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Sample records for restriction site map

  1. Comparison of canine parvovirus with mink enteritis virus by restriction site mapping.

    PubMed Central

    McMaster, G K; Tratschin, J D; Siegl, G

    1981-01-01

    The genomes of canine parvovirus and mink enteritis virus were compared by restriction enzyme analysis of their replicative-form DNAs. Of 79 mapped sites, 68, or 86%, were found to be common for both types of DNA, indicating that canine parvovirus and mink enteritis virus are closely related viruses. Whether they evolved from a common precursor or whether canine parvovirus is derived from mink enteritis virus, however, cannot be deduced from our present data. Images PMID:6264109

  2. Isolation and restriction site maps of the genes encoding five Mycobacterium tuberculosis proteins.

    PubMed

    Shinnick, T M; Krat, C; Schadow, S

    1987-07-01

    A series of recombinant phage expressing five Mycobacterium tuberculosis antigens were isolated. Restriction maps for these antigens were deduced, and the size of the expressed proteins was determined. PMID:3036711

  3. Isolation and restriction site maps of the genes encoding five Mycobacterium tuberculosis proteins.

    PubMed Central

    Shinnick, T M; Krat, C; Schadow, S

    1987-01-01

    A series of recombinant phage expressing five Mycobacterium tuberculosis antigens were isolated. Restriction maps for these antigens were deduced, and the size of the expressed proteins was determined. Images PMID:3036711

  4. Problem-Solving Test: Restriction Endonuclease Mapping

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2011-01-01

    The term "restriction endonuclease mapping" covers a number of related techniques used to identify specific restriction enzyme recognition sites on small DNA molecules. A method for restriction endonuclease mapping of a 1,000-basepair (bp)-long DNA molecule is described in the fictitious experiment of this test. The most important fact needed to…

  5. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    PubMed Central

    2012-01-01

    Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

  6. A User-Friendly Method for Teaching Restriction Enzyme Mapping.

    ERIC Educational Resources Information Center

    Ehrman, Patrick

    1990-01-01

    Presented is a teaching progression that enhances learning through low-cost, manipulative transparencies. Discussed is instruction about restriction enzymes, plasmids, cutting plasmids, plasmid maps, recording data, and mapping restriction sites. Mapping wheels for student use is included. (CW)

  7. Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing.

    PubMed

    Campbell, Nathan R; LaPatra, Scott E; Overturf, Ken; Towner, Richard; Narum, Shawn R

    2014-12-01

    Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site-associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

  8. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  9. Characterization of Leptospira isolates from serovar hardjo by ribotyping, arbitrarily primed PCR, and mapped restriction site polymorphisms.

    PubMed Central

    Perolat, P; Merien, F; Ellis, W A; Baranton, G

    1994-01-01

    Leptospira serovar hardjo isolates of the hardjoprajitno and hardjobovis genotypes were characterized by ribotyping, arbitrarily primed PCR (AP-PCR) fingerprinting, and the study of mapped restriction site polymorphisms (MRSPs) in rrs and rrl genes. After restriction of chromosomal DNA with BglII, EcoRI, or HindIII, each genotype was individualized with a distinct ribotype. The fingerprints produced by AP-PCR with seven primers clearly separated the two groups; primers KF and RSP produced species-specific products which assigned hardjoprajitno and hardjobovis isolates to the species L. interrogans sensu stricto and L. borgpetersenii, respectively. Furthermore, AP-PCR fingerprints gave evidence of a considerable genomic heterogeneity at the strain level among the hardjobovis group. Conversely, the hardjoprajitno group was homogeneous. MRSP profiles in ribosomal genes indicated that hardjoprajitno and hardjobovis isolates belonged to L. interrogans MRSP group B and L. borgpetersenii group C, respectively. AP-PCR and determination of MRSPs in ribosomal genes proved to be quick and reliable methods for typing Leptospira strains and for studying intraspecific population structures. Images PMID:7989548

  10. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.

    PubMed

    Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

    2011-05-01

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne. PMID:21344184

  11. Association Mapping of Disease Resistance Traits in Rainbow Trout Using Restriction Site Associated DNA Sequencing

    PubMed Central

    Campbell, Nathan R.; LaPatra, Scott E.; Overturf, Ken; Towner, Richard; Narum, Shawn R.

    2014-01-01

    Recent advances in genotyping-by-sequencing have enabled genome-wide association studies in nonmodel species including those in aquaculture programs. As with other aquaculture species, rainbow trout and steelhead (Oncorhynchus mykiss) are susceptible to disease and outbreaks can lead to significant losses. Fish culturists have therefore been pursuing strategies to prevent losses to common pathogens such as Flavobacterium psychrophilum (the etiological agent for bacterial cold water disease [CWD]) and infectious hematopoietic necrosis virus (IHNV) by adjusting feed formulations, vaccine development, and selective breeding. However, discovery of genetic markers linked to disease resistance offers the potential to use marker-assisted selection to increase resistance and reduce outbreaks. For this study we sampled juvenile fish from 40 families from 2-yr classes that either survived or died after controlled exposure to either CWD or IHNV. Restriction site−associated DNA sequencing produced 4661 polymorphic single-nucleotide polymorphism loci after strict filtering. Genotypes from individual survivors and mortalities were then used to test for association between disease resistance and genotype at each locus using the program TASSEL. After we accounted for kinship and stratification of the samples, tests revealed 12 single-nucleotide polymorphism markers that were highly associated with resistance to CWD and 19 markers associated with resistance to IHNV. These markers are candidates for further investigation and are expected to be useful for marker assisted selection in future broodstock selection for various aquaculture programs. PMID:25354781

  12. Restriction Enzyme Mapping: A Simple Student Practical.

    ERIC Educational Resources Information Center

    Higgins, Stephen J.; And Others

    1990-01-01

    An experiment that uses the recombinant plasmid pX1108 to illustrate restriction mapping is described. The experiment involves three restriction enzymes and employs single and double restriction enzyme digestions. A list of needed materials, procedures, safety precautions, results, and discussion are included. (KR)

  13. Near BPS skyrmions and restricted harmonic maps

    NASA Astrophysics Data System (ADS)

    Speight, J. M.

    2015-06-01

    Motivated by a class of near BPS Skyrme models introduced by Adam, Sánchez-Guillén and Wereszczyński, the following variant of the harmonic map problem is introduced: a map φ :(M, g) →(N, h) between Riemannian manifolds is restricted harmonic if it locally extremizes E2 on its SDiff(M) orbit, where SDiff(M) denotes the group of volume preserving diffeomorphisms of (M, g), and E2 denotes the Dirichlet energy. It is conjectured that near BPS skyrmions tend to restricted harmonic maps in the BPS limit. It is shown that φ is restricted harmonic if and only if φ∗ h has exact divergence, and a linear stability theory of restricted harmonic maps is developed, from which it follows that all weakly conformal maps are stable restricted harmonic. Examples of restricted harmonic maps in every degree class R3 → SU(2) and R2 →S2 are constructed. It is shown that the axially symmetric BPS skyrmions on which all previous analytic studies of near BPS Skyrme models have been based, are not restricted harmonic, casting doubt on the phenomenological predictions of such studies. The problem of minimizing E2 for φ :Rk → N over all linear volume preserving diffeomorphisms is solved explicitly, and a deformed axially symmetric family of Skyrme fields constructed which are candidates for approximate near BPS skyrmions at low baryon number. The notion of restricted harmonicity is generalized to restricted F-criticality where F is any functional on maps (M, g) →(N, h) which is, in a precise sense, geometrically natural. The case where F is a linear combination of E2 and E4, the usual Skyrme term, is studied in detail, and it is shown that inverse stereographic projection R3 →S3 ≡ SU(2) is stable restricted F-critical for every such F.

  14. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

    PubMed Central

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D.

    2015-01-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1–2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

  15. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.

    PubMed

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D

    2015-12-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1-2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

  16. Construction of an EcoRI restriction map of Mycoplasma pneumoniae and localization of selected genes.

    PubMed Central

    Wenzel, R; Pirkl, E; Herrmann, R

    1992-01-01

    A restriction map of the genome of Mycoplasma pneumoniae, a small human pathogenic bacterium, was constructed by means of an ordered cosmid library which spans the complete bacterial chromosome. The positions of 143 endonuclease EcoRI restriction fragments were determined and aligned with the physical map. In addition, restriction sites for the rare-cutting enzymes XhoI (25 sites), ApaI (13 sites), NotI (2 sites), and SfiI (2 sites) were included. The resulting map consists of 185 restriction sites, has a mean resolution of 4.4 kbp, and predicts a genome size of 809 kbp. In addition, several genes were identified and mapped to their respective genomic EcoRI restriction fragments. Images PMID:1429453

  17. A 12 megabase restriction map at the cystic fibrosis locus.

    PubMed Central

    Fulton, T R; Bowcock, A M; Smith, D R; Daneshvar, L; Green, P; Cavalli-Sforza, L L; Donis-Keller, H

    1989-01-01

    We have constructed a physical map of the chromosomal region containing the cystic fibrosis locus using seven DNA markers and pulsed-field gel electrophoresis methods. The map includes cleavage sites for 8 rare-cutting restriction enzymes and spans over 12 megabases (Mb) of DNA, with one unlinked probe covering an additional 5 Mb. To our knowledge, this is the largest segment of human DNA which has been restriction-mapped to date. We can identify thirteen putative HTF islands spaced at intervals of 0.3-3.2 Mb. The region between loci D7S8 and MET, where the CF gene lies, includes 1.4-1.9 Mb of DNA. Images PMID:2911467

  18. Optimizing Restriction Site Placement for Synthetic Genomes

    NASA Astrophysics Data System (ADS)

    Montes, Pablo; Memelli, Heraldo; Ward, Charles; Kim, Joondong; Mitchell, Joseph S. B.; Skiena, Steven

    Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.

  19. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq).

    PubMed

    Yu, Hui; You, Xinxin; Li, Jia; Liu, Hankui; Meng, Zining; Xiao, Ling; Zhang, Haifa; Lin, Hao-Ran; Zhang, Yong; Shi, Qiong

    2016-01-01

    Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish. PMID:27058532

  20. Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq)

    PubMed Central

    Yu, Hui; You, Xinxin; Li, Jia; Liu, Hankui; Meng, Zining; Xiao, Ling; Zhang, Haifa; Lin, Hao-Ran; Zhang, Yong; Shi, Qiong

    2016-01-01

    Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish. PMID:27058532

  1. Waste Site Mapping

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Old aircraft considered not restorable are melted down in on-site furnaces to reclaim the aluminum in their airframes. The process produces aluminum ingots and leaves a residue known as "dross." Because dross contains contaminants like lead silver cadmium and copper, Pima County, the dross dumping site, wanted to locate areas where dross had been dumped. Dr. Larry Lepley and Sandra L. Perry used the Landsat Thematic Mapper to screen for dross. A special two-step procedure was developed to separate the dross dumps (typically no larger than 50 meters across) from the desert background. The project has opened the door for similar applications.

  2. QTL for resistance in Lolium perenne to a mixed population of Puccinia graminis subsp. graminicola: use of RAD (restriction site associated DNA) markers to rapidly populate a new linkage map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. Susceptible and resistant plants were crossed to produce a pseudo-testcross population. Markers were produced by the Restriction-sit...

  3. Rapid restriction mapping of cosmids by sequence-specific triple-helix-mediated affinity capture

    SciTech Connect

    Ji, Huamin; Francisco, T.; Smith, L.M.; Guilfoyle, R.A.

    1996-01-15

    A simple and rapid strategy for restriction mapping based on sequence-specific triple-helix affinity capture (TAC) was developed. The strategy was applied to the analysis of cosmid clones by the construction of a new cosmid vector, ScosTriplex-II, containing two different triple-helix-forming sequences flanking the cloning site of the original SuperCos-1 cosmid vector. For restriction mapping, the recombinant cosmid DNA is digested with NotI restriction enzyme or with one of four intron-encoded endonucleases for excision of intact inserts followed by controlled partial digestion with a mapping enzyme used in conjunction with the corresponding methyltransferase. The partial digestion products are combined with biotinylated triple-helix-forming oligonucleotides to form a triple-helical complex. The triple-helix complexes are immobilized on streptavidin-coated magnetic beads, washed, and eluted with pH 9 buffer solution. The fragments are separated and directly sized by agarose gel electrophoresis. Bidirectional maps are obtained simultaneously by binding to the two different triple-helix-forming oligonucleotides. No probe labeling, gel drying, blotting to membranes, hybridization, or autoradiography is necessary. Also, TAC conditions that permit gel-free isolation of the terminal restriction fragments from cosmid inserts were found. These advantages afforded by ScosTriplex-II should facilitate the automation of cosmid restriction site fingerprinting needed for large-scale mapping and sequencing projects. 24 refs., 5 figs.

  4. Restriction enzyme mapping of ribosomal DNA can distinguish between fasciolid (liver fluke) species.

    PubMed

    Blair, D; McManus, D P

    1989-10-01

    Recognition sites for nine different restriction endonucleases were mapped on rDNA genes of fasciolid species. Southern blots of digested DNA from individual worms were probed sequentially with three different probes derived from rDNA of Schistosoma mansoni and known to span between them the entire rDNA repeat unit in that species. Eighteen recognition sites were mapped for Fasciola hepatica, and seventeen for Fasciola gigantica and Fascioloides magna. Each fasciolid species had no more than two unique recognition sites, the remainder being common to one or both of the other two species. No intraspecific variation in restriction sites was noted in F. hepatica (individuals from 11 samples studied; hosts were sheep, cattle and laboratory animals; geographical origins. Australia, New Zealand, Mexico, U.K., Hungary and Spain), or in F. gigantica (two samples; Indonesia and Malaysia). Only one sample of F. magna was available. One specimen of Fasciola sp. from Japan (specific identity regarded in the literature as uncertain) yielded a restriction map identical to that of F. gigantica. Almost all recognition sites occurred in or near the putative rRNA coding regions. The non-transcribed spacer region had few or no cut sites despite the fact that this region is up to about one half of the entire repeat unit in length. Length heterogeneity was noted in the non-transcribed spacer, even within individual worms. PMID:2552311

  5. statement of significance, location map, site plan, landscape plan, site ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA

  6. Exceptionally High Levels of Restriction Site Polymorphism in DNA near the Maize Adh1 Gene

    PubMed Central

    Johns, Mitrick A.; Strommer, Judith N.; Freeling, Michael

    1983-01-01

    Restriction maps have been prepared for the chromosomal region near seven biochemically and genetically distinct maize alcohol dehydrogenase-1 (Adh1) alleles using a small cDNA probe for Adh1. Five restriction sites spanning about 4 kb in and near the Adh1 transcription unit appear identical in all seven alleles. Outside this conserved region, variation in restriction site position is the rule. Six of the seven alleles are distinguishable, and the alleles appear to fall into four groups. The DNA flanking the 1S-type alleles seems to share no restriction site homology with the DNA near the 1F-type alleles. Several hypotheses are put forward to explain how such high levels of polymorphism could have arisen in a species that has been domesticated for only about 10,000 years. PMID:17246173

  7. Efficient and scalable scaffolding using optical restriction maps

    PubMed Central

    2014-01-01

    In the next generation sequencing techniques millions of short reads are produced from a genomic sequence at a single run. The chances of low read coverage to some regions of the sequence are very high. The reads are short and very large in number. Due to erroneous base calling, there could be errors in the reads. As a consequence, sequence assemblers often fail to sequence an entire DNA molecule and instead output a set of overlapping segments that together represent a consensus region of the DNA. This set of overlapping segments are collectively called contigs in the literature. The final step of the sequencing process, called scaffolding, is to assemble the contigs into a correct order. Scaffolding techniques typically exploit additional information such as mate-pairs, pair-ends, or optical restriction maps. In this paper we introduce a series of novel algorithms for scaffolding that exploit optical restriction maps (ORMs). Simulation results show that our algorithms are indeed reliable, scalable, and efficient compared to the best known algorithms in the literature. PMID:25081913

  8. RESTRICTION MAPS OF FIVE AUTOGRAPHA CALIFORNICA MNPV VARIANTS, TRICHOPLUSIA NI MNPV, AND GALLERIA MELLONELLA MNPV DNAS WITH ENDONUCLEASES SMAI, KPNI, BAMHI, SACI, XHOI, AND ECORI

    EPA Science Inventory

    The restriction sites of Autographa californica nuclear polyhedrosis virus (AcMNPV) E2 DNA were mapped for the endonucleases SmaI, KpnK, BamHI, SacI, XhoI, and EcoRI. The restriction maps of four other AcMNPV variants, Trichoplusia ni (TnMNPV), and Galleria mellonella (GmMNPV) ge...

  9. Generating Oriented Pointsets From Redundant Depth Maps Using Restricted Quadtrees

    NASA Astrophysics Data System (ADS)

    Rothermel, M.; Haala, N.; Fritsch, D.

    2014-08-01

    In this article we present an algorithm for the fusion of depth images derived by dense image matching (DIM). One key idea of our algorithm is to generate a 2D triangulation for each available depth map in the image sequence using a restricted quadtrees (RQT). On the one hand this guarantees matching triangulations, on the other hand this creates the possibility to reduce points in the noise range not contributing to the geometry in a controlled manner. By vertex decimation computational efforts in subsequent processing steps are eased. In order to reduce IO overhead, the algorithm is designed in an iterative way: an initial triangulation is lifted to 3D space and, if pixel footprints are comparable, updated using depths of the subsequent map in the sequence. Previously not observed surface regions or surface patches observed only with adverse precision are removed from the existing model and updated by more appropriate triangulations. Thereby differences in scale across depth maps are handled which is particularly important to preserve details and obtain surfaces with the best reconstruction geometry. To remove outliers visibility constraints are forced. The input is overlapping depth images and their poses in space, the output are point coordinates representing the surface, their respective normals and to some degree spatial neighbourhood information of points represented as a non-watertight mesh. The performance of the algorithm will be evaluated on a close range and a oblique aerial dataset.

  10. Restriction enzyme maps of the macropodid herpesvirus 2 genome.

    PubMed

    Johnson, M A; Whalley, J M

    1987-01-01

    The DNA of macropodid herpesvirus 2 (dorcopsis wallaby herpesvirus) was analysed using restriction enzymes and molecular cloning techniques. Sets of EcoRI and SalI clones were prepared which represented approximately 85 per cent of the genome, and these clones were used to map the DNA by double-digestion and hybridization experiments. Data on uncloned regions were obtained by analysing fragments excised from agarose gels, and terminal fragments were identified by exonuclease III digestion. The genome was shown to be approximately 135 kilobases (kb) long. It has a long unique sequence (95 kb) bounded by repeat sequences (5.5 kb) and joined at one end to a short unique sequence (15 kb) also bounded by repeat sequences (7.0 kb) in a manner similar to that of herpes simplex viruses 1 and 2. PMID:2889444

  11. Usability Evaluation of Public Web Mapping Sites

    NASA Astrophysics Data System (ADS)

    Wang, C.

    2014-04-01

    Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The

  12. Mapping NEHRP VS30 site classes

    USGS Publications Warehouse

    Holzer, T.L.; Padovani, A.C.; Bennett, M.J.; Noce, T.E.; Tinsley, J. C., III

    2005-01-01

    Site-amplification potential in a 140-km2 area on the eastern shore of San Francisco Bay, California, was mapped with data from 210 seismic cone penetration test (SCPT) soundings. NEHRP VS30 values were computed on a 50-m grid by both taking into account the thickness and using mean values of locally measured shear-wave velocities of shallow geologic units. The resulting map of NEHRP VS30 site classes differs from other published maps that (1) do not include unit thickness and (2) are based on regional compilations of velocity. Although much of the area in the new map is now classified as NEHRP Site Class D, the velocities of the geologic deposits within this area are either near the upper or lower VS30 boundary of Class D. If maps of NEHRP site classes are to be based on geologic maps, velocity distributions of geologic units may need to be considered in the definition of VS30 boundaries of NEHRP site classes. ?? 2005, Earthquake Engineering Research Institute.

  13. Site maps and facilities listings

    SciTech Connect

    Not Available

    1993-11-01

    In September 1989, a Memorandum of Agreement among DOE offices regarding the environmental management of DOE facilities was signed by appropriate Assistant Secretaries and Directors. This Memorandum of Agreement established the criteria for EM line responsibility. It stated that EM would be responsible for all DOE facilities, operations, or sites (1) that have been assigned to DOE for environmental restoration and serve or will serve no future production need; (2) that are used for the storage, treatment, or disposal of hazardous, radioactive, and mixed hazardous waste materials that have been properly characterized, packaged, and labelled, but are not used for production; (3) that have been formally transferred to EM by another DOE office for the purpose of environmental restoration and the eventual return to service as a DOE production facility; or (4) that are used exclusively for long-term storage of DOE waste material and are not actively used for production, with the exception of facilities, operations, or sites under the direction of the DOE Office of Civilian Radioactive Waste Management. As part of the implementation of the Memorandum of Agreement, Field Offices within DOE submitted their listings of facilities, systems, operation, and sites for which EM would have line responsibility. It is intended that EM facility listings will be revised on a yearly basis so that managers at all levels will have a valid reference for the planning, programming, budgeting and execution of EM activities.

  14. 1884, 1889 & 1893 Site Maps Brookland Site Development ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1884, 1889 & 1893 Site Maps - Brookland Site Development Study, Brookland, bounded by B&O Railroad Tracks, Rhode Island & Brentwood Avenues on the south, 18th Street & South Dakota Avenue on the east, and Michigan Avenue on the North, Washington, District of Columbia, DC

  15. Ground water maps of the Hanford Site

    SciTech Connect

    Kasza, G.L.; Harris, S.F.; Hartman, M.J.

    1990-12-01

    This report presents the results of the June 1990, ground water level measurement program at the 100 Areas and 200 Areas of the Hanford Site (Figure 1). The water levels beneath these areas are measured regularly on a semiannual basis and the data received are used to produce the following set of maps for public release. For clarity, the locating prefixes have been omitted from all well numbers shown on the maps. Wells in the 100 Areas have the prefix 199; wells in the 200 Areas have the prefix 299, and the wells outside these areas have the prefix 699. Ground Water Maps of the Hanford Site is prepared by the Geosciences Group, Environmental Division, Westinghouse Hanford Company, for the US Department of Energy, Richland Operations Office. 1 ref., 6 figs., 2 tabs.

  16. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  17. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

    PubMed Central

    Rudd, K E; Miller, W; Ostell, J; Benson, D A

    1990-01-01

    We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects. PMID:2183179

  18. 'SPODOPTERA FRUGIPERDA' NUCLEAR POLYHEDROSIS VIRUS GENOME: PHYSICAL MAPS FOR RESTRICTION ENDONUCLEASES BAMHI AND HINDIII

    EPA Science Inventory

    The physical map for the genome of Spodoptera frugiperda nuclear polyhedrosis virus was constructed for restriction endonucleases BamHI and HindIII. The ordering of the restriction fragments was accomplished by cross-blot hybridization of BamHI, HindIII, and EcoRI fragments. The ...

  19. Using restriction mapping to teach basic skills in the molecular biology lab.

    PubMed

    Walsh, Lauren; Shaker, Elizabeth; De Stasio, Elizabeth A

    2007-05-01

    Digestion of DNA with restriction enzymes, calculation of volumes and concentrations of reagents for reactions, and the separation of DNA fragments by agarose gel electrophoresis are common molecular biology techniques that are best taught through repetition. The following open-ended, investigative laboratory exercise in plasmid restriction mapping allows students to gain technical expertise while simultaneously exploring the utility of gel electrophoresis and restriction mapping. Because of its interpretive nature, this project also provides data suitable for a written report, and can thus be used to reinforce lessons on figure presentation and science writing skills. PMID:21591089

  20. 25 CFR 247.11 - What other restrictions apply to use of the sites?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false What other restrictions apply to use of the sites? 247.11 Section 247.11 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE USE OF COLUMBIA RIVER TREATY FISHING ACCESS SITES § 247.11 What other restrictions apply to use of the sites?...

  1. 25 CFR 247.11 - What other restrictions apply to use of the sites?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false What other restrictions apply to use of the sites? 247.11 Section 247.11 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE USE OF COLUMBIA RIVER TREATY FISHING ACCESS SITES § 247.11 What other restrictions apply to use of the sites?...

  2. 25 CFR 247.11 - What other restrictions apply to use of the sites?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false What other restrictions apply to use of the sites? 247.11 Section 247.11 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE USE OF COLUMBIA RIVER TREATY FISHING ACCESS SITES § 247.11 What other restrictions apply to use of the sites?...

  3. 25 CFR 247.11 - What other restrictions apply to use of the sites?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true What other restrictions apply to use of the sites? 247.11 Section 247.11 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE USE OF COLUMBIA RIVER TREATY FISHING ACCESS SITES § 247.11 What other restrictions apply to use of the sites?...

  4. 23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. Site plan, 1931 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 updated to 1931. - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

  5. 24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. Site plan, 1924 Photocopied from Sanborn Map Company, Insurance Maps of New Haven, v. 5, map no. 540, 1924 - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

  6. Site characterization and petroleum hydrocarbon plume mapping

    SciTech Connect

    Ravishankar, K.

    1996-12-31

    This paper presents a case study of site characterization and hydrocarbon contamination plume mapping/delineation in a gas processing plant in southern Mexico. The paper describes innovative and cost-effective use of passive (non-intrusive) and active (intrusive) techniques, including the use of compound-specific analytical methods for site characterization. The techniques used, on a demonstrative basis, include geophysical, geochemical, and borehole drilling. Geochemical techniques used to delineate the horizontal extent of hydrocarbon contamination at the site include soil gas surveys. The borehole drilling technique used to assess the vertical extent of contamination and confirm geophysical and geochemical data combines conventional hollow-stem auguring with direct push-probe using Geoprobe. Compound-specific analytical methods, such as hydrocarbon fingerprinting and a modified method for gasoline range organics, demonstrate the inherent merit and need for such analyses to properly characterize a site, while revealing the limitations of noncompound-specific total petroleum hydrocarbon analysis. The results indicate that the techniques used in tandem can properly delineate the nature and extent of contamination at a site; often supplement or complement data, while reducing the risk of errors and omissions during the assessment phase; and provide data constructively to focus site-specific remediation efforts. 7 figs.

