Construction of a 780-kb PAC, BAC, and cosmid contig encompassing the minimal critical deletion involved in B cell lymphocytic leukemia at 13q14.3

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

Bouyge-Moreau, I.; Rondeau, G.; Andre, M.T.

A putative tumor suppressor gene involved in B cell chronic lymphocytic leukemia (B-CLL) was mapped to human chromosome 13q14.3 close to the genetic markers D13S25 and D13S319. We constructed a 780-kb-long contig composed of cosmids, bacterial artificial chromosomes, and bacteriophage PI-derived artificial chromosomes that provides essential information and tools for the positional cloning of this gene. The contig contains both flanking markers as well as several additional genetic markers, three ESTs, and one potential CpG island. In addition, using one B-CLL patient, we characterized a small internal deleted region of 550 kb. Comparing this deletion with other recently published deletionsmore » narrows the minimally deleted area to less than 100 kb in our physical map. This deletion core region should contain all or part of the disrupted in B cell malignancies tumor suppressor gene. 27 refs., 3 figs.« less

NF1 Microdeletion Syndrome: Refined FISH Characterization of Sporadic and Familial Deletions with Locus-Specific Probes

PubMed Central

Riva, Paola; Corrado, Lucia; Natacci, Federica; Castorina, Pierangela; Wu, Bai-Li; Schneider, Gretchen H.; Clementi, Maurizio; Tenconi, Romano; Korf, Bruce R.; Larizza, Lidia

2000-01-01

Summary Two familial and seven sporadic patients with neurofibromatosis 1—who showed dysmorphism, learning disabilities/mental retardation, and additional signs and carried deletions of the NF1 gene—were investigated by use of a two-step FISH approach to characterize the deletions. With FISH of YAC clones belonging to a 7-Mb 17q11.2 contig, we estimated the extension of all of the deletions and identified the genomic regions harboring the breakpoints. Mosaicism accounted for the mild phenotype in two patients. In subsequent FISH experiments, performed with locus-specific probes generated from the same YACs by means of a novel procedure, we identified the smallest region of overlapping (SRO), mapped the deletion breakpoints, and identified the genes that map to each deletion interval. From centromere to telomere, the ∼0.8-Mb SRO includes sequence-tagged site 64381, the SUPT6H gene (encoding a transcription factor involved in chromatin structure), and NF1. Extending telomerically from the SRO, two additional genes—BLMH, encoding a hydrolase involved in bleomycin resistance, and ACCN1, encoding an amiloride-sensitive cation channel expressed in the CNS—were located in the deleted intervals of seven and three patients, respectively. An apparently common centromeric deletion breakpoint was shared by all of the patients, whereas a different telomeric breakpoint defined a deletion interval of 0.8–3 Mb. There was no apparent correlation between the extent of the deletion and the phenotype. This characterization of gross NF1 deletions provides the premise for addressing correctly any genotype-phenotype correlation in the subset of patients with NF1 deletions. PMID:10631140

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

PubMed Central

2010-01-01

Background A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. Results Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. Conclusions In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome. PMID:21156062

Molecular Definition of the 22q11 Deletions in Velo-Cardio-Facial Syndrome

PubMed Central

Morrow, Bernice; Goldberg, Rosalie; Carlson, Christine; Gupta, Ruchira Das; Sirotkin, Howard; Collins, John; Dunham, Ian; O'Donnell, Hilary; Scambler, Peter; Shprintzen, Robert; Kucherlapati, Raju

1995-01-01

Velo-cardio-facial syndrome (VCFS) is a common genetic disorder among individuals with cleft palate and is associated with hemizygous deletions in human chromosome 22q11. Toward the molecular definition of the deletions, we constructed a physical map of 22q11 in the form of overlapping YACs. The physical map covers >9 cM of genetic distance, estimated to span 5 Mb of DNA, and contains a total of 64 markers. Eleven highly polymorphic short tandem-repeat polymorphic (STRP) markers were placed on the physical map, and 10 of these were unambiguously ordered. The 11 polymorphic markers were used to type the DNA from a total of 61 VCFS patients and 49 unaffected relatives. Comparison of levels of heterozygosity of these markers in VCFS patients and their unaffected relatives revealed that four of these markers are commonly hemizygous among VCFS patients. To confirm these results and to define further the breakpoints in VCFS patients, 15 VCFS individuals and their unaffected parents were genotyped for the 11 STRP markers. Haplotypes generated from this study revealed that 82% of the patients have deletions that can be defined by the STRP markers. The results revealed that all patients who have a deletion share a common proximal breakpoint, while there are two distinct distal breakpoints. Markers D22S941 and D22S944 appear to be consistently hemizygous in patients with deletions. Both of these markers are located on a single nonchimeric YAC that is 400 kb long. The results also show that the parental origin of the deleted chromosome does not have any effect on the phenotypic manifestation ImagesFigure 2Figure 3 PMID:7762562

Molecular definition of the 22q11 deletions in velo-cardio-facial syndrome

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

Morrow, B.; Carlson, C.; Gupta, R.D.

Velo-cardio-facial syndrome (VCFS) is a common genetic disorder among individuals with cleft plate and is associated with hemizygous deletions in human chromosome 22q11. Toward the molecular definition of the deletions, we constructed a physical map of 22q11 in the form of overlapping YACs. The physical map covers >9 cM of genetic distance, estimated to span 5 Mb of DNA, and contains a total of 64 markers. Eleven highly polymorphic short tandem-repeat polymorphic (STRP) markers were placed on the physical map, and 10 of these were unambiguously ordered. The 11 polymorphic markers were used to type the DNA from a totalmore » of 61 VCFS patients and 49 unaffected relatives. Comparison of levels of heterozygosity of these markers in VCFS patients and their unaffected relatives revealed that four of these markers are commonly hemizygous among VCFS patients. To confirm these results and to define further the breakpoints in VCFS patients, 15 VCFS individuals and their unaffected parents were genotyped for the 11 STRP markers. Haplotypes generated from this study revealed that 82% of the patients have deletions that can be defined by the STRP markers. The results revealed that all patients who have a deletion share a common proximal breakpoint, while there are two distinct distal breakpoints. Markers D22S941 and D22S944 appear to be consistently hemizygous in patients with deletions. Both of these markers are located on a single nonchimeric YAC that is 400 kb long. The results show that the parental origin of the deleted chromosome does not have any effect on the phenotypic manifestation. 58 refs., 6 figs., 2 tabs.« less

Submicroscopic deletions at the WAGR locus, revealed by nonradioactive in situ hybridization.

PubMed

Fantes, J A; Bickmore, W A; Fletcher, J M; Ballesta, F; Hanson, I M; van Heyningen, V

1992-12-01

Fluorescence in situ hybridization (FISH) with biotin-labeled probes mapping to 11p13 has been used for the molecular analysis of deletions of the WAGR (Wilms tumor, aniridia, genitourinary abnormalities, and mental retardation) locus. We have detected a submicroscopic 11p13 deletion in a child with inherited aniridia who subsequently presented with Wilms tumor in a horseshoe kidney, only revealed at surgery. The mother, who has aniridia, was also found to carry a deletion including both the aniridia candidate gene (AN2) and the Wilms tumor predisposition gene (WT1). This is therefore a rare case of an inherited WAGR deletion. Wilms tumor has so far only been associated with sporadic de novo aniridia cases. We have shown that a cosmid probe for a candidate aniridia gene, homologous to the mouse Pax-6 gene, is deleted in cell lines from aniridia patients with previously characterized deletions at 11p13, while another cosmid marker mapping between two aniridia-associated translocation breakpoints (and hence a second candidate marker) is present on both chromosomes. These results support the Pax-6 homologue as a strong candidate for the AN2 gene. FISH with cosmid probes has proved to be a fast and reliable technique for the molecular analysis of deletions. It can be used with limited amounts of material and has strong potential for clinical applications.

