inconsistent data in an easily installable application. DIT was used to completely translate one dataset (133 sites) that was successfully added to GTN-P, nearly translate three datasets (270 sites), and is scheduled to translate 10 more datasets ( 1000 sites) from the legacy inactive site data holdings of the Frozen Ground Data Center (FGDC). Iterative development has provided the permafrost and wider scientific community with an extendable tool designed specifically for the iterative process of translating unruly data.

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure

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

Bouwmeester, Manon C.; Ruiter, Sander; Lommelaars, Tobias

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin,more » arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. - Highlights: • Compound induced effects on DNA methylation in zebrafish embryos • Global methylation not an informative biomarker • Minimal genome wide site specific changes as detected with DREAM • Compound/class specific effects suggested by pyrosequence of specific targets • Zebrafish embryo may be a screening model for epigenetic effects.« less

Implementation of the Generic Safety Analysis Report - Lessons Learned

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

Blanchard, A.

1999-06-02

The Savannah River Site has completed the development, review and approval process for the Generic Safety Analysis Report (GSAR) and implemented this information in facility SARs and BIOs. This includes the yearly revision of the GSAR and the facility-specific SARs. The process has provided us with several lessons learned.

"Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies".

PubMed

Verma, Ved Vrat; Gupta, Rani; Goel, Manisha

2015-09-14

γ-glutamyltranspeptidase (GGT) is a bi-substrate enzyme conserved in all three domains of life. It catalyzes the cleavage and transfer of γ-glutamyl moiety of glutathione to either water (hydrolysis) or substrates like peptides (transpeptidation). GGTs exhibit great variability in their enzyme kinetics although the mechanism of catalysis is conserved. Recently, GGT has been shown to be a virulence factor in microbes like Helicobacter pylori and Bacillus anthracis. In mammalian cells also, GGT inhibition prior to chemotherapy has been shown to sensitize tumors to the therapy. Therefore, lately both bacterial and eukaryotic GGTs have emerged as potential drug targets, but the efforts directed towards finding suitable inhibitors have not yielded any significant results yet. We propose that delineating the residues responsible for the functional diversity associated with these proteins could help in design of species/clade specific inhibitors. In the present study, we have carried out phylogenetic analysis on a set of 47 GGT-like proteins to address the functional diversity. These proteins segregate into various subfamilies, forming separate clades on the tree. Sequence conservation and motif prediction studies show that even though most of the highly conserved residues have been characterized biochemically in previous studies, a significant number of novel putative sites and motifs are discovered that vary in a clade specific manner. Many of the putative sites predicted during the functional divergence type I and type II analysis, lie close to the known catalytic residues and line the walls of the substrate binding cavity, reinforcing their role in modulating the substrate specificity, catalytic rates and stability of this protein. The study offers interesting insights into the evolution of GGT-like proteins in pathogenic vs. non-pathogenic bacteria, archaea and eukaryotes. Our analysis delineates residues that are highly specific to each GGT subfamily. We propose that these sites not only explain the differences in stability and catalytic variability of various GGTs but can also aid in design of specific inhibitors against particular GGTs. Thus, apart from the commonly used in-silico inhibitor screening approaches, evolutionary analysis identifying the functional divergence hotspots in GGT proteins could augment the structure based drug design approaches.

[3H]aniracetam binds to specific recognition sites in brain membranes.

PubMed

Fallarino, F; Genazzani, A A; Silla, S; L'Episcopo, M R; Camici, O; Corazzi, L; Nicoletti, F; Fioretti, M C

1995-08-01

[3H]Aniracetam bound to specific and saturable recognition sites in membranes prepared from discrete regions of rat brain. In crude membrane preparation from rat cerebral cortex, specific binding was Na+ independent, was still largely detectable at low temperature (4 degrees C), and underwent rapid dissociation. Scatchard analysis of [3H]aniracetam binding revealed a single population of sites with an apparent KD value of approximately 70 nM and a maximal density of 3.5 pmol/mg of protein. Specifically bound [3H]aniracetam was not displaced by various metabolites of aniracetam, nor by other pyrrolidinone-containing nootropic drugs such as piracetam or oxiracetam. Subcellular distribution studies showed that a high percentage of specific [3H]aniracetam binding was present in purified synaptosomes or mitochondria, whereas specific binding was low in the myelin fraction. The possibility that at least some [3H]aniracetam binding sites are associated with glutamate receptors is supported by the evidence that specific binding was abolished when membranes were preincubated at 37 degrees C under fast shaking (a procedure that substantially reduced the amount of glutamate trapped in the membranes) and could be restored after addition of either glutamate or alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) but not kainate. The action of AMPA was antagonized by DNQX, which also reduced specific [3H]aniracetam binding in unwashed membranes. High levels of [3H]aniracetam binding were detected in hippocampal, cortical, or cerebellar membranes, which contain a high density of excitatory amino acid receptors.(ABSTRACT TRUNCATED AT 250 WORDS)

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Pharmacological characterization of CCKB receptors in human brain: no evidence for receptor heterogeneity.

PubMed

Kinze, S; Schöneberg, T; Meyer, R; Martin, H; Kaufmann, R

1996-10-11

In this paper, cholecystokinin (CCK) B-type binding sites were characterized with receptor binding studies in different human brain regions (various parts of cerebral cortex, basal ganglia, hippocampus, thalamus, cerebellar cortex) collected from 22 human postmortem brains. With the exception of the thalamus, where no specific CCK binding sites were found, a pharmacological characterization demonstrated a single class of high affinity CCK sites in all brain areas investigated. Receptor densities ranged from 0.5 fmol/mg protein (hippocampus) to 8.4 fmol/mg protein (nucleus caudatus). These CCK binding sites displayed a typical CCKA binding profile as shown in competition studies by using different CCK-related compounds and non peptide CCK antagonists discriminating between CCKA and CCKB sites. The rank order of agonist or antagonist potency in inhibiting specific sulphated [propionyl-3H]cholecystokinin octapeptide binding was similar and highly correlated for the brain regions investigated as demonstrated by a computer-assisted analysis. Therefore it is concluded that CCKB binding sites in human cerebral cortex, basal ganglia, cerebellar cortex share identical ligand binding characteristics.

The use of computers to teach human anatomy and physiology to allied health and nursing students

NASA Astrophysics Data System (ADS)

Bergeron, Valerie J.

Educational institutions are under tremendous pressure to adopt the newest technologies in order to prepare their students to meet the challenges of the twenty-first century. For the last twenty years huge amounts of money have been spent on computers, printers, software, multimedia projection equipment, and so forth. A reasonable question is, "Has it worked?" Has this infusion of resources, financial as well as human, resulted in improved learning? Are the students meeting the intended learning goals? Any attempt to develop answers to these questions should include examining the intended goals and exploring the effects of the changes on students and faculty. This project investigated the impact of a specific application of a computer program in a community college setting on students' attitudes and understanding of human anatomy and physiology. In this investigation two sites of the same community college with seemingly similar students populations, seven miles apart, used different laboratory activities to teach human anatomy and physiology. At one site nursing students were taught using traditional dissections and laboratory activities; at the other site two of the dissections, specifically cat and sheep pluck, were replaced with the A.D.A.M.RTM (Animated Dissection of Anatomy for Medicine) computer program. Analysis of the attitude data indicated that students at both sites were extremely positive about their laboratory experiences. Analysis of the content data indicated a statistically significant difference in performance between the two sites in two of the eight content areas that were studied. For both topics the students using the computer program scored higher. A detailed analysis of the surveys, interviews with faculty and students, examination of laboratory materials, and observations of laboratory facilities in both sites, and cost-benefit analysis led to the development of seven recommendations. The recommendations call for action at the level of the institution requiring investment in additional resources, and at the level of the faculty requiring a commitment to exploration and reflective practice.

Site specific modification of the human plasma proteome by methylglyoxal

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

Kimzey, Michael J.; Kinsky, Owen R.; Yassine, Hussein N.

Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC–MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-argininemore » modification, dihydroxyimidazolidine (R + 72) and hydroimidazolone (R + 54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan–HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. - Highlights: • Methylglyoxal (MG) selectively modifies arginine sites in human plasma proteome. • Dihydroxyimidazolidine and hydroimidazolone adducts on serum albumin identified • MG modification on albumin R257 associated with loss of drug site I binding capacity • MRM-tandem mass spectrometry enables sensitive detection of albumin MG-R257. • Site-specific MG modification may represent a useful monitor of effective therapy of T2DM.« less

Considerations in the statistical analysis of clinical trials in periodontitis.

PubMed

Imrey, P B

1986-05-01

Adult periodontitis has been described as a chronic infectious process exhibiting sporadic, acute exacerbations which cause quantal, localized losses of dental attachment. Many analytic problems of periodontal trials are similar to those of other chronic diseases. However, the episodic, localized, infrequent, and relatively unpredictable behavior of exacerbations, coupled with measurement error difficulties, cause some specific problems. Considerable controversy exists as to the proper selection and treatment of multiple site data from the same patient for group comparisons for epidemiologic or therapeutic evaluative purposes. This paper comments, with varying degrees of emphasis, on several issues pertinent to the analysis of periodontal trials. Considerable attention is given to the ways in which measurement variability may distort analytic results. Statistical treatments of multiple site data for descriptive summaries are distinguished from treatments for formal statistical inference to validate therapeutic effects. Evidence suggesting that sites behave independently is contested. For inferential analyses directed at therapeutic or preventive effects, analytic models based on site independence are deemed unsatisfactory. Methods of summarization that may yield more powerful analyses than all-site mean scores, while retaining appropriate treatment of inter-site associations, are suggested. Brief comments and opinions on an assortment of other issues in clinical trial analysis are preferred.

Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All.

PubMed

Cummins, Peter L; Kannappan, Babu; Gready, Jill E

2018-01-01

The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO 2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.

Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

PubMed

Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

2010-06-01

The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

Application of microtremor horizontal-to-vertical spectral ratio (MHVSR) analysis for site characterization: State of the art

USGS Publications Warehouse

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sanchez-Sesma, F. J.; Yong, Alan

2018-01-01

Nakamura (Q Rep Railway Tech Res Inst 30:25–33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site’s MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

Investigation of the Occurrence of Porcine Reproductive and Respiratory Virus in Swine Herds Participating in an Area Regional Control and Elimination Project in Ontario, Canada.

PubMed

Arruda, A G; Friendship, R; Carpenter, J; Hand, K; Ojkic, D; Poljak, Z

2017-02-01

The main goal of this study was to investigate the occurrence of porcine reproductive and respiratory syndrome virus (PRRSV)-specific genotypes in swine sites in Ontario (Canada) using molecular, spatial and network data from a porcine reproductive and respiratory syndrome (PRRS) regional control project. For each site, location, animal movement service provider (truck companies), PRRSV status and sequencing data of the open reading frame 5 (ORF5) were obtained. Three-kilometre buffers were created to evaluate neighbourhood characteristics for each site. Social network analysis was conducted on swine sites and trucking companies to assemble the network and define network components. Three different PRRSV genotypes were used as outcomes for statistical analysis based on the region's phylogenetic tree of the ORF5. Multivariable exact logistic regression was conducted to investigate the association between being positive for a specific genotype and two main exposures of interest: (i) having at least one neighbour within three km also positive for the same genotype outside the production system and (ii) having at least one positive site for the same genotype in the same truck network component outside the production system. Results showed that the importance of area spread and truck network on PRRSV occurrence differed according to genotype. Additionally, the Ontario PRRS database appears suitable for conducting regional disease investigations. Finally, the use of relatively new tools available for network, spatial and molecular analysis could be useful in investigation, control and prevention of endemic infectious diseases in animal populations. © 2015 Blackwell Verlag GmbH.

A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

USGS Publications Warehouse

Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

2002-01-01

Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

PubMed

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Nucleotide sequence and structural organization of the human vasopressin pituitary receptor (V3) gene.

PubMed

René, P; Lenne, F; Ventura, M A; Bertagna, X; de Keyzer, Y

2000-01-04

In the pituitary, vasopressin triggers ACTH release through a specific receptor subtype, termed V3 or V1b. We cloned the V3 cDNA and showed that its expression was almost exclusive to pituitary corticotrophs and some corticotroph tumors. To study the determinants of this tissue specificity, we have now cloned the gene for the human (h) V3 receptor and characterized its structure. It is composed of two exons, spanning 10kb, with the coding region interrupted between transmembrane domains 6 and 7. We established that the transcription initiation site is located 498 nucleotides upstream of the initiator codon and showed that two polyadenylation sites may be used, while the most frequent is the most downstream. Sequence analysis of the promoter region showed no TATA box but identified consensus binding motifs for Sp1, CREB, and half sites of the estrogen receptor binding site. However comparison with another corticotroph-specific gene, proopiomelanocortin, did not identify common regulatory elements in the two promoters except for a short GC-rich region. Unexpectedly, hV3 gene analysis revealed that a formerly cloned 'artifactual' hV3 cDNA indeed corresponded to a spliced antisense transcript, overlapping the 5' part of the coding sequence in exon 1 and the promoter region. This transcript, hV3rev, was detected in normal pituitary and in many corticotroph tumors expressing hV3 sense mRNA and may therefore play a role in hV3 gene expression.

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

Lord, Anna C.

The U.S. Strategic Petroleum Reserve (SPR) is a stockpile of emergency crude oil to be tapped into if a disruption in the nation's oil supply occurs. The SPR is comprised of four salt dome sites. Subsidence surveys have been conducted either annually or biennially at all four sites over the life of the program. Monitoring of surface behavior is a first line defense to detecting possible subsurface cavern integrity issues. Over the life of the Bryan Mound site, subsidence rates over abandoned Cavern 3 have continuously been the highest at the site. In an effort to try and understand themore » subsurface dynamics, specifically over Bryan Mound Cavern 3, historic interferometric synthetic aperture radar (InSAR) data was acquired and processed by TRE Altamira. InSAR involves the processing of multiple satellite synthetic aperture radar scenes acquired across the same location of the Earth's surface at different times to map surface deformation. The analysis of the data has the ability to detect millimeters of motion spanning days, months, year and decades, across specific sites. The intent in regards to the Bryan Mound site was (1) to confirm the higher subsidence rates recorded over abandoned Cavern 3 indicated by land survey and (2) understand the regional surface behavior. This report describes the InSAR analysis results, how those results compare to the historical collection of land survey data, and what additional information the data has provided towards understanding the response recorded at the surface.« less

Specific strychnine binding sites on acrosome-associated membranes of golden hamster spermatozoa.

PubMed

Llanos, Miguel N; Ronco, Ana M; Aguirre, María C

2003-06-27

This study demonstrates for the first time, that membrane vesicles originated from the hamster sperm head after the occurrence of the acrosome reaction, possess specific strychnine binding sites. [3H]Strychnine binding was saturable and reversible, being displaced by unlabeled strychnine (IC(50)=26.7+/-2.3 microM). Kinetic analysis revealed one binding site with K(d)=120nM and B(max)=142fmol/10(6) spermatozoa. Glycine receptor agonists beta-alanine and taurine inhibited strychnine binding by 20-30%. Surprisingly, glycine stimulated binding by about 40-50%. Results obtained in this study strongly suggest the presence of glycine receptors-with distinctive kinetic properties on the periacrosomal plasma membrane of hamster spermatozoa. Localization of this receptor fits well with its previously proposed role in acrosomal exocytosis during mammalian fertilization.

Specific CA3 neurons decode neural information of dentate granule cells evoked by paired-pulse stimulation in co-cultured networks.

PubMed

Poli, Daniele; DeMarse, Thomas B; Wheeler, Bruce C; Brewer, Gregory J

2017-07-01

CA3 and dentate gyrus (DG) neurons are cultured in two-chamber devices on multi-electrode arrays (MEAs) and connected via micro-tunnels. In order to evoke time-locked activity, paired-pulse stimulation is applied to 22 different sites and repeated 25 times in each well in 5 MEA co-cultures and results compared to CA3-CA3 and DG-DG networks homologous controls. In these hippocampal sub-regions, we focus on the mechanisms underpinning a network's ability to decode the identity of site specific stimulation from analysis of evoked network responses using a support vector machine classifier. Our results indicate that a pool of CA3 neurons is able to reliably decode the identity of DG stimulation site information.

Plasma 25-hydroxyvitamin D concentration and subsequent risk of total and site specific cancers in Japanese population: large case-cohort study within Japan Public Health Center-based Prospective Study cohort.

PubMed

Budhathoki, Sanjeev; Hidaka, Akihisa; Yamaji, Taiki; Sawada, Norie; Tanaka-Mizuno, Sachiko; Kuchiba, Aya; Charvat, Hadrien; Goto, Atsushi; Kojima, Satoshi; Sudo, Natsuki; Shimazu, Taichi; Sasazuki, Shizuka; Inoue, Manami; Tsugane, Shoichiro; Iwasaki, Motoki

2018-03-07

To evaluate the association between pre-diagnostic circulating vitamin D concentration and the subsequent risk of overall and site specific cancer in a large cohort study. Nested case-cohort study within the Japan Public Health Center-based Prospective Study cohort. Nine public health centre areas across Japan. 3301 incident cases of cancer and 4044 randomly selected subcohort participants. Plasma concentration of 25-hydroxyvitamin D measured by enzyme immunoassay. Participants were divided into quarters based on the sex and season specific distribution of 25-hydroxyvitamin D among subcohorts. Weighted Cox proportional hazard models were used to calculate the multivariable adjusted hazard ratios for overall and site specific cancer across categories of 25-hydroxyvitamin D concentration, with the lowest quarter as the reference. Incidence of overall or site specific cancer. Plasma 25-hydroxyvitamin D concentration was inversely associated with the risk of total cancer, with multivariable adjusted hazard ratios for the second to fourth quarters compared with the lowest quarter of 0.81 (95% confidence interval 0.70 to 0.94), 0.75 (0.65 to 0.87), and 0.78 (0.67 to 0.91), respectively (P for trend=0.001). Among the findings for cancers at specific sites, an inverse association was found for liver cancer, with corresponding hazard ratios of 0.70 (0.44 to 1.13), 0.65 (0.40 to 1.06), and 0.45 (0.26 to 0.79) (P for trend=0.006). A sensitivity analysis showed that alternately removing cases of cancer at one specific site from total cancer cases did not substantially change the overall hazard ratios. In this large prospective study, higher vitamin D concentration was associated with lower risk of total cancer. These findings support the hypothesis that vitamin D has protective effects against cancers at many sites. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Contacts between the factor TUF and RPG sequences.

PubMed

Vignais, M L; Huet, J; Buhler, J M; Sentenac, A

1990-08-25

The yeast TUF factor binds specifically to RPG-like sequences involved in multiple functions at enhancers, silencers, and telomeres. We have characterized the interaction of TUF with its optimal binding sequence, rpg-1 (1-ACACCCATACATTT-14), using a gel DNA-binding assay in combination with methylation protection and mutagenesis experiments. As many as 10 base pairs appear to be engaged in factor binding. Analysis of a collection of 30 different RPG mutants demonstrated the importance of 8 base pairs at position 2, 3, 4, 5, 6, 7, 10, and 12 and the critical role of the central GC pair at position 5. Methylation protection data on four different natural sites confirmed a close contact at positions 4, 5, 6, and 10 and suggested additional contacts at base pairs 8, 12, and 13. The derived consensus sequence was RCAAYCCRYNCAYY. A quantitative band shift analysis was used to determine the equilibrium dissociation constant for the complex of TUF and its optimal binding site rpg-1. The specific dissociation constant (K8) was found to be 1.3 x 10(-11) M. The comparison of the K8 value with the dissociation constant obtained for nonspecific DNA sites (Kn8 = 8.7 x 10(-6) M) shows the high binding selectivity of TUF for its specific RPG target.

Analytical methods for characterization of explosives-contaminated sites on U.S. Army installations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas F.; Walsh, Marianne E.; Thorne, Philip G.

1995-10-01

The U.S. Army manufactures munitions at facilities throughout the United States. Many of these facilities are contaminated with residues of explosives from production, disposal of off- specification, and out-of-data munitions. The first step in remediating these sites is careful characterization. Currently sites are being characterized using a combination of on-site field screening and off-site laboratory analysis. Most of the contamination is associated with TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-tri-nitro-1,3,5-triazine) and their manufacturing impurities and environmental transformation products. Both colorimetric and enzyme immunoassay-based field screening methods have been used successfully for on-site characterization. These methods have similar detection capabilities but differ in their selectivity. Although field screening is very cost-effective, laboratory analysis is still required to fully characterize a site. Laboratory analysis for explosives residues in the United States is generally conducted using high-performance liquid chromatography equipped with a UV detector. Air-dried soils are extracted with acetonitrile in an ultrasonic bath. Water is analyzed directly if detection limits in the range of 10 - 20 (mu) g/L are acceptable, or preconcentrated using either salting-out solvent extraction with acetonitrile or solid phase extraction.

USP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A.

PubMed

Uckelmann, Michael; Densham, Ruth M; Baas, Roy; Winterwerp, Herrie H K; Fish, Alexander; Sixma, Titia K; Morris, Joanna R

2018-01-15

BRCA1-BARD1-catalyzed ubiquitination of histone H2A is an important regulator of the DNA damage response, priming chromatin for repair by homologous recombination. However, no specific deubiquitinating enzymes (DUBs) are known to antagonize this function. Here we identify ubiquitin specific protease-48 (USP48) as a H2A DUB, specific for the C-terminal BRCA1 ubiquitination site. Detailed biochemical analysis shows that an auxiliary ubiquitin, an additional ubiquitin that itself does not get cleaved, modulates USP48 activity, which has possible implications for its regulation in vivo. In cells we reveal that USP48 antagonizes BRCA1 E3 ligase function and in BRCA1-proficient cells loss of USP48 results in positioning 53BP1 further from the break site and in extended resection lengths. USP48 repression confers a survival benefit to cells treated with camptothecin and its activity acts to restrain gene conversion and mutagenic single-strand annealing. We propose that USP48 promotes genome stability by antagonizing BRCA1 E3 ligase function.

Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori

PubMed Central

Li, Dandan; Wang, Yanhong; Zhang, Kun; Jiao, Zhujin; Zhu, Xiaopeng; Skogerboe, Geir; Guo, Xiangqian; Chinnusamy, Viswanathan; Bi, Lijun; Huang, Yongping; Dong, Shuanglin; Chen, Runsheng; Kan, Yunchao

2011-01-01

Accumulating evidences show that small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. The silkworm is an important model for studies on insect genetics and control of lepidopterous pests. Here, we have performed the first systematic identification and analysis of intermediate size ncRNAs (50–500 nt) in the silkworm. We identified 189 novel ncRNAs, including 141 snoRNAs, six snRNAs, three tRNAs, one SRP and 38 unclassified ncRNAs. Forty ncRNAs showed significantly altered expression during silkworm development or across specific stage transitions. Genomic comparisons revealed that 123 of these ncRNAs are potentially silkworm-specific. Analysis of the genomic organization of the ncRNA loci showed that 32.62% of the novel snoRNA loci are intergenic, and that all the intronic snoRNAs follow the pattern of one-snoRNA-per-intron. Target site analysis predicted a total of 95 2′-O-methylation and pseudouridylation modification sites of rRNAs, snRNAs and tRNAs. Together, these findings provide new clues for future functional study of ncRNA during insect development and evolution. PMID:21227919

N- and O-glycosylation Analysis of Human C1-inhibitor Reveals Extensive Mucin-type O-Glycosylation.

PubMed

Stavenhagen, Kathrin; Kayili, H Mehmet; Holst, Stephanie; Koeleman, Carolien A M; Engel, Ruchira; Wouters, Diana; Zeerleder, Sacha; Salih, Bekir; Wuhrer, Manfred

2018-06-01

Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N - and O -glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD). Various proteases were applied, partly in combination with PNGase F and exoglycosidase treatment, in order to analyze the (glyco)peptides. The analysis revealed an extensively O -glycosylated N-terminal region. Five novel and five known O -glycosylation sites were identified, carrying mainly core1-type O -glycans. In addition, we detected a heavily O -glycosylated portion spanning from Thr 82 -Ser 121 with up to 16 O -glycans attached. Likewise, all known six N -glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. The glycoforms were in accordance with results on released N -glycans by MALDI-TOF/TOF-MS/MS. The comprehensive characterization of C1-Inh glycosylation described in this study will form the basis for further functional studies on the role of these glycan modifications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Stereoscopically Observing Manipulative Actions

PubMed Central

Ferri, S.; Pauwels, K.; Rizzolatti, G.; Orban, G. A.

2016-01-01

The purpose of this study was to investigate the contribution of stereopsis to the processing of observed manipulative actions. To this end, we first combined the factors “stimulus type” (action, static control, and dynamic control), “stereopsis” (present, absent) and “viewpoint” (frontal, lateral) into a single design. Four sites in premotor, retro-insular (2) and parietal cortex operated specifically when actions were viewed stereoscopically and frontally. A second experiment clarified that the stereo-action-specific regions were driven by actions moving out of the frontoparallel plane, an effect amplified by frontal viewing in premotor cortex. Analysis of single voxels and their discriminatory power showed that the representation of action in the stereo-action-specific areas was more accurate when stereopsis was active. Further analyses showed that the 4 stereo-action-specific sites form a closed network converging onto the premotor node, which connects to parietal and occipitotemporal regions outside the network. Several of the specific sites are known to process vestibular signals, suggesting that the network combines observed actions in peripersonal space with gravitational signals. These findings have wider implications for the function of premotor cortex and the role of stereopsis in human behavior. PMID:27252350

Functional analysis of dengue virus (DENV) type 2 envelope protein domain 3 type-specific and DENV complex-reactive critical epitope residues.

PubMed

Pitcher, Trevor J; Sarathy, Vanessa V; Matsui, Kiyohiko; Gromowski, Gregory D; Huang, Claire Y-H; Barrett, Alan D T

2015-02-01

The dengue virus (DENV) envelope protein domain 3 (ED3) is the target of potent virus neutralizing antibodies. The DENV-2 ED3 contains adjacent type-specific and DENV complex-reactive antigenic sites that are composed of a small number of residues that were previously demonstrated to be critical for antibody binding. Site-directed mutagenesis of a DENV-2 16681 infectious clone was used to mutate critical residues in the DENV-2 type-specific (K305A and P384A) and DENV complex-reactive (K310A) antigenic sites. The K305A mutant virus multiplied like the parent virus in mosquito and mammalian cells, as did the P384A mutant virus, which required a compensatory mutation (G330D) for viability. However, the K310A mutant virus could not be recovered. The DENV-2 type-specific critical residue mutations K305A and P384A+G330D reduced the ability of DENV-2 type-specific, but not DENV complex-reactive, mAbs to neutralize virus infectivity and this was directly correlated with mAb binding affinity to the rED3 mutants. © 2015 The Authors.

Stereoscopically Observing Manipulative Actions.

PubMed

Ferri, S; Pauwels, K; Rizzolatti, G; Orban, G A

2016-08-01

The purpose of this study was to investigate the contribution of stereopsis to the processing of observed manipulative actions. To this end, we first combined the factors "stimulus type" (action, static control, and dynamic control), "stereopsis" (present, absent) and "viewpoint" (frontal, lateral) into a single design. Four sites in premotor, retro-insular (2) and parietal cortex operated specifically when actions were viewed stereoscopically and frontally. A second experiment clarified that the stereo-action-specific regions were driven by actions moving out of the frontoparallel plane, an effect amplified by frontal viewing in premotor cortex. Analysis of single voxels and their discriminatory power showed that the representation of action in the stereo-action-specific areas was more accurate when stereopsis was active. Further analyses showed that the 4 stereo-action-specific sites form a closed network converging onto the premotor node, which connects to parietal and occipitotemporal regions outside the network. Several of the specific sites are known to process vestibular signals, suggesting that the network combines observed actions in peripersonal space with gravitational signals. These findings have wider implications for the function of premotor cortex and the role of stereopsis in human behavior. © The Author 2016. Published by Oxford University Press.

Computational active site analysis of molecular pathways to improve functional classification of enzymes.

PubMed

Ozyurt, A Sinem; Selby, Thomas L

2008-07-01

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

Quantifying Fast and Slow Responses of Terrestrial Carbon Exchange across a Water Availability Gradient in North American Flux Sites

NASA Astrophysics Data System (ADS)

Biederman, J. A.; Scott, R. L.; Goulden, M.

2014-12-01

Climate change is predicted to increase the frequency and severity of water limitation, altering terrestrial ecosystems and their carbon exchange with the atmosphere. Here we compare site-level temporal sensitivity of annual carbon fluxes to interannual variations in water availability against cross-site spatial patterns over a network of 19 eddy covariance flux sites. This network represents one order of magnitude in mean annual productivity and includes western North American desert shrublands and grasslands, savannahs, woodlands, and forests with continuous records of 4 to 12 years. Our analysis reveals site-specific patterns not identifiable in prior syntheses that pooled sites. We interpret temporal variability as an indicator of ecosystem response to annual water availability due to fast-changing factors such as leaf stomatal response and microbial activity, while cross-site spatial patterns are used to infer ecosystem adjustment to climatic water availability through slow-changing factors such as plant community and organic carbon pools. Using variance decomposition, we directly quantify how terrestrial carbon balance depends on slow- and fast-changing components of gross ecosystem production (GEP) and total ecosystem respiration (TER). Slow factors explain the majority of variance in annual net ecosystem production (NEP) across the dataset, and their relative importance is greater at wetter, forest sites than desert ecosystems. Site-specific offsets from spatial patterns of GEP and TER explain one third of NEP variance, likely due to slow-changing factors not directly linked to water, such as disturbance. TER and GEP are correlated across sites as previously shown, but our site-level analysis reveals surprisingly consistent linear relationships between these fluxes in deserts and savannahs, indicating fast coupling of TER and GEP in more arid ecosystems. Based on the uncertainty associated with slow and fast factors, we suggest a framework for improved prediction of terrestrial carbon balance. We will also present results of ongoing work to quantify fast and slow contributions to the relationship between evapotranspiration and precipitation across a precipitation gradient.

Site specific probabilistic seismic hazard analysis at Dubai Creek on the west coast of UAE

NASA Astrophysics Data System (ADS)

Shama, Ayman A.

2011-03-01

A probabilistic seismic hazard analysis (PSHA) was conducted to establish the hazard spectra for a site located at Dubai Creek on the west coast of the United Arab Emirates (UAE). The PSHA considered all the seismogenic sources that affect the site, including plate boundaries such as the Makran subduction zone, the Zagros fold-thrust region and the transition fault system between them; and local crustal faults in UAE. PSHA indicated that local faults dominate the hazard. The peak ground acceleration (PGA) for the 475-year return period spectrum is 0.17 g and 0.33 g for the 2,475-year return period spectrum. The hazard spectra are then employed to establish rock ground motions using the spectral matching technique.

Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

PubMed

Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

2017-08-01

Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

Net Mineralization Response to Fertilizer Application and Site-Specific Setting in a No-Till Dryland Wheat Agroecosystem in the Pacific Northwest (USA)

NASA Astrophysics Data System (ADS)

Bruner, Emily A.; Brown, David J.; Carpenter-Boggs, Lynn

2015-04-01

Application of nitrogen (N) fertilizers is pivotal to maintaining agricultural productivity. Nutrient management is typically guided by a combined assessment of crop yield requirements, residual soil inorganic N concentration, and predicted N supply from organic matter. However, laboratory assays employed to forecast mineralization potential do not reflect in situ processes occurring in soils, processes that can vary spatially within a field. Furthermore, fertilizer application alters biogeochemical cycles through a variety of mechanisms including priming effects and microbial community alterations. This study investigates in-situ ammonification/nitrification rates utilizing mineralization cores as part of a five-year Site-Specific Climate-Friendly Farming (SCF) project. In-depth accounting of nitrate and ammonium production and flux was possible via a six bag mixed-bed ion exchange resin system. Soil cores (7.5 cm diameter by 15 cm deep) were isolated from the surrounding soil by three resin bags sealed in the top and bottom of individual plastic cylinders. Fifteen locations were selected across a commercial direct-seed wheat field based on statistical clustering of primary and secondary topographic variables. In each location surface soil-resin cores were installed in fertilized and unfertilized plots immediately after spring planting and removed before harvest. In situ ammonification/nitrification rates will be analyzed as a function of both fertilizer application and site-specific environmental characteristics as determined from soil moisture monitoring, soil characterization, and crop analysis at each measurement location. This site-specific information on N transformations and availability can then be used to guide site-specific crop management.

Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures*

PubMed Central

Jain, Kanishk; Warmack, Rebeccah A.; Stavropoulos, Peter

2016-01-01

In the family of protein arginine methyltransferases (PRMTs) that predominantly generate either asymmetric or symmetric dimethylarginine (SDMA), PRMT7 is unique in producing solely monomethylarginine (MMA) products. The type of methylation on histones and other proteins dictates changes in gene expression, and numerous studies have linked altered profiles of methyl marks with disease phenotypes. Given the importance of specific inhibitor development, it is crucial to understand the mechanisms by which PRMT product specificity is conferred. We have focused our attention on active-site residues of PRMT7 from the protozoan Trypanosoma brucei. We have designed 26 single and double mutations in the active site, including residues in the Glu-Xaa8-Glu (double E) loop and the Met-Gln-Trp sequence of the canonical Thr-His-Trp (THW) loop known to interact with the methyl-accepting substrate arginine. Analysis of the reaction products by high resolution cation exchange chromatography combined with the knowledge of PRMT crystal structures suggests a model where the size of two distinct subregions in the active site determines PRMT7 product specificity. A dual mutation of Glu-181 to Asp in the double E loop and Gln-329 to Ala in the canonical THW loop enables the enzyme to produce SDMA. Consistent with our model, the mutation of Cys-431 to His in the THW loop of human PRMT9 shifts its product specificity from SDMA toward MMA. Together with previous results, these findings provide a structural basis and a general model for product specificity in PRMTs, which will be useful for the rational design of specific PRMT inhibitors. PMID:27387499

SPICODYN: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings.

PubMed

Pastore, Vito Paolo; Godjoski, Aleksandar; Martinoia, Sergio; Massobrio, Paolo

2018-01-01

We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis. In particular, for inferring network connectivity, a new implementation of the transfer entropy method is presented dealing with multiple time delays (temporal extension) and with multiple binary patterns (high order extension). SPICODYN is specifically tailored to process data coming from different Multi-Electrode Arrays setups, guarantying, in those specific cases, automated processing. The optimized implementation of the Delayed Transfer Entropy and the High-Order Transfer Entropy algorithms, allows performing accurate and rapid analysis on multiple spike trains from thousands of electrodes.

Critical management practices influencing on-site waste minimization in construction projects.

PubMed

Ajayi, Saheed O; Oyedele, Lukumon O; Bilal, Muhammad; Akinade, Olugbenga O; Alaka, Hafiz A; Owolabi, Hakeem A

2017-01-01

As a result of increasing recognition of effective site management as the strategic approach for achieving the required performance in construction projects, this study seeks to identify the key site management practices that are requisite for construction waste minimization. A mixed methods approach, involving field study and survey research were used as means of data collection. After confirmation of construct validity and reliability of scale, data analysis was carried out through a combination of Kruskal-Wallis test, descriptive statistics and exploratory factor analysis. The study suggests that site management functions could significantly reduce waste generation through strict adherence to project drawings, and by ensuring fewer or no design changes during construction process. Provision of waste skips for specific materials and maximisation of on-site reuse of materials are also found to be among the key factors for engendering waste minimization. The result of factor analysis suggests four factors underlying on-site waste management practices with 96.093% of total variance. These measures include contractual provisions for waste minimization, waste segregation, maximisation of materials reuse and effective logistic management. Strategies through which each of the underlying measures could be achieved are further discussed in the paper. Findings of this study would assist construction site managers and other site operatives in reducing waste generated by construction activities. Copyright © 2016 Elsevier Ltd. All rights reserved.

A novel non prophage(-like) gene-intervening element within gerE that is reconstituted during sporulation in Bacillus cereus ATCC10987.

PubMed

Abe, Kimihiro; Shimizu, Shin-Ya; Tsuda, Shuhei; Sato, Tsutomu

2017-09-12

Gene rearrangement is a widely-shared phenomenon in spore forming bacteria, in which prophage(-like) elements interrupting sporulation-specific genes are excised from the host genome to reconstitute the intact gene. Here, we report a novel class of gene-intervening elements, named gin, inserted in the 225 bp gerE-coding region of the B. cereus ATCC10987 genome, which generates a sporulation-specific rearrangement. gin has no phage-related genes and possesses three site-specific recombinase genes; girA, girB, and girC. We demonstrated that the gerE rearrangement occurs at the middle stage of sporulation, in which site-specific DNA recombination took place within the 9 bp consensus sequence flanking the disrupted gerE segments. Deletion analysis of gin uncovered that GirC and an additional factor, GirX, are responsible for gerE reconstitution. Involvement of GirC and GirX in DNA recombination was confirmed by an in vitro recombination assay. These results broaden the definition of the sporulation-specific gene rearrangement phenomenon: gene-intervening elements are not limited to phage DNA but may include non-viral genetic elements that carry a developmentally-regulated site-specific recombination system.

Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences.

PubMed

Chen, Zhen-Yong; Guo, Xiao-Jiang; Chen, Zhong-Xu; Chen, Wei-Ying; Wang, Ji-Rui

2017-06-01

The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5' upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

Western energy related overhead monitoring project. Phase 2: Summary. [Campbell County, Wyoming and coal strip mines in Montana and New Mexico

NASA Technical Reports Server (NTRS)

Anderson, J. E. (Principal Investigator)

1979-01-01

Assistance by NASA to EPA in the establishment and maintenance of a fully operational energy-related monitoring system included: (1) regional analysis applications based on LANDSAT and auxiliary data; (2) development of techniques for using aircraft MSS data to rapidly monitor site specific surface coal mine activities; and (3) registration of aircraft MSS data to a map base. The coal strip mines used in the site specific task were in Campbell County, Wyoming; Big Horn County, Montana; and the Navajo mine in San Juan County, New Mexico. The procedures and software used to accomplish these tasks are described.

Mass Spectrometric Analysis of the Cell Surface N-Glycoproteome by Combining Metabolic Labeling and Click Chemistry

NASA Astrophysics Data System (ADS)

Smeekens, Johanna M.; Chen, Weixuan; Wu, Ronghu

2015-04-01

Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide- N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

PubMed Central

Grimmer, Matthew R.; Stolzenburg, Sabine; Ford, Ethan; Lister, Ryan; Blancafort, Pilar; Farnham, Peggy J.

2014-01-01

Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications. PMID:25122745

An Integrated Assessment of Location-Dependent Scaling for Microalgae Biofuel Production Facilities

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

Coleman, Andre M.; Abodeely, Jared; Skaggs, Richard

Successful development of a large-scale microalgae-based biofuels industry requires comprehensive analysis and understanding of the feedstock supply chain—from facility siting/design through processing/upgrading of the feedstock to a fuel product. The evolution from pilot-scale production facilities to energy-scale operations presents many multi-disciplinary challenges, including a sustainable supply of water and nutrients, operational and infrastructure logistics, and economic competitiveness with petroleum-based fuels. These challenges are addressed in part by applying the Integrated Assessment Framework (IAF)—an integrated multi-scale modeling, analysis, and data management suite—to address key issues in developing and operating an open-pond facility by analyzing how variability and uncertainty in space andmore » time affect algal feedstock production rates, and determining the site-specific “optimum” facility scale to minimize capital and operational expenses. This approach explicitly and systematically assesses the interdependence of biofuel production potential, associated resource requirements, and production system design trade-offs. The IAF was applied to a set of sites previously identified as having the potential to cumulatively produce 5 billion-gallons/year in the southeastern U.S. and results indicate costs can be reduced by selecting the most effective processing technology pathway and scaling downstream processing capabilities to fit site-specific growing conditions, available resources, and algal strains.« less

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

PubMed Central

Glinsky, Gennadi V.

2015-01-01

Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements. PMID:25956794

Teaching Geography and History through GIS: Application on Greek cultural sites

NASA Astrophysics Data System (ADS)

Skentos, Athanasios; Pavlopoulos, Kosmas; Galani, Apostolia; Theodorakopoulou, Katerina; Kritikos, Giorgos

2013-04-01

This study deals with the presentation of cultural succession in Greek space-time through a GIS application, associated with core concepts of geographic and historical education. Through the specific application students will be able to develop five distinct skills: sense of time-scale, historical and geographic comprehension, spatial analysis and interpretation, ability to perform geo-historical research, and procedure of geo-historical decision-making. The methodology is based on the calibration of a set of criteria for each cultural site that covers the topics of economy, geomorphology, society, religion, art and science. Further analysis of these data forms a geodatabase. In addition, palaeogeographic and historical maps of the cultural sites derived by the geodatabase provide information about temporal and spatial changes. As result, students will be able to develop a multidimensional and interdisciplinary approach, in order to reconstruct the evolution of the site.

Influence of culture site-specific MIC distributions on the pharmacokinetic and pharmacodynamic properties of piperacillin/tazobactam and piperacillin: a data analysis.

PubMed

Frei, Christopher R; Hampton, Shanna L; Burgess, David S

2006-07-01

Investigators who perform pharmacokinetic/pharmacodynamic (PK-PD) modeling with Monte Carlo simulation have historically not stratified microbiological data by culture site. This lack of stratification might be problematic if susceptibility patterns differ among sites and might lead to differences in PK-PD. This study compared the PK-PD of 2 antimicrobial regimens against 5 gram-negative bacterial species form 3 culture sites. This data analysis was performed at the Department of Pharmacology, The University of Texas Health Science Center, San Antonio, Texas. Blood, pulmonary (ie, bronchial, endotracheal, lung, respiratory, sputum, and tracheal secretions), and wound distributions of MICs were extracted from the 2002 Intensive Care Unit Surveillance System database. Bacteria included Acinetobacter baumannii, Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The PK properties of piperacillin/tazobactam (3.375 g every 4 hours) and piperacillin (3 g every 4 hours) were obtained from studies in healthy volunteers. Monte Carlo simulation was used in 10,000 patients for each antimicrobial-bacteria-culture site combination. The cumulative fraction of response (CFR) for a free percentage time above the MIC of > or =50% was determined for each combination, and a clinically significant difference was defined a priori as > or =10%. Data from 2408 pulmonary, 490 blood, and 242 wound isolates were included. For piperacillin/tazobactam, the CFR varied <10% by culture site in all 5 bacterial species. Site-specific differences were noted in MIC50 for piperacillin versus E cloacae and E coli and MIC90 for piperacillin/tazobactam versus K pneumoniae and P aeruginosa. Likewise, for piperacillin, the CFR was similar among the 3 culture sites for P aeruginosa. However, the CFR for piperacillin varied by > or =10% for A baumannii (blood > wound), E cloacae (pulmonary > blood), E coli (pulmonary and blood > wound), and K pneumoniae (wound > blood). The PK-PD models based on PK properties found in healthy humans and site-specific MIC distributions in this study suggest that for piperacillin, culture-site differences subsequently resulted in CFR differences that exceeded a predetermined level of clinical significance. Furthermore, these data suggest that traditional reporting strategies for microbiological data (ie, MIC50 and MIC90) might fail to adequately characterize the MIC population.

Open dumps in the Hellenic prefecture of Laconia: statistical analysis of characteristics and restoration prioritization on the basis of a field survey.

PubMed

Tsatsarelis, Thomas; Antonopoulos, Ioannis; Karagiannidis, Avraam; Perkoulidis, George

2007-10-01

This study presents an assessment of the current status of open dumps in Laconia prefecture of Peloponnese in southern Greece, where all open dumps are targeted for closure by 2008. An extensive field survey was conducted in 2005 to register existing sites in the prefecture. The data collected included the site area and age, waste depth, type of disposed waste, distance from nearest populated area, local geographical features and observed practices of open burning and soil coverage. On the basis of the collected data, a GIS database was developed, and the above parameters were statistically analysed. Subsequently, a decision tool for the restoration of open dumps was implemented, which led to the prioritization of site restorations and specific decisions about appropriate restoration steps for each site. The sites requiring restoration were then further classified using Principal Component Analysis, in order to categorize them into groups suitable for similar restoration work, thus facilitating fund allocation and subsequent restoration project management.

Pressure-specific and multiple pressure response of fish assemblages in European running waters☆

PubMed Central

Schinegger, Rafaela; Trautwein, Clemens; Schmutz, Stefan

2013-01-01

We classified homogenous river types across Europe and searched for fish metrics qualified to show responses to specific pressures (hydromorphological pressures or water quality pressures) vs. multiple pressures in these river types. We analysed fish taxa lists from 3105 sites in 16 ecoregions and 14 countries. Sites were pre-classified for 15 selected pressures to separate unimpacted from impacted sites. Hierarchical cluster analysis was used to split unimpacted sites into four homogenous river types based on species composition and geographical location. Classification trees were employed to predict associated river types for impacted sites with four environmental variables. We defined a set of 129 candidate fish metrics to select the best reacting metrics for each river type. The candidate metrics represented tolerances/intolerances of species associated with six metric types: habitat, migration, water quality sensitivity, reproduction, trophic level and biodiversity. The results showed that 17 uncorrelated metrics reacted to pressures in the four river types. Metrics responded specifically to water quality pressures and hydromorphological pressures in three river types and to multiple pressures in all river types. Four metrics associated with water quality sensitivity showed a significant reaction in up to three river types, whereas 13 metrics were specific to individual river types. Our results contribute to the better understanding of fish assemblage response to human pressures at a pan-European scale. The results are especially important for European river management and restoration, as it is necessary to uncover underlying processes and effects of human pressures on aquatic communities. PMID:24003262

CpG methylation at the USF binding site mediates cell-specific transcription of human ascorbate transporter SVCT2 exon 1a

PubMed Central

Qiao, Huan; May, James M.

2013-01-01

SVCT2 is the major transporter mediating vitamin C uptake in most organs. Its expression is driven by two promoters (CpG-poor exon 1a promoter and CpG-rich exon 1b promoter). In this work we mapped discrete elements within the proximal CpG-poor promoter responsible for the exon 1a transcription. We identified two E boxes for USF binding and one Y box for NF-Y binding. We further show that the formation of an NFY/USF complex on the exon 1a promoter amplifies each other's ability to bind to the promoter in a cooperativity-dependent manner and is absolutely required for the full activity of the exon 1a promoter. The analysis of the CpG site located at the upstream USF binding site in the promoter showed a strong correlation between expression and demethylation. It was also shown that the exon 1a transcription was induced in cell culture treated with demethylating agent decitabine. The specific methylation of this CpG site impaired both the binding of USF and the formation of the functional NF-Y/USF complex as well as promoter activity, suggesting its importance for the cell-specific transcription. Thus CpG methylation at the upstream USF binding site functions in establishing and maintaining cell-specific transcription from the CpG-poor SVCT2 exon 1a promoter. PMID:21770893

A cross-study analysis of prenatal exposures to environmental contaminants and the epigenome: support for stress-responsive transcription factor occupancy as a mediator of gene-specific CpG methylation patterning

PubMed Central

Martin, Elizabeth M.; Fry, Rebecca C.

2016-01-01

Abstract A biological mechanism by which exposure to environmental contaminants results in gene-specific CpG methylation patterning is currently unknown. We hypothesize that gene-specific CpG methylation is related to environmentally perturbed transcription factor occupancy. To test this hypothesis, a database of 396 genes with altered CpG methylation either in cord blood leukocytes or placental tissue was compiled from 14 studies representing assessments of six environmental contaminants. Subsequently, an in silico approach was used to identify transcription factor binding sites enriched among the genes with altered CpG methylation in relationship to the suite of environmental contaminants. For each study, the sequences of the promoter regions (representing −1000 to +500 bp from the transcription start site) of all genes with altered CpG methylation were analyzed for enrichment of transcription factor binding sites. Binding sites for a total of 56 unique transcription factors were identified to be enriched within the promoter regions of the genes. Binding sites for the Kidney-Enriched Krupple-like Factor 15, a known responder to endogenous stress, were enriched ( P  < 0.001–0.041) among the genes with altered CpG methylation associated for five of the six environmental contaminants. These data support the transcription factor occupancy theory as a potential mechanism underlying environmentally-induced gene-specific CpG methylation. PMID:27066266

Analysis strategies for longitudinal attachment loss data.

PubMed

Beck, J D; Elter, J R

2000-02-01

The purpose of this invited review is to describe and discuss methods currently in use to quantify the progression of attachment loss in epidemiological studies of periodontal disease, and to make recommendations for specific analytic methods based upon the particular design of the study and structure of the data. The review concentrates on the definition of incident attachment loss (ALOSS) and its component parts; measurement issues including thresholds and regression to the mean; methods of accounting for longitudinal change, including changes in means, changes in proportions of affected sites, incidence density, the effect of tooth loss and reversals, and repeated events; statistical models of longitudinal change, including the incorporation of the time element, use of linear, logistic or Poisson regression or survival analysis, and statistical tests; site vs person level of analysis, including statistical adjustment for correlated data; the strengths and limitations of ALOSS data. Examples from the Piedmont 65+ Dental Study are used to illustrate specific concepts. We conclude that incidence density is the preferred methodology to use for periodontal studies with more than one period of follow-up and that the use of studies not employing methods for dealing with complex samples, correlated data, and repeated measures does not take advantage of our current understanding of the site- and person-level variables important in periodontal disease and may generate biased results.

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

PubMed Central

Miotto, Olivo; Heiny, AT; Tan, Tin Wee; August, J Thomas; Brusic, Vladimir

2008-01-01

Background The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components. Results We compared over 3,000 PB2 protein sequences of human-transmissible and avian isolates, to produce a catalogue of sites involved in adaptation to human-to-human transmission. This analysis identified 17 characteristic sites, five of which have been present in human-transmissible strains since the 1918 Spanish flu pandemic. Sixteen of these sites are located in functional domains, suggesting they may play functional roles in host-range specificity. The catalogue of characteristic sites was used to derive sequence signatures from historical isolates. These signatures, arranged in chronological order, reveal an evolutionary timeline for the adaptation of the PB2 protein to human hosts. Conclusion By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful tool for comparative characterization of sequence sets. In addition to confirming previously reported findings, several novel characteristic sites within PB2 are reported. Sequence signatures generated using the characteristic sites catalogue characterize concisely the adaptation characteristics of individual isolates. Evolutionary timelines derived from signatures of early human influenza isolates suggest that characteristic variants emerged rapidly, and remained remarkably stable through subsequent pandemics. In addition, the signatures of human-infecting H5N1 isolates suggest that this avian subtype has low pandemic potential at present, although it presents more human adaptation components than most avian subtypes. PMID:18315849

Modeling corewood-outerwood transition in loblolly pine using wood specific gravity

Treesearch

Christian R. Mora; H. Lee Allen; Richard F. Daniels; Alexander Clark

2007-01-01

A modified logistic function was used for modeling specific-gravity profiles obtained from X-ray densitometry analysis in 675 loblolly pine (Pinus taeda L.) trees in four regeneration trials. Trees were 21 or 22 years old at the time of the study. The function was used for demarcating corewood, transitional, and outerwood zones. Site and silvicultural effects were...

Economic evaluation of nasogastric versus intravenous hydration in infants with bronchiolitis.

PubMed

Oakley, Ed; Carter, Rob; Murphy, Bridie; Borland, Meredith; Neutze, Jocelyn; Acworth, Jason; Krieser, David; Dalziel, Stuart; Davidson, Andrew; Donath, Susan; Jachno, Kim; South, Mike; Babl, Franz E

2017-06-01

Bronchiolitis is the most common lower respiratory tract infection in infants and the leading cause of hospitalisation. We aimed to assess whether intravenous hydration (IVH) was more cost-effective than nasogastric hydration (NGH) as a planned secondary economic analysis of a randomised trial involving 759 infants (aged 2-12 months) admitted to hospital with a clinical diagnosis of bronchiolitis and requiring non-oral hydration. No Australian cost data exist to aid clinicians in decision-making around interventions in bronchiolitis. Cost data collections included hospital and intervention-specific costs. The economic analysis was reduced to a cost-minimisation study, focusing on intervention-specific costs of IVH versus NGH, as length of stay was equal between groups. All analyses are reported as intention to treat. Intervention costs were greater for IVH than NGH ($113 vs $74; cost difference of $39 per child). The intervention-specific cost advantage to NGH was robust to inter-site variation in unit prices and treatment activity. Intervention-specific costs account for <10% of total costs of bronchiolitis admissions, with NGH having a small cost saving across all sites. © 2016 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea.

PubMed Central

Brown, D P; Idler, K B; Katz, L

1990-01-01

The 18.1-kilobase plasmid pSE211 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site. Restriction analysis of the integrated plasmid, pSE211int, and adjacent chromosomal sequences allowed identification of attP, the plasmid attachment site. Nucleotide sequencing of attP, attB, attL, and attR revealed a 57-base-pair sequence common to all sites with no duplications of adjacent plasmid or chromosomal sequences in the integrated state, indicating that integration takes place through conservative, reciprocal strand exchange. An analysis of the sequences indicated the presence of a putative gene for Phe-tRNA at attB which is preserved at attL after integration has occurred. A comparison of the attB site for a number of actinomycete plasmids is presented. Integration at attB was also observed when a 2.4-kilobase segment of pSE211 containing attP and the adjacent plasmid sequence was used to transform a pSE211- host. Nucleotide sequencing of this segment revealed the presence of two complete open reading frames (ORFs) and a segment of a third ORF. The ORF adjacent to attP encodes a putative polypeptide 437 amino acids in length that shows similarity, at its C-terminal domain, to sequences of site-specific recombinases of the integrase family. The adjacent ORF encodes a putative 98-amino-acid basic polypeptide that contains a helix-turn-helix motif at its N terminus which corresponds to domains in the Xis proteins of a number of bacteriophages. A proposal for the function of this polypeptide is presented. The deduced amino acid sequence of the third ORF did not reveal similarities to polypeptide sequences in the current data banks. Images FIG. 2 FIG. 3 PMID:2180909

Semantic Data And Visualization Techniques Applied To Geologic Field Mapping

NASA Astrophysics Data System (ADS)

Houser, P. I. Q.; Royo-Leon, M.; Munoz, R.; Estrada, E.; Villanueva-Rosales, N.; Pennington, D. D.

2015-12-01

Geologic field mapping involves the use of technology before, during, and after visiting a site. Geologists utilize hardware such as Global Positioning Systems (GPS) connected to mobile computing platforms such as tablets that include software such as ESRI's ArcPad and other software to produce maps and figures for a final analysis and report. Hand written field notes contain important information and drawings or sketches of specific areas within the field study. Our goal is to collect and geo-tag final and raw field data into a cyber-infrastructure environment with an ontology that allows for large data processing, visualization, sharing, and searching, aiding in connecting field research with prior research in the same area and/or aid with experiment replication. Online searches of a specific field area return results such as weather data from NOAA and QuakeML seismic data from USGS. These results that can then be saved to a field mobile device and searched while in the field where there is no Internet connection. To accomplish this we created the GeoField ontology service using the Web Ontology Language (OWL) and Protégé software. Advanced queries on the dataset can be made using reasoning capabilities can be supported that go beyond a standard database service. These improvements include the automated discovery of data relevant to a specific field site and visualization techniques aimed at enhancing analysis and collaboration while in the field by draping data over mobile views of the site using augmented reality. A case study is being performed at University of Texas at El Paso's Indio Mountains Research Station located near Van Horn, Texas, an active multi-disciplinary field study site. The user can interactively move the camera around the study site and view their data digitally. Geologist's can check their data against the site in real-time and improve collaboration with another person as both parties have the same interactive view of the data.

Putative melatonin receptors in a human biological clock

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

Reppert, S.M.; Weaver, D.R.; Rivkees, S.A.

In vitro autoradiography with /sup 125/I-labeled melatonin was used to examine melatonin binding sites in human hypothalamus. Specific /sup 125/I-labeled melatonin binding was localized to the suprachiasmatic nuclei, the site of a putative biological clock, and was not apparent in other hypothalamic regions. Specific /sup 125/I-labeled melatonin binding was consistently found in the suprachiasmatic nuclei of hypothalami from adults and fetuses. Densitometric analysis of competition experiments with varying concentrations of melatonin showed monophasic competition curves, with comparable half-maximal inhibition values for the suprachiasmatic nuclei of adults (150 picomolar) and fetuses (110 picomolar). Micromolar concentrations of the melatonin agonist 6-chloromelatonin completelymore » inhibited specific /sup 125/I-labeled melatonin binding, whereas the same concentrations of serotonin and norepinephrine caused only a partial reduction in specific binding. The results suggest that putative melatonin receptors are located in a human biological clock.« less

A logistic regression equation for estimating the probability of a stream flowing perennially in Massachusetts

USGS Publications Warehouse

Bent, Gardner C.; Archfield, Stacey A.

2002-01-01

A logistic regression equation was developed for estimating the probability of a stream flowing perennially at a specific site in Massachusetts. The equation provides city and town conservation commissions and the Massachusetts Department of Environmental Protection with an additional method for assessing whether streams are perennial or intermittent at a specific site in Massachusetts. This information is needed to assist these environmental agencies, who administer the Commonwealth of Massachusetts Rivers Protection Act of 1996, which establishes a 200-foot-wide protected riverfront area extending along the length of each side of the stream from the mean annual high-water line along each side of perennial streams, with exceptions in some urban areas. The equation was developed by relating the verified perennial or intermittent status of a stream site to selected basin characteristics of naturally flowing streams (no regulation by dams, surface-water withdrawals, ground-water withdrawals, diversion, waste-water discharge, and so forth) in Massachusetts. Stream sites used in the analysis were identified as perennial or intermittent on the basis of review of measured streamflow at sites throughout Massachusetts and on visual observation at sites in the South Coastal Basin, southeastern Massachusetts. Measured or observed zero flow(s) during months of extended drought as defined by the 310 Code of Massachusetts Regulations (CMR) 10.58(2)(a) were not considered when designating the perennial or intermittent status of a stream site. The database used to develop the equation included a total of 305 stream sites (84 intermittent- and 89 perennial-stream sites in the State, and 50 intermittent- and 82 perennial-stream sites in the South Coastal Basin). Stream sites included in the database had drainage areas that ranged from 0.14 to 8.94 square miles in the State and from 0.02 to 7.00 square miles in the South Coastal Basin.Results of the logistic regression analysis indicate that the probability of a stream flowing perennially at a specific site in Massachusetts can be estimated as a function of (1) drainage area (cube root), (2) drainage density, (3) areal percentage of stratified-drift deposits (square root), (4) mean basin slope, and (5) location in the South Coastal Basin or the remainder of the State. Although the equation developed provides an objective means for estimating the probability of a stream flowing perennially at a specific site, the reliability of the equation is constrained by the data used to develop the equation. The equation may not be reliable for (1) drainage areas less than 0.14 square mile in the State or less than 0.02 square mile in the South Coastal Basin, (2) streams with losing reaches, or (3) streams draining the southern part of the South Coastal Basin and the eastern part of the Buzzards Bay Basin and the entire area of Cape Cod and the Islands Basins.

Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing

PubMed Central

Chandran, Anandhakumar; Syed, Junetha; Taylor, Rhys D.; Kashiwazaki, Gengo; Sato, Shinsuke; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

2016-01-01

Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2 showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing. PMID:27098039

Concordance of Beta-papillomavirus across anogenital and oral anatomic sites of men: The HIM Study.

PubMed

Nunes, Emily M; López, Rossana V M; Sudenga, Staci L; Gheit, Tarik; Tommasino, Massimo; Baggio, Maria L; Ferreira, Silvaneide; Galan, Lenice; Silva, Roberto C; Lazcano-Ponce, Eduardo; Giuliano, Anna R; Villa, Luisa L; Sichero, Laura

2017-10-01

We evaluated the concordance between β-HPVs detected in external genital skin, anal canal, and oral cavity specimens collected simultaneously from 717 men that were participating in the multinational HIM Study. Viral genotyping was performed using the Luminex technology. Species- and type-specific concordance was measured using kappa statistics for agreement. Overall, concordance of β-HPVs across sites was low and mainly observed among paired genital/anal canal samples. When grouped by species, solely β-4 HPVs showed moderate concordance in genital/anal pairs (κ = 0.457), which could be attributed to the substantial concordance of HPV-92 in men from Brazil and Mexico (κ > 0.610). β-HPV type concordance was higher in Mexico, where HPV-19 was consistently concordant in all anatomic site combinations. Our analysis indicates that type-specific concordance across sites is limited to few viral types; however, these infections seem to occur more often than would be expected by chance, suggesting that although rare, there is agreement among sites. Copyright © 2017 Elsevier Inc. All rights reserved.