  7. Restriction endonucleases for pulsed field mapping of bacterial genomes.

    PubMed Central

    McClelland, M; Jones, R; Patel, Y; Nelson, M

    1987-01-01

    Fundamental to many bacterial genome mapping strategies currently under development is the need to cleave the genome into a few large DNA fragments that can be resolved by pulsed field gel electrophoresis. Identification of endonucleases that infrequently cut a genome is of key importance in this process. We show that the tetranucleotide CTAG is extremely rare in most bacterial genomes with G+C contents above 45%. As a consequence, most of the sixteen bacterial genomes we have tested are cleaved less than once every 100,000 base pairs by one or more endonucleases that have CTAG in their recognition sequences: Xba I (TCTAGA), Spe I (ACTAGT), Avr II (CCTAGG) and Nhe I (GCTAGC). Similarly, CCG and CGG are the rarest trinucleotides in many genomes with G+C content of less than 45%. Thus, Sma I (CCCGGG), Rsr II (CGGWCCG), Nae I (GCCGGC) and Sac II (CCGCGG) are often suitable endonucleases for producing fragments that average over 100,000 base pairs from such genomes. Pulsed field gel electrophoresis of the fragments that result from cleavage with endonucleases that cleave only a few times per genome should assist in the physical mapping of many prokaryotic genomes. Images PMID:2819819

  8. Mapping of sites in forest stands.

    PubMed

    Netto, Sylvio Péllico; Stefanello, Flavio R; Pelissari, Allan L; David, Hassan C

    2014-12-01

    Generally, the forest companies use the total one year planting area as a minimum stratum of the total population and, consequently, the forest inventory processing has been conducted by applying the stratified random sampling to it. This study was carried out in the National Forest of Tres Barras, Brazil, and it aimed to classify and map the sites of Pinus elliottii stands. A systematic sampling was structured into clusters and applied independently by compartments. The clusters, in maltese cross, were composed of four sampling subunits, using Prodan sampling method with a fixed number of six trees. By analysis of the methodology it was possible to confirm the hypothesis: a) the selective thinning cause expressive increase of volumetric variability within compartments; b) the variation of sites within the compartments causes volumetric expansion of variance and this grows proportionally to the quality of the sites; c) the stratification in sites results in minimum variance within them; d) the stratification in sites resulted in until to 91% reduction of variances within them. PMID:25590737

  9. Dissection of the Salmonella typhimurium genome by use of a Tn5 derivative carrying rare restriction sites.

    PubMed Central

    Wong, K K; McClelland, M

    1992-01-01

    A polylinker with rare restriction sites was introduced into a mini-Tn5 derivative. These sites include M.XbaI-DpnI (TCTAGATCTAGA), which is rare in most bacterial genomes, SwaI (ATTTAAAT) and PacI (TTAATTAA), which are rare in G+C-rich genomes, NotI (GCGGCCGC) and SfiI (GGCCN5GGCC), which are rare in A+T-rich genomes, and BlnI (CCTAGG), SpeI (ACTAGT), and XbaI (TCTAGA), which are rare in the genomes of many gram-negative bacteria. This Tn5(pfm) (pulsed-field mapping) transposon carries resistance to chloramphenicol and kanamycin to allow selection in a wide variety of background genomes. This Tn5(pfm) was integrated randomly into the Salmonella typhimurium and Serratia marcescens genomes. Integration of the new rare SwaI, PacI, BlnI, SpeI, and XbaI sites was assayed by restriction digestion and pulsed-field gel electrophoresis. Tn5(pfm) constructs could be valuable tools for pulsed-field mapping of gram-negative bacterial genomes by assisting in the production of physical maps and restriction fragment catalogs. For the first applications of a Tn5(pfm), we bisected five of the six largest BlnI fragments in the S. typhimurium genome, bisected the linearized 90-kb pSLT plasmid, and used Tn5(pfm) and Tn10 to trisect the largest BlnI fragment. Images PMID:1317382

  10. 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

  11. GIS Surface Effects Map Archive, Nevada Test Site, Nevada

    SciTech Connect

    Grasso, Dennis N.

    2003-08-28

    The GIS Surface Effects Map Archive contains a comprehensive collection of maps showing the surface effects produced by underground nuclear testing at the Nevada Test Site. From 1951 to 1992, scientists with the U.S. Geological Survey and agencies of the U.S. Department of Energy used field and aerial-photo mapping techniques to painstakingly map such surface effects as collapse sinks, craters, cracks, fractures, faults, and pressure ridges. Shortly after each test, a complex surface effects map was produced. Of the more than 920 underground detonations conducted at the Nevada Test Site, 688 were mapped for surface effects. This archive preserves these original maps in digital format. A Geographic Information System (GIS) was used to digitally reproduce each original, hand-drawn surface effects map and to assemble these maps into the digital data sets of this archive. The archive was designed to allow easy access to the maps, while preserving the original maps for perpetuity. Users can query the detonation sites database; prepare, view, and print individual or composite maps; and perform various types of scientific analysis and management tasks. Spatial analyses and queries can be performed on detonation sites and related surface effects in conjunction with other chronological, geographical, geological, or hydrological information via links to external maps and databases. This browser interface provides information about the archive, the history of surface effects mapping at the Nevada Test Site, the methods used to produce the digital surface effects maps, and links to published reports, data tables, and maps. Location maps show testing areas, operational areas, and detonation sites. Demonstration maps illustrate the methods used to produce the digital surface effects maps and exhibit some of the characteristics and uses for these data. Use the links below to view and print individual surface effects maps, retrieve information about the detonations and types of

  12. Topographic Map of Pathfinder Landing Site

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Topographic map of the landing site, to a distance of 60 meters from the lander in the LSC coordinate system. The lander is shown schematically in the center; 2.5 meter radius circle (black) centered on the camera was not mapped. Gentle relief [root mean square (rms) elevation variation 0.5 m; rms a directional slope 4O] and organization of topography into northwest and northeast-trending ridges about 20 meters apart are apparent. Roughly 30% of the illustrated area is hidden from the camera behind these ridges. Contours (0.2 m interval) and color coding of elevations were generated from a digital terrain model, which was interpolated by kriging from approximately 700 measured points. Angular and parallax point coordinates were measured manually on a large (5 m length) anaglyphic uncontrolled mosaic and used to calculate Cartesian (LSC) coordinates. Errors in azimuth on the order of 10 are therefore likely; elevation errors were minimized by referencing elevations to the local horizon. The uncertainty in range measurements increases quadratically with range. Given a measurement error of 1/2 pixel, the expected precision in range is 0.3 meter at 10 meter range, and 10 meters at 60 meter range. Repeated measurements were made, compared, and edited for consistency to improve the range precision. Systematic errors undoubtedly remain and will be corrected in future maps compiled digitally from geometrically controlled images. Cartographic processing by U.S. Geological Survey.

    NOTE: original caption as published in Science Magazine

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California Institute of Technology (Caltech).

  13. A Genetic Linkage Map of the Mouse Using Restriction Landmark Genomic Scanning (Rlgs)

    PubMed Central

    Hayashizaki, Y.; Hirotsune, S.; Okazaki, Y.; Shibata, H.; Akasako, A.; Muramatsu, M.; Kawai, J.; Hirasawa, T.; Watanabe, S.; Shiroishi, T.; Moriwaki, K.; Taylor, B. A.; Matsuda, Y.; Elliott, R. W.; Manly, K. F.; Chapman, V. M.

    1994-01-01

    We have developed a multiplex method of genome analysis, restriction landmark genomic scanning (RLGS) that has been used to construct genetic maps in mice. Restriction landmarks are end-labeled restriction fragments of genomic DNA that are separated by using high resolution, two-dimensional gel electrophoresis identifying as many as two thousand landmark loci in a single gel. Variation for several hundred of these loci has been identified between laboratory strains and between these strains and Mus spretus. The segregation of more than 1100 RLGS loci has been analyxed in recombinant inbred (RI) strains and in two separate interspecific genetic crosses. Genetic maps have been derived that link 1045 RLGS loci to reference loci on all of the autosomes and the X chromosome of the mouse genome. The RLGS method can be applied to genome analysis in many different organisms to identify genomic loci because it used end-labeling of restriction landmarks rather than probe hybridization. Different combinations of restriction enzymes yield different sets of RLGS loci providing expanded power for genetic mapping. PMID:7896102

  14. 25 CFR 247.11 - What other restrictions apply to use of the sites?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false What other restrictions apply to use of the sites? 247.11 Section 247.11 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FISH AND WILDLIFE USE OF COLUMBIA RIVER TREATY FISHING ACCESS SITES § 247.11 What other restrictions apply to use of the sites? The Area Director may prescribe and post...

  15. EcoRI restriction endonuclease map of the composite R plasmid NR1.

    PubMed Central

    Tanak, N; Cramer, J H; Rownd, R H

    1976-01-01

    A physical map of the composite R plasmid NR1 has been constructed using specific cleavage of deoxyribonucleic acid (DNA) by the restriction endonuclease EcoR-. Digestion of composite NR1 DNA by EcoRI yields thirteen fragments. The six largest fragments (designated A to F) are from the resistance transfer factor component that harbors the tetracycline resistance genes (RTF-TC). The seven smallest fragments (designated G to M) are from the r-determinants component that harbors the chloramphenicol (CM), streptomycin-spectinomycin (SM/SP), and sulfonamide (SA) resistance genes. The largest fragment of several RTF-TC segregants of NR1 that have deleted the r-determinants component is 0.8 X 10(6) daltons larger than fragment A of composite NR1. Only a part of fragment H of the r-determinants component is amplified in transitioned NR1 DNA in Proteus mirabilis, which consists of multiple, tandem sequences of r-determinants attached to a single copy of the RTF-TC component. Both of these changes can be explained by the locations of the excision sites at the RTF-TC: r-determinants junctions that are involved in the dissociation and reassociation of the RTF-TC and r-determinants components. The thirteen fragments of composite NR1 DNA produced by EcoRI have been ordered using partial digestion techniques. The order of the fragments is: A-D-C-E-F-B-H-I-L-K-G-M-J. The approximate locations of the TC, CM, SM/SP, and SA resistance genes on the EcoRI map were determined by analyzing several deletion mutants of NR1. Images PMID:776943

  16. Mapping site-specific endonuclease binding to DNA by direct imaging with AFM

    SciTech Connect

    Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J.; Modrich, P.; Isfort, R.J.

    1995-12-31

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  17. Pulsed-field gel electrophoresis for long-range restriction mapping.

    PubMed

    Gemmill, Robert M; Bolin, Richard; Albertsen, Hans; Tomkins, Jeff P; Wing, Rod A

    2002-02-01

    This unit describes procedures for generating long-range restriction maps of genomic DNA and for analysis of large insert clones. The basic protocol details restriction digestion of agarose-embedded DNA, PFGE separation, Southern transfer, and hybridization. Support protocols describe the preparation of high-molecular-weight genomic DNA samples in agarose blocks and in agarose microbeads, respectively. Additional support protocols describe the preparation of DNA size standards from l phage and two yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe. An alternative method of preparing S. cerevisiae size standards using lithium dodecyl sulfate (LiDS) solubilization is provided. The final protocol details the preparation of BAC DNA suitable for digestion, mapping, and sequencing. PMID:18428330

  18. Surface-material maps of Viking landing sites on Mars

    NASA Technical Reports Server (NTRS)

    Moore, H. J.; Keller, J. M.

    1991-01-01

    Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

  19. Restriction mapping of a YAC contig in the hemochromatosis gene region

    SciTech Connect

    Burt, M.J.; Smit, D.J.; Pyper, W.R.

    1994-09-01

    Hemochromatosis is a common inherited disorder of iron metabolism that can lead to cirrhosis, hepatocellular carcinoma, cardiomyopathy, diabetes and anthropathy. We have mapped the hemochromatosis gene to within 1 cM of HLA-A and the microsatellite D6S105, and our allele association studies have shown that D6S105 is the marker most closely associated with the hemochromatosis gene. We are currently constructing a YAC contig and restriction map of this region as part of a positional cloning strategy to identify the hemochromatosis gene. YACs containing HLA-A or D6S105 were selected, and fluorescent-in-situ-hybridization (FISH) was performed to confirm chromosomal location and exclude chimerism. YAC DNA was digested with a panel of rare cutters, separated by pulsed field gel electrophoresis, Southern blotted and probed with the vector arms to create restriction maps. YAC insert terminal ends were isolated using vectorette methodology. A contig extending 600 kb centromeric and 350 kb telomeric of HLA-A has been established. HLA-A, HLA-F and the microsatellite D6S265 have been positioned on this map. The contig does not yet overlap any D6S105 positive YACs but the telomeric end of the contig has been sequenced and is being used to identify additional YACs to bridge this interval. Restriction mapping of three D6S105 YACs has shown the presence of several CpG islands in this region. As these CpG islands are in close proximity to D6S105, they are being used to isolate coding sequences to determine whether any of these mark the position of the hemochromatosis gene.

  20. Disaggregation of soil map units for improved ecological site mapping in rangelands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rangeland soils are often mapped with soil map units consisting of associations, complexes, and undifferentiated groups composed of varied soil components. Because different components may be related to different ecological sites, the unmapped heterogeneity within map units limits the potential uses...

  1. Disaggregation of Soil Map Units for Improved Ecological Site Mapping in Rangelands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rangeland soils are often mapped with soil map units consisting of associations, complexes, and undifferentiated groups composed of varied soil components. Because different components may be related to different ecological sites, the unmapped heterogeneity within map units limits the potential uses...

  2. Ground water maps of Hanford Site Separations Areas, December 1989

    SciTech Connect

    Kasza, G.L.

    1990-06-01

    The Separations Areas consist of the 200 East and 200 West areas and the surrounding vicinity on the Hanford Site. Chemical processing operations are carried out in the Separations Areas by Westinghouse Hanford Company for the US Department of Energy-Richland Operations Office. This set of ground water maps consists of: (1) Separations Areas depth-to-water map, (2) Separations Areas water table map, and (3) a map comparing the potentiometric surface of the Rattlesnake Ridge confined aquifer with the water table of the unconfined aquifer. The field measurements for these maps were collected during December 1989. 3 figs., 1 tab.

  3. Optimizing landfill site selection by using land classification maps.

    PubMed

    Eskandari, M; Homaee, M; Mahmoodi, S; Pazira, E; Van Genuchten, M Th

    2015-05-01

    Municipal solid waste disposal is a major environmental concern throughout the world. Proper landfill siting involves many environmental, economic, technical, and sociocultural challenges. In this study, a new quantitative method for landfill siting that reduces the number of evaluation criteria, simplifies siting procedures, and enhances the utility of available land evaluation maps was proposed. The method is demonstrated by selecting a suitable landfill site near the city of Marvdasht in Iran. The approach involves two separate stages. First, necessary criteria for preliminary landfill siting using four constraints and eight factors were obtained from a land classification map initially prepared for irrigation purposes. Thereafter, the criteria were standardized using a rating approach and then weighted to obtain a suitability map for landfill siting, with ratings in a 0-1 domain and divided into five suitability classes. Results were almost identical to those obtained with a more traditional environmental landfill siting approach. Because of far fewer evaluation criteria, the proposed weighting method was much easier to implement while producing a more convincing database for landfill siting. The classification map also considered land productivity. In the second stage, the six best alternative sites were evaluated for final landfill siting using four additional criteria. Sensitivity analyses were furthermore conducted to assess the stability of the obtained ranking. Results indicate that the method provides a precise siting procedure that should convince all pertinent stakeholders. PMID:25666474

  4. 9. SITE MAP HIGHLIGHTING SIGNIFICANT BUILDINGS AND SHOWING LOCATION LOCATION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. SITE MAP HIGHLIGHTING SIGNIFICANT BUILDINGS AND SHOWING LOCATION LOCATION OF OUTPATIENT CLINIC ADDITION - U.S. Veterans Administration Medical Center, 600 South Seventieth Street, Lincoln, Lancaster County, NE

  5. Groundwater maps of the Hanford Site Separations Area, January 1989

    SciTech Connect

    Kasza, G.L.; Schatz, A.L.

    1989-03-01

    The groundwater maps of the Hanford Site Separations Area, dated January 1989, are prepared by the Environmental Engineering and Technology Function, Environmental Division, Westinghouse Hanford Company. The groundwater maps are updated on a semiannual basis and are complementary to the Hanford Site water table map prepared by Pacific Northwest Laboratory. The Separations Area consists of the 200 East and 200 West areas and the surrounding vicinity on the Hanford Site. Chemical processing operations are carried out in the Separations Area by Westinghouse Hanford for the US Department of Energy - Richland Operations Office. This set of groundwater maps consists of: (1) Separations Area depth-to-water map, (2) Separations Area water table map, and (3) a map comparing the potentiometric surface of the Rattlesnake Ridge confined aquifer with the water table of the unconfined aquifer. The field measurements for these maps were collected during the period January 19 to February 8, 1989, and are listed in Table 1. For clarity, the locating prefixes have been omitted from all well numbers shown on the maps. Wells in the 200 Areas have the prefix 299, and the wells outside of these areas have the prefix 699.

  6. Long range restriction mapping of 13q14. 2 focused on the Wilson disease region

    SciTech Connect

    Bull, P.C. ); Cox, D.W. Univ. of Toronto, Ontario )

    1993-06-01

    The Wilson disease locus (WND) has been mapped by multipoint linkage analysis to a region within 13q14.3 that is flanked proximally by marker D12S21 and distally by marker D13S59 at distances of 0.4 and 1.2 cM, respectively. Long range restriction maps were constructed around these two markers to provide a framework for the detailed physical analysis that will be necessary for the cloning of the gene. The maps, together spanning over 4 Mb, include five newly isolated markers (D13S110, D13S113, D13S194, D13F71S1, and D13S196) and two established markers (D13S56and D13S25) that were previously localized to 13q14.2-q14.3 using a hybrid panel. Markers D13F71S1 and D13S196 map to the region between D13S31 and D13S59 and will therefore be useful for the isolation of YAC, for further molecular studies on Wilson disease. 19 refs., 5 figs., 2 tabs.

  7. Generation of a Restriction Fragment Length Polymorphism Linkage Map for Toxoplasma Gondii

    PubMed Central

    Sibley, L. D.; LeBlanc, A. J.; Pfefferkorn, E. R.; Boothroyd, J. C.

    1992-01-01

    We have constructed a genetic linkage map for the parasitic protozoan, Toxoplasma gondii, using randomly selected low copy number DNA markers that define restriction fragment length polymorphisms (RFLPs). The inheritance patterns of 64 RFLP markers and two phenotypic markers were analyzed among 19 recombinant haploid progeny selected from two parallel genetic crosses between PLK and CEP strains. In these first successful interstrain crosses, these RFLP markers segregated into 11 distinct genetic linkage groups that showed close correlation with physical linkage groups previously defined by molecular karyotype. Separate linkage maps, constructed for each of the 11 chromosomes, indicated recombination frequencies range from approximately 100 to 300 kb per centimorgan. Preliminary linkage assignments were made for the loci regulating sinefungin resistance (snf-1) on chromosome IX and adenine arabinoside (ara-1) on chromosome V by linkage to RFLP markers. Despite random segregation of separate chromosomes, the majority of chromosomes failed to demonstrate internal recombination events and in 3/19 recombinant progeny no intramolecular recombination events were detected. The relatively low rate of intrachromosomal recombination predicts that tight linkage for unknown genes can be established with a relatively small set of markers. This genetic linkage map should prove useful in mapping genes that regulate drug resistance and other biological phenotypes in this important opportunistic pathogen. PMID:1360931

  8. A Restriction Fragment Length Polymorphism Map and Electrophoretic Karyotype of the Fungal Maize Pathogen Cochliobolus Heterostrophus

    PubMed Central

    Tzeng, T. H.; Lyngholm, L. K.; Ford, C. F.; Bronson, C. R.

    1992-01-01

    A restriction fragment length polymorphism (RFLP) map has been constructed of the nuclear genome of the plant pathogenic ascomycete Cochliobolus heterostrophus. The segregation of 128 RFLP and 4 phenotypic markers was analyzed among 91 random progeny of a single cross; linkages were detected among 126 of the markers. The intact chromosomal DNAs of the parents and certain progeny were separated using pulsed field gel electrophoresis and hybridized with probes used to detect the RFLPs. In this way, 125 markers were assigned to specific chromosomes and linkages among 120 of the markers were confirmed. These linkages totalled 941 centimorgans (cM). Several RFLPs and a reciprocal translocation were identified tightly linked to Tox1, a locus controlling host-specific virulence. Other differences in chromosome arrangement between the parents were also detected. Fourteen gaps of at least 40 cM were identified between linkage groups on the same chromosomes; the total map length was therefore estimated to be, at a minimum, 1501 cM. Fifteen A chromosomes ranging from about 1.3 megabases (Mb) to about 3.7 Mb were identified; one of the strains also has an apparent B chromosome. This chromosome appears to be completely dispensable; in some progeny, all of 15 markers that mapped to this chromosome were absent. The total genome size was estimated to be roughly 35 Mb. Based on these estimates of map length and physical genome size, the average kb/cM ratio in this cross was calculated to be approximately 23. This low ratio of physical to map distance should make this RFLP map a useful tool for cloning genes. PMID:1346261

  9. 1996 Hanford site report on land disposal restrictions for mixed waste

    SciTech Connect

    Black, D.G.

    1996-04-01

    This report was submitted to meet the requirements of Hanford Federal Facility Agreement and Consent Order milestone M-26-OIF. This milestone requires the preparation of an annual report that covers characterization, treatment, storage, minimization, and other aspects of land disposal-restricted mixed waste management at the Hanford Site.

  10. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  11. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site...

  12. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site...

  13. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site...

  14. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site...

  15. 47 CFR 73.4108 - FM transmitter site map submissions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site...

  16. Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples

    PubMed Central

    Baldwin, James C.

    2015-01-01

    Introduction Optical restriction genome mapping is a technology in which a genome is linearized on a surface and digested with specific restriction enzymes, giving an arrangement of the genome with gaps whose order and size are unique for a given organism. Current applications of this technology include assisting with the correct scaffolding and ordering of genomes in conjunction with whole-genome sequencing, observation of genetic drift and evolution using comparative genomics and epidemiological monitoring of the spread of infections. Here, we investigated the suitability of genome mapping for use in clinical labs as a potential diagnostic tool. Materials and Methods Using whole genome mapping, we investigated the basic performance of the technology for identifying two bacteria of interest for food-safety (Lactobacilli spp. and Enterohemorrhagic Escherichia coli). We further evaluated the performance for identifying multiple organisms from both simple and complex mixtures. Results We were able to successfully generate optical restriction maps of four Lactobacillus species as well as a strain of Enterohemorrhagic Escherichia coli from within a mixed solution, each distinguished using a common compatible restriction enzyme. Finally, we demonstrated that optical restriction maps were successfully obtained and the correct organism identified within a clinical matrix. Conclusion With additional development, whole genome mapping may be a useful clinical tool for rapid invitro diagnostics. PMID:26435946

  17. Groudwater maps of the Hanford Site Separations Area, June 1989

    SciTech Connect

    Kasza, G.L.; Reidel, S.P.; Schatz, A.L.

    1989-09-01

    The groundwater maps of the Hanford Site Separations Area, recorded June 1989, are prepared by the Environmental Engineering and Technology Function, Environmental Division, Westinghouse Hanford Company. This set of groundwater maps consists of Separations Area depth-to-water map, Separations Area water table map, and a map comparing the potentiometric surface of the Rattlesnake Ridge confined aquifer with the water table of the unconfined aquifer. The field measurements for these maps were collected during June 1989. The Separations Area depth-to-water map depicts the measurement well locations and the depths to the water table at these locations. This map supports engineering or environmental studies which may require the approximate depth from the ground surface to the water table. On the third map, the potentiometric surface of the Rattlesnake Ridge confined aquifer is compared with the water table of the unconfined aquifer in the vicinity of West Lake, Gable Mountain Pond, and the B Pond system. The purpose of this map is to monitor the potential for aquifer intercommunication in this area. 3 figs., 1 tab.

  18. Robotic Mapping of Cultural Heritage Sites

    NASA Astrophysics Data System (ADS)

    Borrmann, D.; Heß, R.; Houshiar, H. R.; Eck, D.; Schilling, K.; Nüchter, A.

    2015-02-01

    In archaeological studies the use of new technologies has moved into focus in the past years creating new challenges such as the processing of the massive amounts of data. In this paper we present steps and processes for smart 3D modelling of environments by use of the mobile robot Irma3D. A robot that is equipped with multiple sensors, most importantly a photo camera and a laser scanner, enables the automation of most of the processes, including data acquisition and registration. The robot was tested in two scenarios, Ostia Antica and the Würzburg Residence. The paper describes the steps for creating 3D color reconstructions of these renown cultural heritage sites.

  19. Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

    PubMed Central

    Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

    2015-01-01

    To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ variety, ‘Yonekura’. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the ‘spiny-leaf type’ as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. PMID:26175625

  20. Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

    PubMed

    Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

    2015-06-01

    To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. PMID:26175625

  1. Groundwater maps of the Hanford Site, December 1995

    SciTech Connect

    Sweeney, M.D., Westinghouse Hanford

    1996-07-02

    This the latest in a series of reports that document the configuration of the water table aquifer beneath the Hanford Site. This series presents the results of the semiannual water level measurement program and the water table maps generated from these measurements. The reports document the changes in the groundwater level at the Hanford Site during the transition from nuclear material production to environmental restoration and remediation. In addition, these reports provide water level data to support the various site characterization and groundwater monitoring programs currently in progress on the Hanford Site.

  2. Hanford site Computer Automated Mapping Information System (CAMIS)

    SciTech Connect

    Rush, S.F.

    1995-09-01

    The Computer Automated Mapping Information System (CAMIS) provides sitewide, networked access to CAD based geographically referenced data. CAMIS allows multiple organizations to maintain and share their data. Information collected and managed according to site-wide standards, enables each organization to focus their limited resources on data issues tied to their own discipline without having to collect or manage reference data outside their respective domains. Sharing information also minimizes redundant data and helps improve the overall quality of the sites` data resources.

  3. Geologic mapping as a prerequisite to hazardous waste facility siting

    SciTech Connect

    LaMoreaux, P.E. )

    1993-03-01

    The nation's welfare is based on its capability to develop the mineral, water, and energy resources of the land. In addition, these resources must be developed with adequate consideration of environmental impact and the future welfare of the country. Geologic maps are an absolute necessity in the discovery and development of natural resources; for managing radioactive, toxic, and hazardous wastes; and for the assessment of hazards and risks such as those associated with volcanic action, earthquakes, landslides, and subsidence. Geologic maps are the basis for depicting rocks and rock materials, minerals, coal, oil, and water at or near the earth's surface. Hazardous waste facility projects require the preparation of detailed geologic maps. Throughout most of the USA, this type of mapping detail is not available. If these maps were available, it is estimated that the duration of an individual project could be reduced by at least one-fourth (1/4). Therefore, adequate site-specific mapping is required if one is to eliminate environmental problems associated with hazardous, toxic, radioactive, and municipal waste sites.

  4. Considerations for applying digital soil mapping to ecological sites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advancements in the spatial prediction of soil properties are not currently being fully utilized for ecological studies. Linking digital soil mapping (DSM) with ecological sites (ES) has the potential to better land management decisions by improving spatial resolution and precision as well as...