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

Lachiewicz, A.; Rao, K.; Aylsworth, A.

A 2-year-old boy with Martin-Bell syndrome was referred for molecular testing and found to have a large deletion of FMRI. His mother was found to have two FMR-1 alleles in the normal range for CGG repeats. DNA probes located both proximal and distal to FRAXA were used to delineate the approximation location of the deletion endpoints. Proximal to the fragile site, DXS312 (pX135) was absent but DXS98 (4D8) was present. Distal to the fragile site, DXS296 (VK21) was absent but DXS304 (U6.2) was present. Our patient does not appear to have clinical findings other than those typically associated with fragilemore » X syndrome suggesting that the deletion does not remove other contiguous genes, e.g., IDS. The deletion in this patient is larger than the patient reported by Gedeon et al., in whom approximately 2.5 megabases were estimated to be deleted. Using the physical map of Schlessinger et al., the physical extent of the deletion can be estimated to be at least 3 megabases. This patient may be useful in physical mapping of the chromosomal region near FMR-1. Continued long-term evaluation of this patient may uncover clinical findings suggestive that the deletion removes other genes near to FMR-1 or, alternatively, no findings atypical of the fragile X syndrome suggesting that no other genes lie in the deletion interval.« less

A fruit quality gene map of Prunus

PubMed Central

2009-01-01

Background Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance. Results A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG. Conclusion The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in Prunus crops. PMID:19995417

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Deutsch, Joseph; Salazar, Walter; Hernandez-Ochoa, Miguel; Grygleski, Edward; Steffan, Shawn; Iorizzo, Massimo; Polashock, James; Vorsa, Nicholi; Zalapa, Juan

2016-06-13

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

The gene for replication factor C subunit 2 (RFC2) is within the 7q11.23 Williams syndrome deletion

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

Peoples, R.; Perez-Jurado, L.; Francke, U.

1996-06-01

Williams syndrome (WS) is a developmental disorder with multiple system manifestations, including supraval var aortic stenosis (SVAS), peripheral pulmonic stenosis, connective tissue abnormalities, short stature, characteristic personality profile and cognitive deficits, and variable hypercalcemia in infancy. It is caused by heterozygosity for a chromosomal deletion of part of band 7q11.23 including the elastin locus (ELN). Since disruption of the ELN gene causes autosomal dominant SVAS, it is assumed that ELN haploinsufficiency is responsible for the cardiovascular features of WS. The deletion that extends from the ELN locus in both directions is {ge}200 kb in size, although estimates of {ge}2 Mbmore » are suggested by high-resolution chromosome banding and physical mapping studies. We have searched for additional dosage-sensitive genes within the deletion that may be responsible for the noncardiovascular features. We report here that the gene for replication factor C subunit 2 (RFC2) maps within the WS deletion region and was found to be deleted in all of 18 WS patients studied. The protein product of RFC2 is part of a multimeric complex involved in DNA elongation during replication. 14 refs., 3 figs.« less

The Genetics of a Small Chromosome Region of DROSOPHILA MELANOGASTER Containing the Structural Gene for Alcohol Dehydrogenase. IV: Scutoid, an Antimorphic Mutation

PubMed Central

Ashburner, M.; Tsubota, S.; Woodruff, R. C.

1982-01-01

Exchange mapping locates the dominant mutation Scutoid to the right of Adh on chromosome arm 2L of D. melanogaster. However, deletion mapping indicates that Sco is to the left of Adh. The phenotype of Sco is sensitive to mutation, or deletion, of noc+ and of three genes, el, l(2)br22, and l(2)br29 mapping immediately distal to noc. The four contiguous loci, el, l(2)br22, l(2)br29 and noc, although separable by deletion end points, interact, because certain (or all) alleles of these four loci show partial failure of complementation, or even negative complementation. The simplest hypothesis is that Sco is a small reciprocal transposition, the genes noc, osp, and Adh exchanging places with three genes normally mapping proximal to them: l(2)br34, l(2)br35 and rd. The Sco phenotype is thought to result from a position effect at the newly created noc/l(2)br28 junction. PMID:6816673

Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents.

PubMed

Ulloa, Mauricio; Hulse-Kemp, Amanda M; De Santiago, Luis M; Stelly, David M; Burke, John J

2017-01-01

High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F 2 , a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD) 1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the A t and D t subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the D t subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral A t -subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum . However, the genomic comparisons revealed evidence of additional unconfirmed possible duplications, inversions and translocations, and unbalance SNP sequence homology or SNP sequence/loci genomic dominance, or homeolog loci bias of the upland tetraploid A t and D t subgenomes. The alignments indicated that 364 SNP-associated previously unintegrated scaffolds can be placed in pseudochromosomes of the NBI G hirsutum assembly. This is the first intraspecific SNP genetic linkage consensus map assembled in G hirsutum with a core of reproducible mendelian SNP markers assayed on different populations and it provides further knowledge of chromosome arrangement of genic and nongenic SNPs. Together, the consensus map and RIL populations provide a synergistically useful platform for localizing and identifying agronomically important loci for improvement of the cotton crop.

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

Basu, Sumit, E-mail: sumit.basu@cern.ch; Chatterjee, Rupa; Nayak, Tapan K.

Heavy-ion collisions at ultra-relativistic energies are often referred to as little bangs. We propose for the first time to map the heavy-ion collisions at ultra-relativistic energies, similar to the maps of the cosmic microwave background radiation, using fluctuations of energy density and temperature in small phase space bins. We study the evolution of fluctuations at each stage of the collision using an event-by-event hydrodynamic framework. We demonstrate the feasibility of making fluctuation maps from experimental data and its usefulness in extracting considerable information regarding the early stages of the collision and its evolution.

Evaluation of potential models for imprinted and nonimprinted components of human chromosome 15q11-q13 syndromes by fine-structure homology mapping in the mouse.

PubMed Central

Nicholls, R D; Gottlieb, W; Russell, L B; Davda, M; Horsthemke, B; Rinchik, E M

1993-01-01

Prader-Willi and Angelman syndromes are complex neurobehavioral contiguous gene syndromes whose expression depends on the unmasking of genomic imprinting for different genetic loci in human chromosome 15q11-q13. The homologous chromosomal region in the mouse genome has been fine-mapped by using interspecific (Mus spretus) crosses and overlapping, radiation-induced deletions to evaluate potential animal models for both imprinted and nonimprinted components of these syndromes. Four evolutionarily conserved sequences from human 15q11-q13, including two cDNAs from fetal brain (DN10, D15S12h; DN34, D15S9h-1), a microdissected clone (MN7; D15F37S1h) expressed in mouse brain, and the gene for the beta 3 subunit of the gamma-aminobutyric acid type A receptor (Gabrb3), were mapped in mouse chromosome 7 by analysis of deletions at the pink-eyed dilution (p) locus. Three of these loci are deleted in pre- and postnatally lethal p-locus mutations, which extend up to 5.5 +/- 1.7 centimorgans (cM) proximal to p; D15S9h-1, which maps 1.1 +/- 0.8 cM distal to p and is the mouse homolog of the human gene D15S9 (which shows a DNA methylation imprint), is not deleted in any of the p-locus deletion series. A transcript from the Gabrb3 gene, but not the transcript detected by MN7 at the D15F37S1h locus, is expressed in mice homozygous for the p6H deletion, which have an abnormal neurological phenotype. Furthermore, the Gabrb3 transcript is expressed equally well from the maternal or paternal chromosome 7 and, therefore, its expression is not imprinted in mouse brain. Deletions at the mouse p locus should serve as intermediate genetic reagents and models with which to analyze the genetics and etiology of individual components of human 15q11-q13 disorders. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 PMID:8095339

Optimized detection of shear peaks in weak lensing maps

NASA Astrophysics Data System (ADS)