Orthogonal use of a human tRNA synthetase active site to achieve multi-functionality

PubMed Central

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B.; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A.; Schimmel, Paul; Yang, Xiang-Lei

2011-01-01

Protein multi-functionality is an emerging explanation for the complexity of higher organisms. In this regard, while aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, some also act in pathways for inflammation, angiogenesis, and apoptosis. How multiple functions evolved and their relationship to the active site is not clear. Here structural modeling analysis, mutagenesis, and cell-based functional studies show that the potent angiostatic, natural fragment of human TrpRS associates via Trp side chains that protrude from the cognate cellular receptor VE-cadherin. Modeling indicates that (I prefer the way it was because the conclusion was reached not only by modeling, but more so by experimental studies.)VE-cadherin Trp side chains fit into the Trp-specific active site of the synthetase. Thus, specific side chains of the receptor mimic (?) amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multi-functionality of human tRNA synthetases and other proteins. PMID:20010843

Groundwater Data Package for the 2004 Composite Analysis

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

Thorne, Paul D.

2004-08-11

This report presents data and information that supports the groundwater module. The conceptual model of groundwater flow and transport at the Hanford Site is described and specific information applied in the numerical implementation module is provided.

Tularosa Basin Play Fairway Analysis

DOE Data Explorer

Adam Brandt

2015-11-15

This submission contains several shapefiles used for a deterministic PFA, as well as a heat composite risk segment with union overlay, and training sites used for weights of evidence. More detailed metadata can be found in the specific file.

Current approaches for the assessment of in situ biodegradation.

PubMed

Bombach, Petra; Richnow, Hans H; Kästner, Matthias; Fischer, Anko

2010-04-01

Considering the high costs and technical difficulties associated with conventional remediation strategies, in situ biodegradation has become a promising approach for cleaning up contaminated aquifers. To verify if in situ biodegradation of organic contaminants is taking place at a contaminated site and to determine if these processes are efficient enough to replace conventional cleanup technologies, a comprehensive characterization of site-specific biodegradation processes is essential. In recent years, several strategies including geochemical analyses, microbial and molecular methods, tracer tests, metabolite analysis, compound-specific isotope analysis, and in situ microcosms have been developed to investigate the relevance of biodegradation processes for cleaning up contaminated aquifers. In this review, we outline current approaches for the assessment of in situ biodegradation and discuss their potential and limitations. We also discuss the benefits of research strategies combining complementary methods to gain a more comprehensive understanding of the complex hydrogeological and microbial interactions governing contaminant biodegradation in the field.

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

Moran, James J.; Kreuzer, Helen W.; Carman, April J.

Acid scavengers are frequently used as stabilizer compounds in a variety of applications. When used to stabilize volatile compounds such as nerve agents, the lower volatility and higher stability of acid scavengers make them more persistent in a post-event forensic setting. We are employing compound-specific stable isotope analysis of the carbon, nitrogen, and hydrogen components of three acid scavenging compounds (N,N-diethylaniline, tributylamine, and triethylamine) as a tool for distinguishing between different samples of the stabilizers. Combined analysis of three stable isotopes in these samples improves the technique’s resolving potential, enhancing sample matching capabilities. The compound specific methods developed here canmore » be applied to instances where these compounds are not pure, such as when mixed with an agent or when found as a residue at an event site. Effective sample matching can be crucial for linking compounds at multiple event sites or linking a supply inventory to an event.« less

Simulation of groundwater flow and streamflow depletion in the Branch Brook, Merriland River, and parts of the Mousam River watersheds in southern Maine

USGS Publications Warehouse

Nielsen, Martha G.; Locke, Daniel B.

2015-01-01

The study evaluated two different methods of calculating in-stream flow requirements for Branch Brook and the Merriland River—a set of statewide equations used to calculate monthly median flows and the MOVE.1 record-extension technique used on site-specific streamflow measurements. The August median in-stream flow requirement in the Merriland River was calculated as 7.18 ft3/s using the statewide equations but was 3.07 ft3/s using the MOVE.1 analysis. In Branch Brook, the August median in-stream flow requirements were calculated as 20.3 ft3/s using the statewide equations and 11.8 ft3/s using the MOVE.1 analysis. In each case, using site-specific data yields an estimate of in-stream flow that is much lower than an estimate the statewide equations provide.

Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

DOE PAGES

Liu, Degao; Hu, Rongbin; Palla, Kaitlin J.; ...

2016-02-18

Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. Here, this article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation ofmore » gene expression, as well as identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.« less

Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

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

Liu, Degao; Hu, Rongbin; Palla, Kaitlin J.

Genome editing with site-specific nucleases has become a powerful tool for functional characterization of plant genes and genetic improvement of agricultural crops. Among the various site-specific nuclease-based technologies available for genome editing, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems have shown the greatest potential for rapid and efficient editing of genomes in plant species. Here, this article reviews the current status of application of CRISPR/Cas9 to plant genomics research, with a focus on loss-of-function and gain-of-function analysis of individual genes in the context of perennial plants and the potential application of CRISPR/Cas9 to perturbation ofmore » gene expression, as well as identification and analysis of gene modules as part of an accelerated domestication and synthetic biology effort.« less

In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

PubMed

Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

2012-05-01

Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.

Local SPTHA through tsunami inundation simulations: a test case for two coastal critical infrastructures in the Mediterranean

NASA Astrophysics Data System (ADS)

Volpe, M.; Selva, J.; Tonini, R.; Romano, F.; Lorito, S.; Brizuela, B.; Argyroudis, S.; Salzano, E.; Piatanesi, A.

2016-12-01

Seismic Probabilistic Tsunami Hazard Analysis (SPTHA) is a methodology to assess the exceedance probability for different thresholds of tsunami hazard intensity, at a specific site or region in a given time period, due to a seismic source. A large amount of high-resolution inundation simulations is typically required for taking into account the full variability of potential seismic sources and their slip distributions. Starting from regional SPTHA offshore results, the computational cost can be reduced by considering for inundation calculations only a subset of `important' scenarios. We here use a method based on an event tree for the treatment of the seismic source aleatory variability; a cluster analysis on the offshore results to define the important sources; epistemic uncertainty treatment through an ensemble modeling approach. We consider two target sites in the Mediterranean (Milazzo, Italy, and Thessaloniki, Greece) where coastal (non nuclear) critical infrastructures (CIs) are located. After performing a regional SPTHA covering the whole Mediterranean, for each target site, few hundreds of representative scenarios are filtered out of all the potential seismic sources and the tsunami inundation is explicitly modeled, obtaining a site-specific SPTHA, with a complete characterization of the tsunami hazard in terms of flow depth and velocity time histories. Moreover, we also explore the variability of SPTHA at the target site accounting for coseismic deformation (i.e. uplift or subsidence) due to near field sources located in very shallow water. The results are suitable and will be applied for subsequent multi-hazard risk analysis for the CIs. These applications have been developed in the framework of the Italian Flagship Project RITMARE, EC FP7 ASTARTE (Grant agreement 603839) and STREST (Grant agreement 603389) projects, and of the INGV-DPC Agreement.

Enumeration of antigen-specific CD8+ T lymphocytes by single-platform, HLA tetramer-based flow cytometry: a European multicenter evaluation.

PubMed

Heijnen, Ingmar A F M; Barnett, David; Arroz, Maria J; Barry, Simon M; Bonneville, Marc; Brando, Bruno; D'hautcourt, Jean-Luc; Kern, Florian; Tötterman, Thomas H; Marijt, Erik W A; Bossy, David; Preijers, Frank W M B; Rothe, Gregor; Gratama, Jan W

2004-11-01

HLA class I peptide tetramers represent powerful diagnostic tools for detection and monitoring of antigen-specific CD8(+) T cells. The impetus for the current multicenter study is the critical need to standardize tetramer flow cytometry if it is to be implemented as a routine diagnostic assay. Hence, the European Working Group on Clinical Cell Analysis set out to develop and evaluate a single-platform tetramer-based method that used cytomegalovirus (CMV) as the antigenic model. Absolute numbers of CMV-specific CD8(+) T cells were obtained by combining the percentage of tetramer-binding cells with the absolute CD8(+) T-cell count. Six send-outs of stabilized blood from healthy individuals or CMV-carrying donors with CMV-specific CD8(+) T-cell counts of 3 to 10 cells/microl were distributed to 7 to 16 clinical sites. These sites were requested to enumerate CD8(+) T cells and, in the case of CMV-positive donors, CMV-specific subsets on three separate occasions using the standard method. Between-site coefficients of variation of less than 10% (absolute CD8(+) T-cell counts) and approximately 30% (percentage and absolute numbers of CMV-specific CD8(+) T cells) were achieved. Within-site coefficients of variation were approximately 5% (absolute CD8(+) T-cell counts), approximately 9% (percentage CMV-specific CD8(+) T cells), and approximately 17% (absolute CMV-specific CD8(+) T-cell counts). The degree of variation tended to correlate inversely with the proportion of CMV-specific CD8(+) T-cell subsets. The single-platform MHC tetramer-based method for antigen-specific CD8(+) T-cell counting has been evaluated by a European group of laboratories and can be considered a reproducible assay for routine enumeration of antigen-specific CD8(+) T cells. (c) 2004 Wiley-Liss, Inc.

Trace Metal Content of Sediments Close to Mine Sites in the Andean Region

PubMed Central

Yacoub, Cristina; Pérez-Foguet, Agustí; Miralles, Nuria

2012-01-01

This study is a preliminary examination of heavy metal pollution in sediments close to two mine sites in the upper part of the Jequetepeque River Basin, Peru. Sediment concentrations of Al, As, Cd, Cu, Cr, Fe, Hg, Ni, Pb, Sb, Sn, and Zn were analyzed. A comparative study of the trace metal content of sediments shows that the highest concentrations are found at the closest points to the mine sites in both cases. The sediment quality analysis was performed using the threshold effect level of the Canadian guidelines (TEL). The sediment samples analyzed show that potential ecological risk is caused frequently at both sites by As, Cd, Cu, Hg, Pb, and Zn. The long-term influence of sediment metals in the environment is also assessed by sequential extraction scheme analysis (SES). The availability of metals in sediments is assessed, and it is considered a significant threat to the environment for As, Cd, and Sb close to one mine site and Cr and Hg close to the other mine site. Statistical analysis of sediment samples provides a characterization of both subbasins, showing low concentrations of a specific set of metals and identifies the main characteristics of the different pollution sources. A tentative relationship between pollution sources and possible ecological risk is established. PMID:22606058

Tropospheric delay ray tracing applied in VLBI analysis

NASA Astrophysics Data System (ADS)

Eriksson, David; MacMillan, D. S.; Gipson, John M.

2014-12-01

Tropospheric delay modeling error continues to be one of the largest sources of error in VLBI (very long baseline interferometry) analysis. For standard operational solutions, we use the VMF1 elevation-dependent mapping functions derived from European Centre for Medium-Range Weather Forecasts data. These mapping functions assume that tropospheric delay at a site is azimuthally symmetric. As this assumption is not true, we have instead determined the ray trace delay along the signal path through the troposphere for each VLBI quasar observation. We determined the troposphere refractivity fields from the pressure, temperature, specific humidity, and geopotential height fields of the NASA Goddard Space Flight Center Goddard Earth Observing System version 5 numerical weather model. When applied in VLBI analysis, baseline length repeatabilities were improved compared with using the VMF1 mapping function model for 72% of the baselines and site vertical repeatabilities were better for 11 of 13 sites during the 2 week CONT11 observing period in September 2011. When applied to a larger data set (2011-2013), we see a similar improvement in baseline length and also in site position repeatabilities for about two thirds of the stations in each of the site topocentric components.

Geohydrology of the Antelope Valley Area, California and design for a ground-water-quality monitoring network

USGS Publications Warehouse

Duell, L.F.

1987-01-01

A basinwide ideal network and an actual network were designed to identify ambient groundwater quality, trends in groundwater quality, and degree of threat from potential pollution sources in Antelope Valley, California. In general, throughout the valley groundwater quality has remained unchanged, and no specific trends are apparent. The main source of groundwater for the valley is generally suitable for domestic, irrigation, and most industrial uses. Water quality data for selected constituents of some network wells and surface-water sites are presented. The ideal network of 77 sites was selected on the basis of site-specific criteria, geohydrology, and current land use (agricultural, residential, and industrial). These sites were used as a guide in the design of the actual network consisting of 44 existing wells. Wells are currently being monitored and were selected whenever possible because of budgetary constraints. Of the remaining ideal sites, 20 have existing wells not part of a current water quality network, and 13 are locations where no wells exist. The methodology used for the selection of sites, constituents monitored, and frequency of analysis will enable network users to make appropriate future changes to the monitoring network. (USGS)

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure

PubMed Central

Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

2014-01-01

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a “site-specific” homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional “non-site-specific” allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view. PMID:24710521

On the design of paleoenvironmental data networks for estimating large-scale patterns of climate

NASA Astrophysics Data System (ADS)

Kutzbach, J. E.; Guetter, P. J.

1980-09-01

Guidelines are determined for the spatial density and location of climatic variables (temperature and precipitation) that are appropriate for estimating the continental- to hemispheric-scale pattern of atmospheric circulation (sea-level pressure). Because instrumental records of temperature and precipitation simulate the climatic information that is contained in certain paleoenvironmental records (tree-ring, pollen, and written-documentary records, for example), these guidelines provide useful sampling strategies for reconstructing the pattern of atmospheric circulation from paleoenvironmental records. The statistical analysis uses a multiple linear regression model. The sampling strategies consist of changes in site density (from 0.5 to 2.5 sites per million square kilometers) and site location (from western North American sites only to sites in Japan, North America, and western Europe) of the climatic data. The results showed that the accuracy of specification of the pattern of sea-level pressure: (1) is improved if sites with climatic records are spread as uniformly as possible over the area of interest; (2) increases with increasing site density-at least up to the maximum site density used in this study; (3) is improved if sites cover an area that extends considerably beyond the limits of the area of interest. The accuracy of specification was lower for independent data than for the data that were used to develop the regression model; some skill was found for almost all sampling strategies.

Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions†

PubMed Central

Naegle, Kristen M.; White, Forest M.; Lauffenburger, Douglas A.; Yaffe, Michael B.

2012-01-01

Cell signaling networks propagate information from extracellular cues via dynamic modulation of protein–protein interactions in a context-dependent manner. Networks based on receptor tyrosine kinases (RTKs), for example, phosphorylate intracellular proteins in response to extracellular ligands, resulting in dynamic protein–protein interactions that drive phenotypic changes. Most commonly used methods for discovering these protein–protein interactions, however, are optimized for detecting stable, longer-lived complexes, rather than the type of transient interactions that are essential components of dynamic signaling networks such as those mediated by RTKs. Substrate phosphorylation downstream of RTK activation modifies substrate activity and induces phospho-specific binding interactions, resulting in the formation of large transient macromolecular signaling complexes. Since protein complex formation should follow the trajectory of events that drive it, we reasoned that mining phosphoproteomic datasets for highly similar dynamic behavior of measured phosphorylation sites on different proteins could be used to predict novel, transient protein–protein interactions that had not been previously identified. We applied this method to explore signaling events downstream of EGFR stimulation. Our computational analysis of robustly co-regulated phosphorylation sites, based on multiple clustering analysis of quantitative time-resolved mass-spectrometry phosphoproteomic data, not only identified known sitewise-specific recruitment of proteins to EGFR, but also predicted novel, a priori interactions. A particularly intriguing prediction of EGFR interaction with the cytoskeleton-associated protein PDLIM1 was verified within cells using co-immunoprecipitation and in situ proximity ligation assays. Our approach thus offers a new way to discover protein–protein interactions in a dynamic context- and phosphorylation site-specific manner. PMID:22851037

Combinatorial multispectral, thermodynamics, docking and site-directed mutagenesis reveal the cognitive characteristics of honey bee chemosensory protein to plant semiochemical.

PubMed

Tan, Jing; Song, Xinmi; Fu, Xiaobin; Wu, Fan; Hu, Fuliang; Li, Hongliang

2018-08-05

In the chemoreceptive system of insects, there are always some soluble binding proteins, such as some antennal-specific chemosensory proteins (CSPs), which are abundantly distributed in the chemosensory sensillar lymph. The antennal-specific CSPs usually have strong capability to bind diverse semiochemicals, while the detailed interaction between CSPs and the semiochemicals remain unclear. Here, by means of the combinatorial multispectral, thermodynamics, docking and site-directed mutagenesis, we detailedly interpreted a binding interaction between a plant semiochemical β-ionone and antennal-specific CSP1 from the worker honey bee. Thermodynamic parameters (ΔH < 0, ΔS > 0) indicate that the interaction is mainly driven by hydrophobic forces and electrostatic interactions. Docking prediction results showed that there are two key amino acids, Phe44 and Gln63, may be involved in the interacting process of CSP1 to β-ionone. In order to confirm the two key amino acids, site-directed mutagenesis were performed and the binding constant (K A ) for two CSP1 mutant proteins was reduced by 60.82% and 46.80% compared to wild-type CSP1. The thermodynamic analysis of mutant proteins furtherly verified that Phe44 maintained an electrostatic interaction and Gln63 contributes hydrophobic and electrostatic forces. Our investigation initially elucidates the physicochemical mechanism of the interaction between antennal-special CSPs in insects including bees to plant semiochemicals, as well as the development of twice thermodynamic analysis (wild type and mutant proteins) combined with multispectral and site-directed mutagenesis methods. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparison of PM10 concentrations and metal content in three different sites of the Venice Lagoon: an analysis of possible aerosol sources.

PubMed

Contini, Daniele; Belosi, Franco; Gambaro, Andrea; Cesari, Daniela; Stortini, Angela Maria; Bove, Maria Chiara

2012-01-01

The Venice Lagoon is exposed to atmospheric pollutants from industrial activities, thermoelectric power plants, petrochemical plants, incinerator, domestic heating, ship traffic, glass factories and vehicular emissions on the mainland. In 2005, construction began on the mobile dams (MOSE), one dam for each channel connecting the lagoon to the Adriatic Sea as a barrier against high tide. These construction works could represent an additional source of pollutants. PM10 samples were taken on random days between 2007 and 2010 at three different sites: Punta Sabbioni, Chioggia and Malamocco, located near the respective dam construction worksites. Chemical analyses of V, Cr, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Sb, Tl and Pb in PM10 samples were performed by Inductively coupled plasma-quadrupole mass spectrometry (ICP-QMS) and results were used to identify the main aerosol sources. The correlation of measured data with meteorology, and source apportionment, failed to highlight a contribution specifically associated to the emissions of the MOSE construction works. The comparison of the measurements at the three sites showed a substantial homogeneity of metal concentrations in the area. Source apportionment with principal component analysis (PCA) and positive matrix factorization (PMF) showed that a four principal factors model could describe the sources of metals in PM10. Three of them were assigned to specific sources in the area and one was characterised as a source of mixed origin (anthropogenic and crustal). A specific anthropogenic source of PM10 rich in Ni and Cr, active at the Chioggia site, was also identified.

Challenges for creating a site-specific groundwater-use record for the Ozark Plateaus aquifer system (central USA) from 1900 to 2010

NASA Astrophysics Data System (ADS)

Knierim, Katherine J.; Nottmeier, Anna M.; Worland, Scott; Westerman, Drew A.; Clark, Brian R.

2017-09-01

Hydrologic budgets to determine groundwater availability are important tools for water-resource managers. One challenging component for developing hydrologic budgets is quantifying water use through time because historical and site-specific water-use data can be sparse or poorly documented. This research developed a groundwater-use record for the Ozark Plateaus aquifer system (central USA) from 1900 to 2010 that related county-level aggregated water-use data to site-specific well locations and aquifer units. A simple population-based linear model, constrained to 0 million liters per day in 1900, provided the best means to extrapolate groundwater-withdrawal rates pre-1950s when there was a paucity of water-use data. To disaggregate county-level data to individual wells across a regional aquifer system, a programmatic hierarchical process was developed, based on the level of confidence that a well pumped groundwater for a specific use during a specific year. Statistical models tested on a subset of the best-available site-specific water-use data provided a mechanism to bracket historic groundwater use, such that groundwater-withdrawal rates ranged, on average, plus or minus 38% from modeled values. Groundwater withdrawn for public supply and domestic use accounted for between 48 and 74% of total groundwater use since 1901, highlighting that groundwater provides an important drinking-water resource. The compilation, analysis, and spatial and temporal extrapolation of water-use data remain a challenging task for water scientists, but is of paramount importance to better quantify groundwater use and availability.

Challenges for creating a site-specific groundwater-use record for the Ozark Plateaus aquifer system (central USA) from 1900 to 2010

USGS Publications Warehouse

Knierim, Katherine J.; Nottmeier, Anna M.; Worland, Scott C.; Westerman, Drew A.; Clark, Brian R.

2017-01-01

Hydrologic budgets to determine groundwater availability are important tools for water-resource managers. One challenging component for developing hydrologic budgets is quantifying water use through time because historical and site-specific water-use data can be sparse or poorly documented. This research developed a groundwater-use record for the Ozark Plateaus aquifer system (central USA) from 1900 to 2010 that related county-level aggregated water-use data to site-specific well locations and aquifer units. A simple population-based linear model, constrained to 0 million liters per day in 1900, provided the best means to extrapolate groundwater-withdrawal rates pre-1950s when there was a paucity of water-use data. To disaggregate county-level data to individual wells across a regional aquifer system, a programmatic hierarchical process was developed, based on the level of confidence that a well pumped groundwater for a specific use during a specific year. Statistical models tested on a subset of the best-available site-specific water-use data provided a mechanism to bracket historic groundwater use, such that groundwater-withdrawal rates ranged, on average, plus or minus 38% from modeled values. Groundwater withdrawn for public supply and domestic use accounted for between 48 and 74% of total groundwater use since 1901, highlighting that groundwater provides an important drinking-water resource. The compilation, analysis, and spatial and temporal extrapolation of water-use data remain a challenging task for water scientists, but is of paramount importance to better quantify groundwater use and availability.

Triplex-mediated analysis of cytosine methylation at CpA sites in DNA.

PubMed

Johannsen, Marie W; Gerrard, Simon R; Melvin, Tracy; Brown, Tom

2014-01-18

Modified triplex-forming oligonucleotides distinguish 5-methyl cytosine from unmethylated cytosine in DNA duplexes by differences in triplex melting temperatures. The discrimination is sequence-specific; dramatic differences in stabilisation are seen for CpA methylation, whereas CpG methylation is not detected. This direct detection of DNA methylation constitutes a new approach for epigenetic analysis.

State Civic Education Policy: Framework and Gap Analysis Tool. Special Report

ERIC Educational Resources Information Center

Baumann, Paul; Brennan, Jan

2017-01-01

The civic education policy framework and gap analysis tool are intended to guide state leaders as they address the complexities of preparing students for college, career and civic life. They allow for adaptation to state- and site-specific circumstances and may be adopted in whole or in piecemeal fashion, according to states' individual…

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data.

PubMed

Bertl, Johanna; Guo, Qianyun; Juul, Malene; Besenbacher, Søren; Nielsen, Morten Muhlig; Hornshøj, Henrik; Pedersen, Jakob Skou; Hobolth, Asger

2018-04-19

Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral mutational process is very complex: whole-genome analyses have revealed that the mutation rate differs between cancer types, between patients and along the genome depending on the genetic and epigenetic context. Therefore, methods that predict the number of different types of mutations in regions or specific genomic elements must consider local genomic explanatory variables. A major drawback of most methods is the need to average the explanatory variables across the entire region or genomic element. This procedure is particularly problematic if the explanatory variable varies dramatically in the element under consideration. To take into account the fine scale of the explanatory variables, we model the probabilities of different types of mutations for each position in the genome by multinomial logistic regression. We analyse 505 cancer genomes from 14 different cancer types and compare the performance in predicting mutation rate for both regional based models and site-specific models. We show that for 1000 randomly selected genomic positions, the site-specific model predicts the mutation rate much better than regional based models. We use a forward selection procedure to identify the most important explanatory variables. The procedure identifies site-specific conservation (phyloP), replication timing, and expression level as the best predictors for the mutation rate. Finally, our model confirms and quantifies certain well-known mutational signatures. We find that our site-specific multinomial regression model outperforms the regional based models. The possibility of including genomic variables on different scales and patient specific variables makes it a versatile framework for studying different mutational mechanisms. Our model can serve as the neutral null model for the mutational process; regions that deviate from the null model are candidates for elements that drive cancer development.

SU-D-BRC-02: Application of Six Sigma Approach to Improve the Efficiency of Patient-Specific QA in Proton Therapy

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

LAH, J; Shin, D; Manger, R

Purpose: To show how the Six Sigma DMAIC (Define-Measure-Analyze-Improve-Control) can be used for improving and optimizing the efficiency of patient-specific QA process by designing site-specific range tolerances. Methods: The Six Sigma tools (process flow diagram, cause and effect, capability analysis, Pareto chart, and control chart) were utilized to determine the steps that need focus for improving the patient-specific QA process. The patient-specific range QA plans were selected according to 7 treatment site groups, a total of 1437 cases. The process capability index, Cpm was used to guide the tolerance design of patient site-specific range. We also analyzed the financial impactmore » of this project. Results: Our results suggested that the patient range measurements were non-capable at the current tolerance level of ±1 mm in clinical proton plans. The optimized tolerances were calculated for treatment sites. Control charts for the patient QA time were constructed to compare QA time before and after the new tolerances were implemented. It is found that overall processing time was decreased by 24.3% after establishing new site-specific range tolerances. The QA failure for whole process in proton therapy would lead up to a 46% increase in total cost. This result can also predict how costs are affected by changes in adopting the tolerance design. Conclusion: We often believe that the quality and performance of proton therapy can easily be improved by merely tightening some or all of its tolerance requirements. This can become costly, however, and it is not necessarily a guarantee of better performance. The tolerance design is not a task to be undertaken without careful thought. The Six Sigma DMAIC can be used to improve the QA process by setting optimized tolerances. When tolerance design is optimized, the quality is reasonably balanced with time and cost demands.« less

Report of sampling and analysis results, Addison Army housing units, Addison, Illinois. Final report

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

Not Available

1990-09-01

The objectives of this sampling and analysis effort include further characterization of environmental contamination identified in an enhanced preliminary assessment carried out in 1989. The specific activities performed at this site were identification, evaluation of the condition, and collection of samples from specific suspected asbestos-containing materials, including floor tiles, pipe run and pipe fitting insulation, dust in the ductwork, and exterior siding, where present. These evaluation were necessary to clarify potential environmental issues identified in the earlier report, prior to the sale or realignment of the property.

Widespread Use of Non-productive Alternative Splice Sites in Saccharomyces cerevisiae

PubMed Central

Kawashima, Tadashi; Douglass, Stephen; Gabunilas, Jason; Pellegrini, Matteo; Chanfreau, Guillaume F.

2014-01-01

Saccharomyces cerevisiae has been used as a model system to investigate the mechanisms of pre-mRNA splicing but only a few examples of alternative splice site usage have been described in this organism. Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many S. cerevisiae intron-containing genes exhibit usage of alternative splice sites, but many transcripts generated by splicing at these sites are non-functional because they introduce premature termination codons, leading to degradation by NMD. Analysis of splicing mutants combined with NMD inactivation revealed the role of specific splicing factors in governing the use of these alternative splice sites and identified novel functions for Prp17p in enhancing the use of branchpoint-proximal upstream 3′ splice sites and for Prp18p in suppressing the usage of a non-canonical AUG 3′-splice site in GCR1. The use of non-productive alternative splice sites can be increased in stress conditions in a promoter-dependent manner, contributing to the down-regulation of genes during stress. These results show that alternative splicing is frequent in S. cerevisiae but masked by RNA degradation and that the use of alternative splice sites in this organism is mostly aimed at controlling transcript levels rather than increasing proteome diversity. PMID:24722551

Automated Scoring of Chromogenic Media for Detection of Methicillin-Resistant Staphylococcus aureus by Use of WASPLab Image Analysis Software.

PubMed

Faron, Matthew L; Buchan, Blake W; Vismara, Chiara; Lacchini, Carla; Bielli, Alessandra; Gesu, Giovanni; Liebregts, Theo; van Bree, Anita; Jansz, Arjan; Soucy, Genevieve; Korver, John; Ledeboer, Nathan A

2016-03-01

Recently, systems have been developed to create total laboratory automation for clinical microbiology. These systems allow for the automation of specimen processing, specimen incubation, and imaging of bacterial growth. In this study, we used the WASPLab to validate software that discriminates and segregates positive and negative chromogenic methicillin-resistant Staphylococcus aureus (MRSA) plates by recognition of pigmented colonies. A total of 57,690 swabs submitted for MRSA screening were enrolled in the study. Four sites enrolled specimens following their standard of care. Chromogenic agar used at these sites included MRSASelect (Bio-Rad Laboratories, Redmond, WA), chromID MRSA (bioMérieux, Marcy l'Etoile, France), and CHROMagar MRSA (BD Diagnostics, Sparks, MD). Specimens were plated and incubated using the WASPLab. The digital camera took images at 0 and 16 to 24 h and the WASPLab software determined the presence of positive colonies based on a hue, saturation, and value (HSV) score. If the HSV score fell within a defined threshold, the plate was called positive. The performance of the digital analysis was compared to manual reading. Overall, the digital software had a sensitivity of 100% and a specificity of 90.7% with the specificity ranging between 90.0 and 96.0 across all sites. The results were similar using the three different agars with a sensitivity of 100% and specificity ranging between 90.7 and 92.4%. These data demonstrate that automated digital analysis can be used to accurately sort positive from negative chromogenic agar cultures regardless of the pigmentation produced. Copyright © 2016 Faron et al.

Food residue fatty acid δ13C and δD values as proxies for evaluating cultural and climatic change at Çatalhöyük, Turkey

NASA Astrophysics Data System (ADS)

Pitter, S.; Evershed, R. P.; Hodder, I.

2012-12-01

Compound specific δ13C stable isotope analysis via gas chromatography-combustion-isotope ratio mass spectrometry (GC-C- IRMS) of C16:0 and C18:0 fatty acids from archaeological pottery has been used previously to probe the organic residue record to identify specific animal origins of fats. By following previously established methods (Evershed et al. 2008) a more comprehensive record of the domestic animal-based subsistence practices of the Neolithic site Çatalhöyük has now been established. Furthermore, a new palaeoenvironmental proxy was also established through δD analysis of C16:0 and C18:0 fatty acids using GC-thermal conversion-IRMS (GC-TC-IRMS). This novel approach has demonstrated a means of observing changes in relative humidity associated with specific pottery types at archaeological sites, creating a proxy that may address several limitations in the field of archaeology with regards to understanding links between humans and their changing environments.

Photoaffinity labeling of protoporphyrinogen oxidase, the molecular target of diphenylether-type herbicides.