  5. Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.

    PubMed

    Ershova, Anna; Rusinov, Ivan; Vasiliev, Mikhail; Spirin, Sergey; Karyagina, Anna

    2016-04-01

    Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes. In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population. PMID:26972562

  6. Self-Avoiding Random Walk with Multiple Site Weightings and Restrictions

    NASA Astrophysics Data System (ADS)

    Krawczyk, J.; Prellberg, T.; Owczarek, A. L.; Rechnitzer, A.

    2006-06-01

    We introduce a new class of models for polymer collapse, given by random walks on regular lattices which are weighted according to multiple site visits. A Boltzmann weight ωl is assigned to each (l+1)-fold visited lattice site, and self-avoidance is incorporated by restricting to a maximal number K of visits to any site via setting ωl=0 for l≥K. In this Letter we study this model on the square and simple cubic lattices for the case K=3. Moreover, we consider a variant of this model, in which we forbid immediate self-reversal of the random walk. We perform simulations for random walks up to n=1024 steps using FlatPERM, a flat histogram stochastic growth algorithm. We find evidence that the existence of a collapse transition depends sensitively on the details of the model and has an unexpected dependence on dimension.

  7. Self-avoiding random walk with multiple site weightings and restrictions.

    PubMed

    Krawczyk, J; Prellberg, T; Owczarek, A L; Rechnitzer, A

    2006-06-23

    We introduce a new class of models for polymer collapse, given by random walks on regular lattices which are weighted according to multiple site visits. A Boltzmann weight omegal is assigned to each (l+1)-fold visited lattice site, and self-avoidance is incorporated by restricting to a maximal number K of visits to any site via setting omegal=0 for l>or=K. In this Letter we study this model on the square and simple cubic lattices for the case K=3. Moreover, we consider a variant of this model, in which we forbid immediate self-reversal of the random walk. We perform simulations for random walks up to n=1024 steps using FlatPERM, a flat histogram stochastic growth algorithm. We find evidence that the existence of a collapse transition depends sensitively on the details of the model and has an unexpected dependence on dimension. PMID:16907227

  8. Preferential site-dependent cleavage by restriction endonuclease PstI.

    PubMed Central

    Armstrong, K; Bauer, W R

    1982-01-01

    The four identical recognition sites for the restriction endonuclease PstI in purified plasmid pSM1 DNA I are cleaved at markedly different rates. The order and relative frequencies of cleavage at these four PstI sites have been determined from the order of appearance of partial cleavage products and from an analysis of production of specific unit length linear molecules. The same pattern of preferential cleavage is also found when linear, nicked circular, or relaxed closed circular forms of the same plasmid DNa are used as substrates for PstI. Inspection of the nucleotide sequences immediately adjoining each of the PstI sites suggests that the presence of adjacent runs of G-C base pairs confers significant resistance to cleavage. Images PMID:6278444

  9. Global Land Survey Impervious Mapping Project Web Site

    NASA Technical Reports Server (NTRS)

    DeColstoun, Eric Brown; Phillips, Jacqueline

    2014-01-01

    The Global Land Survey Impervious Mapping Project (GLS-IMP) aims to produce the first global maps of impervious cover at the 30m spatial resolution of Landsat. The project uses Global Land Survey (GLS) Landsat data as its base but incorporates training data generated from very high resolution commercial satellite data and using a Hierarchical segmentation program called Hseg. The web site contains general project information, a high level description of the science, examples of input and output data, as well as links to other relevant projects.

  10. SDM-Assist software to design site-directed mutagenesis primers introducing “silent” restriction sites

    PubMed Central

    2013-01-01

    Background Over the past decades site-directed mutagenesis (SDM) has become an indispensable tool for biological structure-function studies. In principle, SDM uses modified primer pairs in a PCR reaction to introduce a mutation in a cDNA insert. DpnI digestion of the reaction mixture is used to eliminate template copies before amplification in E. coli; however, this process is inefficient resulting in un-mutated clones which can only be distinguished from mutant clones by sequencing. Results We have developed a program – ‘SDM-Assist’ which creates SDM primers adding a specific identifier: through additional silent mutations a restriction site is included or a previous one removed which allows for highly efficient identification of ‘mutated clones’ by a simple restriction digest. Conclusions The direct identification of SDM clones will save time and money for researchers. SDM-Assist also scores the primers based on factors such as Tm, GC content and secondary structure allowing for simplified selection of optimal primer pairs. PMID:23522286

  11. Optimal mapping of site-specific multivariate soil properties.

    PubMed

    Burrough, P A; Swindell, J

    1997-01-01

    This paper demonstrates how geostatistics and fuzzy k-means classification can be used together to improve our practical understanding of crop yield-site response. Two aspects of soil are important for precision farming: (a) sensible classes for a given crop, and (b) their spatial variation. Local site classifications are more sensitive than general taxonomies and can be provided by the method of fuzzy k-means to transform a multivariate data set with i attributes measured at n sites into k overlapping classes; each site has a membership value mk for each class in the range 0-1. Soil variation is of interest when conditions vary over patches manageable by agricultural machinery. The spatial variation of each of the k classes can be analysed by computing the variograms of mk over the n sites. Memberships for each of the k classes can be mapped by ordinary kriging. Areas of class dominance and the transition zones between them can be identified by an inter-class confusion index; reducing the zones to boundaries gives crisp maps of dominant soil groups that can be used to guide precision farming equipment. Automation of the procedure is straightforward given sufficient data. Time variations in soil properties can be automatically incorporated in the computation of membership values. The procedures are illustrated with multi-year crop yield data collected from a 5 ha demonstration field at the Royal Agricultural College in Cirencester, UK. PMID:9573478

  12. Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein

    PubMed Central

    Belfort, Marlene

    2015-01-01

    Mapping the precise position of endonucleolytic cleavage sites is a fundamental experimental technique used to describe the function of a homing endonuclease. However, these proteins are often recalcitrant to cloning and over-expression in biological systems because of toxicity induced by spurious DNA cleavage events. In this chapter we outline the steps to successfully express a homing endonuclease in vitro and use this product in nucleotide-resolution cleavage assays. PMID:24510259

  13. CisSERS: Customizable in silico sequence evaluation for restriction sites

    DOE PAGESBeta

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit; et al

    2016-04-12

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

  14. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

    PubMed

    Sharpe, Richard M; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies. PMID:27071032

  15. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

    PubMed Central

    Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit

    2016-01-01

    High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies. PMID:27071032

  16. Cartographic Mapping of Mars Landing Sites: A Historical Perspective

    NASA Technical Reports Server (NTRS)

    Duxbury, Thomas C.

    2007-01-01

    Initial mapping of Mars began with the early Mariner 4, 6 and 7 flybys in the 1960's. Mariner 9 obtained the first global coverage of Mars in 1971. Viking Orbiters 1 and 2 added new and higher resolution global coverage. The US Geological Survey produced the first digital global cartographic map products in black and white and in color, the mosaicked digital image models (MDIMs). In 1989, the Phobos 88 mission added imaging as well as multispectral mapping of Mars in the equatorial region. The Mars Global Surveyor (MGS) added to the black and white and color global coverage. The most important development for Mars cartography occurred on MGS with its global coverage of Mars using the Mars Observer Laser Altimeter (MOL A) producing precision ground control in latitude, longitude and radius. The next version of the MDIM was produced at 230 m spatial resolution using MOLA precision cartographic control. The Mars Odyssey mission THEMIS instrument has completed its global infrared mapping of Mars at 100 m spatial resolution. The Mars Express mission is completing its global coverage of Mars in stereo at 100 m spatial resolution or better. MGS, Odyssey and Mars Express continue to provide limited surface coverage at the 1 to 20 m resolution. Currently the new Mars Reconnaissance Orbiter is producing images at the 10's of cm level. All of these datasets provide a rich and historic perspective of Mars covering nearly five decades and allow global cartographic map products to be produced in visual and infrared at the 100 m level with specialized cartographic maps being produced for landing sites at the meter or sub-meter spatial resolution level. This work was produced at the Jet Propulsion Laboratory, California Institute of Technology under contract to the National Aeronautics and Space Administration, NAS 7-7120.5d, within the NASA Mars Data Analysis Program and the MGS, Odyssey, Mars Express and MRO Participating Scientist Programs.

  17. A cosmid contig and high resolution restriction map of the 2 megabase region containing the Huntington's disease gene.

    PubMed

    Baxendale, S; MacDonald, M E; Mott, R; Francis, F; Lin, C; Kirby, S F; James, M; Zehetner, G; Hummerich, H; Valdes, J

    1993-06-01

    The quest for the mutation responsible for Huntington's disease (HD) has required an exceptionally detailed analysis of a large part of 4p16.3 by molecular genetic techniques, making this stretch of 2.2 megabases one of the best characterized regions of the human genome. Here we describe the construction of a cosmid and P1 clone contig spanning the region containing the HD gene, and the establishment of a detailed, high resolution restriction map. This ordered clone library has allowed the identification of several genes from the region, and has played a vital role in the recent identification of the Huntington's disease gene. The restriction map provides the framework for the detailed analysis of a region extremely rich in coding sequences. This study also exemplifies many of the strategies to be used in the analysis of larger regions of the human genome. PMID:8348156

  18. Site classification map for Tbilisi using seismic prospecting methods

    NASA Astrophysics Data System (ADS)

    Goguadze, Nino; Gventcadze, Aleko; Arabidze, Vakhtang; Tsereteli, Emil; Gaphrindashvili, Giorgi

    2013-04-01

    This aspect deserves major attention since it plays considerable role in the definition of the seismic impact to be considered in the design and retrofitting of structures. The most important parameter of soil maps of seismic site conditions, the shear wave velocity in the upper 30 m section of the ground (VS30) on regional scales are relatively rare since they require substantial investment in geological and geotechnical data acquisition and interpretation. Work presented here was initiated by working package wp5 of regional projects EMME (Earthquake Model for Middle East Region). In the frame of the project geophysical field work were done in some parts of Tbilisi. Seismic prospecting measurements were done along some profiles. In seismic= prospecting RAS-24 was used and obtained data is processed by Winsism V.12 (refraction analysis ). Second version of soil classification for Tbilisi city was done on the basis of new geo-engineering map of 1: 25 000 scales. For this the number of engineering-geological researches and generalization on the territory of Tbilisi were processed, All the Geological and Engineer-geological reports, that were collected and processed. Since in the geological reports less attention is paid to the genesis of the quaternary sediments and their lithological description, and in this regard the territory of Tbilisi is very difficult and multi-spectrum, it was necessary to conduct additional field surveys in 10 districts to specify information. Finely combining information that comes from seismoprospecting measurements and geo-engineering map the new site classification map expressed in Vs30 were derived for Tbilisi city.

  19. Evaluation of Mapping Methodologies at a Legacy Test Site

    NASA Astrophysics Data System (ADS)

    Sussman, A. J.; Schultz-Fellenz, E. S.; Roback, R. C.; Kelley, R. E.; Drellack, S.; Reed, D.; Miller, E.; Cooper, D. I.; Sandoval, M.; Wang, R.

    2013-12-01

    On June 12th, 1985, a nuclear test with an announced yield between 20-150kt was detonated in rhyolitic lava in a vertical emplacement borehole at a depth of 608m below the surface. This test did not collapse to the surface and form a crater, but rather resulted in a subsurface collapse with more subtle surface expressions of deformation, providing an opportunity to evaluate the site using a number of surface mapping methodologies. The site was investigated over a two-year time span by several mapping teams. In order to determine the most time efficient and accurate approach for mapping post-shot surface features at a legacy test site, a number of different techniques were employed. The site was initially divided into four quarters, with teams applying various methodologies, techniques, and instrumentations to each quarter. Early methods included transect lines and site gridding with a Brunton pocket transit, flagging tape, measuring tape, and stakes; surveying using a hand-held personal GPS to locate observed features with an accuracy of × 5-10m; and extensive photo-documentation. More recent methods have incorporated the use of near survey grade GPS devices to allow careful location and mapping of surface features. Initially, gridding was employed along with the high resolution GPS surveys, but this was found to be time consuming and of little observational value. Raw visual observation (VOB) data included GPS coordinates for artifacts or features of interest, field notes, and photographs. A categorization system was used to organize the myriad of items, in order to aid in database searches and for visual presentation of findings. The collected data set was imported into a geographic information system (GIS) as points, lines, or polygons and overlain onto a digital color orthophoto map of the test site. Once these data were mapped, spectral data were collected using a high resolution field spectrometer. In addition to geo-locating the field observations with 10cm

  20. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing.

    PubMed

    Leaché, Adam D; Chavez, Andreas S; Jones, Leonard N; Grummer, Jared A; Gottscho, Andrew D; Linkem, Charles W

    2015-03-01

    Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both "recent" and "deep" timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

  1. Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    PubMed Central

    Hilario, Elena; Barron, Lorna; Deng, Cecilia H.; Datson, Paul M.; Davy, Marcus W.; Storey, Roy D.

    2015-01-01

    Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al. method: some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS). By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS) method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145) of BamH I sites shared with the reference genome, compared to only 14% (11,513) by stdGBS. PMID:26633193

  2. Innovative restriction site created PCR-RFLP for detection of benzimidazole resistance in Teladorsagia circumcincta.

    PubMed

    Shayan, Parviz; Eslami, Ali; Borji, Hassan

    2007-04-01

    Benzimidazole compounds, especially albendazole, are the most commonly used anthelmintics for deworming of small ruminants in Iran. It is believed that the therapeutic effects of the benzimidazoles (BZs) come through their binding capacity to the beta-tubulin isotype 1. Substitution of phenylalanine to tyrosine at position 200 of this polypeptide confers resistance to BZs. Several investigators developed different biological- and molecular-based techniques to demonstrate the occurrence of resistance in helminthes against BZs. To address the determination of resistance at position 200 of beta-tubulin isotype 1, we developed an innovative restriction site created polymerase chain reaction-restriction fragment length polymorphism, in which nucleotide A at the position of 637 upstream flanked by the first two coding sequences of the phenylalanine (TT) triplet was substituted through the nucleotide G. The introduced modification in forward primer (UTvet MF-primer) leads to the creation of restriction site (AACGTT) for PSP1. Therefore, in the case of normal allele only, PSP1 can cut the corresponding PCR product. In the first step, the genomic DNA was isolated from each single Teladorsagia circumcincta collected either from the abomasa of untreated (n = 35) or of 5 mg/kg BW 2.5% albendazole suspension-treated (n = 40) sheep. It was amplified with the primer pair, creating PCR product of 403 bp in length. In the second step, the PCR product was extracted from agarose gel and amplified with the modified forward primer (UTvet MF-primer) and the same reverse primer as in step 1, creating a PCR product of 222 bp. The PCR product was then cut with PSP1 to obtain in the case of normal allele two DNA products (183 and 39 bp). Eight of the 35 worms collected from the untreated sheep were BZ(SS) homozygotes, and the rest (27) were BZ(RS) heterozygotes. In our preliminary experiment, we could not find a BZ(RR) homozygote form within the examined samples. Five out of 40 worms

  3. A geostatistical approach to mapping site response spectral amplifications

    USGS Publications Warehouse

    Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Tanaka, Y.; Tanaka, H.

    2010-01-01

    If quantitative estimates of the seismic properties do not exist at a location of interest then the site response spectral amplifications must be estimated from data collected at other locations. Currently, the most common approach employs correlations of site class with maps of surficial geology. Analogously, correlations of site class with topographic slope can be employed where the surficial geology is unknown. Our goal is to identify and validate a method to estimate site response with greater spatial resolution and accuracy for regions where additional effort is warranted. This method consists of three components: region-specific data collection, a spatial model for interpolating seismic properties, and a theoretical method for computing spectral amplifications from the interpolated seismic properties. We consider three spatial interpolation schemes: correlations with surficial geology, termed the geologic trend (GT), ordinary kriging (OK), and kriging with a trend (KT). We estimate the spectral amplifications from seismic properties using the square root of impedance method, thereby linking the frequency-dependent spectral amplifications to the depth-dependent seismic properties. Thus, the range of periods for which this method is applicable is limited by the depth of exploration. A dense survey of near-surface S-wave slowness (Ss) throughout Kobe, Japan shows that the geostatistical methods give more accurate estimates of Ss than the topographic slope and GT methods, and the OK and KT methods perform equally well. We prefer the KT model because it can be seamlessly integrated with geologic maps that cover larger regions. Empirical spectral amplifications show that the region-specific data achieve more accurate estimates of observed median short-period amplifications than the topographic slope method. ?? 2010 Elsevier B.V.

  4. Construction of a cosmid contig and of an EcoRI restriction map of yeast chromosome X.

    PubMed

    Huang, M E; Chuat, J C; Thierry, A; Dujon, B; Galibert, F

    1994-01-01

    We report here the construction of a complete physical map of the chromosome X of yeast Saccharomyces cerevisiae. Fragments resulting from partial Sau3AI digestion of DNA from a diploid strain derived from S288C were ligated to linearized pWE15, a cosmid vector with T3 and T7 promoters. Another library, made in the cosmid vector pOU61 cos, that lacks T3 and T7 promoters, was also used as a source of target clones. Chromosome-X-specific clones were sorted out by hybridization with radiolabelled pulse-field-gel-purified chromosome X as a probe. Then, 254 cosmids were ordered by walking from one to another by hybridization with end-specific T3 or T7 RNA transcripts as probes. The construction was put to the test by hybridization with a battery of chromosome X gene markers, that showed that the physical map and the genetic map were colinear. The validity of the contig was further strengthened by the results of chromosome nested fractionation with meganuclease I-SceI. An EcoRI restriction map of the contig enabled further verification and measurement of the total length of the contig, that was found to be approximately 700 kb in size. In addition to providing a base for the ongoing yeast genome sequencing project, the physical map can be used to map any sequence belonging to chromosome X. PMID:7803814

  5. 1993 report on Hanford Site land disposal restrictions for mixed wastes

    SciTech Connect

    Black, D.

    1993-04-01

    Since the early 1940s, the contractors at the Hanford Site have been involved in the production and purification of nuclear defense materials. These production activities have resulted in the generation of large quantities of liquid and solid radioactive mixed waste (RMW). This waste is subject to regulation under authority of both the Resource Conservation and Recovery Act of 1976{sup 2}(RCRA) and Atomic Energy Act{sup 3}. This report covers mixed waste only. Hazardous waste that is not contaminated with radionuclides is not addressed in this report. The Washington State Department of Ecology, US Environmental Protection Agency, and US Department of Energy have entered into an agreement, the Hanford Federal Facility Agreement and Consent Order{sup 1} (commonly referred to as the Tri-Party Agreement) to bring the Hanford Site operations into compliance with dangerous waste regulations. The Tri-Party Agreement required development of the original land disposal restrictions (LDR) plan and its annual updates to comply with LDR requirements for RMW. This report is the third update of the plan first issued in 1990. The Tri-Party Agreement requires, and the baseline plan and annual update reports provide, the information that follows: Waste characterization information; storage data; treatment information; waste reduction information; schedule; and progress.

  6. Site-specific IGFBP-1 hyper-phosphorylation in fetal growth restriction: clinical and functional relevance.

    PubMed

    Abu Shehab, Majida; Khosravi, Javad; Han, Victor K M; Shilton, Brian H; Gupta, Madhulika B

    2010-04-01

    Phosphorylation enhances IGFBP-1 binding to IGF-I, thereby limiting the bioavailability of IGF-I that may be important in fetal growth. Our goal in this study was to determine whether changes in site-specific IGFBP-1 phosphorylation were unique to fetal growth restriction. To establish a link, we compared IGFBP-1 phosphorylation (sites and degree) in amniotic fluid from FGR (N = 10) and controls (N = 12). The concentration of serine phosphorylated IGFBP-1 showed a negative correlation with birth weight in FGR (P = 0.049). LC-MS/MS analysis revealed all four previously identified phosphorylation sites (Ser98, Ser101, Ser119, and Ser169) to be common to FGR and control groups. Relative phosphopeptide intensities (LC-MS) between FGR and controls demonstrated 4-fold higher intensity for Ser101 (P = 0.026), 7-fold for Ser98/Ser101 (P = 0.02), and 23-fold for Ser169 (P = 0.002) in the FGR group. Preliminary BIAcore data revealed 4-fold higher association and 1.7-fold lower dissociation constants for IGFBP-1/IGF-I in FGR. A structural model of IGFBP-1 bound to IGF-I indicates that all the phosphorylation sites are on relatively mobile regions of the IGFBP-1 sequence. Residues Ser98, Ser101, and Ser169 are close to structured regions that are involved in IGF-I binding and, therefore, could potentially make direct contact with IGF-I. On the other hand, residue Ser119 is in the middle of the unstructured linker that connects the N- and C-terminal domains of IGFBP-1. The model is consistent with the assumption that residues Ser98, Ser101, and Ser169 could directly interact with IGF-I, and therefore phosphorylation at these sites could change IGF-I interactions. We suggest that site-specific increase in IGFBP-1 phosphorylation limits IGF-I bioavailability, which directly contributes to the development of FGR. This study delineates the potential role of higher phosphorylation of IGFBP-1 in FGR and provides the basis to substantiate these findings with larger sample size. PMID

  7. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato.

    PubMed

    Shirasawa, Kenta; Hirakawa, Hideki; Isobe, Sachiko

    2016-04-01

    Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i)in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops. PMID:26932983

  8. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato

    PubMed Central

    Shirasawa, Kenta; Hirakawa, Hideki; Isobe, Sachiko

    2016-01-01

    Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i) in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops. PMID:26932983

  9. Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites.

    PubMed

    Serrao, Erik; Cherepanov, Peter; Engelman, Alan N

    2016-01-01

    Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients. PMID:27023428

  10. Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene).

    PubMed

    Bhushan, Ashish; Mukherjee, Tanmoy; Joshi, Jayadev; Shankar, Pratap; Kalia, Vipin Chandra

    2015-06-01

    Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho. PMID:25805900

  11. Using Restriction Mapping to Teach Basic Skills in the Molecular Biology Lab

    ERIC Educational Resources Information Center

    Walsh, Lauren; Shaker, Elizabeth; De Stasio, Elizabeth A.

    2007-01-01

    Digestion of DNA with restriction enzymes, calculation of volumes and concentrations of reagents for reactions, and the separation of DNA fragments by agarose gel electrophoresis are common molecular biology techniques that are best taught through repetition. The following open-ended, investigative laboratory exercise in plasmid restriction…

  12. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... maps. 3285.103 Section 3285.103 Housing and Urban Development Regulations Relating to Housing and Urban... Considerations § 3285.103 Site suitability with design zone maps. Prior to the initial installation of a new... indicated on the design zone maps provided with the home, are suitable for the site location where the...

  13. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... maps. 3285.103 Section 3285.103 Housing and Urban Development Regulations Relating to Housing and Urban... Considerations § 3285.103 Site suitability with design zone maps. Prior to the initial installation of a new... indicated on the design zone maps provided with the home, are suitable for the site location where the...

  14. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... maps. 3285.103 Section 3285.103 Housing and Urban Development Regulations Relating to Housing and Urban... Considerations § 3285.103 Site suitability with design zone maps. Prior to the initial installation of a new... indicated on the design zone maps provided with the home, are suitable for the site location where the...

  15. 24 CFR 3285.103 - Site suitability with design zone maps.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... maps. 3285.103 Section 3285.103 Housing and Urban Development Regulations Relating to Housing and Urban... Considerations § 3285.103 Site suitability with design zone maps. Prior to the initial installation of a new... indicated on the design zone maps provided with the home, are suitable for the site location where the...

  16. A sequence-tagged site map of human chromosome 11.

    PubMed

    Smith, M W; Clark, S P; Hutchinson, J S; Wei, Y H; Churukian, A C; Daniels, L B; Diggle, K L; Gen, M W; Romo, A J; Lin, Y

    1993-09-01

    We report the construction of 370 sequence-tagged sites (STSs) that are detectable by PCR amplification under sets of standardized conditions and that have been regionally mapped to human chromosome 11. DNA sequences were determined by sequencing directly from cosmid templates using primers complementary to T3 and T7 promoters present in the cloning vector. Oligonucleotide PCR primers were predicted by computer and tested using a battery of genomic DNAs. Cosmids were regionally localized on chromosome 11 by using fluorescence in situ hybridization or by analyzing a somatic cell hybrid panel. Additional STSs corresponding to known genes and markers on chromosome 11 were also produced under the same series of standardized conditions. The resulting STSs provide uniform coverage of chromosome 11 with an average spacing of 340 kb. The DNA sequence determined for use in STS production corresponds to about 0.1% (116 kb) of chromosome 11 and has been analyzed for the presence of repetitive sequences, similarities to known genes and motifs, and possible exons. Computer analysis of this sequence has identified and therefore mapped at least eight new genes on chromosome 11. PMID:8244387

  17. 1997 Hanford site report on land disposal restrictions for mixed waste

    SciTech Connect

    Black, D.G.

    1997-04-07

    The baseline land disposal restrictions (LDR) plan was prepared in 1990 in accordance with the Hanford Federal Facility Agreement and Consent Order (commonly referred to as the Tn-Party Agreement) Milestone M-26-00 (Ecology et al, 1989). The text of this milestone is below. ''LDR requirements include limitations on storage of specified hazardous wastes (including mixed wastes). In accordance with approved plans and schedules, the U.S. Department of Energy (DOE) shall develop and implement technologies necessary to achieve full compliance with LDR requirements for mixed wastes at the Hanford Site. LDR plans and schedules shall be developed with consideration of other action plan milestones and will not become effective until approved by the U.S. Environmental Protection Agency (EPA) (or Washington State Department of Ecology [Ecology]) upon authorization to administer LDRs pursuant to Section 3006 of the Resource Conservation and Recovery Act of 1976 (RCRA). Disposal of LDR wastes at any time is prohibited except in accordance with applicable LDR requirements for nonradioactive wastes at all times. The plan will include, but not be limited to, the following: Waste characterization plan; Storage report; Treatment report; Treatment plan; Waste minimization plan; A schedule depicting the events necessary to achieve full compliance with LDR requirements; and A process for establishing interim milestones.

  18. Application of restriction site amplified polymorphism (RSAP) to genetic diversity in Saccharina japonica

    NASA Astrophysics Data System (ADS)

    Zhao, Cui; Liu, Cui; Li, Wei; Chi, Shan; Feng, Rongfang; Liu, Tao

    2013-07-01

    Restriction site amplified polymorphism (RSAP) was used, for the first time, to analyze the genetic structure and diversity of four, mainly cultivated, varieties of the brown alga, Saccharina japonica. Eighty-eight samples from varieties " Rongfu ", " Fujian ", " Ailunwan " and " Shengchanzhong " were used for the genetic analyses. One hundred and ninety-eight bands were obtained using eight combinations of primers. One hundred and ninety-one (96.46%) were polymorphic bands. Nei's genetic diversity was 0.360, and the coefficient of genetic differentiation was 0.357. No inbreeding-type recession was found in the four brown alga varieties and the results of the " Ailunwan " variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program. Genetic diversity and cluster analyses results were consistent with these genetic relationships. The results show the RSAP method is suitable for genetic analysis. Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.