Marian, Laura; Smith, Robert E.; Hilbert, Stefan; Schneider, Peter

2012-06-01

We present a new method to extract cosmological constraints from weak lensing (WL) peak counts, which we denote as ‘the hierarchical algorithm’. The idea of this method is to combine information from WL maps sequentially smoothed with a series of filters of different size, from the largest down to the smallest, thus increasing the cosmological sensitivity of the resulting peak function. We compare the cosmological constraints resulting from the peak abundance measured in this way and the abundance obtained by using a filter of fixed size, which is the standard practice in WL peak studies. For this purpose, we employ a large set of WL maps generated by ray tracing through N-body simulations, and the Fisher matrix formalism. We find that if low signal-to-noise ratio (?) peaks are included in the analysis (?), the hierarchical method yields constraints significantly better than the single-sized filtering. For a large future survey such as Euclid or Large Synoptic Survey Telescope, combined with information from a cosmic microwave background experiment like Planck, the results for the hierarchical (single-sized) method are Δns= 0.0039 (0.004), ΔΩm= 0.002 (0.0045), Δσ8= 0.003 (0.006) and Δw= 0.019 (0.0525). This forecast is conservative, as we assume no knowledge of the redshifts of the lenses, and consider a single broad bin for the redshifts of the sources. If only peaks with ? are considered, then there is little difference between the results of the two methods. We also examine the statistical properties of the hierarchical peak function: Its covariance matrix has off-diagonal terms for bins with ? and aperture mass of M < 3 × 1014 h-1 M⊙, the higher bins being largely uncorrelated and therefore well described by a Poisson distribution.

An atypical deletion of the Williams–Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism

PubMed Central

Edelmann, Lisa; Prosnitz, Aaron; Pardo, Sherly; Bhatt, Jahnavi; Cohen, Ninette; Lauriat, Tara; Ouchanov, Leonid; González, Patricia J; Manghi, Elina R; Bondy, Pamela; Esquivel, Marcela; Monge, Silvia; Delgado, Marietha F; Splendore, Alessandra; Francke, Uta; Burton, Barbara K; McInnes, L Alison

2007-01-01

Background During a genetic study of autism, a female child who met diagnostic criteria for autism spectrum disorder, but also exhibited the cognitive–behavioural profile (CBP) associated with Williams–Beuren syndrome (WBS) was examined. The WBS CBP includes impaired visuospatial ability, an overly friendly personality, excessive non‐social anxiety and language delay. Methods Using array‐based comparative genomic hybridisation (aCGH), a deletion corresponding to BAC RP11‐89A20 in the distal end of the WBS deletion interval was detected. Hemizygosity was confirmed using fluorescence in situ hybridisation and fine mapping was performed by measuring the copy number of genomic DNA using quantitative polymerase chain reaction. Results The proximal breakpoint was mapped to intron 1 of GTF2IRD1 and the distal breakpoint lies 2.4–3.1 Mb towards the telomere. The subject was completely hemizygous for GTF2I, commonly deleted in carriers of the classic ∼1.5 Mb WBS deletion, and GTF2IRD2, deleted in carriers of the rare ∼1.84 Mb WBS deletion. Conclusion Hemizygosity of the GTF2 family of transcription factors is sufficient to produce many aspects of the WBS CBP, and particularly implicate the GTF2 transcription factors in the visuospatial construction deficit. Symptoms of autism in this case may be due to deletion of additional genes outside the typical WBS interval or remote effects on gene expression at other loci. PMID:16971481

Analyzing the Broken Ridge area of the Indian Ocean using magnetic and gravity anomaly maps and geoid undulation and bathymetry data

NASA Technical Reports Server (NTRS)

Lazarewicz, A. R.; Sailor, R. V. (Principal Investigator)

1982-01-01

A higher resolution anomaly map of the Broken Ridge area (2 degree dipole spacing) was produced and reduced to the pole using quiet time data for this area. The map was compared with equally scaled maps of gravity anomaly, geoid undulation, and bathymetry. The ESMAP results were compared with a NASA MAGSAT map derived by averaging data in two-degree bins. A survey simulation was developed to model the accuracy of MAGSAT anomaly maps as a function of satellite altitude, instrument noise level, external noise model, and crustal anomaly field model. A preliminary analysis of the geophysical structure of Broken Ridge is presented and unresolved questions are listed.

Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) on Mars Reconnaissance Orbiter (MRO)

NASA Astrophysics Data System (ADS)

Murchie, S.; Arvidson, R.; Bedini, P.; Beisser, K.; Bibring, J.-P.; Bishop, J.; Boldt, J.; Cavender, P.; Choo, T.; Clancy, R. T.; Darlington, E. H.; Des Marais, D.; Espiritu, R.; Fort, D.; Green, R.; Guinness, E.; Hayes, J.; Hash, C.; Heffernan, K.; Hemmler, J.; Heyler, G.; Humm, D.; Hutcheson, J.; Izenberg, N.; Lee, R.; Lees, J.; Lohr, D.; Malaret, E.; Martin, T.; McGovern, J. A.; McGuire, P.; Morris, R.; Mustard, J.; Pelkey, S.; Rhodes, E.; Robinson, M.; Roush, T.; Schaefer, E.; Seagrave, G.; Seelos, F.; Silverglate, P.; Slavney, S.; Smith, M.; Shyong, W.-J.; Strohbehn, K.; Taylor, H.; Thompson, P.; Tossman, B.; Wirzburger, M.; Wolff, M.

2007-05-01

The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) is a hyperspectral imager on the Mars Reconnaissance Orbiter (MRO) spacecraft. CRISM consists of three subassemblies, a gimbaled Optical Sensor Unit (OSU), a Data Processing Unit (DPU), and the Gimbal Motor Electronics (GME). CRISM's objectives are (1) to map the entire surface using a subset of bands to characterize crustal mineralogy, (2) to map the mineralogy of key areas at high spectral and spatial resolution, and (3) to measure spatial and seasonal variations in the atmosphere. These objectives are addressed using three major types of observations. In multispectral mapping mode, with the OSU pointed at planet nadir, data are collected at a subset of 72 wavelengths covering key mineralogic absorptions and binned to pixel footprints of 100 or 200 m/pixel. Nearly the entire planet can be mapped in this fashion. In targeted mode the OSU is scanned to remove most along-track motion, and a region of interest is mapped at full spatial and spectral resolution (15-19 m/pixel, 362-3920 nm at 6.55 nm/channel). Ten additional abbreviated, spatially binned images are taken before and after the main image, providing an emission phase function (EPF) of the site for atmospheric study and correction of surface spectra for atmospheric effects. In atmospheric mode, only the EPF is acquired. Global grids of the resulting lower data volume observations are taken repeatedly throughout the Martian year to measure seasonal variations in atmospheric properties. Raw, calibrated, and map-projected data are delivered to the community with a spectral library to aid in interpretation.

DNA sequence analysis of simian virus 40 mutants with deletions mapping in the leader region of the late viral mRNA's: mutants with deletions similar in size and position exhibit varied phenotypes.

PubMed

Barkan, A; Mertz, J E

1981-02-01

The nucleotide sequences of 10 viable yet partially defective deletion mutants of simian virus 40 were determined. The deletions mapped within, and, in many cases, 5' to, the predominant leader sequence of the late viral mRNA's. They ranged from 74 to 187 nucleotide pairs in length. Six of the mutants had lost the sequence that corresponds to the "cap" site (5' terminus) of the most abundant class of 16S mRNA's. One of these mutants had a deletion that extended 103 nucleotide pairs into the region preceding this primary cap site and, therefore, was missing many secondary cap sites as well. A seventh mutant lacked the entire major 16S leader sequence except for the first six nucleotides at its 5' end and the last nine at its 3' end. Although these mutants differed in the size and position of their deletions, we were unable to discover any simple correlations between their growth characteristics and their DNA sequences. This finding indicates that the secondary structures of the RNA transcripts may play a more important role than the exact nucleotide sequence of the RNAs in determining how they function within the cell.