PubMed

Camadro, J M; Matringe, M; Thome, F; Brouillet, N; Mornet, R; Labbe, P

1995-05-01

Diphenylether-type herbicides are extremely potent inhibitors of protoporphyrinogen oxidase, a membrane-bound enzyme involved in the heme and chlorophyll biosynthesis pathways. Tritiated acifluorfen and a diazoketone derivative of tritiated acifluorfen were specifically bound to a single class of high-affinity binding sites on yeast mitochondrial membranes with apparent dissociation constants of 7 nM and 12.5 nM, respectively. The maximum density of specific binding sites, determined by Scatchard analysis, was 3 pmol.mg-1 protein. Protoporphyrinogen oxidase specific activity was estimated to be 2500 nmol protoporphyrinogen oxidized h-1.mol-1 enzyme. The diazoketone derivative of tritiated acifluorfen was used to specifically photolabel yeast protoporphyrinogen oxidase. The specifically labeled polypeptide in wild-type mitochondrial membranes had an apparent molecular mass of 55 kDa, identical to the molecular mass of the purified enzyme. This photolabeled polypeptide was not detected in a protoporphyrinogen-oxidase-deficient yeast strain, but the membranes contained an equivalent amount of inactive immunoreactive protoporphyrinogen oxidase protein.

Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.

PubMed

Hu, Zhan; Ding, Xuezhi; Hu, Shengbiao; Sun, Yunjun; Xia, Liqiu

2013-12-01

Marker-free, genetically-modified rice was created by the tissue-specifically regulated Cre/loxP system, in which the Cre recombinase gene and hygromycin phosphotransferase gene (hpt) were flanked by two directly oriented loxP sites. Cre expression was activated by the tissue-specific promoter OsMADS45 in flower or napin in seed, resulting in simultaneous excision of the recombinase and marker genes. Segregation of T1 progeny was performed to select recombined plants. The excision was confirmed by PCR, Southern blot and sequence analyses indicating that efficiency varied from 10 to 53 % for OsMADS45 and from 12 to 36 % for napin. The expression of cry1Ac and vip3A was detected by RT-PCR analysis in marker-free transgenic rice. These results suggested that our tissue-specifically regulated Cre/loxP system could auto-excise marker genes from transgenic rice and alleviate public concerns about the security of GM crops.

Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures.

PubMed

Jain, Kanishk; Warmack, Rebeccah A; Debler, Erik W; Hadjikyriacou, Andrea; Stavropoulos, Peter; Clarke, Steven G

2016-08-26

In the family of protein arginine methyltransferases (PRMTs) that predominantly generate either asymmetric or symmetric dimethylarginine (SDMA), PRMT7 is unique in producing solely monomethylarginine (MMA) products. The type of methylation on histones and other proteins dictates changes in gene expression, and numerous studies have linked altered profiles of methyl marks with disease phenotypes. Given the importance of specific inhibitor development, it is crucial to understand the mechanisms by which PRMT product specificity is conferred. We have focused our attention on active-site residues of PRMT7 from the protozoan Trypanosoma brucei We have designed 26 single and double mutations in the active site, including residues in the Glu-Xaa8-Glu (double E) loop and the Met-Gln-Trp sequence of the canonical Thr-His-Trp (THW) loop known to interact with the methyl-accepting substrate arginine. Analysis of the reaction products by high resolution cation exchange chromatography combined with the knowledge of PRMT crystal structures suggests a model where the size of two distinct subregions in the active site determines PRMT7 product specificity. A dual mutation of Glu-181 to Asp in the double E loop and Gln-329 to Ala in the canonical THW loop enables the enzyme to produce SDMA. Consistent with our model, the mutation of Cys-431 to His in the THW loop of human PRMT9 shifts its product specificity from SDMA toward MMA. Together with previous results, these findings provide a structural basis and a general model for product specificity in PRMTs, which will be useful for the rational design of specific PRMT inhibitors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Light-stimulated cargo release from a core–shell structured nanocomposite for site-specific delivery

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

Cai, Yun; Ling, Li; Li, Xiaofang

This paper reported a core–shell structured site-specific delivery system with a light switch triggered by low energy light (λ=510 nm). Its core was composed of supermagnetic Fe{sub 3}O{sub 4} nanoparticles for magnetic guiding and targeting. Its outer shell consisted of mesoporous silica molecular sieve MCM-41 which offered highly ordered hexagonal tunnels for cargo capacity. A light switch N1-(4aH-cyclopenta[1,2-b:5,4-b′]dipyridin-5(5aH)-ylidene)benzene-1, 4-diamine (CBD) was covalently grafted into these hexagonal tunnels, serving as light stimuli acceptor with loading content of 1.1 μM/g. This composite was fully characterized and confirmed by SEM, TEM, XRD patterns, N{sub 2} adsorption/desorption, thermogravimetric analysis, IR, UV–vis absorption and emissionmore » spectra. Experimental data suggested that this composite had a core as wide as 150 nm and could be magnetically guided to specific sites. Its hexagonal tunnels were as long as 180 nm. Upon light stimuli of “on” and “off” states, controllable release was observed with short release time of ~900 s (90% capacity). - Graphical abstract: A core–shell structured site-specific delivery system with a light switch triggered by yellow light was constructed. Controllable release was observed with short release time of ~900 s (90% capacity). - Highlights: • A core–shell structured site-specific delivery system was constructed. • It consisted of Fe{sub 3}O{sub 4} core and MCM-41 shell grafted with light switch. • This delivery system was triggered by low energy light. • Controllable release was observed with short release time of ~900 s.« less

Amino Acid Hydrolysis and Analysis System for Investigation of Site Directed Nucleation and Growth of Ceramic Films on Metallic Surfaces

DTIC Science & Technology

2008-09-30

that composed the proteinaceous polymers found at the interface between calcite crystals deposited by oyster cells and the various n1etal substrates...proteinaceous polymers found at the interface between calcite crystals deposited by oyster cells and the various metal substrates. A recently...required for the mechanism of biomineralization and site-specific deposition of ceramic crystals on aluminum alloy substrates. These calcite crystals

Wetlands Research Program. Evaluation of Methods for Sampling Vegetation and Delineating Wetlands Transition Zones in Southern Louisiana, January 1979-May 1981.

DTIC Science & Technology

1983-10-01

sites should be collected and correlated to vegetational response through ordination or factor analysis techniques. 3. If site-specific methods are...specified number of samples is collected . If the 40 ."l ’ - - - .. -’-. - : -. .~ -, .4 .- . -.- , - ...... rb. . o* . -.% o - .- * .-.- v- . J...only, although the data collected were sufficient for determination of such parameters as density, cover, frequency, basal area, and importance value

Analysis of Environmental Issues Related to Small-Scale Hydroelectric Development IV: Fish Mortality Resulting From Turbine Passage

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

Turbak, Susan C.; Reichle, Donna R.; Shriner, Carole R.

1981-01-01

The purpose of this report is to provide summary information for use by potential developers and regulators of small-scale hydroelectric projects (defined as existing dams that can be retrofitted to a total site capacity of ≤30 MW), where turbine-related mortality of fish is a potential issue affecting site-specific development. Mitigation techniques for turbine-related mortality are not covered in this report.

Stochastic ground motion simulation

USGS Publications Warehouse

Rezaeian, Sanaz; Xiaodan, Sun; Beer, Michael; Kougioumtzoglou, Ioannis A.; Patelli, Edoardo; Siu-Kui Au, Ivan

2014-01-01

Strong earthquake ground motion records are fundamental in engineering applications. Ground motion time series are used in response-history dynamic analysis of structural or geotechnical systems. In such analysis, the validity of predicted responses depends on the validity of the input excitations. Ground motion records are also used to develop ground motion prediction equations(GMPEs) for intensity measures such as spectral accelerations that are used in response-spectrum dynamic analysis. Despite the thousands of available strong ground motion records, there remains a shortage of records for large-magnitude earthquakes at short distances or in specific regions, as well as records that sample specific combinations of source, path, and site characteristics.

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

Rowe, M.D.; Pierce, B.L.

This report presents results of tests of different final site selection methods used for siting large-scale facilities such as nuclear power plants. Test data are adapted from a nuclear power plant siting study conducted on Long Island, New York. The purpose of the tests is to determine whether or not different final site selection methods produce different results, and to obtain some understanding of the nature of any differences found. Decision rules and weighting methods are included. Decision rules tested are Weighting Summation, Power Law, Decision Analysis, Goal Programming, and Goal Attainment; weighting methods tested are Categorization, Ranking, Rating Ratiomore » Estimation, Metfessel Allocation, Indifferent Tradeoff, Decision Analysis lottery, and Global Evaluation. Results show that different methods can, indeed, produce different results, but that the probability that they will do so is controlled by the structure of differences among the sites being evaluated. Differences in weights and suitability scores attributable to methods have reduced significance if the alternatives include one or two sites that are superior to all others in many attributes. The more tradeoffs there are among good and bad levels of different attributes at different sites, the more important are the specifics of methods to the final decision. 5 refs., 14 figs., 19 tabs.« less

Shared worlds: multi-sited ethnography and nursing research.

PubMed

Molloy, Luke; Walker, Kim; Lakeman, Richard

2017-03-22

Background Ethnography, originally developed for the study of supposedly small-scale societies, is now faced with an increasingly mobile, changing and globalised world. Cultural identities can exist without reference to a specific location and extend beyond regional and national boundaries. It is therefore no longer imperative that the sole object of the ethnographer's practice should be a geographically bounded site. Aim To present a critical methodological review of multi-sited ethnography. Discussion Understanding that it can no longer be taken with any certainty that location alone determines culture, multi-sited ethnography provides a method of contextualising multi-sited social phenomena. The method enables researchers to examine social phenomena that are simultaneously produced in different locations. It has been used to undertake cultural analysis of diverse areas such as organ trafficking, global organisations, technologies and anorexia. Conclusion The authors contend that multi-sited ethnography is particularly suited to nursing research as it provides researchers with an ethnographic method that is more relevant to the interconnected world of health and healthcare services. Implications for practice Multi-sited ethnography provides nurse researchers with an approach to cultural analysis in areas such as the social determinants of health, healthcare services and the effects of health policies across multiple locations.

Profile analysis of the LTPP SPS-6 site in Arizona.

DOT National Transportation Integrated Search

2010-07-01

"This report characterizes the longitudinal profiles of five pavement sections within the Arizona Specific : Pavement Studies 6 project throughout their service life. This project was built and monitored as part of : the Long-Term Pavement Performanc...

A Measure of the Broad Substrate Specificity of Enzymes Based on ‘Duplicate’ Catalytic Residues

PubMed Central

Chakraborty, Sandeep; Ásgeirsson, Bjarni; Rao, Basuthkar J.

2012-01-01

The ability of an enzyme to select and act upon a specific class of compounds with unerring precision and efficiency is an essential feature of life. Simultaneously, these enzymes often catalyze the reaction of a range of similar substrates of the same class, and also have promiscuous activities on unrelated substrates. Previously, we have established a methodology to quantify promiscuous activities in a wide range of proteins. In the current work, we quantitatively characterize the active site for the ability to catalyze distinct, yet related, substrates (BRASS). A protein with known structure and active site residues provides the framework for computing ‘duplicate’ residues, each of which results in slightly modified replicas of the active site scaffold. Such spatial congruence is supplemented by Finite difference Poisson Boltzmann analysis which filters out electrostatically unfavorable configurations. The congruent configurations are used to compute an index (BrassIndex), which reflects the broad substrate profile of the active site. We identify an acetylhydrolase and a methyltransferase as having the lowest and highest BrassIndex, respectively, from a set of non-homologous proteins extracted from the Catalytic Site Atlas. The acetylhydrolase, a regulatory enzyme, is known to be highly specific for platelet-activating factor. In the methyltransferase (PDB: 1QAM), various combinations of glycine (Gly38/40/42), asparagine (Asn101/11) and glutamic acid (Glu59/36) residues having similar spatial and electrostatic profiles with the specified scaffold (Gly38, Asn101 and Glu59) exemplifies the broad substrate profile such an active site may provide. ‘Duplicate’ residues identified by relaxing the spatial and/or electrostatic constraints can be the target of directed evolution methodologies, like saturation mutagenesis, for modulating the substrate specificity of proteins. PMID:23166637

Transcriptional control of the tissue-specific, developmentally regulated osteocalcin gene requires a binding motif for the Msx family of homeodomain proteins.

PubMed

Hoffmann, H M; Catron, K M; van Wijnen, A J; McCabe, L R; Lian, J B; Stein, G S; Stein, J L

1994-12-20

The OC box of the rat osteocalcin promoter (nt -99 to -76) is the principal proximal regulatory element contributing to both tissue-specific and developmental control of osteocalcin gene expression. The central motif of the OC box includes a perfect consensus DNA binding site for certain homeodomain proteins. Homeodomain proteins are transcription factors that direct proper development by regulating specific temporal and spatial patterns of gene expression. We therefore addressed the role of the homeodomain binding motif in the activity of the OC promoter. In this study, by the combined application of mutagenesis and site-specific protein recognition analysis, we examined interactions of ROS 17/2.8 osteosarcoma cell nuclear proteins and purified Msx-1 homeodomain protein with the OC box. We detected a series of related specific protein-DNA interactions, a subset of which were inhibited by antibodies directed against the Msx-1 homeodomain but which also recognize the Msx-2 homeodomain. Our results show that the sequence requirements for binding the Msx-1 or Msx-2 homeodomain closely parallel those necessary for osteocalcin gene promoter activity in vivo. This functional relationship was demonstrated by transient expression in ROS 17/2.8 osteosarcoma cells of a series of osteocalcin promoter (nt -1097 to +24)-reporter gene constructs containing mutations within and flanking the homeodomain binding site of the OC box. Northern blot analysis of several bone-related cell types showed that all of the cells expressed msx-1, whereas msx-2 expression was restricted to cells transcribing osteocalcin. Taken together, our results suggest a role for Msx-1 and -2 or related homeodomain proteins in transcription of the osteocalcin gene.

Support Vector Machine and Artificial Neural Network Models for the Classification of Grapevine Varieties Using a Portable NIR Spectrophotometer.

PubMed

Gutiérrez, Salvador; Tardaguila, Javier; Fernández-Novales, Juan; Diago, María P

2015-01-01

The identification of different grapevine varieties, currently attended using visual ampelometry, DNA analysis and very recently, by hyperspectral analysis under laboratory conditions, is an issue of great importance in the wine industry. This work presents support vector machine and artificial neural network's modelling for grapevine varietal classification from in-field leaf spectroscopy. Modelling was attempted at two scales: site-specific and a global scale. Spectral measurements were obtained on the near-infrared (NIR) spectral range between 1600 to 2400 nm under field conditions in a non-destructive way using a portable spectrophotometer. For the site specific approach, spectra were collected from the adaxial side of 400 individual leaves of 20 grapevine (Vitis vinifera L.) varieties one week after veraison. For the global model, two additional sets of spectra were collected one week before harvest from two different vineyards in another vintage, each one consisting on 48 measurement from individual leaves of six varieties. Several combinations of spectra scatter correction and smoothing filtering were studied. For the training of the models, support vector machines and artificial neural networks were employed using the pre-processed spectra as input and the varieties as the classes of the models. The results from the pre-processing study showed that there was no influence whether using scatter correction or not. Also, a second-degree derivative with a window size of 5 Savitzky-Golay filtering yielded the highest outcomes. For the site-specific model, with 20 classes, the best results from the classifiers thrown an overall score of 87.25% of correctly classified samples. These results were compared under the same conditions with a model trained using partial least squares discriminant analysis, which showed a worse performance in every case. For the global model, a 6-class dataset involving samples from three different vineyards, two years and leaves monitored at post-veraison and harvest was also built up, reaching a 77.08% of correctly classified samples. The outcomes obtained demonstrate the capability of using a reliable method for fast, in-field, non-destructive grapevine varietal classification that could be very useful in viticulture and wine industry, either global or site-specific.

Unusual interaction of human apurinic/apyrimidinic endonuclease 1 (APE1) with abasic sites via the Schiff-base-dependent mechanism.

PubMed

Ilina, Ekaterina S; Khodyreva, Svetlana N; Lavrik, Olga I

2018-05-03

Clustered apurinic/apyrimidinic (AP) sites are more cytotoxic than isolated AP lesions because double strand breaks (DSB) can be formed during repair of closely positioned bistranded AP sites. Formation of DSB due to simultaneous cleavage of bistranded AP sites may be regulated by proteins specifically interacting with this complex lesion. A set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) was used for search in the extracts of human cells proteins specifically recognizing clustered AP sites. A protein, which formed the Schiff-base-dependent covalent products having an apparent molecular mass of 50 kDa with the subset of BS-AP DNAs, was identified by mass spectrometry as apurinic/apyrimidinic endonuclease 1 (APE1). The identity of trapped protein was confirmed by Western blot analysis with anti-APE1 antibodies. Purified recombinant human APE1 is also capable of forming the 50 kDa-adducts with efficiency of BS-AP DNAs cross-linking to APE1 being dependent on the mutual orientation of AP sites. In spite of formation of the Schiff-base-dependent intermediate, which is prerequisite for the β-elimination mechanism, APE1 is unable to cleave AP sites. APE1 lacking the first 34 amino acids at the N-terminus, unlike wild type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites. The yield of APE1-AP DNA cross-links was found to correlate with the enzyme amount in the extracts estimated by the immunochemical approach; therefore the BS-AP DNA-probes can be useful for comparative analysis of APE1 content in cell extracts. Copyright © 2018. Published by Elsevier B.V.

The neuron-specific RNA-binding protein ELAV regulates neuroglian alternative splicing in neurons and binds directly to its pre-mRNA

PubMed Central

Lisbin, Michael J.; Qiu, Jan; White, Kalpana

2001-01-01

Drosophila melanogaster neural-specific protein, ELAV, has been shown to regulate the neural-specific splicing of three genes: neuroglian (nrg), erect wing, and armadillo. Alternative splicing of the nrg transcript involves alternative inclusion of a 3′-terminal exon. Here, using a minigene reporter, we show that the nrg alternatively spliced intron (nASI) has all the determinants required to recreate proper neural-specific RNA processing seen with the endogenous nrg transcript, including regulation by ELAV. An in vitro UV cross-linking assay revealed that ELAV from nuclear extracts cross-links to four distinct sites along the 3200 nucleotide long nASI; one EXS is positioned at the polypyrimidine tract of the default 3′ splice site. ELAV cross-linking sites (EXSs) have in common long tracts of (U)-rich sequence rather than a precise consensus; moreover, each tract has at least two 8/10U elements; their importance is validated by mutant transgene reporter analysis. Further, we propose criteria for ELAV target sequence recognition based on the four EXSs, sites within the nASI that are (U) rich but do not cross-link with ELAV, and predicted EXSs from a phylogenetic comparison with Drosophila virilis nASI. These results suggest that ELAV regulates nrg alternative splicing by direct interaction with the nASI. PMID:11581160

The neuron-specific RNA-binding protein ELAV regulates neuroglian alternative splicing in neurons and binds directly to its pre-mRNA.

PubMed

Lisbin, M J; Qiu, J; White, K

2001-10-01

Drosophila melanogaster neural-specific protein, ELAV, has been shown to regulate the neural-specific splicing of three genes: neuroglian (nrg), erect wing, and armadillo. Alternative splicing of the nrg transcript involves alternative inclusion of a 3'-terminal exon. Here, using a minigene reporter, we show that the nrg alternatively spliced intron (nASI) has all the determinants required to recreate proper neural-specific RNA processing seen with the endogenous nrg transcript, including regulation by ELAV. An in vitro UV cross-linking assay revealed that ELAV from nuclear extracts cross-links to four distinct sites along the 3200 nucleotide long nASI; one EXS is positioned at the polypyrimidine tract of the default 3' splice site. ELAV cross-linking sites (EXSs) have in common long tracts of (U)-rich sequence rather than a precise consensus; moreover, each tract has at least two 8/10U elements; their importance is validated by mutant transgene reporter analysis. Further, we propose criteria for ELAV target sequence recognition based on the four EXSs, sites within the nASI that are (U) rich but do not cross-link with ELAV, and predicted EXSs from a phylogenetic comparison with Drosophila virilis nASI. These results suggest that ELAV regulates nrg alternative splicing by direct interaction with the nASI.

Incorporating geologic information into hydraulic tomography: A general framework based on geostatistical approach

NASA Astrophysics Data System (ADS)

Zha, Yuanyuan; Yeh, Tian-Chyi J.; Illman, Walter A.; Onoe, Hironori; Mok, Chin Man W.; Wen, Jet-Chau; Huang, Shao-Yang; Wang, Wenke

2017-04-01

Hydraulic tomography (HT) has become a mature aquifer test technology over the last two decades. It collects nonredundant information of aquifer heterogeneity by sequentially stressing the aquifer at different wells and collecting aquifer responses at other wells during each stress. The collected information is then interpreted by inverse models. Among these models, the geostatistical approaches, built upon the Bayesian framework, first conceptualize hydraulic properties to be estimated as random fields, which are characterized by means and covariance functions. They then use the spatial statistics as prior information with the aquifer response data to estimate the spatial distribution of the hydraulic properties at a site. Since the spatial statistics describe the generic spatial structures of the geologic media at the site rather than site-specific ones (e.g., known spatial distributions of facies, faults, or paleochannels), the estimates are often not optimal. To improve the estimates, we introduce a general statistical framework, which allows the inclusion of site-specific spatial patterns of geologic features. Subsequently, we test this approach with synthetic numerical experiments. Results show that this approach, using conditional mean and covariance that reflect site-specific large-scale geologic features, indeed improves the HT estimates. Afterward, this approach is applied to HT surveys at a kilometer-scale-fractured granite field site with a distinct fault zone. We find that by including fault information from outcrops and boreholes for HT analysis, the estimated hydraulic properties are improved. The improved estimates subsequently lead to better prediction of flow during a different pumping test at the site.

Construction of transformed, cultured silkworm cells and transgenic silkworm using the site-specific integrase system from phage φC31.

PubMed

Yin, Yajuan; Cao, Guangli; Xue, Renyu; Gong, Chengliang

2014-10-01

The Streptomyces bacteriophage, φC31, uses a site-specific integrase enzyme to perform efficient recombination. The recombination system uses specific sequences to integrate exogenous DNA from the phage into a host. The sequences are known as the attP site in the phage and the attB site in the host. The system can be used as a genetic manipulation tool. In this study it has been applied to the transformation of cultured BmN cells and the construction of transgenic Bombyx mori individuals. A plasmid, pSK-attB/Pie1-EGFP/Zeo-PASV40, containing a cassette designed to express a egfp-zeocin fusion gene, was co-transfected into cultured BmN cells with a helper plasmid, pSK-Pie1/NLS-Int/NSL. Expression of the egfp-zeocin fusion gene was driven by an ie-1 promoter, downstream of a φC31 attB site. The helper plasmid encoded the φC31 integrase enzyme, which was flanked by two nuclear localization signals. Expression of the egfp-zeocin fusion gene could be observed in transformed cells. The two plasmids were also transferred into silkworm eggs to obtain transgenic silkworms. Successful integration of the fusion gene was indicated by the detection of green fluorescence, which was emitted by the silkworms. Nucleotide sequence analysis demonstrated that the attB site had been cut, to allow recombination between the attB and endogenous pseudo attP sites in the cultured silkworm cells and silkworm individuals.

Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

USGS Publications Warehouse

Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

2000-01-01

A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

PubMed Central

McClelland, M; Nelson, M; Raschke, E

1994-01-01

Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes. PMID:7937074

Improving Site-Specific Radiological Performance Assessments - 13431

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

Tauxe, John; Black, Paul; Catlett, Kate

2013-07-01

An improved approach is presented for conducting complete and defensible radiological site-specific performance assessments (PAs) to support radioactive waste disposal decisions. The basic tenets of PA were initiated some thirty years ago, focusing on geologic disposals and evaluating compliance with regulations. Some of these regulations were inherently probabilistic (i.e., addressing uncertainty in a quantitative fashion), such as the containment requirements of the U.S. Environmental Protection Agency's (EPA's) 40 CFR 191, Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes, Chap. 191.13 [1]. Methods of analysis were developed to meet those requirements, butmore » at their core early PAs used 'conservative' parameter values and modeling approaches. This limited the utility of such PAs to compliance evaluation, and did little to inform decisions about optimizing disposal, closure and long-term monitoring and maintenance, or, in general, maintaining doses 'as low as reasonably achievable' (ALARA). This basic approach to PA development in the United States was employed essentially unchanged through the end of the 20. century, principally by the U.S. Department of Energy (DOE). Performance assessments developed in support of private radioactive waste disposal operations, regulated by the U.S. Nuclear Regulatory Commission (NRC) and its agreement states, were typically not as sophisticated. Discussion of new approaches to PA is timely, since at the time of this writing, the DOE is in the midst of revising its Order 435.1, Radioactive Waste Management [2], and the NRC is revising 10 CFR 61, Licensing Requirements for Land Disposal of Radioactive Waste [3]. Over the previous decade, theoretical developments and improved computational technology have provided the foundation for integrating decision analysis (DA) concepts and objective-focused thinking, plus a Bayesian approach to probabilistic modeling and risk analysis, to guide improvements in PA. This decision-making approach, [4, 5, 6] provides a transparent formal framework for using a value- or objective-focused approach to decision-making. DA, as an analytical means to implement structured decision making, provides a context for both understanding how uncertainty affects decisions and for targeting uncertainty reduction. The proposed DA approach improves defensibility and transparency of decision-making. The DA approach is fully consistent with the need to perform realistic modeling (rather than conservative modeling), including evaluation of site-specific factors. Instead of using generic stylized scenarios for radionuclide fate and transport and for human exposures to radionuclides, site-specific scenarios better represent the advantages and disadvantages of alternative disposal sites or engineered designs, thus clarifying their differences as well as providing a sound basis for evaluation of site performance. The full DA approach to PA is described, from explicitly incorporating societal values through stakeholder involvement to model building. Model building involves scoping by considering features, events, processes, and exposure scenarios (FEPSs), development of a conceptual site model (CSM), translation into numerical models and subsequent computation, and model evaluation. These are implemented in a cycle of uncertainty analysis, sensitivity analysis and value of information analysis so that uncertainty can be reduced until sufficient confidence is gained in the decisions to be made. This includes the traditional focus on hydrogeological processes, but also places emphasis on other FEPSs such as biotically-induced transport and human exposure phenomena. The significance of human exposure scenarios is emphasized by modifying the traditional acronym 'FEPs' to include them, hence 'FEPSs'. The radioactive waste community is also recognizing that disposal sites are to be considered a national (or even global) resource. As such, there is a pressing need to optimize their utility within the constraints of protecting human health and the environment. Failing to do so will result in the need for additional sites or options for storing radioactive waste temporarily, assuming a continued need for radioactive waste disposal. Optimization should be performed using DA, including economic analysis, invoked if necessary through the ALARA process. The economic analysis must recognize the cost of implementation (disposal design, closure, maintenance, etc.), and intra- and inter-generational equity in order to ensure that the best possible radioactive waste management decisions are made for the protection of both current and future generations. In most cases this requires consideration of population or collective risk. (authors)« less

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

PubMed Central

Lin, Zhuoheng; Feng, Xuyang; Jiang, Xue; Songyang, Zhou; Huang, Junjiu

2015-01-01

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1+ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3'UTR lengths while MEFs tend towards longer 3'UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3'UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3'UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis. PMID:26713853

An endoglycosidase-assisted LC-MS/MS-based strategy for the analysis of site-specific core-fucosylation of low-concentrated glycoproteins in human serum using prostate-specific antigen (PSA) as example.

PubMed

Lang, Robert; Leinenbach, Andreas; Karl, Johann; Swiatek-de Lange, Magdalena; Kobold, Uwe; Vogeser, Michael

2018-05-01

Recently, site-specific fucosylation of glycoproteins has attracted attention as it can be associated with several types of cancers including prostate cancer. However, individual glycoproteins, which might serve as potential cancer markers, often are very low-concentrated in complex serum matrices and distinct glycan structures are hard to detect by immunoassays. Here, we present a mass spectrometry-based strategy for the simultaneous analysis of core-fucosylated and total prostate-specific antigen (PSA) in human serum in the low ng/ml concentration range. Sample preparation comprised an immunoaffinity capture step to enrich total PSA from human serum using anti-PSA antibody coated magnetic beads followed by consecutive two-step on-bead partial deglycosylation with endoglycosidase F3 and tryptic digestion prior to LC-MS/MS analysis. The method was shown to be linear from 0.5 to 60 ng/ml total PSA concentrations and allows the simultaneous quantification of core-fucosylated PSA down to 1 ng/ml and total PSA lower than 0.5 ng/ml. The imprecision of the method over two days ranged from 9.7-23.2% for core-fucosylated PSA and 10.3-18.3% for total PSA depending on the PSA level. The feasibility of the method in native sera was shown using three human specimens. To our knowledge, this is the first MS-based method for quantification of core-fucosylated PSA in the low ng/ml concentration range in human serum. This method could be used in large patient cohorts as core-fucosylated PSA may be a diagnostic biomarker for the differentiation of prostate cancer and other prostatic diseases, such as benign prostatic hyperplasia (BPH). Furthermore, the described strategy could be used to monitor potential changes in site-specific core-fucosylation of other low-concentrated glycoproteins, which could serve as more specific markers ("marker refinement") in cancer research. Copyright © 2018 Elsevier B.V. All rights reserved.

Single nucleotide polymorphism-specific regulation of matrix metalloproteinase-9 by multiple miRNAs targeting the coding exon

PubMed Central

Duellman, Tyler; Warren, Christopher; Yang, Jay

2014-01-01

Microribonucleic acids (miRNAs) work with exquisite specificity and are able to distinguish a target from a non-target based on a single nucleotide mismatch in the core nucleotide domain. We questioned whether miRNA regulation of gene expression could occur in a single nucleotide polymorphism (SNP)-specific manner, manifesting as a post-transcriptional control of expression of genetic polymorphisms. In our recent study of the functional consequences of matrix metalloproteinase (MMP)-9 SNPs, we discovered that expression of a coding exon SNP in the pro-domain of the protein resulted in a profound decrease in the secreted protein. This missense SNP results in the N38S amino acid change and a loss of an N-glycosylation site. A systematic study demonstrated that the loss of secreted protein was due not to the loss of an N-glycosylation site, but rather an SNP-specific targeting by miR-671-3p and miR-657. Bioinformatics analysis identified 41 SNP-specific miRNA targeting MMP-9 SNPs, mostly in the coding exon and an extension of the analysis to chromosome 20, where the MMP-9 gene is located, suggesting that SNP-specific miRNAs targeting the coding exon are prevalent. This selective post-transcriptional regulation of a target messenger RNA harboring genetic polymorphisms by miRNAs offers an SNP-dependent post-transcriptional regulatory mechanism, allowing for polymorphic-specific differential gene regulation. PMID:24627221

Site-specific early performance and nutrition of two Salix species in SRIC in southern Quebec (Canada)

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

Labrecque, M.; Teodorescu, T.I.; Daigle, S.