  19. Patterns of Ancestral Human Diversity: An Analysis of Alu-Insertion and Restriction-Site Polymorphisms

    PubMed Central

    Watkins, W. S.; Ricker, C. E.; Bamshad, M. J.; Carroll, M. L.; Nguyen, S. V.; Batzer, M. A.; Harpending, H. C.; Rogers, A. R.; Jorde, L. B.

    2001-01-01

    We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations. PMID:11179020

  20. AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping

    PubMed Central

    Xia, Zhiqiang; Zou, Meiling; Zhang, Shengkui; Feng, Binxiao; Wang, Wenquan

    2014-01-01

    We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding. PMID:25466435

  1. De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

    PubMed Central

    2013-01-01

    Background Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place. Through a National Sunflower Association (NSA) funded initiative, we report on the process of SNP discovery through reductive genome sequencing and local assembly of six diverse sunflower inbred lines that represent oil as well as confection types. Results A combination of Restriction site Associated DNA Sequencing (RAD-Seq) protocols and Illumina paired-end sequencing chemistry generated high quality 89.4 M paired end reads from the six lines which represent 5.3 GB of the sequencing data. Raw reads from the sunflower line, RHA 464 were assembled de novo to serve as a framework reference genome. About 15.2 Mb of sunflower genome distributed over 42,267 contigs were obtained upon assembly of RHA 464 sequencing data, the contig lengths ranged from 200 to 950 bp with an N50 length of 393 bp. SNP calling was performed by aligning sequencing data from the six sunflower lines to the assembled reference RHA 464. On average, 1 SNP was located every 143 bp of the sunflower genome sequence. Based on several filtering criteria, a final set of 16,467 putative sequence variants with characteristics favorable for Illumina Infinium Genotyping Technology (IGT) were mined from the sequence data generated across six diverse sunflower lines. Conclusion Here we report the molecular and computational methodology involved in SNP development for a complex genome like sunflower lacking reference assembly, offering an attractive tool for molecular breeding purposes in sunflower. PMID:23947483

  2. 1994 Report on Hanford Site land disposal restrictions for mixed waste

    SciTech Connect

    Black, D.G.

    1994-04-01

    The baseline land disposal restrictions (LDR) plan was prepared in 1990 in accordance with the Hanford Federal Facility Agreement and Consent Order (commonly referred to as the Tri-Party Agreement) Milestone M-26-00 (Ecology et al. 1992). The text of this milestone is below. LDR requirements include limitations on storage of specified hazardous wastes (including mixed wastes). In accordance with approved plans and schedules, the US Department of Energy (DOE) shall develop and implement technologies necessary to achieve full compliance with LDR requirements for mixed wastes at the Hanford Site. LDR plans and schedules shall be developed with consideration at other action plan milestones and will not become effective until approved by the US Environmental Protection Agency (EPA) (or Washington State Department of Ecology [Ecology]) upon authorization to administer LDRs pursuant to Section 3006 of the Resource Conservation and Recovery Act of 1976 (RCRA). Disposal of LDR wastes at any time is prohibited except in accordance with applicable LDR requirements for nonradioactive wastes at all times. The plan will include, but not be limited to, the following: waste characterization plan; storage report; treatment report; treatment plan; waste minimization plan; a schedule depicting the events necessary to achieve full compliance with LDR requirements; a process for establishing interim milestones. The original plan was published in October 1990. This is the fourth of a series of annual updates required by Tri-Party Agreement Milestone M-26-01. A Tri-Party Agreement change request approved in March 1992 changed the annual due date from October to April and consolidated this report with a similar one prepared under Milestone M-25-00. The reporting period for this report is from April 1, 1993, to March 31, 1994.

  3. Light chain amyloidosis of the urinary bladder. A site restricted deposition of an externally produced immunoglobulin

    PubMed Central

    Livneh, A; Shtrasburg, S; Martin, B; Baniel, J; Gal, R; Pras, M

    2001-01-01

    Aims—To identify the amyloid protein in a patient with amyloidosis localised to the urinary bladder, and to see whether subtyping of the protein by sequence analysis increases the understanding of the selection of the urinary bladder as the site of amyloid deposition. Methods—A patient with gross haematuria and a congophilic mass in his urinary bladder was evaluated further. Characterisation of the amyloid protein was performed using conventional histological and immunohistochemical methods. Determination of the N-terminal amino acid sequence of the amyloid protein was performed using protein sequencers. Results—The patient's history, physical examination, and laboratory evaluation excluded the involvement of other organs, justifying a diagnosis of amyloidosis localised to the urinary bladder. Histological and immunological studies showed that the amyloid protein deposited in the urinary bladder of the patient was probably of the amyloid light chain type. No plasma cells or lymphocytes were seen in sections of the urinary bladder and lower ureter adjacent to the amyloid deposits. Molecular analysis showed the sequence NFMLTQPHSISGSPG, which assigned the amyloid protein to either the VλI or the VλVI immunoglobulin (Ig) light chain families. Conclusions—The findings suggest that the amyloid protein in this patient originated outside the urinary bladder. The heterogeneity of the Ig proteins in known cases of amyloidosis of the lower urinary tract suggests that the amino acid residues, which determine the Vλ subtyping, have no major role in restricting the deposited protein to the urinary bladder. Key Words: primary amyloidosis • urinary bladder • λ light chain • amino acid sequence PMID:11729210

  4. Magnetic mapping and interpretation of an archaeological site in Syria

    NASA Astrophysics Data System (ADS)

    khatib alkontar, Rozan AL; Munschy, Marc; Castel, Corinne; Quenet, Philippe

    2014-05-01

    Among the subsurface methods of exploration that have been developed to meet the new requirements of archaeological research, geophysical methods offer a very wide range of applications in the study of buried deposits. In their latest developments, the prospecting method based on the measurement of the magnetic field is particularly effective at very different types of sites, ranging from prehistoric times to the most recent. The measured magnetic field observed at a place and at a time, results from the vector sum of the main regional field, the effect of subsurface structures, local disturbances such as power lines, buildings, fences, and the diurnal variation (solar influence). The principle of the magnetic method is, from magnetic measurements on a flat plane above the prospected surface, to study the three-dimensional variations of magnetization producing the magnetic anomalies. The use of magnetic surveys for archaeological prospecting is a well-established and versatile technique, and wide ranges of data processing routines are often applied to further enhance acquired data or derive source parameters. The main purpose of this work was to acquire new magnetic data on the field and to propose quantitative interpretations of magnetic maps obtained on three archaeological sites of Bronze Age in Syria (Badiyah ANR program). More precisely, some results are presented concerning one of the three sites, the Tell Al-Rawda-site which corresponds to a circular city of Early Bronze Age with a radius of about 200 m. Several profiles are used to characterize magnetizations. A large portion of archaeological geophysical data are concerned primarily with identifying the location and spatial extent of buried remains, although the data collected are likely to contain further information relating to the depth and geometry of anomalous features. A simple magnetic model corresponding to rectangular structures uniformly magnetized associated to walls cannot explain the magnetic

  5. A computer assisted method for the determination of restriction enzyme recognifion sites.

    PubMed Central

    Gingeras, T R; MIlazzo, J P; Roberts, R J

    1978-01-01

    A computer program has been developed which aids in the determination of restriction enzyme recognition sequences. This is achieved by cleaving DNAs of known sequence with a restriction endonuclease and comparing the fragmentation pattern with a computer-generated set of patterns. The feasibility of this approach has been tested using fragmentation patterns of 0X174 DNA produced by enzymes of both known and unknown specificity. Recognition sequences are predicted for two restriction endonucleases (BbvI and SfaNI) using this method. In addition, recognition sequences are predicted for two other new enzymes (PvuI and MstI) using another computer-assisted method. Images PMID:724510

  6. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms.

    PubMed

    Paterson, A H; Lander, E S; Hewitt, J D; Peterson, S; Lincoln, S E; Tanksley, S D

    1988-10-20

    The conflict between the Mendelian theory of particulate inheritance and the observation of continuous variation for most traits in nature was resolved in the early 1900s by the concept that quantitative traits can result from segregation of multiple genes, modified by environmental effects. Although pioneering experiments showed that linkage could occasionally be detected to such quantitative trait loci (QTLs), accurate and systematic mapping of QTLs has not been possible because the inheritance of an entire genome could not be studied with genetic markers. The use of restriction fragment length polymorphisms (RFLPs) has made such investigations possible, at least in principle. Here, we report the first use of a complete RFLP linkage map to resolve quantitative traits into discrete Mendelian factors, in an interspecific back-cross of tomato. Applying new analytical methods, we mapped at least six QTLs controlling fruit mass, four QTLs for the concentration of soluble solids and five QTLs for fruit pH. This approach is broadly applicable to the genetic dissection of quantitative inheritance of physiological, morphological and behavioural traits in any higher plant or animal. PMID:2902517

  7. Mapping I-A(g7) restricted epitopes in murine G6PC2.

    PubMed

    Yang, Tao; Hohenstein, Anita C; Lee, Catherine E; Hutton, John C; Davidson, Howard W

    2013-03-01

    G6PC2, also known as islet-specific glucose 6-phosphatase catalytic subunit-related protein (IGRP), is a major target of autoreactive CD8(+) T cells in both diabetic human subjects and the non-obese diabetic (NOD) mouse. However, in contrast to the abundant literature regarding the CD8(+) response to this antigen, much less is known about the potential involvement of IGRP-reactive CD4(+) T cells in diabetogenesis. The single previous study that examined this question in NOD mice was based upon a candidate epitope approach and identified three I-A(g7)-restricted epitopes that each elicited spontaneous responses in these animals. However, given the known inaccuracies of MHC class II epitope prediction algorithms, we hypothesized that additional specificities might also be targeted. To address this issue, we immunized NOD mice with membranes from insect cells overexpressing full-length recombinant mouse IGRP and measured recall responses of purified CD4(+) T cells using a library of overlapping peptides encompassing the entire 355-aa primary sequence. Nine peptides representing 8 epitopes gave recall responses, only 1 of which corresponded to any of the previously reported sequences. In each case proliferation was blocked by a monoclonal antibody to I-A(g7), but not the appropriate isotype control. Consistent with a role in diabetogenesis, proliferative responses to 4 of the 9 peptides (3 epitopes) were also detected in CD4(+) T cells purified from the pancreatic draining lymph nodes of pre-diabetic female animals, but not from peripheral lymph nodes or spleens of the same animals. Intriguingly, one of the newly identified spontaneously reactive epitopes (P8 [IGRP(55-72)]) is highly conserved between mice and man, suggesting that it might also be a target of HLA-DQ8-restricted T cells in diabetic human subjects, an hypothesis that we are currently testing. PMID:22983906

  8. Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

    PubMed

    Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

    2016-09-01

    Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

  9. Restriction site detection in repetitive nuclear DNA sequences of Trypanosoma evansi for strain differentiation among different isolates.

    PubMed

    Shyma, K P; Gupta, S K; Gupta, J P; Singh, Ajit; Chaudhari, S S; Singh, Veer

    2016-09-01

    The differences or similarities among different isolates of Trypanosoma evansi through endonuclease profile was identified in the present study. The repetitive nuclear DNA of T. evansi isolated from infected cattle, buffalo and equine blood was initially amplified by PCR using specific primers. A panel of restriction enzymes, EcoRI, Eco91l, HindIII and PstI were for complete digestion of PCR products. Agarose gel electrophoresis of digested product did not show cleavage fragments and only single DNA band of the original size was visible in the ethidium bromide stained agarose gel. This indicated that the 227 bp PCR product from repetitive sequence had no site-specific cleavage sites for the REs used in this study. No heterogeneity in the repetitive nuclear DNA restriction endonuclease profile among the different isolates was recorded. PMID:27605842

  10. A Site Response Map of the Continental U.S

    NASA Astrophysics Data System (ADS)

    Magistrale, H.; Rong, Y.; Thompson, E.; Silva, W. J.

    2012-12-01

    We create a site response map of the continental U.S. using the topographic slope methodology, which uses correlations between slope and Vs30 (Wald and Allen, 2007). We determine new regional correlations for the central and eastern U.S. (CEUS) and western U.S. (WUS) calibrated to the Vs30 observation database of Pacific Engineering and Analysis, and introduce a novel correlation for areas of the WUS that hosted Pleistocene and younger lakes. In the WUS we develop a new correlation by first removing Vs30 observations from Utah basins and the Imperial Valley, California, from the database, and second using a stochastic simulation to choose slope and Vs30 bins and calculate standard deviation and bias. We select the best model based on three criteria: (i) bias and standard deviation is among the smallest; (ii) the correlations will not change dramatically for neighboring bins; and (iii) the Vs30 bin boundaries can be matched to NEHRP categories. Relative to WUS, the Utah and Imperial Valley Vs30 values are low for a given slope. We fit a separate correlation in the manner described above. We attribute the low values to the occupation of these areas by Pleistocene and younger lakes. We posit that when sediment-laden streams entered these lakes, the flow velocity was reduced so that all coarse sediments were deposited at the lake margin, and only very fine grained (and seismically slow) material was distributed over the lake bed. This model is confirmed by: (i) relatively high Vs30 values in the geologically similar Las Vegas Valley that was not occupied by a lake; (ii) ordinary Vs30 values in Utah and Imperial Valley locations above the high lake stands; and (iii) a consistent pattern of Vs30 values in the Reno, Nevada, basin across a paleo-lake boundary. In the CEUS, we use the recent correlation of Silva et al. (2011) that includes better constraints on the correlation at rock sites. In all regions the slopes are determined from SRTM digital elevation data (Jarvis

  11. Integrated Mapping and Imaging at a Legacy Test Site (Invited)

    NASA Astrophysics Data System (ADS)

    Sussman, A. J.; Schultz-Fellenz, E. S.; Kelley, R. E.; Sweeney, J. J.; Vigil, S.; DiBenedetto, J.; Chipman, V.

    2013-12-01

    A team of multi-disciplinary geoscientists was tasked to characterize and evaluate a legacy nuclear detonation site in order to develop research locations with the long-term goal of improving treaty monitoring, verification, and other national security applications. There was a test at the site of interest that was detonated on June 12, 1985 in a vertical emplacement borehole at a depth of 608m below the surface in rhyolites. With announced yield of 20-150 kt, the event did not collapse to the surface and form a crater, but rather experienced a subsurface collapse with more subtle surface expressions of deformation. This result provides the team with an opportunity to evaluate a number of surface and subsurface inspection technologies in a broad context. The team collected ground-based visual observation, ground penetrating radar, electromagnetic, ground-based and airborne LiDAR, ground-based and airborne hyperspectral, gravity and magnetics, dc and induction electrical methods, and active seismic data during field campaigns in the summers of 2012 and 2013. Detection of features was performed using various approaches that were assessed for accuracy, efficiency and diversity of target features. For example, whereas the primary target of the ground-based visual observation survey was to map the surface features, the target of the gravity survey was to attempt the detection of a possible subsurface collapse zone which might be located as little as 200 meters below the surface. The datasets from surveys described above are integrated into a geographical information system (GIS) database for analysis and visualization. Other presentations during this session provide further details as to some of the work conducted. Work by Los Alamos National Laboratory and Lawrence Livermore National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946/NST10-NCNS-PD00. Work by National Security Technologies, LLC, was performed under

  12. 1999 Report on Hanford Site land disposal restriction for mixed waste

    SciTech Connect

    BLACK, D.G.

    1999-03-25

    This report was submitted to meet the requirements of Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) Milestone M-26-011. This milestone requires the preparation of an annual report that covers characterization, treatment, storage, minimization, and other aspects of managing land-disposal-restricted mixed waste at the Hanford Facility.

  13. [Rapid site-directed mutagenesis on full-length plasmid DNA by using designed restriction enzyme assisted mutagenesis].

    PubMed

    Zhang, Baozhong; Ran, Duoliang; Zhang, Xin; An, Xiaoping; Shan, Yunzhu; Zhou, Yusen; Tong, Yigang

    2009-02-01

    To use the designed restriction enzyme assisted mutagenesis technique to perform rapid site-directed mutagenesis on double-stranded plasmid DNA. The target amino acid sequence was reversely translated into DNA sequences with degenerate codons, resulting in large amount of silently mutated sequences containing various restriction endonucleases (REs). Certain mutated sequence with an appropriate RE was selected as the target DNA sequence for designing mutation primers. The full-length plasmid DNA was amplified with high-fidelity Phusion DNA polymerase and the amplified product was 5' phosphorylated by T4 polynucleotide kinase and then self-ligated. After transformation into an E. coli host the transformants were rapidly screened by cutting with the designed RE. With this strategy we successfully performed the site-directed mutagenesis on an 8 kb plasmid pcDNA3.1-pIgR and recovered the wild-type amino acid sequence of human polymeric immunoglobulin receptor (pIgR). A novel site-directed mutagenesis strategy based on DREAM was developed which exploited RE as a rapid screening measure. The highly efficient, high-fidelity Phusion DNA polymerase was applied to ensure the efficient and faithful amplification of the full-length sequence of a plasmid of up to 8 kb. This rapid mutagenesis strategy avoids using any commercial site-directed mutagenesis kits, special host strains or isotopes. PMID:19459340

  14. Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving

    PubMed Central

    2011-01-01

    Background The TaqII enzyme is a member of the Thermus sp. enzyme family that we propounded previously within Type IIS restriction endonucleases, containing related thermophilic bifunctional endonucleases-methyltransferases from various Thermus sp.: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI and TsoI. These enzymes show significant nucleotide and amino acid sequence similarities, a rare phenomenon among restriction endonucleases, along with similarities in biochemical properties, molecular size, DNA recognition sequences and cleavage sites. They also feature some characteristics of Types I and III. Results Barker et al. reported the Type IIS/IIC restriction endonuclease TaqII as recognizing two distinct cognate site variants (5'-GACCGA-3' and 5'-CACCCA-3') while cleaving 11/9 nucleotides downstream. We used four independent methods, namely, shotgun cloning and sequencing, restriction pattern analysis, digestion of particular custom substrates and GeneScan analysis, to demonstrate that the recombinant enzyme recognizes only 5'-GACCGA-3' sites and cleaves 11/9 nucleotides downstream. We did not observe any 5'-CACCCA-3' cleavage under a variety of conditions and site arrangements tested. We also characterized the enzyme biochemically and established new digestion conditions optimal for practical enzyme applications. Finally, we developed and propose a new version of the Fidelity Index - the Fidelity Index for Partial Cleavage (FI-PC). Conclusions The DNA recognition sequence of the bifunctional prototype TaqII endonuclease-methyltransferase from Thermus aquaticus has been redefined as recognizing only 5'-GACCGA-3' cognate sites. The reaction conditions (pH and salt concentrations) were designed either to minimize (pH = 8.0 and 10 mM ammonium sulphate) or to enhance star activity (pH = 6.0 and no salt). Redefinition of the recognition site and reaction conditions makes this prototype endonuclease a useful tool for DNA manipulation; as yet, this enzyme has no practical

  15. 76 FR 19003 - Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-06

    ...: Proposed rule. SUMMARY: EPA is proposing to issue both a site-specific treatment variance to U.S. Ecology... proposes to issue both a site-specific treatment variance to U.S. Ecology Nevada (USEN) located in Beatty... section of this document. II. Does this action apply to me? This proposal applies only to U. S....

  16. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

    PubMed Central

    2010-01-01

    High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

  17. Interactive NCORP Map Details Community Research Sites | Division of Cancer Prevention

    Cancer.gov

    An interactive map of the NCI Community Oncology Research Program (NCORP) with detailed information on hundreds of community sites that take part in clinical trials is available on the NCORP website. |

  18. Is it enough to have one ECa map for the site-specific management delineation?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The soil apparent electrical conductivity (ECa) has been used to map soil spatial variability and to relate it to the variability of various soil properties thus delineating zones of site-specific management. Most often, a single ECa survey is done and the generated ECa map is considered to infer t...

  19. A 405-kb cosmid contig and HindIII restriction map of the progressive myoclonus epilepsy type 1 (EPM1) candidate region in 21q22.3

    SciTech Connect

    Lafreniere, R.G.; Rouleau, G.A.; De Jong, P.J.

    1995-09-01

    As a step toward identifying the molecular defect in patients afflicted with progressive myoclonus epilepsy type 1 (EPM1), we have assembled a cosmid contig of the candidate EPM1 region in 21q22.3. The contig constitutes a collection of 87 different cosmids spanning 405 kb based on a derived HindIII restriction map. Potential CpG-rich islands have been identified based on the restriction map generated from eight different rare-cutting enzymes. This contig contains the genetic material required for the isolation of expressed sequences and the identification of the gene defective in EPM1 and possibly other disorders mapping to this region. 15 refs., 1 fig.

  20. Preliminary Correlation Map of Geomorphic Surfaces in North-Central Frenchman Flat, Nevada Test Site

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    This correlation map (scale = 1:12,000) presents the results of a mapping initiative that was part of the comprehensive site characterization required to operate the Area 5 Radioactive Waste Management Site, a low-level radioactive waste disposal facility located in northern Frenchman Flat at the Nevada Test Site. Eight primary map units are recognized for Quaternary surfaces: remnants of six alluvial fan or terrace surfaces, one unit that includes colluvial aprons associated with hill slopes, and one unit for anthropogenically disturbed surfaces. This surficial geology map provides fundamental data on natural processes for reconstruction of the Quaternary history of northern Frenchman Flat, which in turn will aid in the understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. The bedrock units identified on this map were derived from previous published mapping efforts and are included for completeness.

  1. 1998 report on Hanford Site land disposal restrictions for mixed waste

    SciTech Connect

    Black, D.G.

    1998-04-10

    This report was submitted to meet the requirements of Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) Milestone M-26-01H. This milestone requires the preparation of an annual report that covers characterization, treatment, storage, minimization, and other aspects of managing land-disposal-restricted mixed waste at the Hanford Facility. The US Department of Energy, its predecessors, and contractors on the Hanford Facility were involved in the production and purification of nuclear defense materials from the early 1940s to the late 1980s. These production activities have generated large quantities of liquid and solid mixed waste. This waste is regulated under authority of both the Resource Conservation and Recovery Act of l976 and the Atomic Energy Act of 1954. This report covers only mixed waste. The Washington State Department of Ecology, US Environmental Protection Agency, and US Department of Energy have entered into the Tri-Party Agreement to bring the Hanford Facility operations into compliance with dangerous waste regulations. The Tri-Party Agreement required development of the original land disposal restrictions (LDR) plan and its annual updates to comply with LDR requirements for mixed waste. This report is the eighth update of the plan first issued in 1990. The Tri-Party Agreement requires and the baseline plan and annual update reports provide the following information: (1) Waste Characterization Information -- Provides information about characterizing each LDR mixed waste stream. The sampling and analysis methods and protocols, past characterization results, and, where available, a schedule for providing the characterization information are discussed. (2) Storage Data -- Identifies and describes the mixed waste on the Hanford Facility. Storage data include the Resource Conservation and Recovery Act of 1976 dangerous waste codes, generator process knowledge needed to identify the waste and to make LDR determinations, quantities

  2. Assembly of a 1-Mb restriction-mapped cosmid contig spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1

    SciTech Connect

    Olsen, A.S.; Georgescu, A.; Johnson, S.; Carrano, A.V.

    1996-06-01

    We describe the assembly of a 1-Mb cosmid contig and restriction map spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1. The map was constructed from 16 smaller contigs assembled by fingerprinting, a BAC and a PAC clone, and 42 previously unmapped cosmids. In most cases, single-step cosmid walks were sufficient to join two previously assembled contigs, and all but one gap was filled from this cosmid contig library. The remaining gap of about 19 kb was spanned with a single BAC and a single PAC clone. EcoRI mapping of a dense set of overlapping clones validated the assembly of the map and indicated a length of 1040 kb for the contig. This high-resolution clone map provides an ideal resource for gene identification through cDNA selection, exon trapping, and DNA sequencing. 10 refs., 1 fig.

  3. Mapping epitopes and antigenicity by site-directed masking

    NASA Astrophysics Data System (ADS)

    Paus, Didrik; Winter, Greg

    2006-06-01

    Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to -lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with -lactamase in Freund's adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund's adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. backbone flexibility | Freund's adjuvant | conformational epitope | antisera

  4. Supplemental Investigation Plan for FFACO Use Restrictions, Nevada Test Site, Nevada, Revision 0

    SciTech Connect

    Lynn Kidman

    2008-02-01

    This document is part of an effort to re-evaluate all FFACO URs against the current RBCA criteria (referred to in this document as the Industrial Sites [IS] RBCA process) as defined in the Industrial Sites Project Establishment of Final Action Levels (NNSA/NSO, 2006a). After reviewing all of the existing FFACO URs, the 12 URs addressed in this Supplemental Investigation Plan (SIP) could not be evaluated against the current RBCA criteria as sufficient information about the contamination at each site was not available. This document presents the plan for conducting field investigations to obtain the needed information. This SIP includes URs from Corrective Action Units (CAUs) 326, 339, 358, 452, 454, 464, and 1010, located in Areas 2, 6, 12, 19, 25, and 29 of the Nevada Test Site, which is approximately 65 miles northwest of Las Vegas, Nevada; and CAU 403, located in Area 3 of the Tonopah Test Range, which is approximately 165 miles north of Las Vegas, Nevada.

  5. Orbital-science investigation: Part K: geologic sketch map of the candidate Proclus Apollo landing site

    USGS Publications Warehouse

    Lucchitta, Baerbel Koesters

    1972-01-01

    A panoramic camera frame (fig. 25-69) was used as the base for a geologic sketch map (fig. 25-70) of an area near Proclus Crater. The map was prepared to investigate the usefulness of the Apollo 15 panoramic camera photography in large-scale geologic mapping and to assess the geologic value of this area as a potential Apollo landing site. The area is being considered as a landing site because of the availability of smooth plains terrain and because of the scientific value of investigating plains materials, dark halo craters, and ancient rocks that may be present in the Proclus ray material.