Clinical resistance associated with a novel MAP2K1 mutation in a patient with Langerhans cell histiocytosis.

PubMed

Azorsa, David O; Lee, David W; Wai, Daniel H; Bista, Ranjan; Patel, Apurvi R; Aleem, Eiman; Henry, Michael M; Arceci, Robert J

2018-05-16

Patients with Langerhans cell histiocytosis (LCH) harbor BRAF V600E and activating mutations of MAP2K1/MEK1 in 50% and 25% of cases, respectively. We evaluated a patient with treatment-refractory LCH for mutations in the RAS-RAF-MEK-ERK pathway and identified a novel mutation in the MAP2K1 gene resulting in a p.L98_K104 > Q deletion and predicted to be auto-activating. During treatment with the MEK inhibitor trametinib, the patient's disease showed significant progression. In vitro characterization of the MAP2K1 p.L98_K104 > Q deletion confirmed its effect on cellular activation of the ERK pathway and drug resistance. © 2018 Wiley Periodicals, Inc.

Large-Scale Distributed Coalition Formation

DTIC Science & Technology

2009-09-01

Ripeanu, Matei, Adriana Iamnitchi, and Ian Foster. “Mapping the Gnutella Network”. IEEE Internet Computing, 6(1):50–57, 2002. 78. Rowstron, Antony I...for Search. Working Papers 95-02-010, Santa Fe Institute, February 1995. 97. Xu, Yang, Paul Scerri, Bin Yu, Steven Okamoto, Michael Lewis, and Ka

4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions.

PubMed

Bi, Weimin; Cheung, Sau-Wai; Breman, Amy M; Bacino, Carlos A

2016-10-01

Deletions in the 4p16.3 region cause Wolf-Hirschhorn syndrome, a well known contiguous microdeletion syndrome with the critical region for common phenotype mapped in WHSCR2. Recently, duplications in 4p16.3 were reported in three patients with developmental delay and dysmorphic features. Through chromosomal microarray analysis, we identified 156 patients with a deletion (n = 109) or duplication (n = 47) in 4p16.3 out of approximately 60,000 patients analyzed by Baylor Miraca Genetics Laboratories. Seventy-five of the postnatally detected deletions encompassed the entire critical region, 32 (43%) of which were associated with other chromosome rearrangements, including six patients (8%) that had a duplication adjacent to the terminal deletion. Our data indicate that Wolf-Hirschhorn syndrome deletions with an adjacent duplication occur at a higher frequency than previously appreciated. Pure deletions (n = 14) or duplications (n = 15) without other copy number changes distal to or inside the WHSCR2 were identified for mapping of critical regions. Our data suggest that deletion of the segment from 0.6 to 0.9 Mb from the terminus of 4p causes a seizure phenotype and duplications of a region distal to the previously defined smallest region of overlap for 4p16.3 microduplication syndrome are associated with neurodevelopmental problems. We detected seven Wolf-Hirschhorn syndrome deletions and one 4p16.3 duplication prenatally; all of the seven are either >8 Mb in size and/or associated with large duplications. In conclusion, our study provides deeper insight into the molecular mechanisms, the critical regions and effective prenatal diagnosis for 4p16.3 deletions/ duplications. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Deletion mapping of chromosome 13q in head and neck squamous cell carcinoma in Indian patients: correlation with prognosis of the tumour

PubMed Central

Sabbir, Golam Md; Roy, Anup; Mandal, Syamsundar; Dam, Aniruddha; Roychoudhury, Susanta; Panda, Chinmay Kumar

2006-01-01

Deletions in chromosome (chr.) 13q occur frequently in head and neck squamous cell carcinoma (HNSCC). Previous studies failed to identify common deleted regions in chr.13q, though several candidate tumour suppressor genes (TSGs) loci, e.g. BRCA2, RB1 and BRCAX have been localized in this chromosome, as well as no prognostic significance of the deletion has been reported. Thus, in the present study, deletion mapping of chr. 13q has been done in 55 primary HNSCC samples of Indian patients using 11 highly polymorphic microsatellite markers of which three were intragenic to BRCA2 gene, one intragenic to RB1 gene and another from BRCAX locus. The deletion in chr.13q was significantly associated with progression of HNSCC. High frequencies (27–39%) of loss of heterozygosity were found in 13q13.1 (BRCA2), 13q14.2 (RB1), 13q21.2–22.1 (BRCAX) and 13q31.1 regions. Deletions in the BRCA2 and RB1 regions were significantly correlated. The four highly deleted regions were associated with clinical stage and histological grades of the tumour as well as poor patient outcome. Deletion in the 13q31.1 region was only found to be associated with HPV infection. High frequencies (11–23%) of microsatellite size alteration (MA) were seen to overlap with the highly deleted regions. Forty per cent of the samples showed rare biallelic alteration whereas loss of normal copy of chromosome 13q was seen in five tumours. Thus, it seems that the putative TSGs located in the BRCAX and 13q31.1 regions as well as the BRCA2 and RB1 genes may have some cumulative effect in progression and poor prognosis of HNSCC. Significant association between deletion in BRCA2 and RB1 gene loci may indicate functional relationship between the genes in this tumour progression. PMID:16623759

Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients.

PubMed Central

Carlson, C; Sirotkin, H; Pandita, R; Goldberg, R; McKie, J; Wadey, R; Patanjali, S R; Weissman, S M; Anyane-Yeboa, K; Warburton, D; Scambler, P; Shprintzen, R; Kucherlapati, R; Morrow, B E

1997-01-01

Velo-cardio-facial syndrome (VCFS) is a relatively common developmental disorder characterized by craniofacial anomalies and conotruncal heart defects. Many VCFS patients have hemizygous deletions for a part of 22q11, suggesting that haploinsufficiency in this region is responsible for its etiology. Because most cases of VCFS are sporadic, portions of 22q11 may be prone to rearrangement. To understand the molecular basis for chromosomal deletions, we defined the extent of the deletion, by genotyping 151 VCFS patients and performing haplotype analysis on 105, using 15 consecutive polymorphic markers in 22q11. We found that 83% had a deletion and >90% of these had a similar approximately 3 Mb deletion, suggesting that sequences flanking the common breakpoints are susceptible to rearrangement. We found no correlation between the presence or size of the deletion and the phenotype. To further define the chromosomal breakpoints among the VCFS patients, we developed somatic hybrid cell lines from a set of VCFS patients. An 11-kb resolution physical map of a 1,080-kb region that includes deletion breakpoints was constructed, incorporating genes and expressed sequence tags (ESTs) isolated by the hybridization selection method. The ordered markers were used to examine the two separated copies of chromosome 22 in the somatic hybrid cell lines. In some cases, we were able to map the chromosome breakpoints within a single cosmid. A 480-kb critical region for VCFS has been delineated, including the genes for GSCL, CTP, CLTD, HIRA, and TMVCF, as well as a number of novel ordered ESTs. PMID:9326327

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

PubMed Central

Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

2017-01-01

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding. PMID:28848588

Knowledge-driven binning approach for rare variant association analysis: application to neuroimaging biomarkers in Alzheimer's disease.