1996-12-31

Salix discolor WU and Salix viminalis L. were planted under short-rotation intensive culture (SRIC) in three unirrigated and unfertilized abandoned farmland sites (S1, S2, S3) showing different soil textures: sandy loam, clay silt and clay loam. The aims of the experiment were to: (i) investigate first year response to site nutrient condition and (ii) diagnose factors limiting performance. Over the first season, stem biomass productivity was superior on the sandy site (S1) for S. discolor and did not vary between species on clay sites (S2, S3). The inferior performance of plants on clay sites was related to difficulty implanting unrootedmore » cuttings in compacted soil during an exceptionally dry period (May and June). The change in nutrient status was unapparent solely from comparison of critical levels or optimum ratios because leaf nutrient concentration was less affected by site. Diagnostic techniques based on vector analysis of leaf nutrient concentration, content, and dry mass allowed simultaneous comparison of the nutrient status of two species planted on three sites. The relative deficiency of all nutrients, based on vector magnitude and direction, on the two other clay sites (S2, S3) supports the hypothesis that specific edaphic conditions and dryness induced nutrient disorders in willows. Successful establishment of willows in SRIC depends strongly on the characteristics of the plantation site and on precipitation during the establishment phase in the first year of growth.« less

Hospital site selection using fuzzy AHP and its derivatives.

PubMed

Vahidnia, Mohammad H; Alesheikh, Ali A; Alimohammadi, Abbas

2009-07-01

Environmental managers are commonly faced with sophisticated decisions, such as choosing the location of a new facility subject to multiple conflicting criteria. This paper considers the specific problem of creating a well-distributed network of hospitals that delivers its services to the target population with minimal time, pollution and cost. We develop a Multi-Criteria Decision Analysis process that combines Geographical Information System (GIS) analysis with the Fuzzy Analytical Hierarchy Process (FAHP), and use this process to determine the optimum site for a new hospital in the Tehran urban area. The GIS was used to calculate and classify governing criteria, while FAHP was used to evaluate the decision factors and their impacts on alternative sites. Three methods were used to estimate the total weights and priorities of the candidate sites: fuzzy extent analysis, center-of-area defuzzification, and the alpha-cut method. The three methods yield identical priorities for the five alternatives considered. Fuzzy extent analysis provides less discriminating power, but is simpler to implement and compute than the other two methods. The alpha-cut method is more complicated, but integrates the uncertainty and overall attitude of the decision-maker. The usefulness of the new hospital site is evaluated by computing an accessibility index for each pixel in the GIS, defined as the ratio of population density to travel time. With the addition of a new hospital at the optimum site, this index improved over about 6.5 percent of the geographical area.

Site-specific seismic probabilistic tsunami hazard analysis: performances and potential applications

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Volpe, Manuela; Lorito, Stefano; Selva, Jacopo; Orefice, Simone; Graziani, Laura; Brizuela, Beatriz; Smedile, Alessandra; Romano, Fabrizio; De Martini, Paolo Marco; Maramai, Alessandra; Piatanesi, Alessio; Pantosti, Daniela

2017-04-01

Seismic Probabilistic Tsunami Hazard Analysis (SPTHA) provides probabilities to exceed different thresholds of tsunami hazard intensity, at a specific site or region and in a given time span, for tsunamis caused by seismic sources. Results obtained by SPTHA (i.e., probabilistic hazard curves and inundation maps) represent a very important input to risk analyses and land use planning. However, the large variability of source parameters implies the definition of a huge number of potential tsunami scenarios, whose omission could lead to a biased analysis. Moreover, tsunami propagation from source to target requires the use of very expensive numerical simulations. At regional scale, the computational cost can be reduced using assumptions on the tsunami modeling (i.e., neglecting non-linear effects, using coarse topo-bathymetric meshes, empirically extrapolating maximum wave heights on the coast). On the other hand, moving to local scale, a much higher resolution is required and such assumptions drop out, since detailed inundation maps require significantly greater computational resources. In this work we apply a multi-step method to perform a site-specific SPTHA which can be summarized in the following steps: i) to perform a regional hazard assessment to account for both the aleatory and epistemic uncertainties of the seismic source, by combining the use of an event tree and an ensemble modeling technique; ii) to apply a filtering procedure which use a cluster analysis to define a significantly reduced number of representative scenarios contributing to the hazard of a specific target site; iii) to perform high resolution numerical simulations only for these representative scenarios and for a subset of near field sources placed in very shallow waters and/or whose coseismic displacements induce ground uplift or subsidence at the target. The method is applied to three target areas in the Mediterranean located around the cities of Milazzo (Italy), Thessaloniki (Greece) and Siracusa (Italy). The latter target analysis is enriched by the use of local observed tsunami data, both geological and historical. Indeed, tsunami data-sets available for Siracusa are particularly rich with respect to the scarce and heterogeneous data-sets usually available elsewhere. Therefore, they can represent a further valuable source of information to benchmark and strengthen the results of such kind of studies. The work is funded by the Italian Flagship Project RITMARE, the two EC FP7 ASTARTE (Grant agreement 603839) and STREST (Grant agreement 603389) projects, the TSUMAPS-NEAM (Grant agreement ECHO/SUB/2015/718568/PREV26) project and the INGV-DPC Agreement.

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array.

PubMed

Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina; Guldberg, Per; Dufva, Martin; Wang, Shan X; Hansen, Mikkel F

2017-09-26

Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.

A DNA enzyme with N-glycosylase activity

NASA Technical Reports Server (NTRS)

Sheppard, T. L.; Ordoukhanian, P.; Joyce, G. F.

2000-01-01

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Perceived threat and corroboration: key factors that improve a predictive model of trust in internet-based health information and advice.

PubMed

Harris, Peter R; Sillence, Elizabeth; Briggs, Pam

2011-07-27

How do people decide which sites to use when seeking health advice online? We can assume, from related work in e-commerce, that general design factors known to affect trust in the site are important, but in this paper we also address the impact of factors specific to the health domain. The current study aimed to (1) assess the factorial structure of a general measure of Web trust, (2) model how the resultant factors predicted trust in, and readiness to act on, the advice found on health-related websites, and (3) test whether adding variables from social cognition models to capture elements of the response to threatening, online health-risk information enhanced the prediction of these outcomes. Participants were asked to recall a site they had used to search for health-related information and to think of that site when answering an online questionnaire. The questionnaire consisted of a general Web trust questionnaire plus items assessing appraisals of the site, including threat appraisals, information checking, and corroboration. It was promoted on the hungersite.com website. The URL was distributed via Yahoo and local print media. We assessed the factorial structure of the measures using principal components analysis and modeled how well they predicted the outcome measures using structural equation modeling (SEM) with EQS software. We report an analysis of the responses of participants who searched for health advice for themselves (N = 561). Analysis of the general Web trust questionnaire revealed 4 factors: information quality, personalization, impartiality, and credible design. In the final SEM model, information quality and impartiality were direct predictors of trust. However, variables specific to eHealth (perceived threat, coping, and corroboration) added substantially to the ability of the model to predict variance in trust and readiness to act on advice on the site. The final model achieved a satisfactory fit: χ(2) (5) = 10.8 (P = .21), comparative fit index = .99, root mean square error of approximation = .052. The model accounted for 66% of the variance in trust and 49% of the variance in readiness to act on the advice. Adding variables specific to eHealth enhanced the ability of a model of trust to predict trust and readiness to act on advice.

Perceived Threat and Corroboration: Key Factors That Improve a Predictive Model of Trust in Internet-based Health Information and Advice

PubMed Central

Harris, Peter R; Briggs, Pam

2011-01-01

Background How do people decide which sites to use when seeking health advice online? We can assume, from related work in e-commerce, that general design factors known to affect trust in the site are important, but in this paper we also address the impact of factors specific to the health domain. Objective The current study aimed to (1) assess the factorial structure of a general measure of Web trust, (2) model how the resultant factors predicted trust in, and readiness to act on, the advice found on health-related websites, and (3) test whether adding variables from social cognition models to capture elements of the response to threatening, online health-risk information enhanced the prediction of these outcomes. Methods Participants were asked to recall a site they had used to search for health-related information and to think of that site when answering an online questionnaire. The questionnaire consisted of a general Web trust questionnaire plus items assessing appraisals of the site, including threat appraisals, information checking, and corroboration. It was promoted on the hungersite.com website. The URL was distributed via Yahoo and local print media. We assessed the factorial structure of the measures using principal components analysis and modeled how well they predicted the outcome measures using structural equation modeling (SEM) with EQS software. Results We report an analysis of the responses of participants who searched for health advice for themselves (N = 561). Analysis of the general Web trust questionnaire revealed 4 factors: information quality, personalization, impartiality, and credible design. In the final SEM model, information quality and impartiality were direct predictors of trust. However, variables specific to eHealth (perceived threat, coping, and corroboration) added substantially to the ability of the model to predict variance in trust and readiness to act on advice on the site. The final model achieved a satisfactory fit: χ2 5 = 10.8 (P = .21), comparative fit index = .99, root mean square error of approximation = .052. The model accounted for 66% of the variance in trust and 49% of the variance in readiness to act on the advice. Conclusions Adding variables specific to eHealth enhanced the ability of a model of trust to predict trust and readiness to act on advice. PMID:21795237

Protein crystallography and site-direct mutagenesis analysis of the poly(ethylene terephthalate) hydrolase PETase from Ideonella sakaiensis.

PubMed

Liu, Bing; He, Lihui; Wang, Liping; Li, Tao; Li, Changcheng; Liu, Huayi; Luo, Yunzi; Bao, Rui

2018-03-30

Compared with traditional recycle strategies, biodegradation provides a sustainable solution for poly (ethylene terephthalate) (PET) wastes disposal. PETase, a newly identified enzyme from Ideonella sakaiensis, has high efficiency and specificity towards PET, which provides a prominent prospect on PET degradation. Based on the biochemical analysis, we propose that the wide substrate-binding pocket is critical for its excellent property on crystallized PET hydrolysis. Structure-guided site-directed mutagenesis exhibited improvement in PETase catalytic efficiency, providing valuable insight on how the molecular engineering of PETase can optimize its application in biocatalysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

40 CFR 1508.28 - Tiering.

Code of Federal Regulations, 2014 CFR

2014-07-01

... refers to the coverage of general matters in broader environmental impact statements (such as national... regional or basinwide program statements or ultimately site-specific statements) incorporating by reference..., or policy environmental impact statement to a program, plan, or policy statement or analysis of...

40 CFR 1508.28 - Tiering.

Code of Federal Regulations, 2011 CFR

2011-07-01

... refers to the coverage of general matters in broader environmental impact statements (such as national... regional or basinwide program statements or ultimately site-specific statements) incorporating by reference..., or policy environmental impact statement to a program, plan, or policy statement or analysis of...

40 CFR 1508.28 - Tiering.

Code of Federal Regulations, 2012 CFR

2012-07-01

... refers to the coverage of general matters in broader environmental impact statements (such as national... regional or basinwide program statements or ultimately site-specific statements) incorporating by reference..., or policy environmental impact statement to a program, plan, or policy statement or analysis of...

40 CFR 1508.28 - Tiering.

Code of Federal Regulations, 2013 CFR

2013-07-01

... refers to the coverage of general matters in broader environmental impact statements (such as national... regional or basinwide program statements or ultimately site-specific statements) incorporating by reference..., or policy environmental impact statement to a program, plan, or policy statement or analysis of...

40 CFR 1508.28 - Tiering.

Code of Federal Regulations, 2010 CFR

2010-07-01

... refers to the coverage of general matters in broader environmental impact statements (such as national... regional or basinwide program statements or ultimately site-specific statements) incorporating by reference..., or policy environmental impact statement to a program, plan, or policy statement or analysis of...

Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein.

PubMed

Kemme, Catherine A; Esadze, Alexandre; Iwahara, Junji

2015-11-10

Functions of transcription factors require formation of specific complexes at particular sites in cis-regulatory elements of genes. However, chromosomal DNA contains numerous sites that are similar to the target sequences recognized by transcription factors. The influence of such "quasi-specific" sites on functions of the transcription factors is not well understood at present by experimental means. In this work, using fluorescence methods, we have investigated the influence of quasi-specific DNA sites on the efficiency of target location by the zinc finger DNA-binding domain of the inducible transcription factor Egr-1, which recognizes a 9 bp sequence. By stopped-flow assays, we measured the kinetics of Egr-1's association with a target site on 143 bp DNA in the presence of various competitor DNAs, including nonspecific and quasi-specific sites. The presence of quasi-specific sites on competitor DNA significantly decelerated the target association by the Egr-1 protein. The impact of the quasi-specific sites depended strongly on their affinity, their concentration, and the degree of their binding to the protein. To quantitatively describe the kinetic impact of the quasi-specific sites, we derived an analytical form of the apparent kinetic rate constant for the target association and used it for fitting to the experimental data. Our kinetic data with calf thymus DNA as a competitor suggested that there are millions of high-affinity quasi-specific sites for Egr-1 among the 3 billion bp of genomic DNA. This study quantitatively demonstrates that naturally abundant quasi-specific sites on DNA can considerably impede the target search processes of sequence-specific DNA-binding proteins.

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan

NASA Astrophysics Data System (ADS)

Sakata, Masayuki K.; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-12-01

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan.

PubMed

Sakata, Masayuki K; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-11-14

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases

PubMed Central

Kim, J. Dongun; Senn, Stefan; Harel, Arye; Jelen, Benjamin I.; Falkowski, Paul G.

2013-01-01

Oxidoreductases play a central role in catalysing enzymatic electron-transfer reactions across the tree of life. To first order, the equilibrium thermodynamic properties of these proteins are governed by protein folds associated with specific transition metals and ligands at the active site. A global analysis of holoenzyme structures and functions suggests that there are fewer than approximately 500 fundamental oxidoreductases, which can be further clustered into 35 unique groups. These catalysts evolved in prokaryotes early in the Earth's history and are largely responsible for the emergence of non-equilibrium biogeochemical cycles on the planet's surface. Although the evolutionary history of the amino acid sequences in the oxidoreductases is very difficult to reconstruct due to gene duplication and horizontal gene transfer, the evolution of the folds in the catalytic sites can potentially be used to infer the history of these enzymes. Using a novel, yet simple analysis of the secondary structures associated with the ligands in oxidoreductases, we developed a structural phylogeny of these enzymes. The results of this ‘composome’ analysis suggest an early split from a basal set of a small group of proteins dominated by loop structures into two families of oxidoreductases, one dominated by α-helices and the second by β-sheets. The structural evolutionary patterns in both clades trace redox gradients and increased hydrogen bond energy in the active sites. The overall pattern suggests that the evolution of the oxidoreductases led to decreased entropy in the transition metal folds over approximately 2.5 billion years, allowing the enzymes to use increasingly oxidized substrates with high specificity. PMID:23754810

Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

PubMed Central

Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

Investigating the complexity of precipitation sets within California via the fractal-multifractal method

NASA Astrophysics Data System (ADS)

Puente, Carlos E.; Maskey, Mahesh L.; Sivakumar, Bellie

2017-04-01

A deterministic geometric approach, the fractal-multifractal (FM) method, is adapted in order to encode highly intermittent daily rainfall records observed over a year. Using such a notion, this research investigates the complexity of rainfall in various stations within the State of California. Specifically, records gathered at (from South to North) Cherry Valley, Merced, Sacramento and Shasta Dam, containing 59, 116, 115 and 72 years, all ending at water year 2015, were encoded and analyzed in detail. The analysis reveals that: (a) the FM approach yields faithful encodings of all records, by years, with mean square and maximum errors in accumulated rain that are less than a mere 2% and 10%, respectively; (b) the evolution of the corresponding "best" FM parameters, allowing visualization of the inter-annual rainfall dynamics from a reduced vantage point, exhibit implicit variability that precludes discriminating between sites and extrapolating to the future; (c) the evolution of the FM parameters, restricted to specific regions within space, allows finding sensible future simulations; and (d) the rain signals at all sites may be termed "equally complex," as usage of k-means clustering and conventional phase space analysis of FM parameters yields comparable results for all sites.

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

Namhata, Argha; Oladyshkin, Sergey; Dilmore, Rober

Carbon dioxide (CO2) storage into geological formations is regarded as an important mitigation strategy for anthropogenic CO2 emissions to the atmosphere. This study first simulates the leakage of CO2 and brine from a storage reservoir through the caprock. Then, we estimate the resulting pressure changes at the zone overlying the caprock also known as Above Zone Monitoring Interval (AZMI). A data-driven approach of arbitrary Polynomial Chaos (aPC) Expansion is then used to quantify the uncertainty in the above zone pressure prediction based on the uncertainties in different geologic parameters. Finally, a global sensitivity analysis is performed with Sobol indices basedmore » on the aPC technique to determine the relative importance of different parameters on pressure prediction. The results indicate that there can be uncertainty in pressure prediction locally around the leakage zones. The degree of such uncertainty in prediction depends on the quality of site specific information available for analysis. The scientific results from this study provide substantial insight that there is a need for site-specific data for efficient predictions of risks associated with storage activities. The presented approach can provide a basis of optimized pressure based monitoring network design at carbon storage sites.« less

Implementation of a DOD ELAP Conforming Quality System at a FUSRAP Site Field Temporary Radiological Screening Laboratory - 13500

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

Winters, M.S.; McElheny, G.; Houston, L.M.

2013-07-01

A case study is presented on specific program elements that supported the transition of a temporary field radiological screening lab to an accredited operation capable of meeting client quality objectives for definitive results data. The temporary field lab is located at the Formerly Utilized Sites Remedial Action Program Linde Site in Tonawanda, NY. The site is undergoing remediation under the direction of the United States Army Corps of Engineers - Buffalo District, with Cabrera Services Inc. as the remediation contractor and operator of the on-site lab. Analysis methods employed in the on-site lab include gross counting of alpha and betamore » particle activity on swipes and air filters and gamma spectroscopy of soils and other solid samples. A discussion of key program elements and lessons learned may help other organizations considering pursuit of accreditation for on-site screening laboratories. (authors)« less

Conformations of the HIV-1 protease: A crystal structure data set analysis.

PubMed

Palese, Luigi Leonardo

2017-11-01

The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein. Copyright © 2017 Elsevier B.V. All rights reserved.

Attachment narratives in refugee children: interrater reliability and qualitative analysis in pilot findings from a two-site study.

PubMed

De Haene, Lucia; Dalgaard, Nina Thorup; Montgomery, Edith; Grietens, Hans; Verschueren, Karine

2013-06-01

Although forced migration research on refugee family functioning clearly points to the potential breakdown of parental availability and responsiveness in the context of cumulative migration stressors, studies exploring attachment security in refugee children are surprisingly lacking so far. The authors report their findings from a 2-site, small-scale administration of an attachment measure, adapted for use with refugee children aged between 4 and 9 years from a reliable and validated doll-play procedure. We evaluated interrater reliability and conducted a qualitative analysis of refugee children's narrative response to identify migration-specific representational markers of attachment quality. The level of agreement among 3 independent coders ranged between .54 to 1.00 for both study samples, providing initial psychometric evidence of the measure's value in assessing child attachment security in this population. The exploratory analysis of migration-related narrative markers pointed to specific parameters to be used in parent-child observational assessments in future validation of the attachment measure, such as parental withdrawal or trauma-communication within the parent-child dyad. Copyright © 2013 International Society for Traumatic Stress Studies.

Activity loss by H46A mutation in Mycobacterium tuberculosis isocitrate lyase is due to decrease in structural plasticity and collective motions of the active site.

PubMed

Shukla, Rohit; Shukla, Harish; Tripathi, Timir

2018-01-01

Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a crucial enzyme of the glyoxylate cycle and is a validated anti-tuberculosis drug target. Structurally distant, non-active site mutation (H46A) in MtbICL has been found to cause loss of enzyme activity. The aim of the present work was to explore the structural alterations induced by H46A mutation that caused the loss of enzyme activity. The structural and dynamic consequences of H46A mutation were studied using multiple computational methods such as docking, molecular dynamics simulation and residue interaction network analysis (RIN). Principal component analysis and cross correlation analysis revealed the difference in conformational flexibility and collective modes of motions between the wild-type and mutant enzyme, particularly in the active site region. RIN analysis revealed that the active site geometry was disturbed in the mutant enzyme. Thus, the dynamic perturbation of the active site led to enzyme transition from its active form to inactive form upon mutation. The computational analyses elucidated the mutant-specific conformational alterations, differential dominant motions, and anomalous residue level interactions that contributed to the abrogated function of mutant MtbICL. An understanding of interactions of mutant enzymes may help in modifying the existing drugs and designing improved drugs for successful control of tuberculosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease.

PubMed

Repanas, Kostas; Zingler, Nora; Layer, Liliana E; Schumann, Gerald G; Perrakis, Anastassis; Weichenrieder, Oliver

2007-01-01

The human LINE-1 endonuclease (L1-EN) is the targeting endonuclease encoded by the human LINE-1 (L1) retrotransposon. L1-EN guides the genomic integration of new L1 and Alu elements that presently account for approximately 28% of the human genome. L1-EN bears considerable technological interest, because its target selectivity may ultimately be engineered to allow the site-specific integration of DNA into defined genomic locations. Based on the crystal structure, we generated L1-EN mutants to analyze and manipulate DNA target site recognition. Crystal structures and their dynamic and functional analysis show entire loop grafts to be feasible, resulting in altered specificity, while individual point mutations do not change the nicking pattern of L1-EN. Structural parameters of the DNA target seem more important for recognition than the nucleotide sequence, and nicking profiles on DNA oligonucleotides in vitro are less well defined than the respective integration site consensus in vivo. This suggests that additional factors other than the DNA nicking specificity of L1-EN contribute to the targeted integration of non-LTR retrotransposons.

The Urbis Project: Identification and Characterization of Potential Urban Development Areas as a Web-Based Service

NASA Astrophysics Data System (ADS)

Manzke, Nina; Kada, Martin; Kastler, Thomas; Xu, Shaojuan; de Lange, Norbert; Ehlers, Manfred

2016-06-01

Urban sprawl and the related landscape fragmentation is a Europe-wide challenge in the context of sustainable urban planning. The URBan land recycling Information services for Sustainable cities (URBIS) project aims for the development, implementation, and validation of web-based information services for urban vacant land in European functional urban areas in order to provide end-users with site specific characteristics and to facilitate the identification and evaluation of potential development areas. The URBIS services are developed based on open geospatial data. In particular, the Copernicus Urban Atlas thematic layers serve as the main data source for an initial inventory of sites. In combination with remotely sensed data like SPOT5 images and ancillary datasets like OpenStreetMap, detailed site specific information is extracted. Services are defined for three main categories: i) baseline services, which comprise an initial inventory and typology of urban land, ii) update services, which provide a regular inventory update as well as an analysis of urban land use dynamics and changes, and iii) thematic services, which deliver specific information tailored to end-users' needs.

Interaction of SR 33557 with skeletal muscle calcium channel blocker receptors in the baboon: characterization of its binding sites

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

Sol-Rolland, J.; Joseph, M.; Rinaldi-Carmona, M.

1991-05-01

A procedure for the isolation of primate skeletal microsomal membranes was initiated. Membranes exhibited specific enzymatic markers such as 5'-nucleotidase, Ca{sup 2}{sup +},Mg({sup 2}{sup +})-adenosine triphosphatase and an ATP-dependent calcium uptake. Baboon skeletal microsomes bound specifically with high-affinity potent Ca{sup 2}{sup +} channel blockers such as dihydropyridine, phenylalkylamine and benzothiazepine derivatives. Scatchard analysis of equilibrium binding assays with ({sup 3}H)(+)-PN 200-110, ({sup 3}H)(-)-desmethoxyverapamil (( {sup 3}H)(-)-D888) and ({sup 3}H)-d-cis-dilitiazem were consistent with a single class of binding sites for the three radioligands. The pharmacological profile of SR 33557, an original compound with calcium antagonist properties, was investigated using radioligand bindingmore » studies. SR 33557 totally inhibited the specific binding of the three main classes of Ca{sup 2}{sup +} channel effectors and interacted allosterically with them. In addition, SR 33557 bound with high affinity to a homogeneous population of binding sites in baboon skeletal muscle.« less

Escherichia coli ArgR mutants defective in cer/Xer recombination, but not in DNA binding.

PubMed

Sénéchal, Hélène; Delesques, Jérémy; Szatmari, George

2010-04-01

The Escherichia coli arginine repressor (ArgR) is an L-arginine-dependent DNA-binding protein that controls the expression of the arginine biosynthetic genes and is required as an accessory factor for Xer site-specific recombination at cer and related recombination sites in plasmids. We used the technique of pentapeptide scanning mutagenesis to isolate a series of ArgR mutants that were considerably reduced in cer recombination, but were still able to repress an argA::lacZ fusion. DNA sequence analysis showed that all of the mutants mapped to the same nucleotide, resulting in a five amino acid insertion between residues 149 and 150 of ArgR, corresponding to the end of the alpha6 helix. A truncated ArgR containing a stop codon at residue 150 displayed the same phenotype as the protein with the five amino acid insertion, and both mutants displayed sequence-specific DNA-binding activity that was L-arginine dependent. These results show that the C-terminus of ArgR is more important in cer/Xer site-specific recombination than in DNA binding.

Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge.

PubMed

Lin, Chi-Hung; Krisp, Christoph; Packer, Nicolle H; Molloy, Mark P

2018-02-10

Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of specific sources of airborne particles emitted from within a complex industrial (steelworks) site

NASA Astrophysics Data System (ADS)

Beddows, D. C. S.; Harrison, Roy M.

2018-06-01

A case study is provided of the development and application of methods to identify and quantify specific sources of emissions from within a large complex industrial site. Methods include directional analysis of concentrations, chemical source tracers and correlations with gaseous emissions. Extensive measurements of PM10, PM2.5, trace gases, particulate elements and single particle mass spectra were made at sites around the Port Talbot steelworks in 2012. By using wind direction data in conjunction with real-time or hourly-average pollutant concentration measurements, it has been possible to locate areas within the steelworks associated with enhanced pollutant emissions. Directional analysis highlights the Slag Handling area of the works as the most substantial source of elevated PM10 concentrations during the measurement period. Chemical analyses of air sampled from relevant wind directions is consistent with the anticipated composition of slags, as are single particle mass spectra. Elevated concentrations of PM10 are related to inverse distance from the Slag Handling area, and concentrations increase with increased wind speed, consistent with a wind-driven resuspension source. There also appears to be a lesser source associated with Sinter Plant emissions affecting PM10 concentrations at the Fire Station monitoring site. The results are compared with a ME2 study using some of the same data, and shown to give a clearer view of the location and characteristics of emission sources, including fugitive dusts.

Substrate specificity of mitochondrial intermediate peptidase analysed by a support-bound peptide library

PubMed Central

Marcondes, M.F.M.; Alves, F.M.; Assis, D.M.; Hirata, I.Y.; Juliano, L.; Oliveira, V.; Juliano, M.A.

2015-01-01

The substrate specificity of recombinant human mitochondrial intermediate peptidase (hMIP) using a synthetic support-bound FRET peptide library is presented. The collected fluorescent beads, which contained the hydrolysed peptides generated by hMIP, were sequenced by Edman degradation. The results showed that this peptidase presents a remarkable preference for polar uncharged residues at P1 and P1′ substrate positions: Ser = Gln > Thr at P1 and Ser > Thr at P1′. Non-polar residues were frequent at the substrate P3, P2, P2′ and P3′ positions. Analysis of the predicted MIP processing sites in imported mitochondrial matrix proteins shows these cleavages indeed occur between polar uncharged residues. Previous analysis of these processing sites indicated the importance of positions far from the MIP cleavage site, namely the presence of a hydrophobic residue (Phe or Leu) at P8 and a polar uncharged residue (Ser or Thr) at P5. To evaluate this, additional kinetic analyses were carried out, using fluorogenic substrates synthesized based on the processing sites attributed to MIP. The results described here underscore the importance of the P1 and P1′ substrate positions for the hydrolytic activity of hMIP. The information presented in this work will help in the design of new substrate-based inhibitors for this peptidase. PMID:26082885

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites

PubMed Central

2017-01-01

Quality control of MRI is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. Visual inspection is subjective and impractical for large scale datasets. Although automated quality assessments have been demonstrated on single-site datasets, it is unclear that solutions can generalize to unseen data acquired at new sites. Here, we introduce the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. Our tool can be run both locally and as a free online service via the OpenNeuro.org portal. The classifier is trained on a publicly available, multi-site dataset (17 sites, N = 1102). We perform model selection evaluating different normalization and feature exclusion approaches aimed at maximizing across-site generalization and estimate an accuracy of 76%±13% on new sites, using leave-one-site-out cross-validation. We confirm that result on a held-out dataset (2 sites, N = 265) also obtaining a 76% accuracy. Even though the performance of the trained classifier is statistically above chance, we show that it is susceptible to site effects and unable to account for artifacts specific to new sites. MRIQC performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement which might require more labeled data and new approaches to the between-site variability. Overcoming these limitations is crucial for a more objective quality assessment of neuroimaging data, and to enable the analysis of extremely large and multi-site samples. PMID:28945803

Can Sap Flow Help Us to Better Understand Transpiration Patterns in Landscapes?

NASA Astrophysics Data System (ADS)

Hassler, S. K.; Weiler, M.; Blume, T.

2017-12-01

Transpiration is a key process in the hydrological cycle and a sound understanding and quantification of transpiration and its spatial variability is essential for management decisions and for improving the parameterisation of hydrological and soil-vegetation-atmosphere transfer models. At the tree scale, transpiration is commonly estimated by measuring sap flow. Besides evaporative demand and water availability, tree-specific characteristics such as species, size or social status, stand-specific characteristics such as basal area or stand density and site-specific characteristics such as geology, slope position or aspect control sap flow of individual trees. However, little is known about the relative importance or the dynamic interplay of these controls. We studied these influences with multiple linear regression models to explain the variability of sap velocity measurements in 61 beech and oak trees, located at 24 sites spread over a 290 km²-catchment in Luxembourg. For each of 132 consecutive days of the growing season of 2014 we applied linear models to the daily spatial pattern of sap velocity and determined the importance of the different predictors. By upscaling sap velocities to the tree level with the help of species-dependent empirical estimates for sapwood area we also examined patterns of sap flow as a more direct representation of transpiration. Results indicate that a combination of mainly tree- and site-specific factors controls sap velocity patterns in this landscape, namely tree species, tree diameter, geology and aspect. For sap flow, the site-specific predictors provided the largest contribution to the explained variance, however, in contrast to the sap velocity analysis, geology was more important than aspect. Spatial variability of atmospheric demand and soil moisture explained only a small fraction of the variance. However, the temporal dynamics of the explanatory power of the tree-specific characteristics, especially species, were correlated to the temporal dynamics of potential evaporation. We conclude that spatial representation of transpiration in models could benefit from including patterns according to tree and site characteristics.