  6. Reverse footprinting to map sites of RNA-protein interactions.

    PubMed

    Nilsen, Timothy W

    2014-06-01

    Nuclease protection of a site-specifically labeled RNA by an RNA-binding protein is an extremely powerful method for determining the site of an RNA-protein interaction. If a protein binds to the region that contains the site-specific label, it will protect the label and adjoining sequences from nuclease digestion. The protected region, or "footprint," can then be characterized by extensive fragmentation and gel electrophoresis. As the name implies, reverse footprinting produces a mirror image of a conventional footprint; the footprint is revealed by the presence, not the absence, of bands. This method has a distinct advantage over conventional footprinting in that only a small fraction of the labeled RNA must be bound. PMID:24890211

  7. Mapping epitopes and antigenicity by site-directed masking

    PubMed Central

    Paus, Didrik; Winter, Greg

    2006-01-01

    Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (β-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to β-lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with β-lactamase in Freund’s adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund’s adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. PMID:16754878

  8. Digital geologic map database of the Nevada Test Site area, Nevada

    SciTech Connect

    Wahl, Ronald R.; Sawyer, David A.; Minor, Scott A.; Carr, Michael D.; Cole, James C.; Swadley, W.C.; Laczniak, Randell J.; Warren, Richard G.; Green, Katryn S.; Engle, Colin M.

    1997-09-09

    Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients. The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

  9. A yeast artificial chromosome contig and NotI restriction map that spans the tumor suppressor gene(s) locus, 11q22.2-q23.3

    SciTech Connect

    Arai, Yasuhito; Hosoda, Fumie; Nakayama, Kyoko; Ohki, Misao

    1996-07-01

    Human chromosome 11q22-q23 is a pathologically important region in which a high level of loss of heterozygosity has been reported for breast, ovary, cervical, colon, and lung carcinomas, malignant melanomas, and hematologic malignancies. This strongly indicates that one or more tumor suppressor genes reside within the deleted region. In this report, we report the development of a contig map that covers most of the deleted regions found in these malignancies. The map comprises a contig of 66 overlapping yeast artificial chromosomes (YACs) and spans a region of 17 Mb from the PGR gene at 11q22.2 to the MLL gene at q23.3. In the process of screening the YACs, 50 new sequence-tagged site markers were developed from the termini of the YAC inserts. These markers were used for chromosome walking, and the data were then integrated into the contig map. NotI sites in the region. Using 22 of them, a NotI restriction map of the region from PGR to D11S939 was developed. This YAC contig will provide efficient tools for identification of the putative tumor suppressor gene(s). 49 refs., 3 figs., 2 tabs.

  10. Mapping of phosphorylation sites in polyomavirus large T antigen

    SciTech Connect

    Hassauer, M.; Scheidtmann, K.H.; Walter, G.

    1986-06-01

    The phosphorylation sites of polyomavirus large T antigen from infected or transformed cells were investigated. Tryptic digestion of large T antigen from infected, /sup 32/P/sub i/-labeled cells revealed seven major phosphopeptides. Five of these were phosphorylated only at serine residues, and two were phosphorylated at serine and threonine residues. The overall ratio of phosphoserine to phosphothreonine was 6:1. The transformed cell line B4 expressed two polyomavirus-specific phosphoproteins: large T antigen, which was only weakly phosphorylated, and a truncated form of large T antigen of 34,000 molecular weight which was heavily phosphorylated. Both showed phosphorylation patterns similar to that of large T antigen from infected cells. Peptide analyses of large T antigens encoded by the deletion mutants dl8 and dl23 or of specific fragments of wild-type large T antigen indicated that the phosphorylation sites are located in an amino-terminal region upstream of residue 194. The amino acid composition of the phosphopeptides as revealed by differential labeling with various amino acids indicated that several phosphopeptides contain overlapping sequences and that all phosphorylation sites are located in four tryptic peptides derived from a region between Met71 and Arg191. Two of the potential phosphorylation sites were identified as Ser81 and Thr187. The possible role of this modification of large T antigen is discussed.

  11. Post-Closure Strategy for Use-Restricted Sites on the Nevada National Security Site, Nevada Test and Training Range, and Tonopah Test Range, Nevada

    SciTech Connect

    Silvas, A. J.

    2014-03-26

    The purpose of this Post-Closure Strategy is to provide a consistent methodology for continual evaluation of post-closure requirements for use-restricted areas on the Nevada National Security Site (NNSS), Nevada Test and Training Range (NTTR), and Tonopah Test Range (TTR) to consolidate, modify, or streamline the program. In addition, this document stipulates the creation of a single consolidated Post-Closure Plan that will detail the current post-closure requirements for all active use restrictions (URs) and outlines its implementation and subsequent revision. This strategy will ensure effective management and control of the post-closure sites. There are currently over 200 URs located on the NNSS, NTTR, and TTR. Post-closure requirements were initially established in the Closure Report for each site. In some cases, changes to the post-closure requirements have been implemented through addenda, errata sheets, records of technical change, or letters. Post-closure requirements have been collected from these multiple sources and consolidated into several formats, such as summaries and databases. This structure increases the possibility of inconsistencies and uncertainty. As more URs are established and the post-closure program is expanded, the need for a comprehensive approach for managing the program will increase. Not only should the current requirements be obtainable from a single source that supersedes all previous requirements, but the strategy for modifying the requirements should be standardized. This will enable more effective management of the program into the future. This strategy document and the subsequent comprehensive plan are to be implemented under the assumption that the NNSS and outlying sites will be under the purview of the U.S. Department of Energy, National Nuclear Security Administration for the foreseeable future. This strategy was also developed assuming that regulatory control of the sites remains static. The comprehensive plan is not

  12. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells.

    PubMed

    Kok, Yik Lim; Vongrad, Valentina; Shilaih, Mohaned; Di Giallonardo, Francesca; Kuster, Herbert; Kouyos, Roger; Günthard, Huldrych F; Metzner, Karin J

    2016-01-01

    The host genetic landscape surrounding integrated HIV-1 has an impact on the fate of the provirus. Studies analysing HIV-1 integration sites in macrophages are scarce. We studied HIV-1 integration site patterns in monocyte-derived macrophages (MDMs) and activated CD4(+) T cells derived from seven antiretroviral therapy (ART)-treated HIV-1-infected individuals whose cells were infected ex vivo with autologous HIV-1 isolated during the acute phase of infection. A total of 1,484 unique HIV-1 integration sites were analysed. Their distribution in the human genome and genetic features, and the effects of HIV-1 integrase polymorphisms on the nucleotide selection specificity at these sites were indistinguishable between the two cell types, and among HIV-1 isolates. However, the repertoires of HIV-1-hosting gene clusters overlapped to a higher extent in MDMs than in CD4(+) T cells. The frequencies of HIV-1 integration events in genes encoding HIV-1-interacting proteins were also different between the two cell types. Lastly, HIV-1-hosting genes linked to clonal expansion of latently HIV-1-infected CD4(+) T cells were over-represented in gene hotspots identified in CD4(+) T cells but not in those identified in MDMs. Taken together, the repertoire of genes targeted by HIV-1 in MDMs is distinct from and more restricted than that of CD4(+) T cells. PMID:27067385

  13. Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4+ T cells

    PubMed Central

    Kok, Yik Lim; Vongrad, Valentina; Shilaih, Mohaned; Di Giallonardo, Francesca; Kuster, Herbert; Kouyos, Roger; Günthard, Huldrych F.; Metzner, Karin J.

    2016-01-01

    The host genetic landscape surrounding integrated HIV-1 has an impact on the fate of the provirus. Studies analysing HIV-1 integration sites in macrophages are scarce. We studied HIV-1 integration site patterns in monocyte-derived macrophages (MDMs) and activated CD4+ T cells derived from seven antiretroviral therapy (ART)-treated HIV-1-infected individuals whose cells were infected ex vivo with autologous HIV-1 isolated during the acute phase of infection. A total of 1,484 unique HIV-1 integration sites were analysed. Their distribution in the human genome and genetic features, and the effects of HIV-1 integrase polymorphisms on the nucleotide selection specificity at these sites were indistinguishable between the two cell types, and among HIV-1 isolates. However, the repertoires of HIV-1-hosting gene clusters overlapped to a higher extent in MDMs than in CD4+ T cells. The frequencies of HIV-1 integration events in genes encoding HIV-1-interacting proteins were also different between the two cell types. Lastly, HIV-1-hosting genes linked to clonal expansion of latently HIV-1-infected CD4+ T cells were over-represented in gene hotspots identified in CD4+ T cells but not in those identified in MDMs. Taken together, the repertoire of genes targeted by HIV-1 in MDMs is distinct from and more restricted than that of CD4+ T cells. PMID:27067385

  14. Soils maps supplement to soil moisture ground truth, Lafayette, Indiana, site St. Charles, Missouri, site

    NASA Technical Reports Server (NTRS)

    Jones, E. B.; Olt, S. E.

    1975-01-01

    A compilation of soils information obtained as the result of a library search of data on the Lafayette, Indiana, site and St. Charles, Missouri, site is presented. Soils data for the Lafayette, Indiana, site are shown in Plates 1 and 2; and soils data for the St. Charles, Missouri, site are shown in Plates 3 and 4.

  15. Cytological mapping of the human glucose-6-phosphate dehydrogenase gene distal to the fragile-X site suggests a high rate of meiotic recombination across this site.

    PubMed

    Szabo, P; Purrello, M; Rocchi, M; Archidiacono, N; Alhadeff, B; Filippi, G; Toniolo, D; Martini, G; Luzzatto, L; Siniscalco, M

    1984-12-01

    The human gene for glucose-6-phosphate dehydrogenase (G6PD) has been subregionally mapped to band Xq28 by segregation analysis in rodent-human somatic cell hybrids [Pai, G. S., Sprinkel, J. A., Do, T. T., Mareni, C. E. & Migeon, B. R. (1980) Proc. Natl. Acad. Sci. USA 77, 2810-2813]. We have previously reported a common type of X-linked mental retardation associated with an inducible fragile site at Xq27-Xq28 segregates in a close linkage relationship with a G6PD variant, but the relative position of G6PD with respect to the fragile site has not yet been established. This fragile-X syndrome has been shown to be closely linked also to a Taq I restriction fragment length polymorphism detected by a cDNA probe for factor IX, and the latter locus has been mapped to the subtelomeric region Xq26-Xq28 [Camerino, G., Mattei, M. G., Mattei, G. F., Jaye, B. & Mandel, J. L. (1983) Nature (London) 306, 701-704]. The in situ hybridization studies reported here provide strong evidence that G6PD is located on the Xq telomeric fragment distal to the fragile site. These observations and the well-established knowledge that the genes for Deutan and Protan colorblindness are closely linked to G6PD, but segregate independently of factor IX deficiency, suggest that the fragile site associated with this type of X-linked mental retardation occurs in a region prone to high frequency of meiotic recombination. PMID:6595664

  16. Cytological mapping of the human glucose-6-phosphate dehydrogenase gene distal to the fragile-X site suggests a high rate of meiotic recombination across this site.

    PubMed Central

    Szabo, P; Purrello, M; Rocchi, M; Archidiacono, N; Alhadeff, B; Filippi, G; Toniolo, D; Martini, G; Luzzatto, L; Siniscalco, M

    1984-01-01

    The human gene for glucose-6-phosphate dehydrogenase (G6PD) has been subregionally mapped to band Xq28 by segregation analysis in rodent-human somatic cell hybrids [Pai, G. S., Sprinkel, J. A., Do, T. T., Mareni, C. E. & Migeon, B. R. (1980) Proc. Natl. Acad. Sci. USA 77, 2810-2813]. We have previously reported a common type of X-linked mental retardation associated with an inducible fragile site at Xq27-Xq28 segregates in a close linkage relationship with a G6PD variant, but the relative position of G6PD with respect to the fragile site has not yet been established. This fragile-X syndrome has been shown to be closely linked also to a Taq I restriction fragment length polymorphism detected by a cDNA probe for factor IX, and the latter locus has been mapped to the subtelomeric region Xq26-Xq28 [Camerino, G., Mattei, M. G., Mattei, G. F., Jaye, B. & Mandel, J. L. (1983) Nature (London) 306, 701-704]. The in situ hybridization studies reported here provide strong evidence that G6PD is located on the Xq telomeric fragment distal to the fragile site. These observations and the well-established knowledge that the genes for Deutan and Protan colorblindness are closely linked to G6PD, but segregate independently of factor IX deficiency, suggest that the fragile site associated with this type of X-linked mental retardation occurs in a region prone to high frequency of meiotic recombination. Images PMID:6595664

  17. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-01

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2-3 cm-1. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  18. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy.

    PubMed

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2-3 cm(-1). This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance. PMID:26277120

  19. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    SciTech Connect

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  20. Mapping of multiple HLA class II-restricted T-cell epitopes of the mycobacterial 70-kilodalton heat shock protein.

    PubMed Central

    Oftung, F; Geluk, A; Lundin, K E; Meloen, R H; Thole, J E; Mustafa, A S; Ottenhoff, T H

    1994-01-01

    By combining a DNA subclone and synthetic-peptide approach, we mapped epitopes of the immunogenic mycobacterial 70-kDa heat shock protein (HSP70) recognized by human CD4+ T-cell clones and lines. In addition, we identified the respective HLA-DR molecules used in antigen presentation. The donor groups used were healthy persons immunized with killed Mycobacterium leprae and tuberculoid leprosy patients. The results show that the N-terminal part of the HSP70 molecule contains three different T-cell epitopes, of which two were presented by DR7 (amino acids [aa] 66 to 82 and 210 to 226) and one was presented by DR3 (aa 262 to 274). The C-terminal part contains one epitope (aa 413 to 424) presented by HLA-DR2. The C-terminal epitope shows extensive homology to the corresponding region of the human HSP70 sequence. All of the T-cell epitopes identified were presented by only one particular HLA-DR molecule. We also found that HLA-DR5 and DRw53 can present HSP70 to T cells, demonstrating the presence of additional epitopes not yet defined at the peptide level. On the basis of the donors used in this study, recognition of HSP70 at the epitope level seems to be ruled by the restriction elements expressed by the donor rather than by any difference in reactivity between healthy individuals and patients. In conclusion, mycobacterial HSP70 is relevant to subunit vaccine design since it contains a variety of T-cell epitopes presented in the context of multiple HLA-DR molecules. PMID:7525484

  1. Complete Bouguer gravity map of the Nevada Test Site and vicinity, Nevada

    SciTech Connect

    Healey, D.L.; Harris, R.N.; Ponce, D.A.; Oliver, H.W.

    1987-12-31

    About 15,000 gravity stations were used to create the gravity map. Gravity studies at the Nevada Test Site were undertaken to help locate geologically favorable areas for underground nuclear tests and to help characterize potential high-level nuclear waste storage sites. 48 refs. (TEM)

  2. Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

    DOEpatents

    Goodman, Mark M.; Faraj, Bahjat

    1999-01-01

    Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

  3. Halogenated naphthyl methoxy piperidines for mapping serotonin transporter sites

    DOEpatents

    Goodman, M.M.; Faraj, B.

    1999-07-06

    Halogenated naphthyl methoxy piperidines having a strong affinity for the serotonin transporter are disclosed. Those compounds can be labeled with positron-emitting and/or gamma emitting halogen isotopes by a late step synthesis that maximizes the useable lifeterm of the label. The labeled compounds are useful for localizing serotonin transporter sites by positron emission tomography and/or single photon emission computed tomography.

  4. Comparison of Kriging and coKriging for soil contamination mapping in abandoned mine sites

    NASA Astrophysics Data System (ADS)

    Lee, Hyeongyu; Choi, Yosoon

    2015-04-01

    Soil contamination mapping around abandoned mines is an important task for the planning and design of mine reclamation. This study compared the ordinary Kriging and the co-Kriging methods for the soil contamination mapping in abandoned mine sites. Four approaches were conducted as follows: (1) soil contamination mapping using the ordinary Kriging and Inductively Coupled Plasma (ICP) data only; (2) soil contamination mapping using the ordinary Kriging and Portable X-Ray Fluorescence (PXRF) data only; (3) soil contamination mapping using the ordinary Kriging and integrated data from ICP and PXRF; and (4) soil contamination mapping using the co-Kriging and integrated data from ICP and PXRF. Results indicate that the approach 3 provides substantial improvements over other three approaches including a more reasonable spatial pattern of soil contamination and reduction in the error of its estimates.

  5. Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994

    SciTech Connect

    Knoche, K.; Selman, S.; Hung, L.

    1994-06-01

    Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

  6. Frequent occurrence of recognition Site-like sequences in the restriction endonucleases

    PubMed Central

    Biro, Jan C; Biro, Josephine MK

    2004-01-01

    Background There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while Crick argued that any connection between codons and amino acids is only the result of an "accident". This question is fundamental to understand the nature of specific protein-nucleic acid interactions. Results The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5–6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS. Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 Å distance to the C1' atoms in the DNA. The average distance between the closest atoms in the codons and amino acids is 5.5 +/- 0.2 Å (mean +/- S.E.M, n = 55), while the distance between the nitrogen and oxygen atoms of the co-localized molecules is significantly shorter, (3.4 +/- 0.2 Å, p < 0.001, n = 15), when positively charged amino acids are involved. This is indicating that an interaction between the nucleic- and amino acids might occur. Conclusion We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids. PMID:15113406

  7. AthaMap: from in silico data to real transcription factor binding sites.

    PubMed

    Bülow, Lorenz; Steffens, Nils Ole; Galuschka, Claudia; Schindler, Martin; Hehl, Reinhard

    2006-01-01

    AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available at http://www.athamap.de. PMID:16922688

  8. Topographic Mapping and Rover Localization in MER 2003 Mission Landing Sites

    NASA Astrophysics Data System (ADS)

    Li, R.; di, K.; Matthies, L.; Maimone, M.; Arvidson, R.; Crumpler, L.; Xu, F.; Wang, J.; Niu, X.; Serafy, C.; Ming, D.; Richter, L.; Marais, D.; Golombek, M.; Squyres, S.; Johnson, J.; Bell, J.; Maki, J.; Malin, M.; Parker, T.; Edwards, L.; Sims, M.; Wang, A.; Garvin, J.; Soderblom, L.

    2004-05-01

    This presentation illustrates results of topographic mapping and rover localization in Spirit and Opportunity landing sites. MOC/NA images, DIMES descent images, and surface Pancam and Navcam images are used to map regional and local topographic features of the landing sites. A new bundle adjustment method builds an image network with improved visual odometric data to supply enhance pointing data that are essential for high accuracy mapping and rover localization. Special 3D mapping products of the crater where Opportunity spacecraft landed are produced first time using rover images acquired from inside of a planetary crater. Traverse maps will show the comparison result of rover positions computed from the rover telemetry data with those from the image-based localization method. Analysis of the differences will be performed considering wheel slippage, IMU drift, and other factors. High quality topographic mapping products such as orthoimage base maps, 3D digital terrain models, and 3D interactive viewing tools are developed to support a series of mission operations and outreach activities, including long term science planning, rover path planning, geological mapping, wheel track property investigation, rock distribution estimation, crater modeling, and TV simulation scenes.

  9. Electroanatomic mapping to identify breakthrough sites in recurrent typical human flutter.

    PubMed

    Sra, J; Bhatia, A; Dhala, A; Blanck, Z; Rathod, S; Boveja, B; Deshpande, S; Cooley, R; Akhtar, M

    2000-10-01

    The accuracy of conventional techniques in localizing previous radiofrequency (RF) ablation sites and thus breakthrough sites of recurrent atrial flutter is somewhat limited. We investigated the role of electroanatomic mapping for identifying breakthrough sites or "gaps" at the tricuspid annulus and inferior vena cava (IVC)/eustachian ridge isthmus to help RF ablation in patients with recurrent typical flutter. Twelve patients (8 men, 4 women, age 63 +/- 10 years) with recurrent typical atrial flutter were included in the study. An electroanatomic mapping system (CARTO) was used to create a voltage map and activation and propagation patterns in the right atrium. Detailed voltage, activation, and propagation mapping of the tricuspid annulus and IVC/eustachian ridge isthmus allowed precise identification of gaps in all 12 patients at the tricuspid annulus (eight sites), IVC ridges (two sites), mid-isthmus region (one site), and tricuspid annulus and IVC ridges (one site). Radiofrequency energy directed at these sites eliminated atrial flutter in all 12 patients, confirmed by noninducibility of atrial flutter and demonstration of conduction block during atrial pacing on either side of the lesion lines. During a mean follow-up of 14.8 +/- 3.5 months (range 8-19 months), paroxysmal atrial flutter recurred in only one patient and was subsequently treated with amiodarone, although this had been ineffective prior to ablation. Electroanatomic mapping can precisely identify gaps in the lesion line responsible for breakthrough of recurrent typical atrial flutter at the tricuspid annulus and at the IVC/eustachian ridge isthmus. These sites can be targeted with RF ablation with a high degree of success. PMID:11060868

  10. Mapping protein binding sites on the biomolecular corona of nanoparticles

    NASA Astrophysics Data System (ADS)

    Kelly, Philip M.; Åberg, Christoffer; Polo, Ester; O'Connell, Ann; Cookman, Jennifer; Fallon, Jonathan; Krpetić, Željka; Dawson, Kenneth A.

    2015-05-01

    Nanoparticles in a biological milieu are known to form a sufficiently long-lived and well-organized ‘corona’ of biomolecules to confer a biological identity to the particle. Because this nanoparticle-biomolecule complex interacts with cells and biological barriers, potentially engaging with different biological pathways, it is important to clarify the presentation of functional biomolecular motifs at its interface. Here, we demonstrate that by using antibody-labelled gold nanoparticles, differential centrifugal sedimentation and various imaging techniques it is possible to identify the spatial location of proteins, their functional motifs and their binding sites. We show that for transferrin-coated polystyrene nanoparticles only a minority of adsorbed proteins exhibit functional motifs and the spatial organization appears random, which is consistent, overall, with a stochastic and irreversible adsorption process. Our methods are applicable to a wide array of nanoparticles and can offer a microscopic molecular description of the biological identity of nanoparticles.

  11. Mapping in vivo initiation sites of RNA transcription and determining their relative use.

    PubMed Central

    Kessler, M; Aloni, Y

    1984-01-01

    Runoff transcripts were generated on viral transcriptional complexes cleaved with restriction enzymes and incubated in vitro with [alpha-32P]UTP under pulse-chase conditions. As viral transcriptional complexes in vitro elongated the nascent RNA preinitiated in vivo, size analysis by gel electrophoresis of the runoff transcripts allowed identification of the in vivo initiation sites. Moreover, scanning the intensities of the runoff bands as they appeared in the autoradiogram of the gel allowed determination of the relative use of these sites. A model system in which the initiation sites of simian virus 40 late RNA were identified and their relative use determined is presented. Images PMID:6090704

  12. BamI, KpnI, and SalI restriction enzyme maps of the DNAs of herpes simplex virus strains Justin and F: occurrence of heterogeneities in defined regions of the viral DNA.

    PubMed Central

    Locker, H; Frenkel, N

    1979-01-01

    We present the locations of the cleavage sites for the BamI, KpnI, and SalI restriction endonucleases within the DNA molecules of herpes simplex virus type 1 (HSV-1) strains Justin and F. These restriction enzymes cleave the HSV-1 DNA at many sites, producing relatively small fragments which should prove useful in future studies of HSV-1 gene structure and function. The mapping data revealed the occurrence of heterogeneity within three regions of the viral genome including (i) the region spanning map coordinates 0.74--0.76, (ii) the ends of the large (L) DNA component, and (iii) the junction between the large (L) and the small (S) components. The heterogeneity in the ends of L and the S-L junctions of HSV-1 (Justin) and HSV-1 (F) DNAs was grossly similar to that previously reported to occur in the ends of L and the S-L junctions of the HSV-1 (KOS) DNA (M. J. Wagner and W. C. Summers, J. Virol. 27:374--387, 1978). Thus, cleavage of these regions with restriction endonucleases yielded sets of minor fragments differing in size by constant increments. However, the various strains of HSV-1 differed with respect to the numbers, size increments, and relative molarities of the various minor fragments, suggesting that the parameters of the heterogeneity are inherited in the structural makeup of the HSV-1 genome. The strain dependence of the pattern of heterogeneity can be most easily explained in terms of variable sizes of the terminally reiterated a sequence, contained in the DNA molecules of these three strains of HSV-1. Images PMID:228068

  13. Geomorphic Surface Maps of Northern Frenchman Flat, Nevada Test Site, Southern Nevada

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    Large-scale (1:6000) surficial geology maps of northern Frenchman Flat were developed in 1995 as part of comprehensive site characterization required to operate a low-level radioactive waste disposal facility in that area. Seven surficial geology maps provide fundamental data on natural processes and are the platform needed to reconstruct the Quaternary history of northern Frenchman Flat. Reconstruction of the Quaternary history provides an understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. Seven geomorphic surfaces (Units 1 through 7) are recognized, spanning from the early Quaternary to present time.

  14. Satellite Power System (SPS) mapping of exclusion areas for rectenna sites

    NASA Technical Reports Server (NTRS)

    Blackburn, J. B., Jr.; Bavinger, B. A.

    1978-01-01

    The areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System concept are presented. Thirty-six variables with the potential to exclude the rectenna were mapped and coded in a computer. Some of these variables exclude a rectenna from locating within the area of its spatial influence, and other variables potentially exclude the rectenna. These maps of variables were assembled from existing data and were mapped on a grid system.

  15. Hazard maps of earthquake induced permanent displacements validated by site numerical simulation

    NASA Astrophysics Data System (ADS)

    Vessia, Giovanna; Pisano, Luca; Parise, Mario; Tromba, Giuseppe

    2016-04-01

    Hazard maps of seismically induced instability at the urban scale can be drawn by means of GIS spatial interpolation tools starting from (1) a Digital terrain model (DTM) and (2) geological and geotechnical hydro-mechanical site characterization. These maps are commonly related to a fixed return period of the natural phenomenon under study, or to a particular hazard scenario from the most significant past events. The maps could be used to guide the planning activity as well as the emergency actions, but the main limit of such maps is that typically no reliability analyses is performed. Spatial variability and uncertainties in subsoil properties, poor description of geomorphological evidence of active instability, and geometrical approximations and simplifications in DTMs, among the others, could be responsible for inaccurate maps. In this study, a possible method is proposed to control and increase the overall reliability of an hazard scenario map for earthquake-induced slope instability. The procedure can be summarized as follows: (1) GIS Statistical tools are used to improve the spatial distribution of the hydro-mechanical properties of the surface lithologies; (2) Hazard maps are drawn from the preceding information layer on both groundwater and mechanical properties of surficial deposits combined with seismic parameters propagated by means of Ground Motion Propagation Equations; (3) Point numerical stability analyses carried out by means of the Finite Element Method (e.g. Geostudio 2004) are performed to anchor hazard maps prediction to point quantitative analyses. These numerical analyses are used to generate a conversion scale from urban to point estimates in terms of permanent displacements. Although this conversion scale differs from case to case, it could be suggested as a general method to convert the results of large scale map analyses to site hazard assessment. In this study, the procedure is applied to the urban area of Castelfranci (Avellino province

  16. EttA regulates translation by binding to the ribosomal E site and restricting ribosome-tRNA dynamics

    PubMed Central

    Chen, Bo; Boël, Grégory; Hashem, Yaser; Ning, Wei; Fei, Jingyi; Wang, Chi; Gonzalez, Ruben L.; Hunt, John F.; Frank, Joachim

    2014-01-01

    Cells express many ribosome-interacting factors whose functions and molecular mechanisms remain unknown. Here, we elucidate the mechanism of a newly characterized regulatory translation factor, Energy-dependent Translational Throttle A (EttA), which is an Escherichia coli representative of the ATP-binding cassette F (ABC-F) protein family. Using cryo-EM, we demonstrate that the ATP-bound form of EttA binds to the ribosomal tRNA exit (E) site, where it forms bridging interactions between the ribosomal L1 stalk and the tRNA bound in the peptidyl-tRNA binding (P) site. Using single-molecule fluorescence resonance energy transfer (smFRET), we show that the ATP-bound form of EttA restricts ribosome and tRNA dynamics required for protein synthesis. This work represents the first example, to our knowledge, where the detailed molecular mechanism of any ABC-F family protein has been determined and establishes a framework for elucidating the mechanisms of other regulatory translation factors. PMID:24389465

  17. Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites.