PubMed

Kim, Dokyoon; Basile, Anna O; Bang, Lisa; Horgusluoglu, Emrin; Lee, Seunggeun; Ritchie, Marylyn D; Saykin, Andrew J; Nho, Kwangsik

2017-05-18

Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer's disease (LOAD). For rare-variant analysis, we used the knowledge-driven binning approach implemented in Bin-KAT, an automated tool, that provides 1) binning/collapsing methods for multi-level variant aggregation with a flexible, biologically informed binning strategy and 2) an option of performing unified collapsing and statistical rare variant analyses in one tool. A total of 750 non-Hispanic Caucasian participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort who had both WGS data and magnetic resonance imaging (MRI) scans were used in this study. Mean bilateral cortical thickness of the entorhinal cortex extracted from MRI scans was used as an AD-related neuroimaging endophenotype. SKAT was used for a genome-wide gene- and region-based association analysis of rare variants (MAF (minor allele frequency) < 0.05) and potential confounding factors (age, gender, years of education, intracranial volume (ICV) and MRI field strength) for entorhinal cortex thickness were used as covariates. Significant associations were determined using FDR adjustment for multiple comparisons. Our knowledge-driven binning approach identified 16 functional exonic rare variants in FANCC significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In addition, the approach identified 7 evolutionary conserved regions, which were mapped to FAF1, RFX7, LYPLAL1 and GOLGA3, significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In further analysis, the functional exonic rare variants in FANCC were also significantly associated with hippocampal volume and cerebrospinal fluid (CSF) Aβ 1-42 (p-value < 0.05). Our novel binning approach identified rare variants in FANCC as well as 7 evolutionary conserved regions significantly associated with a LOAD-related neuroimaging endophenotype. FANCC (fanconi anemia complementation group C) has been shown to modulate TLR and p38 MAPK-dependent expression of IL-1β in macrophages. Our results warrant further investigation in a larger independent cohort and demonstrate that the biological knowledge-driven binning approach is a powerful strategy to identify rare variants associated with AD and other complex disease.

VizieR Online Data Catalog: Diffuse ionized gas in the Antennae galaxy (Weilbacher+, 2018)

NASA Astrophysics Data System (ADS)

Weilbacher, P. M.; Monreal-Ibero, A.; Verhamme, A.; Sandin, C.; Steinmetz, M.; Kollatschny, W.; Krajnovic, D.; Kamann, S.; Roth, M. M.; Erroz-Ferrer, S.; Marino, R. A.; Maseda, M. V.; Wendt, M.; Bacon, R.; Dreizler, S.; Richard, J.; Wisotzki, L.

2017-11-01

We provide two-dimensional maps of two different ways to measure the diffuse ionized gas as traced by the Halpha emission line in the Antennae Galaxy, both for the central field and the field at the end of the southern tidal tail. We provide a velocity map derived from the Halpha emission line, binned to a S/N~30. Finally, we provide line measurements and derived properties for all HII regions discussed in the paper. (4 data files).

Testing statistical isotropy in cosmic microwave background polarization maps

NASA Astrophysics Data System (ADS)

Rath, Pranati K.; Samal, Pramoda Kumar; Panda, Srikanta; Mishra, Debesh D.; Aluri, Pavan K.

2018-04-01

We apply our symmetry based Power tensor technique to test conformity of PLANCK Polarization maps with statistical isotropy. On a wide range of angular scales (l = 40 - 150), our preliminary analysis detects many statistically anisotropic multipoles in foreground cleaned full sky PLANCK polarization maps viz., COMMANDER and NILC. We also study the effect of residual foregrounds that may still be present in the Galactic plane using both common UPB77 polarization mask, as well as the individual component separation method specific polarization masks. However, some of the statistically anisotropic modes still persist, albeit significantly in NILC map. We further probed the data for any coherent alignments across multipoles in several bins from the chosen multipole range.

The Relationship between Mono-abundance and Mono-age Stellar Populations in the Milky Way Disk

NASA Astrophysics Data System (ADS)

Minchev, I.; Steinmetz, M.; Chiappini, C.; Martig, M.; Anders, F.; Matijevic, G.; de Jong, R. S.

2017-01-01

Studying the Milky Way disk structure using stars in narrow bins of [Fe/H] and [α/Fe] has recently been proposed as a powerful method to understand the Galactic thick and thin disk formation. It has been assumed so far that these mono-abundance populations (MAPs) are also coeval, or mono-age, populations. Here we study this relationship for a Milky Way chemodynamical model and show that equivalence between MAPs and mono-age populations exists only for the high-[α/Fe] tail, where the chemical evolution curves of different Galactic radii are far apart. At lower [α/Fe]-values an MAP is composed of stars with a range in ages, even for small observational uncertainties and a small MAP bin size. Due to the disk inside-out formation, for these MAPs younger stars are typically located at larger radii, which results in negative radial age gradients that can be as large as 2 Gyr kpc-1. Positive radial age gradients can result for MAPs at the lowest [α/Fe] and highest [Fe/H] end. Such variations with age prevent the simple interpretation of observations for which accurate ages are not available. Studying the variation with radius of the stellar surface density and scale height in our model, we find good agreement to recent analyses of the APOGEE red-clump (RC) sample when 1-4 Gyr old stars dominate (as expected for the RC). Our results suggest that the APOGEE data are consistent with a Milky Way model for which mono-age populations flare for all ages. We propose observational tests for the validity of our predictions and argue that using accurate age measurements, such as from asteroseismology, is crucial for putting constraints on Galactic formation and evolution.

Multi-step-ahead Method for Wind Speed Prediction Correction Based on Numerical Weather Prediction and Historical Measurement Data

NASA Astrophysics Data System (ADS)

Wang, Han; Yan, Jie; Liu, Yongqian; Han, Shuang; Li, Li; Zhao, Jing

2017-11-01

Increasing the accuracy of wind speed prediction lays solid foundation to the reliability of wind power forecasting. Most traditional correction methods for wind speed prediction establish the mapping relationship between wind speed of the numerical weather prediction (NWP) and the historical measurement data (HMD) at the corresponding time slot, which is free of time-dependent impacts of wind speed time series. In this paper, a multi-step-ahead wind speed prediction correction method is proposed with consideration of the passing effects from wind speed at the previous time slot. To this end, the proposed method employs both NWP and HMD as model inputs and the training labels. First, the probabilistic analysis of the NWP deviation for different wind speed bins is calculated to illustrate the inadequacy of the traditional time-independent mapping strategy. Then, support vector machine (SVM) is utilized as example to implement the proposed mapping strategy and to establish the correction model for all the wind speed bins. One Chinese wind farm in northern part of China is taken as example to validate the proposed method. Three benchmark methods of wind speed prediction are used to compare the performance. The results show that the proposed model has the best performance under different time horizons.

Deletions of the long arm of chromosome 5 define subgroups of T-cell acute lymphoblastic leukemia

PubMed Central

La Starza, Roberta; Barba, Gianluca; Demeyer, Sofie; Pierini, Valentina; Di Giacomo, Danika; Gianfelici, Valentina; Schwab, Claire; Matteucci, Caterina; Vicente, Carmen; Cools, Jan; Messina, Monica; Crescenzi, Barbara; Chiaretti, Sabina; Foà, Robin; Basso, Giuseppe; Harrison, Christine J.; Mecucci, Cristina

2016-01-01

Recurrent deletions of the long arm of chromosome 5 were detected in 23/200 cases of T-cell acute lymphoblastic leukemia. Genomic studies identified two types of deletions: interstitial and terminal. Interstitial 5q deletions, found in five cases, were present in both adults and children with a female predominance (chi-square, P=0.012). Interestingly, these cases resembled immature/early T-cell precursor acute lymphoblastic leukemia showing significant down-regulation of five out of the ten top differentially expressed genes in this leukemia group, including TCF7 which maps within the 5q31 common deleted region. Mutations of genes known to be associated with immature/early T-cell precursor acute lymphoblastic leukemia, i.e. WT1, ETV6, JAK1, JAK3, and RUNX1, were present, while CDKN2A/B deletions/mutations were never detected. All patients had relapsed/resistant disease and blasts showed an early differentiation arrest with expression of myeloid markers. Terminal 5q deletions, found in 18 of patients, were more prevalent in adults (chi-square, P=0.010) and defined a subgroup of HOXA-positive T-cell acute lymphoblastic leukemia characterized by 130 up- and 197 down-regulated genes. Down-regulated genes included TRIM41, ZFP62, MAPK9, MGAT1, and CNOT6, all mapping within the 1.4 Mb common deleted region at 5q35.3. Of interest, besides CNOT6 down-regulation, these cases also showed low BTG1 expression and a high incidence of CNOT3 mutations, suggesting that the CCR4-NOT complex plays a crucial role in the pathogenesis of HOXA-positive T-cell acute lymphoblastic leukemia with terminal 5q deletions. In conclusion, interstitial and terminal 5q deletions are recurrent genomic losses identifying distinct subtypes of T-cell acute lymphoblastic leukemia. PMID:27151989

Deletions of the long arm of chromosome 5 define subgroups of T-cell acute lymphoblastic leukemia.