The effect of distant metastases sites on survival in de novo stage-IV breast cancer: A SEER database analysis.

PubMed

Wu, San-Gang; Li, Hui; Tang, Li-Ying; Sun, Jia-Yuan; Zhang, Wen-Wen; Li, Feng-Yan; Chen, Yong-Xiong; He, Zhen-Yu

2017-06-01

To investigate the effect of distant metastases sites on survival in patients with de novo stage-IV breast cancer. From 2010 to 2013, patients with a diagnosis of de novo stage-IV breast cancer were identified using the Surveillance, Epidemiology, and End Results database. Univariate and multivariate Cox regression analyses were performed to analyze the effect of distant metastases sites on breast cancer-specific survival and overall survival. A total of 7575 patients were identified. The most common metastatic sites were bone, followed by lung, liver, and brain. Patients with hormone receptor+/human epidermal growth factor receptor 2- and hormone receptor+/human epidermal growth factor receptor 2+ status were more prone to bone metastases. Lung and brain metastases were common in hormone receptor-/human epidermal growth factor receptor 2+ and hormone receptor-/human epidermal growth factor receptor 2- subtypes, and patients with hormone receptor+/ human epidermal growth factor receptor 2+ and hormone receptor-/human epidermal growth factor receptor 2+ subtypes were more prone to liver metastases. Patients with liver and brain metastases had unfavorable prognosis for breast cancer-specific survival and overall survival, whereas bone and lung metastases had no effect on patient survival in multivariate analyses. The hormone receptor-/human epidermal growth factor receptor 2- subtype conferred a significantly poorer outcome in terms of breast cancer-specific survival and overall survival. hormone receptor+/human epidermal growth factor receptor 2+ disease was associated with the best prognosis in terms of breast cancer-specific survival and overall survival. Patients with liver and brain metastases were more likely to experience poor prognosis for breast cancer-specific survival and overall survival by various breast cancer subtypes. Distant metastases sites have differential impact on clinical outcomes in stage-IV breast cancer. Follow-up screening for brain and liver metastases might be effective in improving breast cancer-specific survival and overall survival.

Recent findings and technological advances in phosphoproteomics for cells and tissues.

PubMed

von Stechow, Louise; Francavilla, Chiara; Olsen, Jesper V

2015-01-01

Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins - termed phosphoproteomics - strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.

A new detection method for the K variant of butyrylcholinesterase based on PCR primer introduced restriction analysis (PCR-PIRA).

PubMed Central

Shibuta, K; Abe, M; Suzuki, T

1994-01-01

The K variant of human butyrylcholinesterase is caused by a G/A transition in the butyrylcholinesterase gene, which neither creates nor destroys any restriction site. In an attempt to detect the K variant both simply and rapidly, we developed a two step method of "PCR primer introduced restriction analysis" (PCR-PIRA). The first step was used to introduce a new Fun4HI site into the normal allele for a screening test, while the second step was performed to create a new MaeIII site on the variant allele for a specific test. This method thus enabled us to distinguish clearly the K variant from the normal allele, and also showed that the frequency of the K variant allele is 0.164 in the Japanese population. Images PMID:7966197

75 FR 65310 - Environmental Management Site-Specific Advisory Board, Nevada

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-22

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Nevada AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Nevada Test Site. The Federal Advisory... Board is to make recommendations to DOE-EM and site management in the areas of environmental restoration...

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules.

PubMed

Carpenter, Megan R; Kalburge, Sai S; Borowski, Joseph D; Peters, Molly C; Colwell, Rita R; Boyd, E Fidelma

2017-05-15

Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB , via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs. IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and catalyze their incorporation into bacterial chromosomes, which could convert a strain into a pathogen with very different disease pathologies. Each island had the ability to excise from the chromosome as distinct, complete units for possible transfer. Evolutionary analysis of these regions indicates that they were acquired by horizontal transfer and that PAIs are the units of transfer. Similar to the case for phage evolution, PAIs have a modular structure where different functional regions are acquired by identical recombination modules. Copyright © 2017 American Society for Microbiology.

Influence of Quasi-Specific Sites on Kinetics of Target DNA Search by a Sequence-Specific DNA-Binding Protein

PubMed Central

2015-01-01

Functions of transcription factors require formation of specific complexes at particular sites in cis-regulatory elements of genes. However, chromosomal DNA contains numerous sites that are similar to the target sequences recognized by transcription factors. The influence of such “quasi-specific” sites on functions of the transcription factors is not well understood at present by experimental means. In this work, using fluorescence methods, we have investigated the influence of quasi-specific DNA sites on the efficiency of target location by the zinc finger DNA-binding domain of the inducible transcription factor Egr-1, which recognizes a 9 bp sequence. By stopped-flow assays, we measured the kinetics of Egr-1’s association with a target site on 143 bp DNA in the presence of various competitor DNAs, including nonspecific and quasi-specific sites. The presence of quasi-specific sites on competitor DNA significantly decelerated the target association by the Egr-1 protein. The impact of the quasi-specific sites depended strongly on their affinity, their concentration, and the degree of their binding to the protein. To quantitatively describe the kinetic impact of the quasi-specific sites, we derived an analytical form of the apparent kinetic rate constant for the target association and used it for fitting to the experimental data. Our kinetic data with calf thymus DNA as a competitor suggested that there are millions of high-affinity quasi-specific sites for Egr-1 among the 3 billion bp of genomic DNA. This study quantitatively demonstrates that naturally abundant quasi-specific sites on DNA can considerably impede the target search processes of sequence-specific DNA-binding proteins. PMID:26502071

Assignment of sockeye salmon (Oncorhynchus nerka) to spawning sites using DNA markers.

PubMed

Corley-Smith, Graham E; Wennerberg, Liv; Schembri, Joy A; Lim, Chinten J; Cooper, Karen L; Brandhorst, Bruce P

2005-01-01

Randomly amplified polymorphic DNA (RAPD) markers were used to assign individual adult sockeye salmon to their spawning sites using a genotype assignment test. Six primers were selected for use by screening bulked DNA samples for markers missing in fish from one or more of 5 sites in British Columbia or Alaska. Of 73 markers scored, 54 showed variation between or within sites among the sampled fish. Thirty-seven of the variable markers were not detected in any fish from one or more sites; 18 variable markers were detected in all fish from one or more other sites. Thus 25% of markers scored were found in all fish of some sites and in no fish of some other sites. An assignment test placed all 70 fish tested into their correct populations. Principal coordinate analysis of genetic variation produced clusters of fish corresponding to each sampling site. No sex-specific RAPD markers were detected among more than 1300 screened.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

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

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE PAGES

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.; ...

2017-07-07

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

National hydroelectric power resources study. Preliminary inventory of hydropower resources. Volume 1. Pacific Northwest region

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

None

1979-07-01

The preliminary inventory and analysis procedures provide a comprehensive assessment of the undeveloped hydroelectric power potential in the US and determines which sites merit more thorough investigation. Over 5400 existing structures have been identified as having the physical potential to add hydropower plants or increase hydropower output thereby increasing our present hydropower capacity from a total of 64,000 MW to 158,000 MW and our energy from 280,000 GWH to 503,000 GWH. While the physical potential for this increase is clearly available, some of these projects will undoubtedly not satisfy more-detailed economic analysis as well as the institutional and environmental criteriamore » which will be imposed upon them. Summary tables include estimates of the potential capacity and energy at each site in the inventory. In some cases, individual projects may be site alternatives to others in the same general location, when only one can be considered for hydropower development. The number of sites per state is identified, but specific information is included for only the sites in Alaska, Idaho, Oregon, and Washington in this first volume.« less

Idaho's surface-water-quality monitoring program: results from five sites sampled during water years 1990-93

USGS Publications Warehouse

,

1994-01-01

In 1990, the U.S. Geological Survey (USGS), in cooperation with the Idaho Department of Health and Welfare, Division of Environmental Quality, implemented a statewide water-quality monitoring program in response to Idaho's antidegradation policy as required by the Clean Water Act. The program objective is to provide water-quality managers with a coordinated statewide network to detect trends in surface-water quality. The monitoring program includes the collection and analysis of samples from 56 sites on the Bear, Clearwater, Kootenai, Pend Oreille, Salmon, Snake, and Spokane Rivers and their tributaries (fig. 1). Samples are collected every year at 5 sites (annual sites) in drainage basins where long-term water-quality management is practiced, every other year at 19 sites (biennial sites) in basins where land and water uses change slowly, and every third year at 32 sites (triennial sites) where future development may affect water quality. Each year, 25 of the 56 sites are sampled. This report discusses results of sampling at five annual sites. During water years 1990-93 (October 1, 1989, through September 30, 1993), samples were collected six times per year at the five annual sites (fig. 1). Onsite analyses were made for discharge, specific conductance, pH, temperature, dissolved oxygen, bacteria (fecal coliform and fecal streptococci), and alkalinity. Laboratory analyses were made for major ions, nutrients, trace elements, and suspended sediment. Suspended sediment, nitrate, fecal coliform, trace elements, and specific conductance were used to characterize surface-water quality. Because concentrations of all trace elements except zinc were near detection limits, only zinc is discussed.

Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates.

PubMed

Curran, Amy; Chang, Ing-Feng; Chang, Chia-Lun; Garg, Shilpi; Miguel, Rodriguez Milla; Barron, Yoshimi D; Li, Ying; Romanowsky, Shawn; Cushman, John C; Gribskov, Michael; Harmon, Alice C; Harper, Jeffrey F

2011-01-01

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca(2+)-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with K(M) ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies.

Calcium-Dependent Protein Kinases from Arabidopsis Show Substrate Specificity Differences in an Analysis of 103 Substrates

PubMed Central

Curran, Amy; Chang, Ing-Feng; Chang, Chia-Lun; Garg, Shilpi; Miguel, Rodriguez Milla; Barron, Yoshimi D.; Li, Ying; Romanowsky, Shawn; Cushman, John C.; Gribskov, Michael; Harmon, Alice C.; Harper, Jeffrey F.

2011-01-01

The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca2+-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with KM ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies. PMID:22645532

Expanding the scope of site-specific recombinases for genetic and metabolic engineering.

PubMed

Gaj, Thomas; Sirk, Shannon J; Barbas, Carlos F

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. © 2013 Wiley Periodicals, Inc.

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

PubMed

Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

2015-12-11

Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Immunological Reactivity Using Monoclonal and Polyclonal Antibodies of Autoimmune Thyroid Target Sites with Dietary Proteins

PubMed Central

Herbert, Martha

2017-01-01

Many hypothyroid and autoimmune thyroid patients experience reactions with specific foods. Additionally, food interactions may play a role in a subset of individuals who have difficulty finding a suitable thyroid hormone dosage. Our study was designed to investigate the potential role of dietary protein immune reactivity with thyroid hormones and thyroid axis target sites. We identified immune reactivity between dietary proteins and target sites on the thyroid axis that includes thyroid hormones, thyroid receptors, enzymes, and transport proteins. We also measured immune reactivity of either target specific monoclonal or polyclonal antibodies for thyroid-stimulating hormone (TSH) receptor, 5′deiodinase, thyroid peroxidase, thyroglobulin, thyroxine-binding globulin, thyroxine, and triiodothyronine against 204 purified dietary proteins commonly consumed in cooked and raw forms. Dietary protein determinants included unmodified (raw) and modified (cooked and roasted) foods, herbs, spices, food gums, brewed beverages, and additives. There were no dietary protein immune reactions with TSH receptor, thyroid peroxidase, and thyroxine-binding globulin. However, specific antigen-antibody immune reactivity was identified with several purified food proteins with triiodothyronine, thyroxine, thyroglobulin, and 5′deiodinase. Laboratory analysis of immunological cross-reactivity between thyroid target sites and dietary proteins is the initial step necessary in determining whether dietary proteins may play a potential immunoreactive role in autoimmune thyroid disease. PMID:28894619

A neural network based methodology to predict site-specific spectral acceleration values

NASA Astrophysics Data System (ADS)

Kamatchi, P.; Rajasankar, J.; Ramana, G. V.; Nagpal, A. K.

2010-12-01

A general neural network based methodology that has the potential to replace the computationally-intensive site-specific seismic analysis of structures is proposed in this paper. The basic framework of the methodology consists of a feed forward back propagation neural network algorithm with one hidden layer to represent the seismic potential of a region and soil amplification effects. The methodology is implemented and verified with parameters corresponding to Delhi city in India. For this purpose, strong ground motions are generated at bedrock level for a chosen site in Delhi due to earthquakes considered to originate from the central seismic gap of the Himalayan belt using necessary geological as well as geotechnical data. Surface level ground motions and corresponding site-specific response spectra are obtained by using a one-dimensional equivalent linear wave propagation model. Spectral acceleration values are considered as a target parameter to verify the performance of the methodology. Numerical studies carried out to validate the proposed methodology show that the errors in predicted spectral acceleration values are within acceptable limits for design purposes. The methodology is general in the sense that it can be applied to other seismically vulnerable regions and also can be updated by including more parameters depending on the state-of-the-art in the subject.

Stage-specific control of connective tissue growth factor (CTGF/CCN2) expression in chondrocytes by Sox9 and beta-catenin.

PubMed

Huang, Bau-Lin; Brugger, Sean M; Lyons, Karen M

2010-09-03

CCN2/connective tissue growth factor is highly expressed in hypertrophic chondrocytes and is required for chondrogenesis. However, the transcriptional mechanisms controlling its expression in cartilage are largely unknown. The activity of the Ccn2 promoter was, therefore, investigated in osteochondro-progenitor cells and hypertrophic chondrocytes to ascertain these mechanisms. Sox9 and T-cell factor (TCF) x lymphoid enhancer factor (LEF) factors contain HMG domains and bind to related consensus sites. TCF x LEF factors are normally repressive but when bound to DNA in a complex with beta-catenin become activators of gene expression. In silico analysis of the Ccn2 proximal promoter identified multiple consensus TCF x LEF elements, one of which was also a consensus binding site for Sox9. Using luciferase reporter constructs, the TCF x LEF x Sox9 site was found to be involved in stage-specific expression of Ccn2. Luciferase, electrophoretic mobility shift assay (EMSA), and ChIP analysis revealed that Sox9 represses Ccn2 expression by binding to the consensus TCF x LEF x Sox9 site. On the other hand, the same assays showed that in hypertrophic chondrocytes, TCF x LEF x beta-catenin complexes occupy the consensus TCF x LEF x Sox9 site and activate Ccn2 expression. Furthermore, transgenic mice in which lacZ expression is driven under the control of the proximal Ccn2 promoter revealed that the proximal Ccn2 promoter responded to Wnt signaling in cartilage. Hence, we propose that differential occupancy of the TCF x LEF x Sox9 site by Sox9 versus beta-catenin restricts high levels of Ccn2 expression to hypertrophic chondrocytes.

Reassessment of the NH4 NO3 thermal decomposition technique for calibration of the N2 O isotopic composition.

PubMed

Mohn, Joachim; Gutjahr, Wilhelm; Toyoda, Sakae; Harris, Eliza; Ibraim, Erkan; Geilmann, Heike; Schleppi, Patrick; Kuhn, Thomas; Lehmann, Moritz F; Decock, Charlotte; Werner, Roland A; Yoshida, Naohiro; Brand, Willi A

2016-09-08

In the last few years, the study of N 2 O site-specific nitrogen isotope composition has been established as a powerful technique to disentangle N 2 O emission pathways. This trend has been accelerated by significant analytical progress in the field of isotope-ratio mass-spectrometry (IRMS) and more recently quantum cascade laser absorption spectroscopy (QCLAS). Methods The ammonium nitrate (NH 4 NO 3 ) decomposition technique provides a strategy to scale the 15 N site-specific (SP ≡ δ 15 N α - δ 15 N β ) and bulk (δ 15 N bulk  = (δ 15 N α  + δ 15 N β )/2) isotopic composition of N 2 O against the international standard for the 15 N/ 14 N isotope ratio (AIR-N 2 ). Within the current project 15 N fractionation effects during thermal decomposition of NH 4 NO 3 on the N 2 O site preference were studied using static and dynamic decomposition techniques. The validity of the NH 4 NO 3 decomposition technique to link NH 4 + and NO 3 - moiety-specific δ 15 N analysis by IRMS to the site-specific nitrogen isotopic composition of N 2 O was confirmed. However, the accuracy of this approach for the calibration of δ 15 N α and δ 15 N β values was found to be limited by non-quantitative NH 4 NO 3 decomposition in combination with substantially different isotope enrichment factors for the conversion of the NO 3 - or NH 4 + nitrogen atom into the α or β position of the N 2 O molecule. The study reveals that the completeness and reproducibility of the NH 4 NO 3 decomposition reaction currently confine the anchoring of N 2 O site-specific isotopic composition to the international isotope ratio scale AIR-N 2 . The authors suggest establishing a set of N 2 O isotope reference materials with appropriate site-specific isotopic composition, as community standards, to improve inter-laboratory compatibility. This article is protected by copyright. All rights reserved.

Thin-plate spline (TPS) graphical analysis of the mandible on cephalometric radiographs.

PubMed

Chang, H P; Liu, P H; Chang, H F; Chang, C H

2002-03-01

We describe two cases of Class III malocclusion with and without orthodontic treatment. A thin-plate spline (TPS) analysis of lateral cephalometric radiographs was used to visualize transformations of the mandible. The actual sites of mandibular skeletal change are not detectable with conventional cephalometric analysis. These case analyses indicate that specific patterns of mandibular transformation are associated with Class III malocclusion with or without orthopaedic therapy, and visualization of these deformations is feasible using TPS graphical analysis.

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

PubMed Central

2013-01-01

Background The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations – changes specific to a tumor and not within an individual’s germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. Results We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. Conclusion We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic. PMID:23642077

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.

PubMed

Christoforides, Alexis; Carpten, John D; Weiss, Glen J; Demeure, Michael J; Von Hoff, Daniel D; Craig, David W

2013-05-04

The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations--changes specific to a tumor and not within an individual's germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific. We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity. We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic.

Michael T. Guarnieri | NREL

Science.gov Websites

accumulation," J. Proteomics (2013) "Comparative Proteomics Lends Insight into Genotype-Specific Pathogenicity," J. Proteomics (2013) "De Novo Transcriptomic Analysis of Hydrogen Production in the amino acid changes in the small envelope protein and rescued by a novel glycosolation site," J

Feasibility of a web-based system for police crash report review and information recording.

DOT National Transportation Integrated Search

2016-04-01

Police crash reports include useful additional information that is not available in crash summary records. : This information may include police sketches and narratives and is often needed for detailed site-specific : safety analysis. In addition, so...

Virtual Beach v2.2 User Guide

EPA Science Inventory

Virtual Beach version 2.2 (VB 2.2) is a decision support tool. It is designed to construct site-specific Multi-Linear Regression (MLR) models to predict pathogen indicator levels (or fecal indicator bacteria, FIB) at recreational beaches. MLR analysis has outperformed persisten...

Conformational dynamics of abasic DNA upon interactions with AP endonuclease 1 revealed by stopped-flow fluorescence analysis.

PubMed

Kanazhevskaya, Lyubov Yu; Koval, Vladimir V; Vorobjev, Yury N; Fedorova, Olga S

2012-02-14

Apurinic/apyrimidinic (AP) sites are abundant DNA lesions arising from exposure to UV light, ionizing radiation, alkylating agents, and oxygen radicals. In human cells, AP endonuclease 1 (APE1) recognizes this mutagenic lesion and initiates its repair via a specific incision of the phosphodiester backbone 5' to the AP site. We have investigated a detailed mechanism of APE1 functioning using fluorescently labeled DNA substrates. A fluorescent adenine analogue, 2-aminopurine, was introduced into DNA substrates adjacent to the abasic site to serve as an on-site reporter of conformational transitions in DNA during the catalytic cycle. Application of a pre-steady-state stopped-flow technique allows us to observe changes in the fluorescence intensity corresponding to different stages of the process in real time. We also detected an intrinsic Trp fluorescence of the enzyme during interactions with 2-aPu-containing substrates. Our data have revealed a conformational flexibility of the abasic DNA being processed by APE1. Quantitative analysis of fluorescent traces has yielded a minimal kinetic scheme and appropriate rate constants consisting of four steps. The results obtained from stopped-flow data have shown a substantial influence of the 2-aPu base location on completion of certain reaction steps. Using detailed molecular dynamics simulations of the DNA substrates, we have attributed structural distortions of AP-DNA to realization of specific binding, effective locking, and incision of the damaged DNA. The findings allowed us to accurately discern the step that corresponds to insertion of specific APE1 amino acid residues into the abasic DNA void in the course of stabilization of the precatalytic complex.

Bioinformatics Identification of Modules of Transcription Factor Binding Sites in Alzheimer's Disease-Related Genes by In Silico Promoter Analysis and Microarrays

PubMed Central

Augustin, Regina; Lichtenthaler, Stefan F.; Greeff, Michael; Hansen, Jens; Wurst, Wolfgang; Trümbach, Dietrich

2011-01-01

The molecular mechanisms and genetic risk factors underlying Alzheimer's disease (AD) pathogenesis are only partly understood. To identify new factors, which may contribute to AD, different approaches are taken including proteomics, genetics, and functional genomics. Here, we used a bioinformatics approach and found that distinct AD-related genes share modules of transcription factor binding sites, suggesting a transcriptional coregulation. To detect additional coregulated genes, which may potentially contribute to AD, we established a new bioinformatics workflow with known multivariate methods like support vector machines, biclustering, and predicted transcription factor binding site modules by using in silico analysis and over 400 expression arrays from human and mouse. Two significant modules are composed of three transcription factor families: CTCF, SP1F, and EGRF/ZBPF, which are conserved between human and mouse APP promoter sequences. The specific combination of in silico promoter and multivariate analysis can identify regulation mechanisms of genes involved in multifactorial diseases. PMID:21559189

Performance assessment for the disposal of low-level waste in the 200 West Area Burial Grounds

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

Wood, M.I.; Khaleel, R.; Rittmann, P.D.

1995-06-01

This document reports the findings of a performance assessment (PA) analysis for the disposal of solid low-level radioactive waste (LLW) in the 200 West Area Low-Level Waste Burial Grounds (LLBG) in the northwest corner of the 200 West Area of the Hanford Site. This PA analysis is required by US Department of Energy (DOE) Order 5820.2A (DOE 1988a) to demonstrate that a given disposal practice is in compliance with a set of performance objectives quantified in the order. These performance objectives are applicable to the disposal of DOE-generated LLW at any DOE-operated site after the finalization of the order inmore » September 1988. At the Hanford Site, DOE, Richland Operations Office (RL) has issued a site-specific supplement to DOE Order 5820.2A, DOE-RL 5820.2A (DOE 1993), which provides additiona I ce objectives that must be satisfied.« less

Can the benefits of physical seabed restoration justify the costs? An assessment of a disused aggregate extraction site off the Thames Estuary, UK.

PubMed

Cooper, Keith; Burdon, Daryl; Atkins, Jonathan P; Weiss, Laura; Somerfield, Paul; Elliott, Michael; Turner, Kerry; Ware, Suzanne; Vivian, Chris

2013-10-15

Physical and biological seabed impacts can persist long after the cessation of marine aggregate dredging. Whilst small-scale experimental studies have shown that it may be possible to mitigate such impacts, it is unclear whether the costs of restoration are justified on an industrial scale. Here we explore this question using a case study off the Thames Estuary, UK. By understanding the nature and scale of persistent impacts, we identify possible techniques to restore the physical properties of the seabed, and the costs and the likelihood of success. An analysis of the ecosystem services and goods/benefits produced by the site is used to determine whether intervention is justified. Whilst a comparison of costs and benefits at this site suggests restoration would not be warranted, the analysis is site-specific. We emphasise the need to better define what is, and is not, an acceptable seabed condition post-dredging. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Buffer zone monitoring plan for the Dos Rios subdivision, Gunnison, Colorado

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

NONE

1996-02-01

This report presents a plan for water quality monitoring at the Dos Rios subdivision (Units 2, 3, and the Island Unit) that is intended to satisfy the informational needs of residents who live southwest (downgradient) of the former Gunnison processing site. Water quality monitoring activities described in this report are designed to protect the public from residual contamination that entered the ground water as a result of previous uranium milling operations. Requirements presented in this monitoring plan are also included in the water sampling and analysis plan (WSAP) for the Gunnison Uranium Mill Tailings Remedial Action (UMTRA) Project site. Themore » Gunnison WSAP is a site-specific document prepared by the U.S. Department of Energy (DOE) that provides background, guidance, and justification for future ground water sampling and analysis activities for the UMTRA Project Gunnison processing and disposal sites. The WSAP will be updated annually, as additional water quality data are collected and interpreted, to provide ongoing protection for public health and the environment.« less

Geophysical detection of on-site wastewater plumes in the North Carolina Coastal Plain, USA

NASA Astrophysics Data System (ADS)

Smith, Matthew

Nonpoint source pollution (NPS) continues to be the leading cause of water quality degradation in the United States. On-site wastewater systems (OWS) contribute to NPS; however, due to the range of system designs and complexity of the subsurface, OWS contributions to groundwater pollution are not well understood. As the population of coastal North Carolina continues to increase, better methods to locate and characterize wastewater impacted groundwater are needed. Previous studies have demonstrated the ability of non-intrusive geophysical methods to provide high resolution information on various contaminants in different geologic settings. The goals of this study were to evaluate the utility of ground penetrating radar (GPR) and capacitively coupled resistivity (CCR) for detecting OWS components, delineating associated wastewater plumes, and monitoring temporal variations in groundwater quality. Cross-sectional and three dimensional (3D) geophysical surveys were conducted periodically over a one year period (February 2011--January 2012) at two schools utilizing OWS in the lower Neuse River Basin (NRB) in the North Carolina Coastal Plain (NCCP). Cores were collected at both study sites; as well as monthly groundwater depth, temperature, and specific conductivity measurements to better constrain the geophysical interpretations. Additionally, dissolved inorganic nitrogen (DIN) and Cl concentrations were monitored bi-monthly to assess nutrient transport at the sites. The 3D GPR surveys effectively located the wastewater drainage trenches at both sites, in close agreement with locations described in as-built OWS blueprints. Regression analysis of resistivity versus groundwater specific conductivity revealed an inverse relationship, suggesting resistivity ≤ 250 ohm.m was indicative of wastewater impacted groundwater at both sites. The 3D resistivity models identified regions of low resistivity beneath the drainfields relative to background values. Regression analysis of GPR signal absolute peak amplitude (APA) versus groundwater specific conductivity revealed a decrease in APA indicative of radar signal attenuation at locations where groundwater specific conductivity was elevated. The 3D GPR models identified regions of attenuated radar signal beneath the drainfields relative to background locations. Comparisons of groundwater specific conductivity, GPR, and CCR lateral wastewater plume estimates indicated similar dimensions at both sites. The sensitivity of resistivity measurements tended to decline with increased water-table depth; although, differences in resistivity associated with seasonal water-table depth changes were noticeable. Overall, results of this study suggest that GPR and CCR surveys combined with sediment, hydrologic, and water quality data may provide reliable information on the location of OWS components and extent of associated wastewater plumes. The GPR surveys successfully located the wastewater drainage trenches and helped image the uppermost surface of the wastewater plumes. The CCR surveys delineated the lateral wastewater plume dimensions and revealed temporal changes in groundwater quality associated with differences in groundwater recharge.

Comparison of mosquito control programs in seven urban sites in Africa, the Middle East, and the Americas.

PubMed

Impoinvil, Daniel E; Ahmad, Sajjad; Troyo, Adriana; Keating, Joseph; Githeko, Andrew K; Mbogo, Charles M; Kibe, Lydiah; Githure, John I; Gad, Adel M; Hassan, Ali N; Orshan, Laor; Warburg, Alon; Calderón-Arguedas, Olger; Sánchez-Loría, Victoria M; Velit-Suarez, Rosanna; Chadee, Dave D; Novak, Robert J; Beier, John C

2007-10-01

Mosquito control programs at seven urban sites in Kenya, Egypt, Israel, Costa Rica, and Trinidad are described and compared. Site-specific urban and disease characteristics, organizational diagrams, and strengths, weaknesses, obstacles and threats (SWOT) analysis tools are used to provide a descriptive assessment of each mosquito control program, and provide a comparison of the factors affecting mosquito abatement. The information for SWOT analysis is collected from surveys, focus-group discussions, and personal communication. SWOT analysis identified various issues affecting the efficiency and sustainability of mosquito control operations. The main outcome of our work was the description and comparison of mosquito control operations within the context of each study site's biological, social, political, management, and economic conditions. The issues identified in this study ranged from lack of inter-sector collaboration to operational issues of mosquito control efforts. A lack of sustainable funding for mosquito control was a common problem for most sites. Many unique problems were also identified, which included lack of mosquito surveillance, lack of law enforcement, and negative consequences of human behavior. Identifying common virtues and shortcomings of mosquito control operations is useful in identifying "best practices" for mosquito control operations, thus leading to better control of mosquito biting and mosquito-borne disease transmission.

Source identification of uranium-containing materials at mine legacy sites in Portugal.

PubMed

Keatley, A C; Martin, P G; Hallam, K R; Payton, O D; Awbery, R; Carvalho, F P; Oliveira, J M; Silva, L; Malta, M; Scott, T B

2018-03-01

Whilst prior nuclear forensic studies have focused on identifying signatures to distinguish between different uranium deposit types, this paper focuses on providing a scientific basis for source identification of materials from different uranium mine sites within a single region, which can then be potentially used within nuclear forensics. A number of different tools, including gamma spectrometry, alpha spectrometry, mineralogy and major and minor elemental analysis, have been utilised to determine the provenance of uranium mineral samples collected at eight mine sites, located within three different uranium provinces, in Portugal. A radiation survey was initially conducted by foot and/or unmanned aerial vehicle at each site to assist sample collection. The results from each mine site were then compared to determine if individual mine sites could be distinguished based on characteristic elemental and isotopic signatures. Gamma and alpha spectrometry were used to differentiate between samples from different sites and also give an indication of past milling and mining activities. Ore samples from the different mine sites were found to be very similar in terms of gangue and uranium mineralogy. However, rarer minerals or specific impurity elements, such as calcium and copper, did permit some separation of the sites examined. In addition, classification rates using linear discriminant analysis were comparable to those in the literature. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

An alternative approach to probabilistic seismic hazard analysis in the Aegean region using Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Weatherill, Graeme; Burton, Paul W.