    PubMed

    Pinto, Filipe; Pacheco, Catarina C; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C; Urchueguía, Javier F; Tamagnini, Paula

    2015-12-01

    The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. PMID:26490728

  18. Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites

    PubMed Central

    Pinto, Filipe; Pacheco, Catarina C.; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C.; Urchueguía, Javier F.; Tamagnini, Paula

    2015-01-01

    The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. PMID:26490728

  19. A novel lipid binding site formed by the MAP kinase insert in p38 alpha.

    PubMed

    Diskin, Ron; Engelberg, David; Livnah, Oded

    2008-01-01

    The p38 mitogen-activated protein (MAP) kinases function as signaling molecules essential for many cellular processes, particularly mediating stress response. The activity of p38 MAP kinases is meticulously regulated to reach the desired cellular phenotype. Several alternative activation and attenuation mechanisms have been characterized recently which include new phosphorylation sites. Here we present the crystal structure of p38 alpha MAP kinase in complex with n-octyl-beta-glucopyranoside detergent. The complex unveils a novel lipid-binding site formed by a local conformational change of the MAP kinase insert. This binding is the first attribution for a possible role of the MAP kinase insert in p38. The binding site can accommodate a large selection of lipidic molecules. In addition, we also show via biophysical methods that arachidonic acid and its derivatives bind p38 alpha in vitro. Based on our analysis we propose that the binding of lipids could fine-tune p38 alpha catalytic activity towards a preferred phenotype. PMID:17999933

  20. Orthogonal electrode catheter array for mapping of endocardial focal site of ventricular activation

    SciTech Connect

    Desai, J.M.; Nyo, H.; Vera, Z.; Seibert, J.A.; Vogelsang, P.J. )

    1991-04-01

    Precise location of the endocardial site of origin of ventricular tachycardia may facilitate surgical and catheter ablation of this arrhythmia. The endocardial catheter mapping technique can locate the site of ventricular tachycardia within 4-8 cm2 of the earliest site recorded by the catheter. This report describes an orthogonal electrode catheter array (OECA) for mapping and radiofrequency ablation (RFA) of endocardial focal site of origin of a plunge electrode paced model of ventricular activation in dogs. The OECA is an 8 F five pole catheter with four peripheral electrodes and one central electrode (total surface area 0.8 cm{sup 2}). In eight mongrel dogs, mapping was performed by arbitrarily dividing the left ventricle (LV) into four segments. Each segment was mapped with OECA to find the earliest segment. Bipolar and unipolar electrograms were obtained. The plunge electrode (not visible on fluoroscopy) site was identified by the earliest wave front arrival times of -30 msec or earlier at two or more electrodes (unipolar electrograms) with reference to the earliest recorded surface ECG (I, AVF, and V1). Validation of the proximity of the five electrodes of the OECA to the plunge electrode was performed by digital radiography and RFA. Pathological examination was performed to document the proximity of the OECA to the plunge electrode and also for the width, depth, and microscopic changes of the ablation. To find the segment with the earliest LV activation a total of 10 {plus minus} 3 (mean {plus minus} SD) positions were mapped. Mean arrival times at the two earlier electrodes were -39 {plus minus} 4 msec and -35 {plus minus} 3 msec. Digital radiography showed the plunge electrode to be within the area covered by all five electrodes in all eight dogs. The plunge electrode was within 1 cm2 area of the region of RFA in all eight dogs.

  1. Mapping of anion binding sites on cytochrome c by differential chemical modification of lysine residues.

    PubMed Central

    Osheroff, N; Brautigan, D L; Margoliash, E

    1980-01-01

    The carbonate binding site on horse cytochrome c was mapped by comparing the yields of carboxydinitrophenyl-cytochromes c, each with a single carboxydinitrophenyl-substituted lysine residue per molecule, when the modification reaction was carried out in the presence and absence of carbonate. The site is located on the "left surface" of the protein and consists of lysine residues 72 and/or 73 as well as 86 and/or 87 (Carbonate Site). Although one of the binding sites for phosphate on cytochrome c (Phosphat Site I) is located near the carbonate site, the sites are distinctly different since carbonate does not displace bound phosphate, as monitored by 31P NMR. Furthermore, citrate interacts with Phosphate Site I with high affinity, whereas chloride, acetate, borate, and cacodylate have a much lower affinity for this site, if they bind to it at all. The affinity of phosphate for Phosphate Site I (KD = 2 X 10(-4) M) is at least 1 order of magnitude higher than it is for other sites of interaction. Images PMID:6254024

  2. Microchip-based terminal restriction fragment length polymorphism for on-site analysis of bacterial communities in freshwater.

    PubMed

    Yamaguchi, Nobuyasu; Matsukawa, Syuhei; Shintome, Yoko; Ichijo, Tomoaki; Nasu, Masao

    2013-01-01

    Assessing microbiological quality assurance by monitoring bacteria in various sources of freshwater used for human consumption, recreation, and food preparation is important for a healthy life. Bacterial number and their community structure in freshwater should be determined as quickly as possible, and "real-time" and "on-site" microbiological methods are required. In this study, we examined the protocol for microchip-based terminal restriction fragment length polymorphism (T-RFLP) analysis, which uses microchip electrophoresis for rapid microbial community analysis. The availability of microchip-based T-RFLP was compared with conventional T-RFLP analysis, which uses a capillary electrophoresis system, with freshwater samples (spring water, river water, groundwater, and hydroponics solution). The detection limit of targeted bacteria by on-chip T-RFLP analysis was 1% (10(3) cells/mL). The fragment sizes determined by the two analysis methods were highly correlated (r(2)=0.98). On-chip T-RFLP analysis was completed within 15 min. T-RFLP profiles of nine hydroponics solution samples were analyzed by multidimensional scaling. Considerable changes and stability in bacterial community structure during hydroponic culture were detected by both analyses. These results show that on-chip T-RFLP analysis can monitor changes in bacterial community structure, as well as conventional T-RFLP analysis. The present results indicate that on-chip T-RFLP analysis is an effective tool for rapid and "on-site" bacterial community profiling in freshwater environments, as well as freshwater used for medical and industrial purposes. PMID:23902975

  3. Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers.

    PubMed

    Zohren, Jasmin; Wang, Nian; Kardailsky, Igor; Borrell, James S; Joecker, Anika; Nichols, Richard A; Buggs, Richard J A

    2016-06-01

    Hybridization may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridizing species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here, we analyse introgression among these species using 51 237 variants in restriction site-associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridization due to Holocene reduction in the range of B. nana and expansion in the range of B. pubescens. PMID:27065091

  4. Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

    PubMed

    Mastretta-Yanes, A; Arrigo, N; Alvarez, N; Jorgensen, T H; Piñero, D; Emerson, B C

    2015-01-01

    Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico. PMID:24916682

  5. An approach to mapping haplotype-specific recombination sites in human MHC class III

    SciTech Connect

    Levo, A.; Westman, P.; Partanen, J.

    1996-12-31

    Studies of the major histocompatibility complex (MHC) in mouse indicate that the recombination sites are not randomly distributed and their occurrence is haplotype-dependent. No data concerning haplotype-specific recombination sites in human are available due to the low number of informative families. To investigate haplotype-specific recombination sites in human MHC, we describe an approach based on identification of recombinant haplotypes derived from one conserved haplotype at the population level. The recombination sites were mapped by comparing polymorphic markers between the recombinant and assumed original haplotypes. We tested this approach on the extended haplotype HLA A3; B47; Bf{sup *}F; C4A{sup *}1; C4B{sup *}Q0; DR7, which is most suitable for this analysis. First, it carries a number of rare markers, and second, the haplotype, albeit rare in the general population, is frequent in patients with 21-hydroxylase (21OH) defect. We observed recombinants derived from this haplotype in patients with 21OH defect. All these haplotypes had the centromeric part (from Bf to DR) identical to the original haplotype, but they differed in HLA A and B. We therefore assumed that they underwent recombinations in the segment that separates the Bf and HLA B genes. Polymorphic markers indicated that all break points mapped to two segments near the TNF locus. This approach makes possible the mapping of preferential recombination sites in different haplotypes. 20 refs., 1 fig., 1 tab.

  6. Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping

    PubMed Central

    Agostino, Mark; Yuriev, Elizabeth; Ramsland, Paul A.

    2012-01-01

    Modified gangliosides may be overexpressed in certain types of cancer, thus, they are considered a valuable target in cancer immunotherapy. Structural knowledge of their interaction with antibodies is currently limited, due to the large size and high flexibility of these ligands. In this study, we apply our previously developed site mapping technique to investigate the recognition of cancer-related gangliosides by anti-ganglioside antibodies. The results reveal a potential ganglioside-binding motif in the four antibodies studied, suggesting the possibility of structural convergence in the anti-ganglioside immune response. The structural basis of the recognition of ganglioside-mimetic peptides is also investigated using site mapping and compared to ganglioside recognition. The peptides are shown to act as structural mimics of gangliosides by interacting with many of the same binding site residues as the cognate carbohydrate epitopes. These studies provide important clues as to the structural basis of immunological mimicry of carbohydrates. PMID:22536387

  7. [Identification of SHV-type extended spectrum beta-lactamase genes in Pseudomonas aeruginosa by PCR-restriction fragment length polymorphism and insertion site restriction-PCR].

    PubMed

    Kalai Blagui, S; Achour, W; Abdeladhim, A; Ben Hassen, A

    2009-07-01

    We propose a simple and rapid method to discriminate SHV-type extended spectrum beta-lactamase (ESBL) genes in P. aeruginosa based on PCR techniques (PCR-RFLP and RSI-PCR). We studied 22 producing ESBL P. aeruginosa strains isolated from seven immunocompromised patients (19 isolates) and from environmental swabs (three isolates) at the Bone Marrow Transplantation Center of Tunis. Screening PCR with primer pairs designed to detect gene encoding TEM, SHV, OXA group I, OXA group II, OXA-18 and PER-1 ESBL was positive for bla(OXA18) and bla(SHV) genes in all isolates. Pulsed field gel electrophoresis using SpeI endonuclease defined five genotypic groups. For at least one isolate corresponding to each genotype observed, restriction of PCR products by DdeI and BsrI revealed the same restriction pattern that the bla(SHV-1) negative control; in the same way, RSI-PCR products digestion by NruI, thus excluding 35, 238 and 240 mutations characterizing reported ESBL in P. aeruginosa (SHV-2a, SHV5 et SHV12), and suggesting that studied bla(SHV) genes were not ESBL ones. Genomic DNA hybridization by southern blot with probe consisting in bla(SHV-1) gene was positive in these isolates. Sequencing the full-length open reading frame revealed nucleotide sequence of the bla(SHV-1). PCR-RFLP and RSI-PCR results were then confirmed. This approach is effective for screening P. aeruginosa for ESBL genes carriage in epidemiological studies and for detecting new variants. PMID:18838231

  8. Preliminary Site Classification using the Geologic Map of the Korean Peninsula

    NASA Astrophysics Data System (ADS)

    Kang, S.; Kim, K.; Suk, B.

    2008-12-01

    Studies of the earthquake ground motion consider the soil properties or the bed rock properties in the upper 30 m. The average shear wave velocity in the upper 30 m defined from borehole data is routinely used for classifying the site conditions. However, it is difficult to classify the site condition using the limited borehole data to cover the whole Korean Peninsula. In the study of Lee et al. (2001), site classification of Taiwan was refined using surface geology from the geologic map, geomorphologic data, and borehole data following the guidelines of National Earthquake Reduction Program (NEHRP). Wald and Allen (2007) defined shear wave velocity using slope of topography or gradient in global scale. They also compared their results in the Taiwan region to those proposed by Lee et al. (2001). In this study, we used geologic map, geomorphologic data, estimated average shear wave velocity from slope of topography, and borehole data to define the site conditions of the Korean Peninsula. We compared our results to the borehole data or seismic site condition data which include seismometer locations and ground conditions. There are some differences between our results and seismic site condition data. The discrepancy is attributed to the relatively large scale geologic map (1:250000) which may not include accurate site condition of the regions. Estimated site conditions of the study, however, agree with those from borehole data when a 1-mile buffering distance is applied to geologic condition boundaries. These results provide useful information for the further study of regional hazard estimation, risk management, and other seismological and geotechnical applications.

  9. Comparative Analysis of Infrequent-Restriction-Site PCR and Pulsed-Field Gel Electrophoresis for Epidemiological Typing of Legionella pneumophila Serogroup 1 Strains

    PubMed Central

    Riffard, Serge; Presti, François Lo; Vandenesch, François; Forey, Françoise; Reyrolle, Monique; Etienne, Jerome

    1998-01-01

    Two methods were compared for the analysis of 48 unrelated and epidemiologically related Legionella pneumophila serogroup 1 isolates. These are the infrequent-restriction-site PCR (IRS-PCR) assay with adapters designed for XbaI and PstI restriction sites and the pulsed-field gel electrophoresis (PFGE) analysis determined after DNA restriction with SfiI. Both methods demonstrated a high level of discrimination with a similar capacity for differentiating 23 of the 24 unrelated isolates. PFGE analysis and IRS-PCR assay were both able to identify epidemiologically related isolates of L. pneumophila from three outbreaks. Hence, IRS-PCR assay appears to be a reproducible (intergel reproducibility, 100%) and discriminative (discriminatory index, ≥0.996) tool for typing of Legionella. Compared to PFGE, however, IRS-PCR presented an advantage through ease of performance and with attributes of rapidity and sensitivity of target DNA. PMID:9431941

  10. Repeated mapping of reefs constructed by Sabellaria spinulosa Leuckart 1849 at an offshore wind farm site

    NASA Astrophysics Data System (ADS)

    Pearce, Bryony; Fariñas-Franco, Jose M.; Wilson, Christian; Pitts, Jack; deBurgh, Angela; Somerfield, Paul J.

    2014-07-01

    Sabellaria spinulosa reefs are considered to be sensitive and of high conservation status. This article evaluates the feasibility of using remote sensing technology to delineate S. spinulosa reefs. S. spinulosa reef habitats associated with the Thanet Offshore Windfarm site were mapped using high resolution sidescan sonar (410 kHz) and multibeam echo sounder (<1 m2) data in 2005 (baseline), 2007 (pre-construction baseline) and 2012 (post-construction). The S. spinulosa reefs were identified in the acoustic data as areas of distinct irregular texturing. Maps created using acoustic data were validated using quantitative measures of reef quality, namely tube density (as a proxy for the density of live S. spinulosa), percentage cover of S. spinulosa structures (both living and dead) and associated macrofauna derived from seabed images taken across the development site. Statistically significant differences were observed in all physical measures of S. spinulosa as well the number (S) and diversity (H') of associated species, derived from seabed images classified according to the presence or absence of reef, validating the use of high resolution sidescan sonar to map these important biogenic habitats. High precision mapping in the early stages allowed for the micro-siting of wind turbines in a way that caused minimal damage to S. spinulosa reefs during construction. These habitats have since recovered and expanded in extent. The surveys undertaken at the Thanet Offshore Windfarm site demonstrate the importance of repeat mapping for this emerging industry, allowing habitat enhancement to be attributed to the development whilst preventing background habitat degradation from being wrongly attributed to the development.

  11. Geological mapping of the Oak Ridge K-25 Site, Oak Ridge, Tennessee

    SciTech Connect

    Lemiszki, P.J.

    1994-01-01

    The Oak Ridge K-25 Site (formerly known as the Oak Ridge Gaseous Diffusion Plant) is located in the southern Appalachian Valley and Ridge province of east Tennessee and overlies an area of folded and faulted Cambrian through Ordovician sedimentary rocks in the footwall of the Whiteoak Mountain fault. Environmental restoration plans for the area require that the geology of the site be well understood because various aspects of the groundwater system are directly influenced by stratigraphic and structural characteristics of the bedrock. This study involved mapping the bedrock geology of an 18-square mile area in and around the plant site. Field mapping focused on: (1) checking the accuracy of previously mapped stratigraphic and fault contacts, (2) dividing the bedrock into distinct stratigraphic units based on field criteria, (3) determining the geometry of map-scale folds and faults, and (4) documenting various aspects of the local fracture system. Besides accomplishing all of the above tasks, results from this study have led to a number of new hypotheses regarding various aspects of the site geology. First, faulting and folding within carbonates of the Chickamauga Supergroup in the plant area has repeated certain rock units, which requires that there be a thrust fault in the subsurface below them. This thrust fault may project to the surface with the Carters Limestone. Second, thrust slices of the Rome Formation that overlie the Chickamauga carbonates may be extremely thin and have a limited aerial extent. Third, part of the Knox Group on McKinney Ridge is folded into an anticline. Evaluating the above hypotheses will require information about the subsurface that can only be acquired through drilling and surface geophysical surveys. The geologic map produced from this study can be used to evaluate the location of coreholes that will more effectively intersect a combination of stratigraphic, structural, and hydrologic targets.

  12. Shear wave velocity mapping of Hat Yai district, southern Thailand: implication for seismic site classification

    NASA Astrophysics Data System (ADS)

    Yordkayhun, Sawasdee; Sujitapan, Chedtaporn; Chalermyanont, Tanit

    2015-02-01

    Soil characteristics play an important role in the degree of ground shaking due to local site amplification during an earthquake. The objectives of this work are to study shear wave velocity (Vs) distribution in the near surface, and to develop a seismic site classification map for soil effect characterization and seismic hazard assessment in Hat Yai district, southern Thailand. The Vs determination based on the multichannel analysis of surface waves technique, has been carried out and analyzed at 70 measuring sites throughout the district. On the basis of the weighted-average Vs in the upper 30 m depth (Vs30), a seismic site classification map, based on the National Earthquake Hazards Reduction Program (NEHRP) standard has been developed. It is found that the NEHRP site class in Hat Yai can be classified into four groups in accordance with the value of Vs30 within the range of about 150 to 1160 m s-1. Most parts of the study area are typically classified as site class C and D. Site class C is mostly found within the colluvial and terrace deposits in the western and eastern part of the area, whereas site class D is concentrated in the alluvial sediment of the middle and northern flood plain areas. A small portion of site class B is observed in the western mountain ranges, where there is a thin overburden on the firm rock. There is a remarkably low Vs30 value at only one site, located near the main stream in the northern part of the study area. The results imply that the soil characteristics in the central and northern Hat Yai district pose a medium to high amplification rate with respect to the other regions. Although Vs data alone are insufficient to verify the potential of the amplification of ground shaking, this study provides an initial attempt to understand seismic hazards in the study area.

  13. Localization by restriction fragment length polymorphism mapping in potato of a major dominant gene conferring resistance to the potato cyst nematode Globodera rostochiensis.

    PubMed

    Barone, A; Ritter, E; Schachtschabel, U; Debener, T; Salamini, F; Gebhardt, C

    1990-11-01

    A major dominant locus conferring resistance against several pathotypes of the root cyst nematode Globodera rostochiensis was mapped on the linkage map of potato using restriction fragment length polymorphism (RFLP) markers. The assessment of resistance versus susceptibility of the plants in the experimental population considered was based on an in vivo (pot) and an in vitro (petri dish) test. By linkage to nine RFLP markers the resistance locus Gro1 was assigned to the potato linkage group IX which is homologous to the tomato linkage group 7. Deviations from the additivity of recombination frequencies between Gro1 and its neighbouring markers in the pot test led to the detection of a few phenotypic misclassifications of small plants with poor root systems that limited the observation of cysts on susceptible roots. Pooled data from both tests provided better estimates of recombination frequencies in the linkage interval defined by the markers flanking the resistance locus. PMID:1980523

  14. The distribution of transgene insertion sites in barley determined by physical and genetic mapping.

    PubMed Central

    Salvo-Garrido, Haroldo; Travella, Silvia; Bilham, Lorelei J; Harwood, Wendy A; Snape, John W

    2004-01-01

    The exact site of transgene insertion into a plant host genome is one feature of the genetic transformation process that cannot, at present, be controlled and is often poorly understood. The site of transgene insertion may have implications for transgene stability and for potential unintended effects of the transgene on plant metabolism. To increase our understanding of transgene insertion sites in barley, a detailed analysis of transgene integration in independently derived transgenic barley lines was carried out. Fluorescence in situ hybridization (FISH) was used to physically map 23 transgene integration sites from 19 independent barley lines. Genetic mapping further confirmed the location of the transgenes in 11 of these lines. Transgene integration sites were present only on five of the seven barley chromosomes. The pattern of transgene integration appeared to be nonrandom and there was evidence of clustering of independent transgene insertion events within the barley genome. In addition, barley genomic regions flanking the transgene insertion site were isolated for seven independent lines. The data from the transgene flanking regions indicated that transgene insertions were preferentially located in gene-rich areas of the genome. These results are discussed in relation to the structure of the barley genome. PMID:15280249

  15. Mapping Site Response Parameters on Cal Poly Pomona Campus Using the Spectral Ratio Method

    NASA Astrophysics Data System (ADS)

    HO, K. Y. K.; Polet, J.

    2014-12-01

    Site characteristics are an important factor in earthquake hazard assessment. To better understand site response differences on a small scale, as well as the seismic hazard of the area, we develop site response parameter maps of Cal Poly Pomona campus. Cal Poly Pomona is located in southern California about 40 km east of Los Angeles, within 50 km of San Andreas Fault. The campus is situated on top of the San Jose Fault. With about twenty two thousand students on campus, it is important to know the site response in this area. To this end, we apply the Horizontal-to-Vertical (H/V) spectral ratio technique, which is an empirical method that can be used in an urban environment with no environmental impact. This well-established method is based on the computation of the ratio of vertical ambient noise ground motion over horizontal ambient noise ground motion as a function of frequency. By applying the spectral ratio method and the criteria from Site Effects Assessment Using Ambient Excitations (SESAME) guidelines, we can determine fundamental frequency and a minimum site amplification factor. We installed broadband seismometers throughout the Cal Poly Pomona campus, with an initial number of about 15 sites. The sites are approximately 50 to 150 meters apart and about two hours of waveforms were recorded at each site. We used the Geopsy software to make measurements of the peak frequency and the amplitude of the main peak from the spectral ratio. These two parameters have been determined to be estimates of fundamental frequency and a minimum site amplification factor, respectively. Based on the geological map from the U.S. Geological Survey (USGS) and our data collected from Cal Poly Pomona campus, our preliminary results suggest that the area of campus that is covered by alluvial fan material tends to have a single significant spectral peak with a fundamental frequency of ~1Hz and a minimum amplification factor of ~3.7. The minimum depth of the surface layer is about 56

  16. Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168.

    PubMed

    Anjum, Awais; Brathwaite, Kelly J; Aidley, Jack; Connerton, Phillippa L; Cummings, Nicola J; Parkhill, Julian; Connerton, Ian; Bayliss, Christopher D

    2016-06-01

    Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5'CCCGA and 5'CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. PMID:26786317

  17. Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168

    PubMed Central

    Anjum, Awais; Brathwaite, Kelly J.; Aidley, Jack; Connerton, Phillippa L.; Cummings, Nicola J.; Parkhill, Julian; Connerton, Ian; Bayliss, Christopher D.

    2016-01-01

    Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5′CCCGA and 5′CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. PMID:26786317

  18. Collaborative community hazard exposure mapping: Distant Early Warning radar sites in Alaska's North Slope

    NASA Astrophysics Data System (ADS)

    Brady, M.

    2015-12-01

    A method to produce hazard exposure maps that are developed in collaboration with local coastal communities is the focus of this research. Typically efforts to map community exposure to climate threats over large areas have limited consideration of local perspectives about associated risks, constraining their utility for local management. This problem is especially acute in remote locations such as the Arctic where there are unique vulnerabilities to coastal threats that can be fully understood only through inclusion of community stakeholders. Through collaboration with community members, this study identifies important coastal assets and places and surveys local perspectives of exposure to climate threats along Alaska's vast North Slope coastline spanning multiple municipalities. To model physical exposure, the study adapts the U.S. Geological Survey's (USGS) coastal vulnerability index (CVI) to the Arctic context by incorporating the effects of open water distance determined by sea ice extent, and assigning CVI values to coastal assets and places according to direction and proximity. The study found that in addition to concerns about exposed municipal and industrial assets, North Slope communities viewed exposure of traditional activity sites as presenting a particular risk for communities. Highly exposed legacy Cold War Distant Early Warning Line sites are of particular concern with impacts ranging from financial risk to contamination of sensitive coastal marine environments. This research demonstrates a method to collaboratively map community exposure to coastal climate threats to better understand local risks and produce locally usable exposure maps.

  19. Covariance of biophysical data with digital topograpic and land use maps over the FIFE site

    NASA Technical Reports Server (NTRS)

    Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

    1992-01-01

    This paper discusses the biophysical stratification of the FIFE site, implementation of the stratification utilizing geographic information system methods, and validation of the stratification with respect to field measurements of biomass, Bowen ratio, soil moisture, and the greenness vegetation index (GVI) derived from TM satellite data. Maps of burning and topographic position were significantly associated with variation in GVI, biomass, and Bowen ratio. The stratified design did not significantly alter the estimated site-wide means for surface climate parameters but accounted for between 25 and 45 percent of the sample variance depending on the variable.

  20. Validation of Innovative Exploration Technologies for Newberry Volcano: Drill Site Location Map 2010

    DOE Data Explorer

    Jaffe, Todd

    2012-01-01

    Newberry seeks to explore "blind" (no surface evidence) convective hydrothermal systems associated with a young silicic pluton on the flanks of Newberry Volcano. This project will employ a combination of innovative and conventional techniques to identify the location of subsurface geothermal fluids associated with the hot pluton. Newberry project drill site location map 2010. Once the exploration mythology is validated, it can be applied throughout the Cascade Range and elsewhere to locate and develop “blind” geothermal resources.