PubMed

La Starza, Roberta; Barba, Gianluca; Demeyer, Sofie; Pierini, Valentina; Di Giacomo, Danika; Gianfelici, Valentina; Schwab, Claire; Matteucci, Caterina; Vicente, Carmen; Cools, Jan; Messina, Monica; Crescenzi, Barbara; Chiaretti, Sabina; Foà, Robin; Basso, Giuseppe; Harrison, Christine J; Mecucci, Cristina

2016-08-01

Recurrent deletions of the long arm of chromosome 5 were detected in 23/200 cases of T-cell acute lymphoblastic leukemia. Genomic studies identified two types of deletions: interstitial and terminal. Interstitial 5q deletions, found in five cases, were present in both adults and children with a female predominance (chi-square, P=0.012). Interestingly, these cases resembled immature/early T-cell precursor acute lymphoblastic leukemia showing significant down-regulation of five out of the ten top differentially expressed genes in this leukemia group, including TCF7 which maps within the 5q31 common deleted region. Mutations of genes known to be associated with immature/early T-cell precursor acute lymphoblastic leukemia, i.e. WT1, ETV6, JAK1, JAK3, and RUNX1, were present, while CDKN2A/B deletions/mutations were never detected. All patients had relapsed/resistant disease and blasts showed an early differentiation arrest with expression of myeloid markers. Terminal 5q deletions, found in 18 of patients, were more prevalent in adults (chi-square, P=0.010) and defined a subgroup of HOXA-positive T-cell acute lymphoblastic leukemia characterized by 130 up- and 197 down-regulated genes. Down-regulated genes included TRIM41, ZFP62, MAPK9, MGAT1, and CNOT6, all mapping within the 1.4 Mb common deleted region at 5q35.3. Of interest, besides CNOT6 down-regulation, these cases also showed low BTG1 expression and a high incidence of CNOT3 mutations, suggesting that the CCR4-NOT complex plays a crucial role in the pathogenesis of HOXA-positive T-cell acute lymphoblastic leukemia with terminal 5q deletions. In conclusion, interstitial and terminal 5q deletions are recurrent genomic losses identifying distinct subtypes of T-cell acute lymphoblastic leukemia. Copyright© Ferrata Storti Foundation.

A 1.5-Mb deletion in 17p11.2-p12 is frequently observed in Italian families with hereditary neuropathy with liability to pressure palsies

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

Lorenzetti, D.; Pandolfo, M.; Pareyson, D.

1995-01-01

Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant disorder characterized by recurrent mononeuropathies. A 1.5-Mb deletion in chromosome 17p11.2-p12 has been associated with HNPP. Duplication of the same 1.5-Mb region is known to be associated with Charcot-Marie-Tooth disease type 1 (CMT1A), a more severe peripheral neuropathy characterized by symmetrically slowed nerve conduction velocity (NCV). The CMT1A duplication and HNPP deletion appear to be the reciprocal products of a recombination event involving a repeat element (CMT1A-REP) that flanks the 1.5-Mb region involved in the duplication/deletion. Patients from nine unrelated Italian families who were diagnosed with HNPP onmore » the basis of clinical, electrophysiological, and histological evaluations were analyzed by molecular methods for DNA deletion on chromosome 17p. In all nine families, Southern analysis using a CMT1A-REP probe detected a reduced hybridization signal of a 6.0-kb EcoRI fragment mapping within the distal CMT1A-REP, indicating deletion of one copy of CMT1A-REP in these HNPP patients. Families were also typed with a polymorphic (CA){sub n} repeat and with RFLPs corresponding to loci D17S122, D17S125, and D17S61, which all map within the deleted region. Lack of allelic transmission from affected parent to affected offspring was observed in four informative families, providing an independent indication for deletion. Furthermore, pulsed-field gel electrophoresis analysis of SacII-digested genomic DNA detected junction fragments specific to the 1.5-Mb HNPP deletion in seven of nine Italian families included in this study. These findings suggest that a 1.5-Mb deletion on 17p11.2-p12 is the most common mutation associated with HNPP. 51 refs., 5 figs., 1 tab.« less

Identification of three critical regions within mouse interleukin 2 by fine structural deletion analysis.

PubMed Central

Zurawski, S M; Zurawski, G

1988-01-01

We have analyzed structure--function relationships of the protein hormone murine interleukin 2 by fine structural deletion mapping. A total of 130 deletion mutant proteins, together with some substitution and insertion mutant proteins, was expressed in Escherichia coli and analyzed for their ability to sustain the proliferation of a cloned murine T cell line. This analysis has permitted a functional map of the protein to be drawn and classifies five segments of the protein, which together contain 48% of the sequence, as unessential to the biological activity of the protein. A further 26% of the protein is classified as important, but not crucial, for the activity. Three regions, consisting of amino acids 32-35, 66-77 and 119-141 contain the remaining 26% of the protein and are critical to the biological activity of the protein. The functional map is discussed in the context of the possible role of the identified critical regions in the structure of the hormone and its binding to the interleukin 2 receptor complex. Images PMID:3261239

System design of the CRISM (compact reconnaissance imaging spectrometer for Mars) hyperspectral imager

NASA Astrophysics Data System (ADS)

Silverglate, Peter R.; Fort, Dennis E.

2004-01-01

CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) is a hyperspectral imager that will be launched on the MRO (Mars Reconnaissance Orbiter) in August 2005. The MRO will circle Mars in a polar orbit at a nominal altitude of 325 km. The CRISM spectral range spans the ultraviolet (UV) to the mid-wave infrared (MWIR), 400 nm to 4050 nm. The instrument utilizes a Ritchey-Chretien telescope with a 2.06º field of view (FOV) to focus light on the entrance slit of a dual spectrometer. Within the spectrometer light is split by a dichroic into VNIR (visible-near infrared) (λ <= 1.05 μm) and IR (infrared) (λ >= 1.05 μm) beams. Each beam is directed into a separate modified Offner spectrometer that focuses a spectrally dispersed image of the slit onto a two dimensional focal plane (FP). The IR FP is a 640 x 480 HgCdTe area array; the VNIR FP is a 640 x 480 silicon photodiode area array. The spectral image is contiguously sampled with a 6.55 nm spectral spacing and an instantaneous field of view of 60 μradians. The orbital motion of the MRO pushbroom scans the spectrometer slit across the Martian surface, allowing the planet to be mapped in 558 spectral bands. There are four major mapping modes: A quick initial multi-spectral mapping of a major portion of the Martian surface in 59 selected spectral bands at a spatial resolution of 600 μradians (10:1 binning); an extended multi-spectral mapping of the entire Martian surface in 59 selected spectral bands at a spatial resolution of 300 μradians (5:1 binning); a high resolution Target Mode, performing hyperspectral mapping of selected targets of interest at full spatial and spectral resolution; and an atmospheric Emission Phase Function (EPF) mode for atmospheric study and correction at full spectral resolution at a spatial resolution of 300 μradians (5:1 binning). The instrument is gimbaled to allow scanning over +/-60° for the EPF and Target modes. The scanning also permits orbital motion compensation, enabling longer integration times and consequently higher signal-to-noise ratios for selected areas on the Martian surface in Target Mode.