2010-09-01

The Aegean is the most seismically active and tectonically complex region in Europe. Damaging earthquakes have occurred here throughout recorded history, often resulting in considerable loss of life. The Monte Carlo method of probabilistic seismic hazard analysis (PSHA) is used to determine the level of ground motion likely to be exceeded in a given time period. Multiple random simulations of seismicity are generated to calculate, directly, the ground motion for a given site. Within the seismic hazard analysis we explore the impact of different seismic source models, incorporating both uniform zones and distributed seismicity. A new, simplified, seismic source model, derived from seismotectonic interpretation, is presented for the Aegean region. This is combined into the epistemic uncertainty analysis alongside existing source models for the region, and models derived by a K-means cluster analysis approach. Seismic source models derived using the K-means approach offer a degree of objectivity and reproducibility into the otherwise subjective approach of delineating seismic sources using expert judgment. Similar review and analysis is undertaken for the selection of peak ground acceleration (PGA) attenuation models, incorporating into the epistemic analysis Greek-specific models, European models and a Next Generation Attenuation model. Hazard maps for PGA on a "rock" site with a 10% probability of being exceeded in 50 years are produced and different source and attenuation models are compared. These indicate that Greek-specific attenuation models, with their smaller aleatory variability terms, produce lower PGA hazard, whilst recent European models and Next Generation Attenuation (NGA) model produce similar results. The Monte Carlo method is extended further to assimilate epistemic uncertainty into the hazard calculation, thus integrating across several appropriate source and PGA attenuation models. Site condition and fault-type are also integrated into the hazard mapping calculations. These hazard maps are in general agreement with previous maps for the Aegean, recognising the highest hazard in the Ionian Islands, Gulf of Corinth and Hellenic Arc. Peak Ground Accelerations for some sites in these regions reach as high as 500-600 cm s -2 using European/NGA attenuation models, and 400-500 cm s -2 using Greek attenuation models.

Seismic hazard assessment of the Province of Murcia (SE Spain): analysis of source contribution to hazard

NASA Astrophysics Data System (ADS)

García-Mayordomo, J.; Gaspar-Escribano, J. M.; Benito, B.

2007-10-01

A probabilistic seismic hazard assessment of the Province of Murcia in terms of peak ground acceleration (PGA) and spectral accelerations [SA( T)] is presented in this paper. In contrast to most of the previous studies in the region, which were performed for PGA making use of intensity-to-PGA relationships, hazard is here calculated in terms of magnitude and using European spectral ground-motion models. Moreover, we have considered the most important faults in the region as specific seismic sources, and also comprehensively reviewed the earthquake catalogue. Hazard calculations are performed following the Probabilistic Seismic Hazard Assessment (PSHA) methodology using a logic tree, which accounts for three different seismic source zonings and three different ground-motion models. Hazard maps in terms of PGA and SA(0.1, 0.2, 0.5, 1.0 and 2.0 s) and coefficient of variation (COV) for the 475-year return period are shown. Subsequent analysis is focused on three sites of the province, namely, the cities of Murcia, Lorca and Cartagena, which are important industrial and tourism centres. Results at these sites have been analysed to evaluate the influence of the different input options. The most important factor affecting the results is the choice of the attenuation relationship, whereas the influence of the selected seismic source zonings appears strongly site dependant. Finally, we have performed an analysis of source contribution to hazard at each of these cities to provide preliminary guidance in devising specific risk scenarios. We have found that local source zones control the hazard for PGA and SA( T ≤ 1.0 s), although contribution from specific fault sources and long-distance north Algerian sources becomes significant from SA(0.5 s) onwards.

Quantification of in Situ Biodegradation Rate Constants Using a Novel Combined Isotope Approach

NASA Astrophysics Data System (ADS)

Blum, P.; Sültenfuß, J.; Martus, P.

2014-12-01

Numerous studies have shown the enormous potential of the compound-specific isotope analysis (CSIA) for studying the biodegradation of organic compounds such as monoaromatic hydrocarbons (BTEX), polyaromatic hydrocarbons (PAH), chlorinated solvents and other organic contaminants and environmental transformation mechanisms in groundwater. In addition, two-dimensional isotope analysis such as carbon and hydrogen have been successfully studied indicating the potential to also investigate site-specific reaction mechanisms. The main objective of the current study however is to quantify real effective in situ biodegradation rate constants in a coal-tar contaminated aquifer by combining compound-specific isotope analysis (CSIA) and tracer-based (3H-3He) ground-water dating (TGD). Hence, groundwater samples are used to determine groundwater residence times, and carbon and hydrogen stable isotopes are analyzed for selected BTEX and PAH. The results of the hydrogen stable isotopes surprisingly indicate no isotope fractionation and therefore no biodegradation. In contrast, for stable carbon isotopes of selected BTEX such as o-xylene and toluene, isotope shifts are detected indicating active biodegradation under sulfate-reducing conditions. These and previous results of stable carbon isotopes show that only for o-xylene a clear evidence for biodegradation is possible for the studied site. Nevertheless, in combining these results with the groundwater residence times, which range between 1 year for the shallow wells (20 m below surface) and 41 years for the deeper wells (40 m below surface), it is feasible to effectively determine in situ biodegradation rate constants for o-xylene. Conversely, the outcome also evidently demonstrate the major limitations of the novel combined isotope approach for a successful implementation of monitored natural attenuation (MNA) at such field sites.

Evaluation of chemical data from selected sites in the Surface-Water Ambient Monitoring Program (SWAMP) in Florida

USGS Publications Warehouse

Katz, B.G.; Collins, J.J.

1998-01-01

A cooperative study between the Florida Department of Environmental Protection (FDEP) and the U.S. Geological Survey was conducted to assess the integrity of selected water-quality data collected at 150 sites in the FDEP Surface-Water Ambient Monitoring Program (SWAMP) in Florida. The assessment included determining the consistency of the water-quality data collected statewide, including commonality of monitoring procedures and analytes, screening of the gross validity of a chemical analysis, and quality assurance and quality control (QA/QC) procedures. Four tests were used to screen data at selected SWAMP sites to estimate the gross validity of selected chemical data: (1) the ratio of dissolved solids (in milligrams per liter) to specific conductance (in microsiemens per centimeter); (2) the ratio of total cations (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); (3) the ratio of total anions (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); and (4) the ionic charge-balance error. Although the results of the four screening tests indicate that the chemical data generally are quite reliable, the extremely small number of samples (less than 5 percent of the total number of samples) with sufficient chemical information to run the tests may not provide a representative indication of the analytical accuracy of all laboratories in the program. In addition to the four screening tests, unusually low or high values were flagged for field and laboratory pH (less than 4.0 and greater than 9.0) and specific conductance (less than 10 and greater than 10,000 microsiemens per centimeter). The numbers of flagged data were less than 1 percent of the 19,937 water samples with pH values and less than 0.6 percent of the 16,553 water samples with specific conductance values. Thirty-four agencies responded to a detailed questionnaire that was sent to more than 60 agencies involved in the collection and analysis of surface-water-quality data for SWAMP. The purpose of the survey was to evaluate quality assurance methods and consistency of methods statewide. Information was compiled and summarized on monitoring network design, data review and upload procedures, laboratory and field sampling methods, and data practices. Currently, most agencies that responded to the survey follow FDEP-approved QA/QC protocol for sampling and have quality assurance practices for recording and reporting data. Also, most agencies responded that calibration procedures were followed in the laboratory for analysis of data, but no responses were given about the specific procedures. Approximately 50 percent of the respondents indicated that laboratory analysis methods have changed over time. With so many laboratories involved in analyzing samples for SWAMP, it is difficult to compare water quality from one site to another due to different reporting conventions for chemical constituents and different analytical methods over time. Most agencies responded that calibration methods are followed in the field, but no specific details were provided. Grab samples are the most common method of collection. Other data screening procedures are necessary to further evaluate the validity of chemical data collected at SWAMP sites. High variability in the concentration of targeted constituents may signal analytical problems, but more likely changes in concentration are related to hydrologic conditions. This underscores the need for accurate measurements of discharge, lake stage, tidal stage at the time of sampling so that changes in constituent concentrations can be properly evaluated and fluxes (loads) of nutrients or metals, for example, can be calculated and compared over time.

Regression modeling of gas-particle partitioning of atmospheric oxidized mercury from temperature data

NASA Astrophysics Data System (ADS)

Cheng, Irene; Zhang, Leiming; Blanchard, Pierrette

2014-10-01

Models describing the partitioning of atmospheric oxidized mercury (Hg(II)) between the gas and fine particulate phases were developed as a function of temperature. The models were derived from regression analysis of the gas-particle partitioning parameters, defined by a partition coefficient (Kp) and Hg(II) fraction in fine particles (fPBM) and temperature data from 10 North American sites. The generalized model, log(1/Kp) = 12.69-3485.30(1/T) (R2 = 0.55; root-mean-square error (RMSE) of 1.06 m3/µg for Kp), predicted the observed average Kp at 7 of the 10 sites. Discrepancies between the predicted and observed average Kp were found at the sites impacted by large Hg sources because the model had not accounted for the different mercury speciation profile and aerosol compositions of different sources. Site-specific equations were also generated from average Kp and fPBM corresponding to temperature interval data. The site-specific models were more accurate than the generalized Kp model at predicting the observations at 9 of the 10 sites as indicated by RMSE of 0.22-0.5 m3/µg for Kp and 0.03-0.08 for fPBM. Both models reproduced the observed monthly average values, except for a peak in Hg(II) partitioning observed during summer at two locations. Weak correlations between the site-specific model Kp or fPBM and observations suggest the role of aerosol composition, aerosol water content, and relative humidity factors on Hg(II) partitioning. The use of local temperature data to parameterize Hg(II) partitioning in the proposed models potentially improves the estimation of mercury cycling in chemical transport models and elsewhere.

Monitoring the recovery of Juncus roemerianus marsh burns with the normalized difference vegetation index and Landsat Thematic Mapper data

USGS Publications Warehouse

Ramsey, Elijah W.; Sapkota, S.K.; Barnes, F.G.; Nelson, G.A.

2002-01-01

Nine atmospherically corrected Landsat Thematic Mapper images were used to generate mean normalized difference vegetation indices (NDVI) at 11 burn sites throughout a coastal Juncus roemerianus marsh in St. Marks National Wildlife Refuge, Florida. Time-since-burn, the time lapse from the date of burn to the date of image collection, was related to variation in mean NDVI over time. Regression analysis showed that NDVI increased for about 300 to 400 days immediately after the burn, overshooting the typical mean NDVI of a nonburned marsh. For about another 500 to 600 days NDVI decreased until reaching a nearly constant NDVI of about 0.40. During the phase of increasing NDVI the ability to predict time-since-burn was within about ??60 days. Within the decreasing phase this dropped to about ??88 days. Examination of each burn site revealed some nonburn related influences on NDVI (e.g., seasonality). Normalization of burn NDVI by site-specific nonburn control NDVI eliminated most influences. However, differential responses at the site-specific level remained related to either storm impacts or secondary burning. At these sites, collateral data helped clarify the abnormal changes in NDVI. Accounting for these abnormalities, site-specific burn recovery trends could be broadly standardized into four general phases: Phase 1-preburn, Phase 2-initial recovery (increasing NDVI), Phase 3-late recovery (decreasing NDVI), and Phase 4-final coalescence (unchanging NDVI). Phase 2 tended to last about 300 to 500 days, Phase 3 an additional 500 to 600 days, and finally reaching Phase 4, 900 to 1,000 days after burn.

Alu elements shape the primate transcriptome by cis-regulation of RNA editing

PubMed Central

2014-01-01

Background RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought. PMID:24485196

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

PubMed Central

Mazzoni, Esteban O; Mahony, Shaun; Closser, Michael; Morrison, Carolyn A; Nedelec, Stephane; Williams, Damian J; An, Disi; Gifford, David K; Wichterle, Hynek

2013-01-01

Efficient transcriptional programming promises to open new frontiers in regenerative medicine. However, mechanisms by which programming factors transform cell fate are unknown, preventing more rational selection of factors to generate desirable cell types. Three transcription factors, Ngn2, Isl1 and Lhx3, were sufficient to program rapidly and efficiently spinal motor neuron identity when expressed in differentiating mouse embryonic stem cells. Replacement of Lhx3 by Phox2a led to specification of cranial, rather than spinal, motor neurons. Chromatin immunoprecipitation–sequencing analysis of Isl1, Lhx3 and Phox2a binding sites revealed that the two cell fates were programmed by the recruitment of Isl1-Lhx3 and Isl1-Phox2a complexes to distinct genomic locations characterized by a unique grammar of homeodomain binding motifs. Our findings suggest that synergistic interactions among transcription factors determine the specificity of their recruitment to cell type–specific binding sites and illustrate how a single transcription factor can be repurposed to program different cell types. PMID:23872598

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project

PubMed Central

Vecchio-Pagan, Briana; Bewick, Sharon; Mainali, Kumar; Karig, David K.; Fagan, William F.

2017-01-01

Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates. PMID:28769875

A novel site-specific recombination system derived from bacteriophage phiMR11.

PubMed

Rashel, Mohammad; Uchiyama, Jumpei; Ujihara, Takako; Takemura, Iyo; Hoshiba, Hiroshi; Matsuzaki, Shigenobu

2008-04-04

We report identification of a novel site-specific DNA recombination system that functions in both in vivo and in vitro, derived from lysogenic Staphylococcus aureus phage phiMR11. In silico analysis of the phiMR11 genome indicated orf1 as a putative integrase gene. Phage and bacterial attachment sites (attP and attB, respectively) and attachment junctions were determined and their nucleotide sequences decoded. Sequences of attP and attB were mostly different to each other except for a two bp common core that was the crossover point. We found several inverted repeats adjacent to the core sequence of attP as potential protein binding sites. The precise and efficient integration properties of phiMR11 integrase were shown on attP and attB in Escherichia coli and the minimum size of attP was found to be 34bp. In in vitro assays using crude or purified integrase, only buffer and substrate DNAs were required for the recombination reaction, indicating that other bacterially encoded factors are not essential for activity.

A pharmacophore model specific to active site of CYP1A2 with a novel molecular modeling explorer and CoMFA.

PubMed

Zhang, Tao; Wei, Dong-Qing; Chou, Kuo-Chen

2012-03-01

Comparative molecular field analysis (CoMFA) is a widely used 3D-QSAR method by which we can investigate the potential relation between biological activity of compounds and their structural features. In this study, a new application of this approach is presented by combining the molecular modeling with a new developed pharmacophore model specific to CYP1A2 active site. During constructing the model, we used the molecular dynamics simulation and molecular docking method to select the sensible binding conformations for 17 CYP1A2 substrates based on the experimental data. Subsequently, the results obtained via the alignment of binding conformations of substrates were projected onto the active- site residues, upon which a simple blueprint of active site was produced. It was validated by the experimental and computational results that the model did exhibit the high degree of rationality and provide useful insights into the substrate binding. It is anticipated that our approach can be extended to investigate the protein-ligand interactions for many other enzyme-catalyzed systems as well.

Pedestrian and motorists' actions at pedestrian hybrid beacon sites: findings from a pilot study.

PubMed

Pulugurtha, Srinivas S; Self, Debbie R

2015-01-01

This paper focuses on an analysis of pedestrian and motorists' actions at sites with pedestrian hybrid beacons and assesses their effectiveness in improving the safety of pedestrians. Descriptive and statistical analyses (one-tail two-sample T-test and two-proportion Z-test) were conducted using field data collected during morning and evening peak hours at three study sites in the city of Charlotte, NC, before and after the installation of pedestrian hybrid beacons. Further, an analysis was conducted to assess the change in pedestrian and motorists' actions over time (before the installation; 1 month, 3 months, 6 months, and 12 months after the installation). Results showed an increase in average traffic speed at one of the pedestrian hybrid beacon sites while no specific trends were observed at the other two pedestrian hybrid beacon sites. A decrease in the number of motorists not yielding to pedestrians, pedestrians trapped in the middle of the street, and pedestrian-vehicle conflicts were observed at all the three pedestrian hybrid beacon sites. The installation of pedestrian hybrid beacons did not have a negative effect on pedestrian actions at two out of the three sites. Improvements seem to be relatively more consistent 3 months after the installation of the pedestrian hybrid beacon.

An analysis of benefits and risk information on pharmaceutical web sites for the treatment of menopause.

PubMed

Charbonneau, Deborah H

2013-09-01

As the Internet is a source of information for many health consumers, there is a need to evaluate the information about prescription drugs provided on pharmaceutical manufacturers' web sites. Using a sample of pharmaceutical manufacturers' web sites for the treatment of menopause, the main objective of this study was to evaluate consumer-oriented information about benefits and risks of prescription drugs for the treatment of menopause provided on pharmaceutical web sites. Pharmaceutical manufacturers' web sites for analysis were identified using a list of U.S. FDA-approved hormone therapies for the treatment of menopause. This study revealed substantial gaps in how benefits and risk information were presented on the web sites. Specifically, information about the benefits was prominent while risk information was incomplete and challenging to find. Further, references to the scientific literature to support claims advertised about prescription drug benefits were not provided. Given the lack of scientific evidence to support claims of benefits and limited disclosure about risks, more information is needed for consumers to be able to weigh the benefits and risks of these treatments for menopause. Overall, these findings provide guidance for evaluating drug information provided on pharmaceutical web sites. © 2013 The author. Health Information and Libraries Journal © 2013 Health Libraries Group.

Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames.

PubMed

Behrens, R; Hayles, J; Nurse, P

2000-12-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.

Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

PubMed Central

Behrens, Ralf; Hayles, Jacky; Nurse, Paul

2000-01-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

Cancer-specific SNPs originate from low-level heteroplasmic variants in human mitochondrial genomes of a matched cell line pair.

PubMed

Hedberg, Annica; Knutsen, Erik; Løvhaugen, Anne Silje; Jørgensen, Tor Erik; Perander, Maria; Johansen, Steinar D

2018-04-19

Low-level mitochondrial heteroplasmy is a common phenomenon in both normal and cancer cells. Here, we investigate the link between low-level heteroplasmy and mitogenome mutations in a human breast cancer matched cell line by high-throughput sequencing. We identified 23 heteroplasmic sites, of which 15 were common between normal cells (Hs578Bst) and cancer cells (Hs578T). Most sites were clustered within the highly conserved Complex IV and ribosomal RNA genes. Two heteroplasmic variants in normal cells were found as fixed mutations in cancer cells. This indicates a positive selection of these variants in cancer cells. RNA-Seq analysis identified upregulated L-strand specific transcripts in cancer cells, which include three mitochondrial long non-coding RNA molecules. We hypothesize that this is due to two cancer cell-specific mutations in the control region.

GIS Toolsets for Planetary Geomorphology and Landing-Site Analysis

NASA Astrophysics Data System (ADS)

Nass, Andrea; van Gasselt, Stephan

2015-04-01

Modern Geographic Information Systems (GIS) allow expert and lay users alike to load and position geographic data and perform simple to highly complex surface analyses. For many applications dedicated and ready-to-use GIS tools are available in standard software systems while other applications require the modular combination of available basic tools to answer more specific questions. This also applies to analyses in modern planetary geomorphology where many of such (basic) tools can be used to build complex analysis tools, e.g. in image- and terrain model analysis. Apart from the simple application of sets of different tools, many complex tasks require a more sophisticated design for storing and accessing data using databases (e.g. ArcHydro for hydrological data analysis). In planetary sciences, complex database-driven models are often required to efficiently analyse potential landings sites or store rover data, but also geologic mapping data can be efficiently stored and accessed using database models rather than stand-alone shapefiles. For landings-site analyses, relief and surface roughness estimates are two common concepts that are of particular interest and for both, a number of different definitions co-exist. We here present an advanced toolset for the analysis of image and terrain-model data with an emphasis on extraction of landing site characteristics using established criteria. We provide working examples and particularly focus on the concepts of terrain roughness as it is interpreted in geomorphology and engineering studies.

High-Density Association Study of 383 Candidate Genes for Volumetric BMD at the Femoral Neck and Lumbar Spine Among Older Men

PubMed Central

Yerges, Laura M.; Klei, Lambertus; Cauley, Jane A.; Roeder, Kathryn; Kammerer, Candace M.; Moffett, Susan P.; Ensrud, Kristine E.; Nestlerode, Cara S.; Marshall, Lynn M.; Hoffman, Andrew R.; Lewis, Cora; Lang, Thomas F.; Barrett-Connor, Elizabeth; Ferrell, Robert E.; Orwoll, Eric S.

2009-01-01

Genetics is a well-established but poorly understood determinant of BMD. Whereas some genetic variants may influence BMD throughout the body, others may be skeletal site specific. We initially screened for associations between 4608 tagging and potentially functional single nucleotide polymorphisms (SNPs) in 383 candidate genes and femoral neck and lumbar spine volumetric BMD (vBMD) measured from QCT scans among 862 community-dwelling white men ≥65 yr of age in the Osteoporotic Fractures in Men Study (MrOS). The most promising SNP associations (p < 0.01) were validated by genotyping an additional 1156 white men from MrOS. This analysis identified 8 SNPs in 6 genes (APC, DMP1, FGFR2, FLT1, HOXA, and PTN) that were associated with femoral neck vBMD and 13 SNPs in 7 genes (APC, BMPR1B, FOXC2, HOXA, IGFBP2, NFATC1, and SOST) that were associated with lumbar spine vBMD in both genotyping samples (p < 0.05). Although most associations were specific to one skeletal site, SNPs in the APC and HOXA gene regions were associated with both femoral neck and lumbar spine BMD. This analysis identifies several novel and robust genetic associations for volumetric BMD, and these findings in combination with other data suggest the presence of genetic loci for volumetric BMD that are at least to some extent skeletal-site specific. PMID:19453261

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

Dissanayake, V.U.; Hughes, J.; Hunter, J.C.

The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE boundmore » with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.« less

Genetic code expansion and live cell imaging reveal that Thr308 phosphorylation is irreplaceable and sufficient for Akt1 activity.

PubMed

Balasuriya, Nileeka; Kunkel, Maya T; Liu, Xuguang; Biggar, Kyle K; Li, Shawn S-C; Newton, Alexandra C; O'Donoghue, Patrick

2018-05-17

The proto-oncogene Akt/protein kinase B (PKB) is a pivotal signal transducer for growth and survival. Growth factor stimulation leads to Akt phosphorylation at two regulatory sites (Thr308, Ser473), acutely activating Akt signaling. Delineating the exact role of each regulatory site is, however, technically challenging and has remained elusive. Here, we used genetic code expansion to produce site-specifically phosphorylated Akt1 in order to dissect the contribution of each regulatory site to Akt1 activity. We achieved recombinant production of full length Akt1 containing site-specific pThr and pSer residues for the first time. Our analysis of Akt1 site-specifically phosphorylated at either or both sites revealed that phosphorylation at both sites increases the apparent catalytic rate 1500-fold relative to un-phosphorylated Akt1, an increase attributable primarily to phosphorylation at Thr308. Live imaging of COS7 cells confirmed that phosphorylation of Thr308, but not Ser473, is required for cellular activation of Akt. We found in vitro and in the cell that pThr308 function cannot be mimicked with acidic residues nor could unphosphorylated Thr308 be mimicked by an Ala mutation. An Akt1 variant with pSer308 achieved only partial enzymatic and cellular signaling activity, revealing a critical interaction between the γ-methyl group of pThr308 and Cys310 in the Akt1 active site. Thus, pThr308 is necessary and sufficient to stimulate Akt signaling in cells and the common use of phosphomimetics is not appropriate for studying the biology of Akt signaling. Our data also indicate that pThr308 should be regarded as the primary diagnostic marker of Akt activity. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Adam Warren | NREL

Science.gov Websites

, 2014 Wind Power Opportunities in St. Thomas, USVI: A Site-Specific Evaluation and Analysis. NREL , Canada B.S., Chemical Engineering, Texas A&M University, College Station, Texas Featured Publications Low Carbon Desalination: Status and Research, Development, and Demonstration Needs. Report of a

Analysis of Virginia-specific traffic data inputs for use with the mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2010-02-01

This study developed traffic inputs for use with the Guide for the Mechanistic-Empirical Design of New & Rehabilitated Pavement Structures (MEPDG) in Virginia and sought to determine if the predicted distresses showed differences between site-specifi...

Atom probe tomography of intermetallic phases and interfaces formed in dissimilar joining between Al alloys and steel

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

Lemmens, B.

While Si additions to Al are widely used to reduce the thickness of the brittle intermetallic seam formed at the interface during joining of Al alloys to steel, the underlying mechanisms are not clarified yet. The developed approach for the site specific atom probe tomography analysis revealed Si enrichments at grain and phase boundaries between the θ (Fe{sub 4}Al{sub 13}) and η (Fe{sub 2}Al{sub 5}) phase, up to about ten times that of the concentration in Al. The increase in Si concentration could play an important role for the growth kinetics of the intermetallic phases formed for example in hot-dipmore » aluminizing of steel. - Highlights: •Si additions to Al reduce thickness of intermetallic seam in joining with steel. •Approach developed for the site specific APT analysis of the intermetallic seam •Si enrichment at grain and phase boundaries possibly affects growth of intermetallics.« less

Global site-specific analysis of glycoprotein N-glycan processing.

PubMed

Cao, Liwei; Diedrich, Jolene K; Ma, Yuanhui; Wang, Nianshuang; Pauthner, Matthias; Park, Sung-Kyu Robin; Delahunty, Claire M; McLellan, Jason S; Burton, Dennis R; Yates, John R; Paulson, James C

2018-06-01

N-glycans contribute to the folding, stability and functions of the proteins they decorate. They are produced by transfer of the glycan precursor to the sequon Asn-X-Thr/Ser, followed by enzymatic trimming to a high-mannose-type core and sequential addition of monosaccharides to generate complex-type and hybrid glycans. This process, mediated by the concerted action of multiple enzymes, produces a mixture of related glycoforms at each glycosite, making analysis of glycosylation difficult. To address this analytical challenge, we developed a robust semiquantitative mass spectrometry (MS)-based method that determines the degree of glycan occupancy at each glycosite and the proportion of N-glycans processed from high-mannose type to complex type. It is applicable to virtually any glycoprotein, and a complete analysis can be conducted with 30 μg of protein. Here, we provide a detailed description of the method that includes procedures for (i) proteolytic digestion of glycoprotein(s) with specific and nonspecific proteases; (ii) denaturation of proteases by heating; (iii) sequential treatment of the glycopeptide mixture with two endoglycosidases, Endo H and PNGase F, to create unique mass signatures for the three glycosylation states; (iv) LC-MS/MS analysis; and (v) data analysis for identification and quantitation of peptides for the three glycosylation states. Full coverage of site-specific glycosylation of glycoproteins is achieved, with up to thousands of high-confidence spectra hits for each glycosite. The protocol can be performed by an experienced technician or student/postdoc with basic skills for proteomics experiments and takes ∼7 d to complete.

Analysis of the distributions of hourly NO2 concentrations contributing to annual average NO2 concentrations across the European monitoring network between 2000 and 2014

NASA Astrophysics Data System (ADS)

Malley, Christopher S.; von Schneidemesser, Erika; Moller, Sarah; Braban, Christine F.; Hicks, W. Kevin; Heal, Mathew R.

2018-03-01

Exposure to nitrogen dioxide (NO2) is associated with negative human health effects, both for short-term peak concentrations and from long-term exposure to a wider range of NO2 concentrations. For the latter, the European Union has established an air quality limit value of 40 µg m-3 as an annual average. However, factors such as proximity and strength of local emissions, atmospheric chemistry, and meteorological conditions mean that there is substantial variation in the hourly NO2 concentrations contributing to an annual average concentration. The aim of this analysis was to quantify the nature of this variation at thousands of monitoring sites across Europe through the calculation of a standard set of chemical climatology statistics. Specifically, at each monitoring site that satisfied data capture criteria for inclusion in this analysis, annual NO2 concentrations, as well as the percentage contribution from each month, hour of the day, and hourly NO2 concentrations divided into 5 µg m-3 bins were calculated. Across Europe, 2010-2014 average annual NO2 concentrations (NO2AA) exceeded the annual NO2 limit value at 8 % of > 2500 monitoring sites. The application of this chemical climatology approach showed that sites with distinct monthly, hour of day, and hourly NO2 concentration bin contributions to NO2AA were not grouped into specific regions of Europe, furthermore, within relatively small geographic regions there were sites with similar NO2AA, but with differences in these contributions. Specifically, at sites with highest NO2AA, there were generally similar contributions from across the year, but there were also differences in the contribution of peak vs. moderate hourly NO2 concentrations to NO2AA, and from different hours across the day. Trends between 2000 and 2014 for 259 sites indicate that, in general, the contribution to NO2AA from winter months has increased, as has the contribution from the rush-hour periods of the day, while the contribution from peak hourly NO2 concentrations has decreased. The variety of monthly, hour of day and hourly NO2 concentration bin contributions to NO2AA, across cities, countries and regions of Europe indicate that within relatively small geographic areas different interactions between emissions, atmospheric chemistry and meteorology produce variation in NO2AA and the conditions that produce it. Therefore, measures implemented to reduce NO2AA in one location may not be as effective in others. The development of strategies to reduce NO2AA for an area should therefore consider (i) the variation in monthly, hour of day, and hourly NO2 concentration bin contributions to NO2AA within that area; and (ii) how specific mitigation actions will affect variability in hourly NO2 concentrations.

Preliminary design package for prototype solar heating system

NASA Technical Reports Server (NTRS)

1978-01-01

A summary is given of the preliminary analysis and design activity on solar heating systems. The analysis was made without site specific data other than weather; therefore, the results indicate performance expected under these special conditions. Major items include system candidates, design approaches, trade studies and other special data required to evaluate the preliminary analysis and design. The program calls for the development and delivery of eight prototype solar heating and cooling systems for installation and operational test.

Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4.