  1. Novel Electrophilic and Photoaffinity Covalent Probes for Mapping the Cannabinoid 1 Receptor Allosteric Site(s)

    PubMed Central

    2015-01-01

    Undesirable side effects associated with orthosteric agonists/antagonists of cannabinoid 1 receptor (CB1R), a tractable target for treating several pathologies affecting humans, have greatly limited their translational potential. Recent discovery of CB1R negative allosteric modulators (NAMs) has renewed interest in CB1R by offering a potentially safer therapeutic avenue. To elucidate the CB1R allosteric binding motif and thereby facilitate rational drug discovery, we report the synthesis and biochemical characterization of first covalent ligands designed to bind irreversibly to the CB1R allosteric site. Either an electrophilic or a photoactivatable group was introduced at key positions of two classical CB1R NAMs: Org27569 (1) and PSNCBAM-1 (2). Among these, 20 (GAT100) emerged as the most potent NAM in functional assays, did not exhibit inverse agonism, and behaved as a robust positive allosteric modulator of binding of orthosteric agonist CP55,940. This novel covalent probe can serve as a useful tool for characterizing CB1R allosteric ligand-binding motifs. PMID:26529344

  2. Novel Electrophilic and Photoaffinity Covalent Probes for Mapping the Cannabinoid 1 Receptor Allosteric Site(s).

    PubMed

    Kulkarni, Pushkar M; Kulkarni, Abhijit R; Korde, Anisha; Tichkule, Ritesh B; Laprairie, Robert B; Denovan-Wright, Eileen M; Zhou, Han; Janero, David R; Zvonok, Nikolai; Makriyannis, Alexandros; Cascio, Maria G; Pertwee, Roger G; Thakur, Ganesh A

    2016-01-14

    Undesirable side effects associated with orthosteric agonists/antagonists of cannabinoid 1 receptor (CB1R), a tractable target for treating several pathologies affecting humans, have greatly limited their translational potential. Recent discovery of CB1R negative allosteric modulators (NAMs) has renewed interest in CB1R by offering a potentially safer therapeutic avenue. To elucidate the CB1R allosteric binding motif and thereby facilitate rational drug discovery, we report the synthesis and biochemical characterization of first covalent ligands designed to bind irreversibly to the CB1R allosteric site. Either an electrophilic or a photoactivatable group was introduced at key positions of two classical CB1R NAMs: Org27569 (1) and PSNCBAM-1 (2). Among these, 20 (GAT100) emerged as the most potent NAM in functional assays, did not exhibit inverse agonism, and behaved as a robust positive allosteric modulator of binding of orthosteric agonist CP55,940. This novel covalent probe can serve as a useful tool for characterizing CB1R allosteric ligand-binding motifs. PMID:26529344

  3. Restriction maps of the regions coding for methicillin and tobramycin resistances on chromosomal DNA in methicillin-resistant staphylococci.

    PubMed Central

    Ubukata, K; Nonoguchi, R; Matsuhashi, M; Song, M D; Konno, M

    1989-01-01

    Chromosomal BamHI DNA fragments containing both the mecA gene encoding the penicillin-binding protein responsible for methicillin resistance and the aadD gene encoding 4',4"-adenylyltransferase responsible for tobramycin resistance were cloned from three methicillin- and tobramycin-resistant strains of Staphylococcus aureus and one strain of Staphylococcus epidermidis. Physical maps of the fragments were similar, suggesting their unique origin. Images PMID:2817861

  4. A simulation of Earthquake Loss Estimation in Southeastern Korea using HAZUS and the local site classification Map

    NASA Astrophysics Data System (ADS)

    Kang, S.; Kim, K.

    2013-12-01

    Regionally varying seismic hazards can be estimated using an earthquake loss estimation system (e.g. HAZUS-MH). The estimations for actual earthquakes help federal and local authorities develop rapid, effective recovery measures. Estimates for scenario earthquakes help in designing a comprehensive earthquake hazard mitigation plan. Local site characteristics influence the ground motion. Although direct measurements are desirable to construct a site-amplification map, such data are expensive and time consuming to collect. Thus we derived a site classification map of the southern Korean Peninsula using geologic and geomorphologic data, which are readily available for the entire southern Korean Peninsula. Class B sites (mainly rock) are predominant in the area, although localized areas of softer soils are found along major rivers and seashores. The site classification map is compared with independent site classification studies to confirm our site classification map effectively represents the local behavior of site amplification during an earthquake. We then estimated the losses due to a magnitude 6.7 scenario earthquake in Gyeongju, southeastern Korea, with and without the site classification map. Significant differences in loss estimates were observed. The loss without the site classification map decreased without variation with increasing epicentral distance, while the loss with the site classification map varied from region to region, due to both the epicentral distance and local site effects. The major cause of the large loss expected in Gyeongju is the short epicentral distance. Pohang Nam-Gu is located farther from the earthquake source region. Nonetheless, the loss estimates in the remote city are as large as those in Gyeongju and are attributed to the site effect of soft soil found widely in the area.

  5. A genome-wide map of hyper-edited RNA reveals numerous new sites.

    PubMed

    Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

    2014-01-01

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

  6. Appliation of rad-sequencing to linkage mapping in citrus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

  7. Operation and research at the Ithaca MAP3S regional precipitation chemistry site

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1991-07-01

    Annual precipitation chemistry data from network start-up through 1988 is presented for the nine MAP3S sites. Time trends show significant negative linear regressions (P < 0.10) for SO{sub 4}{sup 2-} at 2 sites, H{sup +} at 4 sites, Ca{sup ++} at 1 site, and Na{sup +} at 1 site. Significant positive regressions over time include: NH{sub 4}{sup +} at 2 sites, Ca{sup ++} at 1 site, K{sup +} at 4 sites, and Cl{sup {minus}} at 2 sites. The Ithaca site shows the highest number of significant trends, with positive trends for Cl{sup {minus}}, NH{sub 4}{sup +}, Ca{sup ++}, and K{sup +}, and a negative trend for H{sup +}. Linear regressions of annual SO{sub 4}{sup 2-} concentrations on SO2 emissions show a significant positive relationship for Whiteface, Illinois, and Ohio at p < 0.10, 0.02, and 0.05 respectively. Overall for all MAP3S sites, plus Hubbard Brook a 25% decline in SO2 emissions over the region has been accompanied by a 16.5% decline in annual precipitation concentrations of SO{sub 4}{sup 2-}. For the region as a whole, a 20% decline in combined emissions has been accompanied to a 20% decline in H{sup +} concentrations. Thus a linear relationship exists between combined emissions and precipitation H{sup +} concentrations. No strong relationship exists for NOx emissions and precipitation NO{sub 3}{sup {minus}} concentration at the annual, seasonal or monthly level. Removing the NOx transportation sector, removing high and low precipitation values, or high pH values also does little to improve the NOx -- NO{sub 3}{sup {minus}} concentration relationships. Dry deposition components such a PAN, NO2, gaseous HNO{sub 3}, or aerosol NO{sub 3}{sup {minus}} should be included in the future with precipitation NO{sub 3}{sup {minus}} to relate emissions of NOx to nitrogen deposition. 11 refs., 27 figs.,1 tab.

  8. Comparative restriction endonuclease maps of proviral DNA of the primate type C simian sarcoma-associated virus and gibbon ape leukemia virus group.

    PubMed Central

    Trainor, C D; Wong-Staal, F; Reitz, M S

    1982-01-01

    Extrachromosomal DNA was purified from canine thymus cells acutely infected with different strains of infectious primate type C viruses of the woolly monkey (simian) sarcoma helper virus and gibbon ape leukemia virus group. All DNA preparations contained linear proviral molecules of 9.1 to 9.2 kilobases, at least some of which represent complete infectious proviral DNA. Cells infected with a replication-defective fibroblast-transforming sarcoma virus and its helper, a replication-competent nontransforming helper virus, also contained a 6.6- to 6.7-kilobase DNA. These proviral DNA molecules were digested with different restriction endonucleases, and the resultant fragments were oriented to the viral RNA by a combination of partial digestions, codigestion with more than one endonuclease, digestion of integrated proviral DNA, and hybridization with 3'- and 5'-specific viral probes. The 3'- and 5'-specific probes each hybridized to fragments from both ends of proviral DNA, indicating that, in common with those of other retroviruses, these proviruses contain a large terminal redundancy at both ends, each of which consists of sequences derived from both the 3' and 5' regions of the viral RNA. The proviral sequences are organized 3',5'-unique-3',5'. Four restriction enzymes (KpnI, SmaI, PstI, and SstI) recognized sites within the large terminal redundancies, and these sites were conserved within all the isolates tested. This suggests that both the 3' and 5' ends of the genomic RNA of these viruses are extremely closely related. In contrast, the restriction sites within the unique portion of the provirus were not strongly conserved within this group of viruses, even though they were related along most of their genomes. Whereas the 5' 60 to 70% of the RNA of these viruses was more closely related by liquid hybridization experiments than was the 3' 30 to 40%, restriction sites within this region were not preferentially conserved, suggesting that small sequence differences or

  9. Including Faults Detected By Near-Surface Seismic Methods in the USGS National Seismic Hazard Maps - Some Restrictions Apply

    NASA Astrophysics Data System (ADS)

    Williams, R. A.; Haller, K. M.

    2014-12-01

    Every 6 years, the USGS updates the National Seismic Hazard Maps (new version released July 2014) that are intended to help society reduce risk from earthquakes. These maps affect hundreds of billions of dollars in construction costs each year as they are used to develop seismic-design criteria of buildings, bridges, highways, railroads, and provide data for risk assessment that help determine insurance rates. Seismic source characterization, an essential component of hazard model development, ranges from detailed trench excavations across faults at the ground surface to less detailed analysis of broad regions defined mainly on the basis of historical seismicity. Though it is a priority for the USGS to discover new Quaternary fault sources, the discovered faults only become a part of the hazard model if there are corresponding constraints on their geometry (length and depth extent) and slip-rate (or recurrence interval). When combined with fault geometry and slip-rate constraints, near-surface seismic studies that detect young (Quaternary) faults have become important parts of the hazard source model. Examples of seismic imaging studies with significant hazard impact include the Southern Whidbey Island fault, Washington; Santa Monica fault, San Andreas fault, and Palos Verdes fault zone, California; and Commerce fault, Missouri. There are many more faults in the hazard model in the western U.S. than in the expansive region east of the Rocky Mountains due to the higher rate of tectonic deformation, frequent surface-rupturing earthquakes and, in some cases, lower erosion rates. However, the recent increase in earthquakes in the central U.S. has revealed previously unknown faults for which we need additional constraints before we can include them in the seismic hazard maps. Some of these new faults may be opportunities for seismic imaging studies to provide basic data on location, dip, style of faulting, and recurrence.

  10. Depth-to-Ice Map of an Arctic Site on Mars

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Color coding in this map of a far-northern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

    The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

    The depth to the top of the icy layer estimated from these observations, as little as 5 centimeters (2 inches), matches modeling of where it would be if Mars has an active cycle of water being exchanged by diffusion between atmospheric water vapor and subsurface water ice.

    This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67.5 degrees north latitude, 132 degrees east longitude, in the Martian arctic plains called Vastitas Borealis. It was formerly a candidate landing site for NASA's Phoenix Mars Lander mission. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is averaged over patches of ground hundreds of kilometers

  11. Mapping potential of digitized aerial photographs and space images for site-specific crop management

    NASA Astrophysics Data System (ADS)

    Nielsen, Gerald A.; Long, Daniel S.; Queen, Lloyd P.

    1996-11-01

    In site-specific crop management, treatments (e.g., fertilizer and herbicides) are applied precisely where they are needed. Global positioning system receivers allow accurate navigation of field implements and creation of crop yield maps. Remote sensing products help producers explain the wide range of yields shown on these maps and become the basis for digitized field management maps. Previous sources of remote sensing products for agriculture did not provide services that generated a sustained demand by crop producers, often because data were not delivered quickly enough. Public Access Resource Centers could provide a nearly uninterrupted electronic flow of data from NASA's MODIS and other sensors that could help producers and their advisors monitor crop conditions. This early warning/opportunity system would provide a low-cost way to discover conditions that merit examination on the ground. High-spatial-resolution digital aerial photographs or data from new commercial satellite companies would provide the basis for site-specific treatments. These detailed data are too expensive to acquire often and must be timed so as to represent differences in water supply characteristics and crop yield potentials. Remote sensing products must be linked to specific prescriptions that crop produces use to control operations and improve outcomes.

  12. Comprehensive mapping of O-GlcNAc modification sites using a chemically cleavable tag.

    PubMed

    Griffin, Matthew E; Jensen, Elizabeth H; Mason, Daniel E; Jenkins, Courtney L; Stone, Shannon E; Peters, Eric C; Hsieh-Wilson, Linda C

    2016-05-24

    The post-translational modification of serine or threonine residues of proteins with a single N-acetylglucosamine monosaccharide (O-GlcNAcylation) is essential for cell survival and function. However, relatively few O-GlcNAc modification sites have been mapped due to the difficulty of enriching and detecting O-GlcNAcylated peptides from complex samples. Here we describe an improved approach to quantitatively label and enrich O-GlcNAcylated proteins for site identification. Chemoenzymatic labelling followed by copper(i)-catalysed azide-alkyne cycloaddition (CuAAC) installs a new mass spectrometry (MS)-compatible linker designed for facile purification of O-GlcNAcylated proteins from cell lysates. The linker also allows subsequent quantitative release of O-GlcNAcylated proteins for downstream MS analysis. We validate the approach by unambiguously identifying several established O-GlcNAc sites on the proteins α-crystallin and O-GlcNAc transferase (OGT), as well as discovering new, previously unreported sites on OGT. Notably, these novel sites on OGT lie in key functional domains of the protein, underscoring how this site identification method may reveal important biological insights into protein activity and regulation. PMID:27063346

  13. Identifying Potential Areas for Siting Interim Nuclear Waste Facilities Using Map Algebra and Optimization Approaches

    SciTech Connect

    Omitaomu, Olufemi A; Liu, Cheng; Cetiner, Sacit M; Belles, Randy; Mays, Gary T; Tuttle, Mark A

    2013-01-01

    The renewed interest in siting new nuclear power plants in the United States has brought to the center stage, the need to site interim facilities for long-term management of spent nuclear fuel (SNF). In this paper, a two-stage approach for identifying potential areas for siting interim SNF facilities is presented. In the first stage, the land area is discretized into grids of uniform size (e.g., 100m x 100m grids). For the continental United States, this process resulted in a data matrix of about 700 million cells. Each cell of the matrix is then characterized as a binary decision variable to indicate whether an exclusion criterion is satisfied or not. A binary data matrix is created for each of the 25 siting criteria considered in this study. Using map algebra approach, cells that satisfy all criteria are clustered and regarded as potential siting areas. In the second stage, an optimization problem is formulated as a p-median problem on a rail network such that the sum of the shortest distance between nuclear power plants with SNF and the potential storage sites from the first stage is minimized. The implications of obtained results for energy policies are presented and discussed.

  14. New polymorphic mtDNA restriction site in the 12S rRNA gene detected in Tunisian patients with non-syndromic hearing loss

    SciTech Connect

    Mkaouar-Rebai, Emna Tlili, Abdelaziz; Masmoudi, Saber; Charfeddine, Ilhem; Fakhfakh, Faiza

    2008-05-09

    The 12S rRNA gene was shown to be a hot spot for aminoglycoside-induced and non-syndromic hearing loss since several deafness-associated mtDNA mutations were identified in this gene. Among them, we distinguished the A1555G, the C1494T and the T1095C mutations and C-insertion or deletion at position 961. One hundred Tunisian patients with non-syndromic hearing loss and 100 hearing individuals were analysed in this study. A PCR-RFLP analysis with HaeIII restriction enzyme showed the presence of the A1555G mutation in the 12S rRNA gene in only one out of the 100 patients. In addition, PCR-RFLP and radioactive PCR revealed the presence of a new HaeIII polymorphic restriction site in the same gene of 12S rRNA site in 4 patients with non-syndromic hearing loss. UVIDOC-008-XD analyses showed the presence of this new polymorphic restriction site with a variable heteroplasmic rates at position +1517 of the human mitochondrial genome. On the other hand, direct sequencing of the entire mitochondrial 12S rRNA gene in the 100 patients and in 100 hearing individuals revealed the presence of the A750G and A1438G polymorphisms and the absence of the C1494T, T1095C and 961insC mutations in all the tested individuals. Sequencing of the whole mitochondrial genome in the 4 patients showing the new HaeIII polymorphic restriction site revealed only the presence of the A8860G transition in the MT-ATP6 gene and the A4769G polymorphism in the ND2 gene.

  15. A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites

    SciTech Connect

    Madueno, E.; Modolell, J.; Papagiannakis, G.

    1995-04-01

    A physical map of the euchromatic X chromosome of Drosophila melanogaster has been constructed by assembling contiguous arrays of cosmids that were selected by screening a library with DNA isolated from microamplified chromosomal divisions. This map, consisting of 893 cosmids, covers {approximately}64% of the euchromatic part of the chromosome. In addition, 568 sequence tagged sites (STS), in aggregate representing 120 kb of sequenced DNA, were derived from selected cosmids. Most of these STSs, spaced at an average distance of {approximately} 35 kb along the euchromatic region of the chromosome, represent DNA tags that can be used as entry points to the fruitfly genome. Furthermore, 42 genes have been placed on the physical map, either through the hybridization of specific probes to the cosmids or through the fact that they were represented among the STSs. These provide a link between the physical and the genetic maps of D. melanogaster. Nine novel genes have been tentatively identified in Drosophila on the basis of matches between STS sequences and sequences from other species. 32 refs., 3 figs., 4 tabs.

  16. New predictive equations and site amplification estimates for the next-generation Swiss ShakeMaps

    NASA Astrophysics Data System (ADS)

    Cauzzi, Carlo; Edwards, Benjamin; Fäh, Donat; Clinton, John; Wiemer, Stefan; Kästli, Philipp; Cua, Georgia; Giardini, Domenico

    2014-01-01

    We present a comprehensive scientific and technical update of the Swiss customization of United States Geological Survey ShakeMap, in use at the Swiss Seismological Service since 2007. The new Swiss ShakeMaps are based on predictive equations for peak ground-motions and response spectra derived from stochastic simulations tailored to Swiss seismicity. Using synthetics allows overcoming the difficulties posed by: (i) the paucity of strong-motion data recordings in Switzerland; (ii) the regional dependence of shear wave energy attenuation and focal depth distribution in the Swiss Alps and foreland; (iii) the depth dependence of stress parameters suggested by macroseismic and instrumental observations. In the new Swiss ShakeMaps, VS,30 is no longer used as proxy for site amplification at regional scale, and is replaced by macroseismic intensity increments for different soil classes, based on the recently revised earthquake catalogue of Switzerland (ECOS-09). The new implementation converts ground-motion levels into macroseismic intensity by means of ground-motion to intensity conversion equations based on the Italian strong-motion and intensity databanks and is therefore well constrained for intensities larger than VII. The new Swiss ShakeMaps show a satisfactory agreement with the macroseimic fields of both large historical events and recent well-recorded earthquakes of moderate magnitude. The new implementation is now fully consistent with the state-of-the-art in engineering seismology in Switzerland.

  17. Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity

    USGS Publications Warehouse

    Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

    2007-01-01

    This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

  18. Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti

    SciTech Connect

    Severson, D.W.; Thathy, V.; Mori, A.

    1995-04-01

    Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F{sub 2} populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs [2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI], is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filaria nematode Brugia malayi and the yellow fever virus. 35 refs., 2 figs., 3 tabs.

  19. Depth-to-Ice Map of a Southern Mars Site Near Melea Planum

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Color coding in this map of a far-southern site on Mars indicates the change in nighttime ground-surface temperature between summer and fall. This site, like most of high-latitude Mars, has water ice mixed with soil near the surface. The ice is probably in a rock-hard frozen layer beneath a few centimeters or inches of looser, dry soil. The amount of temperature change at the surface likely corresponds to how close to the surface the icy material lies.

    The dense, icy layer retains heat better than the looser soil above it, so where the icy layer is closer to the surface, the surface temperature changes more slowly than where the icy layer is buried deeper. On the map, areas of the surface that cooled more slowly between summer and autumn (interpreted as having the ice closer to the surface) are coded blue and green. Areas that cooled more quickly (interpreted as having more distance to the ice) are coded red and yellow.

    The depth to the top of the icy layer estimated from these observations suggests that in some areas, but not others, water is being exchanged by diffusion between atmospheric water vapor and subsurface water ice. Differences in what type of material lies above the ice appear to affect the depth to the ice. The area in this image with the greatest seasonal change in surface temperature corresponds to an area of sand dunes.

    This map and its interpretation are in a May 3, 2007, report in the journal Nature by Joshua Bandfield of Arizona State University, Tempe. The Thermal Emission Imaging System camera on NASA's Mars Odyssey orbiter collected the data presented in the map. The site is centered near 67 degrees south latitude, 36.5 degrees east longitude, near a plain named Melea Planum. This site is within the portion of the planet where, in 2002, the Gamma Ray Spectrometer suite of instruments on Mars Odyssey found evidence for water ice lying just below the surface. The information from the Gamma Ray Spectrometer is

  20. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis.

    PubMed Central

    Yoon, Y; Sanchez, J A; Brun, C; Huberman, J A

    1995-01-01

    New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit. PMID:7739533

  1. Detecting cell-adhesive sites in extracellular matrix using force spectroscopy mapping

    PubMed Central

    Chirasatitsin, Somyot; Engler, Adam J

    2010-01-01

    The cell microenvironment is composed of extracellular matrix (ECM), which contains specific binding sites that allow the cell to adhere to its surroundings. Cells employ focal adhesion proteins, which must be able to resist a variety of forces to bind to ECM. Current techniques for detecting the spatial arrangement of these adhesions, however, have limited resolution and those that detect adhesive forces lack sufficient spatial characterization or resolution. Using a unique application of force spectroscopy, we demonstrate here the ability to determine local changes in the adhesive property of a fibronectin substrate down to the resolution of the fibronectin antibody-functionalized tip diameter, ~20 nm. To verify the detection capabilities of force spectroscopy mapping (FSM), changes in loading rate and temperature were used to alter the bond dynamics and change the adhesion force. Microcontact printing was also used to pattern fluorescein isothiocyanate-conjugated fibronectin in order to mimic the discontinuous adhesion domains of native ECM. Fluorescent detection was used to identify the pattern while FSM was used to map cell adhesion sites in registry with the initial fluorescent image. The results show that FSM can be used to detect the adhesion domains at high resolution and may subsequently be applied to native ECM with randomly distributed cell adhesion sites. PMID:21152375

  2. MicroCT analysis of calcium/phosphorus ratio maps at different bone sites

    NASA Astrophysics Data System (ADS)

    Speller, R.; Pani, S.; Tzaphlidou, M.; Horrocks, J.

    2005-08-01

    The Ca/P ratio was measured in cortical bone samples from the femoral neck, front and rear tibia of rats, rabbits and lambs using synchrotron microCT. Use of a monoenergetic X-ray beam, as provided by the synchrotron facility, generates accurate 3-D maps of the linear attenuation coefficient within the sample and hence gives the ability to map different chemical components. Data were taken at 20 keV for each bone sample and calibration phantoms. From the 3-D data sets, multiple 2-D slices were reconstructed with a slice thickness of ˜28 μm and converted to Ca/P ratios using the calibration phantom results. Average values for each animal and bone site were estimated. Differences between the same bone sites from different animals are not significant (0.3< p<0.5) while those between different bone sites and different animals are highly significant ( p<10-3) demonstrating a dependence upon lifestyle and bone use. The spatial distribution of Ca/P was found to be non-uniform for some bones and some animals possibly indicating the structural mechanism for obtaining bone strength.

  3. Development of Historical Water Table Maps of the 200 West Area of the Hanford Site (1950-1970)

    SciTech Connect

    Kinney, Teena M.; McDonald, John P.

    2006-09-15

    A series of detailed historical water-table maps for the 200-West Area of the Hanford Site was made to aid interpretation of contaminant distribution in the upper aquifer. The contaminants are the result of disposal of large volumes of waste to the ground during Hanford Site operations, which began in 1944 and continued into the mid-1990s. Examination of the contaminant plumes that currently exist on site shows that the groundwater beneath the 200-West Area has deviated from its pre-Hanford west-to-east flow direction during the past 50 years. By using historical water-level measurements from wells around the 200-West Area, it was possible to create water-table contour maps that show probable historic flow directions. These maps are more detailed than previously published water-table maps that encompass the entire Hanford Site.

  4. Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Gao, Guangtu; Liu, Sixin; Hernandez, Alvaro G.; Rexroad, Caird E.

    2015-01-01

    Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellite markers in a genome scan, we previously detected significant and suggestive QTL affecting phenotypic variation in survival following challenge with Flavobacterium psychrophilum, the causative agent of BCWD in rainbow trout. In this study, we performed selective genotyping of SNPs from restriction-site associated DNA (RAD) sequence data from two pedigreed families (2009070 and 2009196) to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and in addition, a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were also detected, and the previously suggestive QTL on Omy1, 7 and 25 were also validated in family 2009070. In family 2009196, the microsatellite significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected, but none of the previously detected suggestive QTL were validated. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling and confinement stress response QTL that our group has previously identified in a separate pedigreed family. With the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or a mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to include 100 positional candidate genes. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential

  5. VS30 mapping and soil classification for seismic site effect evaluation in Dinar region, SW Turkey

    NASA Astrophysics Data System (ADS)

    Ismet Kanlı, Ali; Tildy, Péter; Prónay, Zsolt; Pınar, Ali; Hermann, László

    2006-04-01

    The Dinar earthquake (MS= 6.1) of 1995 October 1 killed 90 people and destroyed more than 4000 buildings. Despite the moderate size of the earthquake, the level of damage was extremely high, which led to many studies that were carried out in the region. The majority of these studies concluded that the main reasons for the damage were the construction errors and the poor soil conditions. However, at that time no appropriate soil condition map based on extended, high density measurements was available. Shear wave velocity is an important parameter for evaluating the dynamic behaviour of soil in the shallow subsurface. Thus site characterization in calculating seismic hazards is usually based on the near surface shear wave velocity values. The average shear wave velocity for the top 30 m of soil is referred to as VS30. For earthquake engineering design purposes, both the Uniform Building Code (UBC) and Eurocode 8 (EC8) codes use VS30 to classify sites according to the soil type. The Vs30 values calculated by using multichannel analysis of surface waves (MASW) were used to create a new soil classification map of the Dinar region. Surface seismic measurements were carried out at 50 locations mostly in Dinar city and its surroundings. The dispersion data of the recorded Rayleigh waves were inverted using a Genetic Algorithm (GA) method to obtain shear wave velocity profiles of the investigated sites. Thus the derived Vs30 map of the Dinar region was transformed to the UBC and EC8 standards. Soil classification results show that most parts of the region, located in alluvial basin, have low shear wave velocity values. These values are within the range of 160-240 m s-1 and thus fall into the SD and SE categories according to the UBC and the C and D categories according to EC8. Within the region, some parts located on the hill zone and the transition zone have better soil conditions [corresponding to SC (UBC) and B (EC8) categories] and have comparatively high shear wave

  6. Contribution of physical modelling to climate-driven landslide hazard mapping: an alpine test site

    NASA Astrophysics Data System (ADS)

    Vandromme, R.; Desramaut, N.; Baills, A.; Hohmann, A.; Grandjean, G.; Sedan, O.; Mallet, J. P.