System design of the CRISM (compact reconnaissance imaging spectrometer for Mars) hyperspectral imager

NASA Astrophysics Data System (ADS)

Silverglate, Peter R.; Fort, Dennis E.

2003-12-01

CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) is a hyperspectral imager that will be launched on the MRO (Mars Reconnaissance Orbiter) in August 2005. The MRO will circle Mars in a polar orbit at a nominal altitude of 325 km. The CRISM spectral range spans the ultraviolet (UV) to the mid-wave infrared (MWIR), 400 nm to 4050 nm. The instrument utilizes a Ritchey-Chretien telescope with a 2.06º field of view (FOV) to focus light on the entrance slit of a dual spectrometer. Within the spectrometer light is split by a dichroic into VNIR (visible-near infrared) (λ <= 1.05 μm) and IR (infrared) (λ >= 1.05 μm) beams. Each beam is directed into a separate modified Offner spectrometer that focuses a spectrally dispersed image of the slit onto a two dimensional focal plane (FP). The IR FP is a 640 x 480 HgCdTe area array; the VNIR FP is a 640 x 480 silicon photodiode area array. The spectral image is contiguously sampled with a 6.55 nm spectral spacing and an instantaneous field of view of 60 μradians. The orbital motion of the MRO pushbroom scans the spectrometer slit across the Martian surface, allowing the planet to be mapped in 558 spectral bands. There are four major mapping modes: A quick initial multi-spectral mapping of a major portion of the Martian surface in 59 selected spectral bands at a spatial resolution of 600 μradians (10:1 binning); an extended multi-spectral mapping of the entire Martian surface in 59 selected spectral bands at a spatial resolution of 300 μradians (5:1 binning); a high resolution Target Mode, performing hyperspectral mapping of selected targets of interest at full spatial and spectral resolution; and an atmospheric Emission Phase Function (EPF) mode for atmospheric study and correction at full spectral resolution at a spatial resolution of 300 μradians (5:1 binning). The instrument is gimbaled to allow scanning over +/-60° for the EPF and Target modes. The scanning also permits orbital motion compensation, enabling longer integration times and consequently higher signal-to-noise ratios for selected areas on the Martian surface in Target Mode.

Wireless Sensor Node Data Gathering and Location Mapping

DTIC Science & Technology

2012-03-01

adaptive two-phase approach to WiFi location sensing,” 4 th Int. Conf. on Pervasive Computing and Communications Workshops, Pisa, Italy, 2006, pp. 452...wrt.v24_micro_generic.bin, March 2010. [11] P. Asadoorian and L. Pesce, Linksys WRT54G Ultimate Hacking , Burlington, MA: Syngress, 2007, pp. 25. 32

Comparison of Aerosol Volume Size Distributions between Surface and Ground-based Remote Sensing Measurements Downwind of Seoul, Korea during MAPS-Seoul

NASA Astrophysics Data System (ADS)

Kim, P.; Choi, Y.; Ghim, Y. S.

2016-12-01

Both sunphotometer (Cimel, CE-318) and skyradiometer (Prede, POM-02) were operated in May, 2015 as a part of the Megacity Air Pollution Studies-Seoul (MAPS-Seoul) campaign. These instruments were collocated at the Hankuk University of Foreign Studies (Hankuk_UFS) site of AErosol RObotic NETwork (AERONET) and the Yongin (YGN) site of SKYradiometer NETwork (SKYNET). The aerosol volume size distribution at the surface was measured using a wide range aerosol spectrometer (WRAS) system consisting of a scanning mobility particle sizer (Grimm, Model 5.416; 45 bins, 0.01-1.09 μm) and an optical particle counter (Grimm, Model 1.109; 31 bins, 0.27-34 μm). The measurement site (37.34oN, 127.27oE, 167 m above sea level) is located about 35 km southeast of downtown Seoul. To investigate the discrepancies in volume concentrations, effective diameters and fine mode volume fractions, we compared the volume size distributions from sunphotometer, skyradiometer, and WRAS system when the measurement time coincided within 5 minutes considering that the measurement intervals were different between instruments.

Differential deletions in 3p are associated with the development of head and neck squamous cell carcinoma in Indian patients.

PubMed

Chakraborty, Suman Bhusan; Dasgupta, Santanu; Roy, Anup; Sengupta, Arunava; Ray, Bidyut; Roychoudhury, Susanta; Panda, Chinmay Kumar

2003-10-15

In this study we performed detailed deletion mapping of two broad regions in the short arm (p) of chromosome 3 (i.e., 3p21.2 approximately p22 and 3p12 approximately p13), which were shown to have a high rate of deletions in head and neck lesions in our previous study. Using 18 highly polymorphic microsatellite markers, the deletion mapping was done in 35 dysplastic lesions and 46 primary head and neck squamous cell carcinoma (HNSCC) samples from Indian patients. Within the 21.6-megabase (Mb) region of 3p21.1 approximately p21.33, we have identified four areas (D1, 3p21.33; D2, 3p21.32; D3, 3p21.31; D4, 3p21.1) that showed a high frequency (46%-69%) of deletions in our samples. In the 3p12 approximately p13 region, we narrowed down the deletion within the 0.7-Mb region (D5, 3p12.1). Among these five regions (D1-D5), deletion in D3 is suggested to be necessary for the development of early dysplastic lesions, whereas the deletion in D2 may be necessary for dysplastic lesions and tumor progression. On the other hand, the deletion in D5 is significantly associated with progression of the lesions from mild/moderate to severe dysplasia. The deletions in D1 and D4, however, are required for tumor progression. As in our previous study, microsatellite size alterations (MA) were observed to be high in and around the highly deleted regions and gradually increased during the progression of the tumor. Loss of normal copy/interstitial alterations of chromosome 3 in the late stages of the tumor as well as rare biallelic alterations around the highly deleted regions also were seen in our samples. Human papilloma virus infection has been found to be associated with the deletion in the D5 region and MA in the D1 region, whereas nodal involvement of the tumor correlated only with the MA in D1 and D5. Thus, this study indicates that multiple tumor suppressor genes whose differential deletions are associated with the development of HNSCC may be present in 3p.

Mapping Cortical Morphology in Youth with Velocardiofacial (22q11.2 Deletion) Syndrome

ERIC Educational Resources Information Center

Kates, Wendy R.; Bansal, Ravi; Fremont, Wanda; Antshel, Kevin M.; Hao, Xuejun; Higgins, Anne Marie; Liu, Jun; Shprintzen, Robert J.; Peterson, Bradley S.

2011-01-01

Objective: Velocardiofacial syndrome (VCFS; 22q11.2 deletion syndrome) represents one of the highest known risk factors for schizophrenia. Insofar as up to 30% of individuals with this genetic disorder develop schizophrenia, VCFS constitutes a unique, etiologically homogeneous model for understanding the pathogenesis of schizophrenia. Method:…

Intracistronic complementation in the simian virus 40 A gene.

PubMed Central

Tornow, J; Cole, C N

1983-01-01

A set of eight simian virus 40 mutants was constructed with lesions in the A gene, which encodes the large tumor (T) antigen. These mutants have small deletions (3-20 base pairs) at either 0.497, 0.288, or 0.243 map units. Mutants having both in-phase and frameshift mutations at each site were isolated. Neither plaque formation nor replication of the mutant DNAs could be detected after transfection of monkey kidney cells. Another nonviable mutant, dlA2459, had a 14-base-pair deletion at 0.193 map unit and was positive for viral DNA replication. Each of the eight mutants were tested for ability to form plaques after cotransfection with dlA2459 DNA. The four mutants that had in-phase deletions were able to complement dlA2459. The other four, which had frameshift deletions, did not. No plaques were formed after cotransfection of cells with any other pair of group A mutants. This suggests that the defect in dlA2459 defines a distinct functional domain of simian virus 40 T antigen. Images PMID:6312452

Contiguous deletion of the NDP, MAOA, MAOB, and EFHC2 genes in a patient with Norrie disease, severe psychomotor retardation and myoclonic epilepsy.