PubMed

Lin, H; Rao, V B; Black, L W

1999-06-04

Bacteriophage DNA packaging results from an ATP-driven translocation of concatemeric DNA into the prohead by the phage terminase complexed with the portal vertex dodecamer of the prohead. Functional domains of the bacteriophage T4 terminase and portal gene 20 product (gp20) were determined by mutant analysis and sequence localization within the structural genes. Interaction regions of the portal vertex and large terminase subunit (gp17) were determined by genetic (terminase-portal intergenic suppressor mutations), biochemical (column retention of gp17 and inhibition of in vitro DNA packaging by gp20 peptides), and immunological (co-immunoprecipitation of polymerized gp20 peptide and gp17) studies. The specificity of the interaction was tested by means of a phage T4 HOC (highly antigenicoutercapsid protein) display system in which wild-type, cs20, and scrambled portal peptide sequences were displayed on the HOC protein of phage T4. Binding affinities of these recombinant phages as determined by the retention of these phages by a His-tag immobilized gp17 column, and by co-immunoprecipitation with purified terminase supported the specific nature of the portal protein and terminase interaction sites. In further support of specificity, a gp20 peptide corresponding to a portion of the identified site inhibited packaging whereas the scrambled sequence peptide did not block DNA packaging in vitro. The portal interaction site is localized to 28 residues in the central portion of the linear sequence of gp20 (524 residues). As judged by two pairs of intergenic portal-terminase suppressor mutations, two separate regions of the terminase large subunit gp17 (central and COOH-terminal) interact through hydrophobic contacts at the portal site. Although the terminase apparently interacts with this gp20 portal peptide, polyclonal antibody against the portal peptide appears unable to access it in the native structure, suggesting intimate association of gp20 and gp17 possibly internalizes terminase regions within the portal in the packasome complex. Both similarities and differences are seen in comparison to analogous sites which have been identified in phages T3 and lambda. Copyright 1999 Academic Press.

78 FR 59012 - Environmental Management Site-Specific Advisory Board Chairs

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-25

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board Chairs AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB) Chairs. The Federal Advisory Committee Act (Pub... and site management in the areas of environmental restoration, waste management, and related...

76 FR 30027 - Land Disposal Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste Treated by U.S. Ecology.... Ecology Nevada in Beatty, Nevada and withdrew an existing site- specific treatment variance issued to... 268.44(o)) by granting a site-specific treatment variance to U.S. Ecology Nevada in Beatty, Nevada and...

3D TOCSY-HSQC NMR for metabolic flux analysis using non-uniform sampling

DOE PAGES

Reardon, Patrick N.; Marean-Reardon, Carrie L.; Bukovec, Melanie A.; ...

2016-02-05

13C-Metabolic Flux Analysis ( 13C-MFA) is rapidly being recognized as the authoritative method for determining fluxes through metabolic networks. Site-specific 13C enrichment information obtained using NMR spectroscopy is a valuable input for 13C-MFA experiments. Chemical shift overlaps in the 1D or 2D NMR experiments typically used for 13C-MFA frequently hinder assignment and quantitation of site-specific 13C enrichment. Here we propose the use of a 3D TOCSY-HSQC experiment for 13C-MFA. We employ Non-Uniform Sampling (NUS) to reduce the acquisition time of the experiment to a few hours, making it practical for use in 13C-MFA experiments. Our data show that the NUSmore » experiment is linear and quantitative. Identification of metabolites in complex mixtures, such as a biomass hydrolysate, is simplified by virtue of the 13C chemical shift obtained in the experiment. In addition, the experiment reports 13C-labeling information that reveals the position specific labeling of subsets of isotopomers. As a result, the information provided by this technique will enable more accurate estimation of metabolic fluxes in larger metabolic networks.« less

Detection of DNA double-strand breaks and chromosome translocations using ligation-mediated PCR and inverse PCR.

PubMed

Singh, Sheetal; Shih, Shyh-Jen; Vaughan, Andrew T M

2014-01-01

Current techniques for examining the global creation and repair of DNA double-strand breaks are restricted in their sensitivity, and such techniques mask any site-dependent variations in breakage and repair rate or fidelity. We present here a system for analyzing the fate of documented DNA breaks, using the MLL gene as an example, through application of ligation-mediated PCR. Here, a simple asymmetric double-stranded DNA adapter molecule is ligated to experimentally induced DNA breaks and subjected to seminested PCR using adapter- and gene-specific primers. The rate of appearance and loss of specific PCR products allows detection of both the break and its repair. Using the additional technique of inverse PCR, the presence of misrepaired products (translocations) can be detected at the same site, providing information on the fidelity of the ligation reaction in intact cells. Such techniques may be adapted for the analysis of DNA breaks and rearrangements introduced into any identifiable genomic location. We have also applied parallel sequencing for the high-throughput analysis of inverse PCR products to facilitate the unbiased recording of all rearrangements located at a specific genomic location.

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

PubMed Central

Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

2015-01-01

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

PubMed Central

Jablonski, Joseph; Clementz, Mark; Ryan, Kevin; Valente, Susana T.

2014-01-01

The 3’ end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3’ end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5’ cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3’ end processing of HIV-1 mRNAs. PMID:24835792

Identification of Mitosis-Specific Phosphorylation in Mitotic Chromosome-Associated Proteins.

PubMed

Ohta, Shinya; Kimura, Michiko; Takagi, Shunsuke; Toramoto, Iyo; Ishihama, Yasushi

2016-09-02

During mitosis, phosphorylation of chromosome-associated proteins is a key regulatory mechanism. Mass spectrometry has been successfully applied to determine the complete protein composition of mitotic chromosomes, but not to identify post-translational modifications. Here, we quantitatively compared the phosphoproteome of isolated mitotic chromosomes with that of chromosomes in nonsynchronized cells. We identified 4274 total phosphorylation sites and 350 mitosis-specific phosphorylation sites in mitotic chromosome-associated proteins. Significant mitosis-specific phosphorylation in centromere/kinetochore proteins was detected, although the chromosomal association of these proteins did not change throughout the cell cycle. This mitosis-specific phosphorylation might play a key role in regulation of mitosis. Further analysis revealed strong dependency of phosphorylation dynamics on kinase consensus patterns, thus linking the identified phosphorylation sites to known key mitotic kinases. Remarkably, chromosomal axial proteins such as non-SMC subunits of condensin, TopoIIα, and Kif4A, together with the chromosomal periphery protein Ki67 involved in the establishment of the mitotic chromosomal structure, demonstrated high phosphorylation during mitosis. These findings suggest a novel mechanism for regulation of chromosome restructuring in mitosis via protein phosphorylation. Our study generated a large quantitative database on protein phosphorylation in mitotic and nonmitotic chromosomes, thus providing insights into the dynamics of chromatin protein phosphorylation at mitosis onset.

Precipitation Depth-Duration-Frequency Analysis for the Nevada National Security Site and Surrounding Areas

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

Chen, Li; Miller, Julianne J.

Accurate precipitation frequency data are important for Environmental Management Soils Activities on the Nevada National Security Site (NNSS). These data are important for environmental assessments performed for regulatory closure of Soils Corrective Action Unit (CAU) Sites, as well as engineering mitigation designs and post-closure monitoring strategies to assess and minimize potential contaminant migration from Soils CAU Sites. Although the National Oceanic and Atmospheric Administration (NOAA) Atlas 14 (Bonnin et al., 2011) provides precipitation frequency data for the NNSS area, the NNSS-specific observed precipitation data were not consistent with the NOAA Atlas 14 predicted data. This is primarily due to themore » NOAA Atlas 14 products being produced from analyses without including the approximately 30 NNSS precipitation gage records, several of which approach or exceed 50 year of record. Therefore, a study of precipitation frequency that incorporated the NNSS precipitation gage records into the NOAA Atlas 14 dataset, was performed specifically for the NNSS to derive more accurate site-specific precipitation data products. Precipitation frequency information, such as the depth-duration-frequency (DDF) relationships, are required to generate synthetic standard design storm hydrographs and assess actual precipitation events. In this study, the actual long-term NNSS precipitation gage records, some of which are the longest gage records in southern and central Nevada, were analyzed to allow for more accurate precipitation DDF estimates to be developed for the NNSS. Gridded maps of precipitation frequency for the NNSS and surrounding areas were then produced.« less

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

PubMed

Liu, C Tony; Layfield, Joshua P; Stewart, Robert J; French, Jarrod B; Hanoian, Philip; Asbury, John B; Hammes-Schiffer, Sharon; Benkovic, Stephen J

2014-07-23

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR.

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

PubMed Central

2015-01-01

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and 13C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR. PMID:24977791

Analysis of chorioallantoic membranes to assess PCB accumulation in American alligators and Loggerhead sea turtles from the coast of South Carolina

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

Cobb, G.P.; Wood, P.D.; O`Quinn, M.

1995-12-31

Investigation of contaminant burdens in threatened and endangered species is difficult due to the small number of samples that can be collected. Many samples can be collected if the sampling methods are non-lethal and more specifically non-invasive. Analysis of chorioallantoic membranes is demonstrated for American alligators and Loggerhead sea turtles. Significant differences were found in PCB, uptake by alligators from the Ashepoo-Combahee-Edisto Basin reference site and a contaminated site in Winyah Bay. Intrasite and intersite differences in uptake and distribution of PCB homologues were noted. These data will be discussed as they relate to egg viability and embryo development.

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

PubMed

Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

2008-06-01

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 is an Inorganic Pyrophosphatase+

PubMed Central

Huang, Hua; Yury, Patskovsky; Toro, Rafael; Farelli, Jeremiah D.; Pandya, Chetanya; Almo, Steven C.; Allen, Karen N.; Dunaway-Mariano, Debra

2012-01-01

The explosion of protein sequence information requires that current strategies for function assignment must evolve to complement experimental approaches with computationally-based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown Haloalkanoate Dehalogenase superfamily member BT2127 (Uniprot accession # Q8A5V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics/structure/mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with kcat/Km value for pyrophosphate of ∼1 × 105 M−1 s−1), together with the gene context, supports the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of the wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure guided site directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. Based on this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172 and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue β-phosphoglucomutase control the leaving group size (phosphate vs. glucose-phosphate) and the position of the Asp acid/base in the open vs. closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases. PMID:21894910

Economic Analysis Case Studies of Battery Energy Storage with SAM

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

DiOrio, Nicholas; Dobos, Aron; Janzou, Steven

2015-11-01

Interest in energy storage has continued to increase as states like California have introduced mandates and subsidies to spur adoption. This energy storage includes customer sited behind-the-meter storage coupled with photovoltaics (PV). This paper presents case study results from California and Tennessee, which were performed to assess the economic benefit of customer-installed systems. Different dispatch strategies, including manual scheduling and automated peak-shaving were explored to determine ideal ways to use the storage system to increase the system value and mitigate demand charges. Incentives, complex electric tariffs, and site specific load and PV data were used to perform detailed analysis. Themore » analysis was performed using the free, publically available System Advisor Model (SAM) tool. We find that installation of photovoltaics with a lithium-ion battery system priced at $300/kWh in Los Angeles under a high demand charge utility rate structure and dispatched using perfect day-ahead forecasting yields a positive net-present value, while all other scenarios cost the customer more than the savings accrued. Different dispatch strategies, including manual scheduling and automated peak-shaving were explored to determine ideal ways to use the storage system to increase the system value and mitigate demand charges. Incentives, complex electric tariffs, and site specific load and PV data were used to perform detailed analysis. The analysis was performed using the free, publically available System Advisor Model (SAM) tool. We find that installation of photovoltaics with a lithium-ion battery system priced at $300/kWh in Los Angeles under a high demand charge utility rate structure and dispatched using perfect day-ahead forecasting yields a positive net-present value, while all other scenarios cost the customer more than the savings accrued.« less

Regional-specific Stochastic Simulation of Spatially-distributed Ground-motion Time Histories using Wavelet Packet Analysis

NASA Astrophysics Data System (ADS)

Huang, D.; Wang, G.

2014-12-01

Stochastic simulation of spatially distributed ground-motion time histories is important for performance-based earthquake design of geographically distributed systems. In this study, we develop a novel technique to stochastically simulate regionalized ground-motion time histories using wavelet packet analysis. First, a transient acceleration time history is characterized by wavelet-packet parameters proposed by Yamamoto and Baker (2013). The wavelet-packet parameters fully characterize ground-motion time histories in terms of energy content, time- frequency-domain characteristics and time-frequency nonstationarity. This study further investigates the spatial cross-correlations of wavelet-packet parameters based on geostatistical analysis of 1500 regionalized ground motion data from eight well-recorded earthquakes in California, Mexico, Japan and Taiwan. The linear model of coregionalization (LMC) is used to develop a permissible spatial cross-correlation model for each parameter group. The geostatistical analysis of ground-motion data from different regions reveals significant dependence of the LMC structure on regional site conditions, which can be characterized by the correlation range of Vs30 in each region. In general, the spatial correlation and cross-correlation of wavelet-packet parameters are stronger if the site condition is more homogeneous. Using the regional-specific spatial cross-correlation model and cokriging technique, wavelet packet parameters at unmeasured locations can be best estimated, and regionalized ground-motion time histories can be synthesized. Case studies and blind tests demonstrated that the simulated ground motions generally agree well with the actual recorded data, if the influence of regional-site conditions is considered. The developed method has great potential to be used in computational-based seismic analysis and loss estimation in a regional scale.

Comparison of unmanned aircraft systems (UAS) to LiDAR for streambank erosion measurement at the site-specific and river network scales

NASA Astrophysics Data System (ADS)

Hamshaw, S. D.; Dewoolkar, M. M.; Rizzo, D.; ONeil-Dunne, J.; Frolik, J.

2016-12-01

Measurement of rates and extent of streambank erosion along river corridors is an important component of many catchment studies and necessary for engineering projects such as river restoration, hazard assessment, and total maximum daily load (TMDL) development. A variety of methods have been developed to quantify streambank erosion, including bank pins, ground surveys, photogrammetry, LiDAR, and analytical models. However, these methods are not only resource intensive, but many are feasible and appropriate only for site-specific studies and not practical for erosion estimates at larger scales. Recent advancements in unmanned aircraft systems (UAS) and photogrammetry software provide capabilities for more rapid and economical quantification of streambank erosion and deposition at multiple scales (from site-specific to river network). At the site-specific scale, the capability of UAS to quantify streambank erosion was compared to terrestrial laser scanning (TLS) and RTK-GPS ground survey and assessed at seven streambank monitoring sites in central Vermont. Across all sites, the UAS-derived bank topography had mean errors of 0.21 m compared to TLS and GPS data. Highest accuracies were achieved in early spring conditions where mean errors approached 10 cm. The cross sectional area of bank erosion at a typical, vegetated streambank site was found to be reliably calculated within 10% of actual for erosion areas greater than 3.5 m2. At the river network-level scale, 20 km of river corridor along the New Haven, Winooski, and Mad Rivers was flown on multiple dates with UAS and used to generate digital elevation models (DEMs) that were then compared for change detection analysis. Airborne LiDAR data collected prior to UAS surveys was also compared to UAS data to determine multi-year rates of bank erosion. UAS-based photogrammetry for generation of fine scale topographic data shows promise for the monitoring of streambank erosion both at the individual site scale and river-network scale in areas that are not densely covered with vegetation year-round.

[Insect cholinesterases and irreversible inhibitors. Statistical treatment of the data].

PubMed

Moralev, S N

2010-01-01

The data on sensitivity of cholinesterases (ChE) of different insects to reversible inhibitors, as well as the data on physico-chemical parameters of amino acids constituting their active centers, were treated by factor analysis and juxtaposed. It is shown that both these characteristics are related to taxonomical belonging of insects. It is revealed the "material substrate" of the factors determining inhibitor action specificity, which are specific sites in ChE active center.

Soil load above Hanford waste storage tanks (2 volumes)

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

Pianka, E.W.

1995-01-25

This document is a compilation of work performed as part of the Dome Load Control Project in 1994. Section 2 contains the calculations of the weight of the soil over the tank dome for each of the 75-feet-diameter waste-storage tanks located at the Hanford Site. The chosen soil specific weight and soil depth measured at the apex of the dome crown are the same as those used in the primary analysis that qualified the design. Section 3 provides reference dimensions for each of the tank farm sites. The reference dimensions spatially orient the tanks and provide an outer diameter formore » each tank. Section 4 summarizes the available soil surface elevation data. It also provides examples of the calculations performed to establish the present soil elevation estimates. The survey data and other data sources from which the elevation data has been obtained are printed separately in Volume 2 of this Supporting Document. Section 5 contains tables that provide an overall summary of the present status of dome loads. Tables summarizing the load state corresponding to the soil depth and soil specific weight for the original qualification analysis, the gravity load requalification for soil depth and soil specific weight greater than the expected actual values, and a best estimate condition of soil depth and specific weight are presented for the Double-Shell Tanks. For the Single-Shell Tanks, only the original qualification analysis is available; thus, the tabulated results are for this case only. Section 6 provides a brief overview of past analysis and testing results that given an indication of the load capacity of the waste storage tanks that corresponds to a condition approaching ultimate failure of the tank. 31 refs.« less

Detection of cervical lesions by multivariate analysis of diffuse reflectance spectra: a clinical study.

PubMed

Prabitha, Vasumathi Gopala; Suchetha, Sambasivan; Jayanthi, Jayaraj Lalitha; Baiju, Kamalasanan Vijayakumary; Rema, Prabhakaran; Anuraj, Koyippurath; Mathews, Anita; Sebastian, Paul; Subhash, Narayanan

2016-01-01

Diffuse reflectance (DR) spectroscopy is a non-invasive, real-time, and cost-effective tool for early detection of malignant changes in squamous epithelial tissues. The present study aims to evaluate the diagnostic power of diffuse reflectance spectroscopy for non-invasive discrimination of cervical lesions in vivo. A clinical trial was carried out on 48 sites in 34 patients by recording DR spectra using a point-monitoring device with white light illumination. The acquired data were analyzed and classified using multivariate statistical analysis based on principal component analysis (PCA) and linear discriminant analysis (LDA). Diagnostic accuracies were validated using random number generators. The receiver operating characteristic (ROC) curves were plotted for evaluating the discriminating power of the proposed statistical technique. An algorithm was developed and used to classify non-diseased (normal) from diseased sites (abnormal) with a sensitivity of 72 % and specificity of 87 %. While low-grade squamous intraepithelial lesion (LSIL) could be discriminated from normal with a sensitivity of 56 % and specificity of 80 %, and high-grade squamous intraepithelial lesion (HSIL) from normal with a sensitivity of 89 % and specificity of 97 %, LSIL could be discriminated from HSIL with 100 % sensitivity and specificity. The areas under the ROC curves were 0.993 (95 % confidence interval (CI) 0.0 to 1) and 1 (95 % CI 1) for the discrimination of HSIL from normal and HSIL from LSIL, respectively. The results of the study show that DR spectroscopy could be used along with multivariate analytical techniques as a non-invasive technique to monitor cervical disease status in real time.

Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts

PubMed Central

Ishii, Genichiro; Aoyagi, Kazuhiko; Sasaki, Hiroki; Ochiai, Atsushi

2015-01-01

Background Fibroblasts are the principal stromal cells that exist in whole organs and play vital roles in many biological processes. Although the functional diversity of fibroblasts has been estimated, a comprehensive analysis of fibroblasts from the whole body has not been performed and their transcriptional diversity has not been sufficiently explored. The aim of this study was to elucidate the transcriptional diversity of human fibroblasts within the whole body. Methods Global gene expression analysis was performed on 63 human primary fibroblasts from 13 organs. Of these, 32 fibroblasts from gastrointestinal organs (gastrointestinal fibroblasts: GIFs) were obtained from a pair of 2 anatomical sites: the submucosal layer (submucosal fibroblasts: SMFs) and the subperitoneal layer (subperitoneal fibroblasts: SPFs). Using hierarchical clustering analysis, we elucidated identifiable subgroups of fibroblasts and analyzed the transcriptional character of each subgroup. Results In unsupervised clustering, 2 major clusters that separate GIFs and non-GIFs were observed. Organ- and anatomical site-dependent clusters within GIFs were also observed. The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling. Conclusions GIFs are characteristic fibroblasts with specific gene expressions from transcriptional regulation, signaling ligands, and extracellular matrix remodeling related genes. In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered. These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract. PMID:26046848

Development of a New Data Tool for Computing Launch and Landing Availability with Respect to Surface Weather

NASA Technical Reports Server (NTRS)

Burns, K. Lee; Altino, Karen

2008-01-01

The Marshall Space Flight Center Natural Environments Branch has a long history of expertise in the modeling and computation of statistical launch availabilities with respect to weather conditions. Their existing data analysis product, the Atmospheric Parametric Risk Assessment (APRA) tool, computes launch availability given an input set of vehicle hardware and/or operational weather constraints by calculating the climatological probability of exceeding the specified constraint limits, APRA has been used extensively to provide the Space Shuttle program the ability to estimate impacts that various proposed design modifications would have to overall launch availability. The model accounts for both seasonal and diurnal variability at a single geographic location and provides output probabilities for a single arbitrary launch attempt. Recently, the Shuttle program has shown interest in having additional capabilities added to the APRA model, including analysis of humidity parameters, inclusion of landing site weather to produce landing availability, and concurrent analysis of multiple sites, to assist in operational landing site selection. In addition, the Constellation program has also expressed interest in the APRA tool, and has requested several additional capabilities to address some Constellation-specific issues, both in the specification and verification of design requirements and in the development of operations concepts. The combined scope of the requested capability enhancements suggests an evolution of the model beyond a simple revision process. Development has begun for a new data analysis tool that will satisfy the requests of both programs. This new tool, Probabilities of Atmospheric Conditions and Environmental Risk (PACER), will provide greater flexibility and significantly enhanced functionality compared to the currently existing tool.

Qualitative data collection and analysis methods: the INSTINCT trial.

PubMed

Meurer, William J; Frederiksen, Shirley M; Majersik, Jennifer J; Zhang, Lingling; Sandretto, Annette; Scott, Phillip A

2007-11-01

Patient care practices often lag behind current scientific evidence and professional guidelines. The failure of such knowledge translation (KT) efforts may reflect inadequate assessment and management of specific barriers confronting both physicians and patients at the point of treatment level. Effective KT in this setting may benefit from the use of qualitative methods to identify and overcome these barriers. Qualitative methodology allows in-depth exploration of the barriers involved in adopting practice change and has been infrequently used in emergency medicine research. The authors describe the methodology for qualitative analysis within the INcreasing Stroke Treatment through INteractive behavioral Change Tactics (INSTINCT) trial. This includes processes for valid data collection and reliable analysis of the textual data from focus group and interview transcripts. INSTINCT is a 24-hospital, randomized, controlled study that is designed to evaluate a system-based barrier assessment and interactive educational intervention to increase appropriate tissue plasminogen activator (tPA) use in ischemic stroke. Intervention hospitals undergo baseline barrier assessment using both qualitative as well as quantitative (survey) techniques. Investigators obtain data on local barriers to tPA use, as well as information on local attitudes, knowledge, and beliefs regarding acute stroke treatment. Targeted groups at each site include emergency physicians, emergency nurses, neurologists, radiologists, and hospital administrators. Transcript analysis using NVivo7 with a predefined barrier taxonomy is described. This will provide both qualitative insight on thrombolytic use and importance of specific barrier types for each site. The qualitative findings subsequently direct the form of professional education efforts and system interventions at treatment sites.

Site-Specific Analyses for Demonstrating Compliance with 10 CFR 61 Performance Objectives - 12179

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

Grossman, C.J.; Esh, D.W.; Yadav, P.

2012-07-01

The U.S. Nuclear Regulatory Commission (NRC) is proposing to amend its regulations at 10 CFR Part 61 to require low-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance with the performance objectives in Subpart C. The amendments would require licensees to conduct site-specific analyses for protection of the public and inadvertent intruders as well as analyses for long-lived waste. The amendments would ensure protection of public health and safety, while providing flexibility to demonstrate compliance with the performance objectives, for current and potential future waste streams. NRC staff intends to submit proposed rule language and associated regulatorymore » basis to the Commission for its approval in early 2012. The NRC staff also intends to develop associated guidance to accompany any proposed amendments. The guidance is intended to supplement existing low-level radioactive waste guidance on issues pertinent to conducting site-specific analyses to demonstrate compliance with the performance objectives. The guidance will facilitate implementation of the proposed amendments by licensees and assist competent regulatory authorities in reviewing the site-specific analyses. Specifically, the guidance provides staff recommendations on general considerations for the site-specific analyses, modeling issues for assessments to demonstrate compliance with the performance objectives including the performance assessment, intruder assessment, stability assessment, and analyses for long-lived waste. This paper describes the technical basis for changes to the rule language and the proposed guidance associated with implementation of the rule language. The NRC staff, per Commission direction, intends to propose amendments to 10 CFR Part 61 to require licensees to conduct site-specific analyses to demonstrate compliance with performance objectives for the protection of public health and the environment. The amendments would require a performance assessment to demonstrate protection of the general population from releases of radioactivity, an assessment to demonstrate protection of a potential inadvertent intruder, and a long-term analysis to assess how the design of the facility considers the potential radiological impacts associated with disposal of long-lived waste streams. Concurrently, the NRC staff intends to propose associated guidance to facilitate the implementation of the requirements to conduct site-specific analyses. In proposing these amendments to the regulation and associated guidance, the NRC staff has conducted extensive public outreach since 2009 including three public meetings and four briefings of the NRC's Advisory Committee on Reactor Safeguards. The NRC staff plans to submit the proposed amendments to the regulations to the Commission in early 2012. Subsequently, the proposed amendments and associated guidance would be published in the Federal Register for public comment pending approval of the proposed amendments to the regulations by the Commission. Following the public comment period, NRC staff plans to address public comments and revise, as necessary, the regulations and associated guidance before publishing a final rule, which is anticipated in 2013. (authors)« less

77 FR 59598 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 9404 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-02

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 61711 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-06

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 56526 - Environmental Management Site-Specific Advisory Board, Portsmouth

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-16

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Portsmouth AGENCY... Initiative Workshop of the Environmental Management Site-Specific Advisory Board (EM SSAB), Portsmouth. The... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 66074 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 54600 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-08

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

76 FR 5147 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-28

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

75 FR 24686 - Environmental Management Site-Specific Advisory Board, Paducah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-05

... DEPARTMENT OF ENERGY Environmental Management Site-Specific Advisory Board, Paducah AGENCY... Environmental Management Site-Specific Advisory Board (EM SSAB), Paducah. The Federal Advisory Committee Act... recommendations to DOE-EM and site management in the areas of environmental restoration, waste management and...

Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

PubMed Central

Chandler, Kevin Brown; Pompach, Petr; Goldman, Radoslav

2013-01-01

Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something which detached N-glycan and de-glycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy which takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false-discovery-rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at false-discovery-rate 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at false-discovery-rate 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http://edwardslab.bmcb.georgetown.edu/GPS. PMID:23829323

Critical review of decision support tools for sustainability assessment of site remediation options.

PubMed

Huysegoms, Lies; Cappuyns, Valérie

2017-07-01

In Europe alone, there are more than 2,5 million potentially contaminated sites of which 14% are expected to require remediation. Contaminated soil and groundwater can cause damage to human health as well as to valuable ecosystems. Globally more attention has been paid to this problem of soil contamination in the past decades. For example, more than 58 000 sites have been remediated in Europe between 2006 and 2011. Together with this increase in remediation projects there has been a surge in the development of new remediation technologies and decision support tools to be able to match every site and its specific characteristics to the best possible remediation alternative. In the past years the development of decision support tools (DST) has evolved in a more sustainable direction. Several DSTs added the claim not only to denote effective or technologically and economically feasible remediation alternatives but also to point out the more or most sustainable remediation alternatives. These trends in the evaluation of site remediation options left users with a confusing clew of possibly applicable tools to assist them in decision making for contaminated site remediation. This review provides a structured overview on the extent decision support tools for contaminated site remediation, that claim to assist in choosing the most sustainable remediation alternative, actually include the different elements of sustainability proposed in our assessment framework. The review contains an in-depth analysis of thirteen tools specifically developed to assess the sustainability of site remediation alternatives. This analysis is based on six criteria derived from the definition of sustainable development of the Brundtland report. The six criteria were concretized by using the three pillars of sustainability, applied to site remediation according to the SuRF-UK framework, two criteria derived from Life Cycle Assessment and Cost-Benefit Analysis, and an 'User friendly' criterion. These elements come together in a framework, drafted for this study, containing six criteria covering the environmental, economic, social, time, uncertainty aspects and user friendliness of a sustainable site remediation. The main remarks uncovered by this review are the imbalance of used indicators still expressing a strong preference for the environmental aspect at the expense of the economic and social aspects of sustainability, the lack of consistency in the terminology used within the field and the failure in adapting released tools to recent legislation or scientific advancements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stonehenge's Greater Cursus

NASA Astrophysics Data System (ADS)

Burley, Paul; Mooers, Howard D.

2016-01-01

Archaeological investigations have emphasized relationships between solar and lunar phenomena and architectural features of prehistoric sites located on the Stonehenge ritual landscape. However, no over-riding landscape design has been identified to explain the purpose of placing hundreds of Neolithic through Iron Age burial sites upon the landscape. Our research and analysis shows the mid-4th millennium BC (mid-Neolithic) landscape represents an 'above, so below' cosmo-geographical relationship. Type, shape, size and orientation of specific elements (such as long barrows, henges, cursus and topography) created a hierotopy representing the Winter Hexagon asterism, Milky Way, ecliptic and other stellar features. The resulting pattern of ritual sites represents translocation of the astronomical Otherworld - the Spirit World - onto the plain. Results of the analysis create a new paradigm of purpose for the built landscape circa 3500 BC, and identifies the reason why Stonehenge is located where it is with respect to other contemorary monuments.

Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12.

PubMed

Jiang, Xukai; Li, Wen; Chen, Guanjun; Wang, Lushan

2017-02-27

The temperature dependence of enzyme catalysis is highly debated. Specifically, how high temperatures induce enzyme inactivation has broad implications for both fundamental and applied science. Here, we explored the mechanism of the reversible thermal inactivation in glycoside hydrolase family 12 (GH12) using comparative molecular dynamics simulations. First, we investigated the distribution of structural flexibility over the enzyme and found that the active site was the general thermal-sensitive region in GH12 cellulases. The dynamic perturbation of the active site before enzyme denaturation was explored through principal-component analysis, which indicated that variations in the collective motion and conformational ensemble of the active site may precisely correspond to enzyme transition from its active form to the inactive form. Furthermore, the degree of dynamic perturbation of the active site was found to be negatively correlated with the melting temperatures of GH12 enzymes, further proving the importance of the dynamic stability of the active site. Additionally, analysis of the residue-interaction network revealed that the active site in thermophilic enzyme was capable of forming additional contacts with other amino acids than those observed in the mesophilic enzyme. These interactions are likely the key mechanisms underlying the differences in rigidity of the active site. These findings provide further biophysical insights into the reversible thermal inactivation of enzymes and potential applications in future protein engineering.