    2012-04-01

    The aim of this work is to develop a methodology for integrating climate change scenarios into quantitative hazard assessment and especially their precipitation component. The effects of climate change will be different depending on both the location of the site and the type of landslide considered. Indeed, mass movements can be triggered by different factors. This paper describes a methodology to address this issue and shows an application on an alpine test site. Mechanical approaches represent a solution for quantitative landslide susceptibility and hazard modeling. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account the uncertainty in the analysis. In this perspective, a new hazard modeling method is developed and integrated in a program named ALICE. This program integrates mechanical stability analysis through a GIS software taking into account data uncertainty. This method proposes a quantitative classification of landslide hazard and offers a useful tool to gain time and efficiency in hazard mapping. However, an expertise approach is still necessary to finalize the maps. Indeed it is the only way to take into account some influent factors in slope stability such as heterogeneity of the geological formations or effects of anthropic interventions. To go further, the alpine test site (Barcelonnette area, France) is being used to integrate climate change scenarios into ALICE program, and especially their precipitation component with the help of a hydrological model (GARDENIA) and the regional climate model REMO (Jacob, 2001). From a DEM, land-cover map, geology, geotechnical data and so forth the program classifies hazard zones depending on geotechnics and different hydrological contexts varying in time. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological

  7. Map showing drainage basins and locations of streamflow-measuring sites, Fairfax County, Virginia

    USGS Publications Warehouse

    Mohler, E.H.

    1977-01-01

    A drainage basin map of Fairfax County shows basins for named streams with drainage areas of 1.1 sq mi (2.8 sq km) or more. Areas of minor streams draining directly into the Potomac River and Occoquan Creek are tabulated. The locations of continuous-record and partial-record (peak-flow and low-flow) flow sites are shown. The use of topographic and climatic characteristics of drainage basins to transfer flow data from gaged areas to ungaged areas is discussed. (Woodard-USGS)

  8. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  9. Computer-aided mapping of stream channels beneath the Lawrence Livermore National Laboratory Super Fund Site

    SciTech Connect

    Sick, M.

    1994-12-01

    The Lawrence Livermore National Laboratory (LLNL) site rests upon 300-400 feet of highly heterogeneous braided stream sediments which have been contaminated by a plume of Volatile Organic Compounds (VOCs). The stream channels are filled with highly permeable coarse grained materials that provide quick avenues for contaminant transport. The plume of VOCs has migrated off site in the TFA area, making it the area of greatest concern. I mapped the paleo-stream channels in the TFA area using SLICE an LLNL Auto-CADD routine. SLICE constructed 2D cross sections and sub-horizontal views of chemical, geophysical, and lithologic data sets. I interpreted these 2D views as a braided stream environment, delineating the edges of stream channels. The interpretations were extracted from Auto-CADD and placed into Earth Vision`s 3D modeling and viewing routines. Several 3D correlations have been generated, but no model has yet been chosen as a best fit.

  10. Archaeological field survey automation: concurrent multisensor site mapping and automated analysis

    NASA Astrophysics Data System (ADS)

    Józefowicz, Mateusz; Sokolov, Oleksandr; Meszyński, Sebastian; Siemińska, Dominika; Kołosowski, Przemysław

    2016-04-01

    ABM SE develops mobile robots (rovers) used for analog research of Mars exploration missions. The rovers are all-terrain exploration platforms, carrying third-party payloads: scientific instrumentation. "Wisdom" ground penetrating radar for Exomars mission has been tested onboard, as well as electrical resistivity module and other devices. Robot has operated in various environments, such as Central European countryside, Dachstein ice caves or Sahara, Morocco (controlled remotely via satellite from Toruń, Poland. Currently ABM SE works on local and global positioning system for a Mars rover basing on image and IMU data. This is performed under a project from ESA. In the next Mars rover missions a Mars GIS model will be build, including an acquired GPR profile, DEM and regular image data, integrated into a concurrent 3D terrain model. It is proposed to use similar approach in surveys of archaeological sites, especially those, where solid architecture remains can be expected at shallow depths or being partially exposed. It is possible to deploy a rover that will concurrently map a selected site with GPR, 2D and 3D cameras to create a site model. The rover image processing algorithms are capable of automatic tracing of distinctive features (such as exposed structure remains on a desert ground, differences in color of the ground, etc.) and to mark regularities on a created map. It is also possible to correlate the 3D map with an aerial photo taken under any angle to achieve interpretation synergy. Currently the algorithms are an interpretation aid and their results must be confirmed by a human. The advantages of a rover over traditional approaches, such as a manual cart or a drone include: a) long hours of continuous work or work in unfavorable environment, such as high desert, frozen water pools or large areas, b) concurrent multisensory data acquisition, c) working from the ground level enables capturing of sites obstructed from the air (trees), d) it is possible to

  11. Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

    SciTech Connect

    Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele; Goedken, Eric R.; Gum, Rebecca J.; Borhani, David W.; Argiriadi, Maria; Groebe, Duncan R.; Jia, Yong; Clampit, Jill E.; Haasch, Deanna L.; Smith, Harriet T.; Wang, Sanyi; Song, Danying; Coen, Michael L.; Cloutier, Timothy E.; Tang, Hua; Cheng, Xueheng; Quinn, Christopher; Liu, Bo; Xin, Zhili; Liu, Gang; Fry, Elizabeth H.; Stoll, Vincent; Ng, Teresa I.; Banach, David; Marcotte, Doug; Burns, David J.; Calderwood, David J.; Hajduk, Philip J.

    2012-03-02

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in

  12. Identification and mapping of natural vegetation on a coastal site using a Worldview-2 satellite image.

    PubMed

    Rapinel, Sébastien; Clément, Bernard; Magnanon, Sylvie; Sellin, Vanessa; Hubert-Moy, Laurence

    2014-11-01

    Identification and mapping of natural vegetation are major issues for biodiversity management and conservation. Remotely sensed data with very high spatial resolution are currently used to study vegetation, but most satellite sensors are limited to four spectral bands, which is insufficient to identify some natural vegetation formations. The study objectives are to discriminate natural vegetation and identify natural vegetation formations using a Worldview-2 satellite image. The classification of the Worldview-2 image and ancillary thematic data was performed using a hybrid pixel-based and object-oriented approach. A hierarchical scheme using three levels was implemented, from land cover at a field scale to vegetation formation. This method was applied on a 48 km² site located on the French Atlantic coast which includes a classified NATURA 2000 dune and marsh system. The classification accuracy was very high, the Kappa index varying between 0.90 and 0.74 at land cover and vegetation formation levels respectively. These results show that Wordlview-2 images are suitable to identify natural vegetation. Vegetation maps derived from Worldview-2 images are more detailed than existing ones. They provide a useful medium for environmental management of vulnerable areas. The approach used to map natural vegetation is reproducible for a wider application by environmental managers. PMID:24973612

  13. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies. PMID:27432793

  14. Mapping the Sea Floor of the Historic Area Remediation Site (HARS) Offshore of New York City

    USGS Publications Warehouse

    Butman, Bradford

    2002-01-01

    The area offshore of New York City has been used for the disposal of dredged material for over a century. The area has also been used for the disposal of other materials such as acid waste, industrial waste, municipal sewage sludge, cellar dirt, and wood. Between 1976 and 1995, the New York Bight Dredged Material Disposal Site, also known as the Mud Dump Site (MDS), received on average about 6 million cubic yards of dredged material annually. In September 1997 the MDS was closed as a disposal site, and it and the surrounding area were designated as the Historic Area Remediation Site (HARS). The sea floor of the HARS, approximately 9 square nautical miles in area, currently is being remediated by placing a minimum 1-m-thick cap of clean dredged material on top of the surficial sediments that are contaminated from previous disposal of dredged and other materials. The U.S. Geological Survey (USGS) is working cooperatively with the U.S. Army Corps of Engineers (USACE) to map the sea floor geology of the HARS and changes in the characteristics of the surficial sediments over time.

  15. Human uroporphyrinogen III synthase: NMR-based mapping of the active site.

    PubMed

    Cunha, Luis; Kuti, Miklos; Bishop, David F; Mezei, Mihaly; Zeng, Lei; Zhou, Ming-Ming; Desnick, Robert J

    2008-05-01

    Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex. PMID:18004775

  16. LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

    PubMed Central

    Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew

    2011-01-01

    Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains. PMID:21789174

  17. Acoustic mapping of the regional seafloor geology in and around Hawaiian ocean dredged-material disposal sites

    USGS Publications Warehouse

    Torresan, Michael E.; Gardner, James V.

    2000-01-01

    During January and February 1998 the U.S. Geological Survey Coastal and Marine Geology Team (USGS) conducted regional high-resolution multibeam mapping surveys of the area surrounding EPA-designated ocean disposal sites located offshore of the Hawaiian Islands of Oahu, Kauai, Maui, and Hawaii. The sites are all located within 5 nautical miles of shore on insular shelves or slopes. Regional maps were required of areas much larger than the disposal sites themselves to assess both the regional seafloor geology and the immediate vicinity of the disposal sites. The purpose of the disposal site surveys was to delimit the extent of disposal material by producing detailed bathymetric and backscatter maps of the seafloor with a ± 1 m spatial accuracy and <1% depth error. The advantage of using multibeam over conventional towed, single-beam sidescan sonar is that the multibeam data are accurately georeferenced for precise location of all imaged features. The multibeam produces a coregistered acoustic-backscatter map that is often required to locate individual disposal deposits. These data were collected by the USGS as part of its regional seafloor mapping and in support of ocean disposal site monitoring studies conducted in cooperation with the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (COE).

  18. Quantitative analysis of anthropogenic relief features: automated mapping of charcoal kiln sites from high-resolution ALS data

    NASA Astrophysics Data System (ADS)

    Schneider, Anna; Takla, Melanie; Nicolay, Alexander; Raab, Alexandra; Raab, Thomas

    2014-05-01

    High-resolution digital elevation data from airborne laser scanning (ALS) allow for identification and mapping of so far unknown small-scale relief features that are hidden by forest cover. Especially as a result of historic land use, small anthropogenic landforms can occur, e.g., remains of charcoal kilns on sites that were used for charcoal production or ridge and furrow systems in former farmland areas. Mapping such relief features and analyzing their spatial distribution patterns can help to understand past land-use systems and their effects on landscapes. To efficiently detect and quantify small-scale relief features from high-resolution DEMs for larger areas, (semi-) automated mapping routines are required. In order to describe the number and spatial distribution of historic charcoal kiln sites in the area around Cottbus, Germany, we developed a GIS-based routine for the detection and mapping of kiln remnants from ALS elevation models with a resolution of 1 or 2 meters. The method is based on a template matching algorithm, using a combination of morphometric parameters, and is implemented within ArcGIS. The mapping results could be validated against a comprehensive database of kiln sites and diameters recorded from archaeological excavations in the forefield of the opencast mine Jänschwalde and from manual digitization of kiln remnants from Shaded Relief maps for the Jänschwalder Heide and the Tauersche Forst, north of Cottbus. A considerably high number of charcoal kiln sites could be detected in ALS data, and the diameters of the identified charcoal kilns are remarkable large in the area. For the Jänschwalder Heide, more than 5000 kiln sites in an area of 32 km2 were detected by manual digitization, with 1355 kiln sites that are wider than 12 m. These relatively large kiln sites could be mapped with detection rates that are close to those of manual digitization using the automated mapping routine. Detection quality was improved by the combination of

  19. A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease

    PubMed Central

    Bellamy, Stuart R.W.; Milsom, Susan E.; Kovacheva, Yana S.; Sessions, Richard B.; Halford, Stephen E.

    2007-01-01

    While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the subunits, SfiI is a tetramer of identical subunits. Two of its subunits (a dimeric unit) create one DNA-binding cleft, and the other two create a second cleft on the opposite side of the protein. The two clefts bind specific DNA cooperatively to give a complex of SfiI with two recognition sites. This complex is responsible for essentially all of the DNA-cleavage reactions by SfiI: virtually none is due to the complex with one site. The communication between the DNA-binding clefts was examined by disrupting one of the very few polar interactions in the otherwise hydrophobic interface between the dimeric units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The mutant protein remained tetrameric in solution and could bind two DNA sites. But instead of being activated by binding two sites, like wild-type SfiI, it showed maximal activity when bound to a single site and had a lower activity when bound to two sites. This interaction across the dimer interface thus enforces in wild-type SfiI a cooperative transition between inactive and active states in both dimers, but without this interaction as in the mutant protein, a single dimer can undergo the transition to give a stable intermediate with one inactive dimer and one active dimer. PMID:17870087

  20. Digital Geologic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California

    USGS Publications Warehouse

    Slate, Janet L.; Berry, Margaret E.; Rowley, Peter D.; Fridrich, Christopher J.; Morgan, Karen S.; Workman, Jeremiah B.; Young, Owen D.; Dixon, Gary L.; Williams, Van S.; McKee, Edwin H.; Ponce, David A.; Hildenbrand, Thomas G.; Swadley, W.C.; Lundstrom, Scott C.; Ekren, E. Bartlett; Warren, Richard G.; Cole, James C.; Fleck, Robert J.; Lanphere, Marvin A.; Sawyer, David A.; Minor, Scott A.; Grunwald, Daniel J.; Laczniak, Randell J.; Menges, Christopher M.; Yount, James C.; Jayko, Angela S.

    1999-01-01

    This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map compilation presents new polygon (geologic map unit contacts), line (fault, fold axis, metamorphic isograd, dike, and caldera wall) and point (structural attitude) vector data for the NTS and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California. The map area covers two 30 x 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7.5-minute quadrangles on the east side-72 quadrangles in all. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area (Wahl and others, 1997) by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. Concurrent publications to this one include a new isostatic gravity map (Ponce and others, 1999) and a new aeromagnetic map (Ponce, 1999).

  1. Differentiation of Meat Samples from Domestic Horses (Equus caballus) and Asiatic Wild Asses (Equus hemionus) Using a Species-Specific Restriction Site in the Mitochondrial Cytochrome b Region

    PubMed Central

    Kuehn, Ralph; Kaczensky, Petra; Lkhagvasuren, Davaa; Pietsch, Stephanie; Walzer, Chris

    2011-01-01

    Recent studies suggest that Asiatic wild asses (Equus hemionus) are being increasingly poached in a commercial fashion. Part of the meat is believed to reach the meat markets in the capital Ulaanbaatar. To test this hypothesis, we collected 500 meat samples between February and May 2006. To differentiate between domestic horse (Equus caballus) and wild ass meat, we developed a restriction fragment length polymorphism (RFLP) assay based on the polymerase chain reaction (PCR). We amplified and sequenced a cytochrome b fragment (335 bp) and carried out a multialignment of the generated sequences for the domestic horse, the Asiatic wild ass, the domestic donkey (Equus asinus) and the Przewalski’s horse (Equus ferus przewalskii). We detected a species-specific restriction site (AatII) for the Asiatic wild ass, resulting in a specific restriction fragment length polymorphism (RFLP) band pattern. This RFLP assay represents a rapid and cost-effective method to detect wild ass meat. All of the 500 meat samples we collected and analysed within this pilot project proved to be domestic horsemeat as declared by the sales people. Thus, either the assumption that wild ass meat is sold as “cheap horse meat” is wrong, or we picked the wrong markets, products or season. PMID:22059088

  2. Mapping of noise impact provoked by the execution of foundation piles at high rise building sites.

    PubMed

    de Araújo, Adolpho Guido; Gusmão, Alexandre Duarte; Rabbani, Emilia Rahnemay Kohman; Fucale, Stela Paulino

    2012-01-01

    The objective of this work is to map, in a limited area inside and outside of the worksite, the environmental impact generated by sound pollution coming from the driving of foundation piles for high rise buildings, as well as to observe and check if the noise levels produced by the emitting source are tolerable in the urban environment. The methodology of the work includes a survey of technical references about the subject; measurement of noises surrounding the worksite during the foundation phase for four distinct buildings, with different types of piles: prefabricated piles, continuous helical displacement piles , traditional compaction piles and Terra Probe compaction piles. A grid of points was built due to the time of driving and after that the measurements of environmental noises were performed emitted by the execution of each type of pile using a sound level meter. The interpretation of the measurements and their impacts on the neighborhood of the building were performed using the computational tool Suffer for creating noise level contours. The X and Y axes of the grid represent the distances in meters of the area studied and the Z axis represents the noise measured in dB. The contours developed represent the mapping of the noise at the worksites and their surroundings. The mapping of the urban impact of noise, the measurement of its dimensions, and the examination of its propagation around the building are important subsides to adequate individual and collective protection procedures. Seventy one points were measured at four building sites with different types of piles, and the results showed that at only three points was the noise within the limits of the Municipal Law of Recife of 70 dB, which proves the relevance of the research. Finally, the comparative analysis between the four types of piles shows that the continuous helical displacement pile emits the lowest noise level among the four pile types studied. PMID:22317218

  3. Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin.

    PubMed

    Radeva, Nedyalka; Krimmer, Stefan G; Stieler, Martin; Fu, Kan; Wang, Xiaojie; Ehrmann, Frederik R; Metz, Alexander; Huschmann, Franziska U; Weiss, Manfred S; Mueller, Uwe; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard

    2016-08-25

    Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and β-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family. PMID:27463859

  4. Global transcriptional start site mapping in Geobacter sulfurreducens during growth with two different electron acceptors.

    PubMed

    González, Getzabeth; Labastida, Aurora; Jímenez-Jacinto, Verónica; Vega-Alvarado, Leticia; Olvera, Maricela; Morett, Enrique; Juárez, Katy

    2016-09-01

    Geobacter sulfurreducens is an anaerobic soil bacterium that is involved in biogeochemical cycles of elements such as Fe and Mn. Although significant progress has been made in the understanding of the electron transfer processes in G. sulfurreducens, little is known about the regulatory mechanisms involved in their control. To expand the study of gene regulation in G. sulfurreducens, we carried out a genome-wide identification of transcription start sites (TSS) by 5'RACE and by deep RNA sequencing of primary mRNAs in two growth conditions. TSSs were identified along G. sulfurreducens genome and over 50% of them were located in the upstream region of the associated gene, and in some cases we detected genes with more than one TSS. Our global mapping of TSSs contributes with valuable information, which is needed for the study of transcript structure and transcription regulation signals and can ultimately contribute to the understanding of transcription initiation phenomena in G. sulfurreducens. PMID:27488344

  5. Geologic map of the Mine Mountain area, Nevada Test Site, southern Nevada

    SciTech Connect

    Cashman, P.H.; Cole, J.C.

    1998-10-05

    The Mine Mountain area is a small range of hills on the west side of the central Yucca Flat basin on the Nevada Test Site, Nye County, Nevada. This map portrays the very complex relationships among the pre-Tertiary stratigraphic units of the region. Rocks and structures of the Mine Mountain area record the compounded effects of: (1) eastward-directed, foreland-vergent thrusting; (2) younger folds and thrusts formed by hinterland vergence in a general westerly direction; and (3) low-angle normal faulting formed by extension along a northeast-southwest trend. All of these structures are older than the oldest middle Miocene volcanic rocks that were deposited on the flanks of the Mine Mountain terrane. High-angle faults that post-date these volcanic rocks locally show displacements of several hundred meters, but do not strongly affect patterns in the pre-Tertiary rocks.

  6. Using Hadoop File System and MapReduce in a small/medium Grid site

    NASA Astrophysics Data System (ADS)

    Riahi, H.; Donvito, G.; Fanò, L.; Fasi, M.; Marzulli, G.; Spiga, D.; Valentini, A.

    2012-12-01

    Data storage and data access represent the key of CPU-intensive and data-intensive high performance Grid computing. Hadoop is an open-source data processing framework that includes fault-tolerant and scalable distributed data processing model and execution environment, named MapReduce, and distributed File System, named Hadoop distributed File System (HDFS). HDFS was deployed and tested within the Open Science Grid (OSG) middleware stack. Efforts have been taken to integrate HDFS with gLite middleware. We have tested the File System thoroughly in order to understand its scalability and fault-tolerance while dealing with small/medium site environment constraints. To benefit entirely from this File System, we made it working in conjunction with Hadoop Job scheduler to optimize the executions of the local physics analysis workflows. The performance of the analysis jobs which used such architecture seems to be promising, making it useful to follow up in the future.

  7. Mapping air pollution using Earth observation techniques for cultural heritage sites

    NASA Astrophysics Data System (ADS)

    Agapiou, Athos; Nisantzi, Argyro; Lysandrou, Vasiliki; Mamouri, Rodanthi; Alexakis, Dimitrios D.; Themistocleous, Kyriacos; Sarris, Apostolos; Hadjimitsis, Diofantos G.

    2013-08-01

    Air pollutants, together with climatic parameters, are of major importance for the deterioration of cultural heritage monuments. Atmospheric pollution is widely recognized as one of the major anthropogenic threats to architectural cultural heritage, in particular when associated with water absorption phenomena. Atmospheric particle deposition on surfaces of Monuments (of cultural heritage interest) may cause an aesthetic impact induced by a series of chemical reactions. Therefore there is a need for systematic monitoring and mapping of air pollution for areas where important archaeological sites and monuments are found. observation techniques, such as the use of satellite image for the retrieval of Aerosol Optical Thickness (AOT), are ideal for this purpose. In this paper, all important monuments of the Paphos District, listed by the Department of Antiquities of Cyprus, have been mapped using Geographical Information Systems. Several recent (2012) MODIS satellite images (both Aqua and Terra) have been used to extract the AOT values in this area. Multi-temporal analysis was performed to identify areas of high risk where AOT values are considered to be high. In situ observations have been also carried out to verify the results.

  8. Landing Site Selection and Surface Traverse Planning using the Lunar Mapping & Modeling Portal

    NASA Astrophysics Data System (ADS)

    Law, E.; Chang, G.; Bui, B.; Sadaqathullah, S.; Kim, R.; Dodge, K.; Malhotra, S.

    2013-12-01

    Introduction: The Lunar Mapping and Modeling Portal (LMMP), is a web-based Portal and a suite of interactive visualization and analysis tools for users to access mapped lunar data products (including image mosaics, digital elevation models, etc.) from past and current lunar missions (e.g., Lunar Reconnaissance Orbiter, Apollo, etc.), and to perform in-depth analyses to support lunar surface mission planning and system design for future lunar exploration and science missions. It has been widely used by many scientists mission planners, as well as educators and public outreach (e.g., Google Lunar XPRICE teams, RESOLVE project, museums etc.) This year, LMMP was used by the Lunar and Planetary Institute (LPI)'s Lunar Exploration internship program to perform lighting analysis and local hazard assessments, such as, slope, surface roughness and crater/boulder distribution to research landing sites and surface pathfinding and traversal. Our talk will include an overview of LMMP, a demonstration of the tools as well as a summary of the LPI Lunar Exploration summer interns' experience in using those tools.

  9. Covariance of biophysical data with digital topographic and land use maps over the FIFE site

    NASA Astrophysics Data System (ADS)

    Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

    1992-11-01

    Sampling design is critical in locating ground sampling stations for large-scale climatological field experiments. In the stratified sampling design adopted for the First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE), the study region was stratified into 14 different terrain units based on land use/land cover and topographic variables that were hypothesized to have a strong influence on surface biophysical properties. Digital terrain maps were produced to facilitate ground data integration and extrapolation. This paper describes the biophysical stratification of the FIFE site, implementation of the stratification using geographic information system (GIS) techniques, and validation of the stratification with respect to field measurements of biomass, soil moisture, Bowen ratio (β), and the greenness vegetation index (GVI) derived from thematic mapper satellite data. Maps of burning and topographic position were significantly associated with variation in biomass, GVI, and β. The effects of burning and topography were stronger for the Konza Prairie Long-Term Ecological Research (KPLTER) site than for the rest of the FIFE site, where cattle grazing was a major confounding effect. The stratified design did not appreciably change the estimated site-wide means for surface climate parameters but accounted for between 25 and 45% of the sample variance depending on the variable. The design was weakened by undersampling of several strata, by high within-station variance in soil and vegetation data, and by failure to account for diverse land management practices on private lands surrounding KPLTER. We recommend that future large-scale climatological studies include the development of a digital terrain data base well in advance of field campaigns and that multitemporal imagery be used to obtain preliminary estimates of spatial and temporal variance in surface biophysical properties. We also recommend that sampling for the most

  10. Application of time domain induced polarization to the mapping of lithotypes in a landfill site

    NASA Astrophysics Data System (ADS)

    Gazoty, A.; Fiandaca, G.; Pedersen, J.; Auken, E.; Christiansen, A. V.; Pedersen, J. K.

    2012-06-01

    A direct current (DC) resistivity and time domain induced polarization (TDIP) survey was undertaken at a decommissioned landfill site situated in Hørløkke, Denmark, for the purpose of mapping the waste deposits and to discriminate important geological units that control the hydrology of the surrounding area. It is known that both waste deposits and clay have clear signatures in TDIP data, making it possible to enhance the resolution of geological structures compared to DC surveys alone. Four DC/TDIP profiles were carried out crossing the landfill, and another seven profiles in the surroundings provide a sufficiently dense coverage of the entire area. The whole dataset was inverted using a 1-D laterally constrained inversion scheme, recently implemented for TDIP data, in order to use the entire decay curves for reconstructing the electrical parameters of the soil in terms of the Cole-Cole polarization model. Results show that it is possible to resolve both the geometry of the buried waste body and key geological structures. In particular, it was possible to find a silt/clay lens at depth that correlates with the flow direction of the pollution plume spreading out from the landfill and to map a shallow sandy layer rich in clay that likely has a strong influence on the hydrology of the site. This interpretation of the geophysical findings was constrained by borehole data, in terms of geology and gamma ray logging. The results of this study are important for the impact of the resolved geological units on the hydrology of the area, making it possible to construct more realistic scenarios of the variation of the pollution plume as a function of the climate change.