PubMed

Rodriguez-Revenga, L; Madrigal, I; Alkhalidi, L S; Armengol, L; González, E; Badenas, C; Estivill, X; Milà, M

2007-05-01

Norrie disease (ND) is an X-linked disorder, inherited as a recessive trait that, therefore, mostly affects males. The gene responsible for ND, called NDP, maps to the short arm of chromosome X (Xp11.4-p11.3). We report here an atypical case of ND, consisting of a patient harboring a large submicroscopic deletion affecting not only the NDP gene but also the MAOA, MAOB, and EFHC2 genes. Microarray comparative genomic hybridization (CGH) analysis showed that 11 consecutive bacterial artificial chromosome (BAC) clones, mapping around the NDP gene, were deleted. These clones span a region of about 1 Mb on Xp11.3. The deletion was ascertained by fluorescent in situ hybridization (FISH) analysis with different BAC clones located within the region. Clinical features of the proband include bilateral retinal detachment, microcephaly, severe psychomotor retardation without verbal language skills acquired, and epilepsy. The identification and molecular characterization of this case reinforces the idea of a new contiguous gene syndrome that would explain the complex phenotype shared by atypical ND patients.

Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization

PubMed Central

Sabath, Daniel E.; Bender, Michael A.; Sankaran, Vijay G.; Vamos, Esther; Kentsis, Alex; Yi, Hye-Son; Greisman, Harvey A.

2017-01-01

Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing β-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --SEA and --FIL. In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods. PMID:26612711

Characterization of genetic deletions in Becker muscular dystrophy using monoclonal antibodies against a deletion-prone region of dystrophin

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

Thanh, L.T.; Man, Nguyen Thi; Morris, G.E.

1995-08-28

We have produced a new panel of 20 monoclonal antibodies (mAbs) against a region of the dystrophin protein corresponding to a deletion-prone region of the Duchenne muscular dystrophy gene (exons 45-50). We show that immunohistochemistry or Western blotting with these {open_quotes}exon-specific{close_quotes} mAbs can provide a valuable addition to Southern blotting or PCR methods for the accurate identification of genetic deletions in Becker muscular dystrophy patients. The antibodies were mapped to the following exons: exon 45 (2 mAbs), exon 46 (6), exon 47 (1), exons 47/48 (4), exons 48-50 (6), and exon 50 (1). PCR amplification of single exons or groupsmore » of exons was used both to produce specific dystrophin immunogens and to map the mAbs obtained. PCR-mediated mutagenesis was also used to identify regions of dystrophin important for mAb binding. Because the mAbs can be used to characterize the dystrophin produced by individual muscle fibres, they will also be useful for studying {open_quotes}revertant{close_quotes} fibres in Duchenne muscle and for monitoring the results of myoblast therapy trials in MD patients with deletions in this region of the dystrophin gene. 27 refs., 7 figs., 3 tabs.« less

Genomic anatomy of the Tyrp1 (brown) deletion complex

PubMed Central

Smyth, Ian M.; Wilming, Laurens; Lee, Angela W.; Taylor, Martin S.; Gautier, Phillipe; Barlow, Karen; Wallis, Justine; Martin, Sancha; Glithero, Rebecca; Phillimore, Ben; Pelan, Sarah; Andrew, Rob; Holt, Karen; Taylor, Ruth; McLaren, Stuart; Burton, John; Bailey, Jonathon; Sims, Sarah; Squares, Jan; Plumb, Bob; Joy, Ann; Gibson, Richard; Gilbert, James; Hart, Elizabeth; Laird, Gavin; Loveland, Jane; Mudge, Jonathan; Steward, Charlie; Swarbreck, David; Harrow, Jennifer; North, Philip; Leaves, Nicholas; Greystrong, John; Coppola, Maria; Manjunath, Shilpa; Campbell, Mark; Smith, Mark; Strachan, Gregory; Tofts, Calli; Boal, Esther; Cobley, Victoria; Hunter, Giselle; Kimberley, Christopher; Thomas, Daniel; Cave-Berry, Lee; Weston, Paul; Botcherby, Marc R. M.; White, Sharon; Edgar, Ruth; Cross, Sally H.; Irvani, Marjan; Hummerich, Holger; Simpson, Eleanor H.; Johnson, Dabney; Hunsicker, Patricia R.; Little, Peter F. R.; Hubbard, Tim; Campbell, R. Duncan; Rogers, Jane; Jackson, Ian J.

2006-01-01

Chromosome deletions in the mouse have proven invaluable in the dissection of gene function. The brown deletion complex comprises >28 independent genome rearrangements, which have been used to identify several functional loci on chromosome 4 required for normal embryonic and postnatal development. We have constructed a 172-bacterial artificial chromosome contig that spans this 22-megabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones. The deletion complex is strikingly gene-poor, containing only 52 protein-coding genes (of which only 39 are supported by human homologues) and has several further notable genomic features, including several segments of >1 Mb, apparently devoid of a coding sequence. We have used sequence polymorphisms to finely map the deletion breakpoints and identify strong candidate genes for the known phenotypes that map to this region, including three lethal loci (l4Rn1, l4Rn2, and l4Rn3) and the fitness mutant brown-associated fitness (baf). We have also characterized misexpression of the basonuclin homologue, Bnc2, associated with the inversion-mediated coat color mutant white-based brown (Bw). This study provides a molecular insight into the basis of several characterized mouse mutants, which will allow further dissection of this region by targeted or chemical mutagenesis. PMID:16505357

Genetic Mapping of Brain Plasticity Across Development in Williams Syndrome: ERP Markers of Face and Language Processing

PubMed Central

Mills, D. L.; Dai, L.; Fishman, I.; Yam, A.; Appelbaum, L. G.; Galaburda, A.; Bellugi, U.; Korenberg, J. R.

2014-01-01

In Williams Syndrome (WS), a known genetic deletion results in atypical brain function with strengths in face and language processing. We examined how genetic influences on brain activity change with development. In three studies, ERPs from large samples of children, adolescents, and adults with the full genetic deletion for WS were compared to typically developing controls, and two adults with partial deletions for WS. Studies 1 and 2 identified ERP markers of brain plasticity in WS across development. Study 3 suggested that in adults with partial deletions for WS, specific genes may be differentially implicated in face and language processing. PMID:24219698

Fine mapping of genetic variants in BIN1, CLU, CR1 and PICALM for association with cerebrospinal fluid biomarkers for Alzheimer's disease.

PubMed

Kauwe, John S K; Cruchaga, Carlos; Karch, Celeste M; Sadler, Brooke; Lee, Mo; Mayo, Kevin; Latu, Wayne; Su'a, Manti; Fagan, Anne M; Holtzman, David M; Morris, John C; Goate, Alison M

2011-02-09

Recent genome-wide association studies of Alzheimer's disease (AD) have identified variants in BIN1, CLU, CR1 and PICALM that show replicable association with risk for disease. We have thoroughly sampled common variation in these genes, genotyping 355 variants in over 600 individuals for whom measurements of two AD biomarkers, cerebrospinal fluid (CSF) 42 amino acid amyloid beta fragments (Aβ(42)) and tau phosphorylated at threonine 181 (ptau(181)), have been obtained. Association analyses were performed to determine whether variants in BIN1, CLU, CR1 or PICALM are associated with changes in the CSF levels of these biomarkers. Despite adequate power to detect effects as small as a 1.05 fold difference, we have failed to detect evidence for association between SNPs in these genes and CSF Aβ(42) or ptau(181) levels in our sample. Our results suggest that these variants do not affect risk via a mechanism that results in a strong additive effect on CSF levels of Aβ(42) or ptau(181).

Structural analysis of chromosomal rearrangements associated with the developmental mutations Ph, W19H, and Rw on mouse chromosome 5.

PubMed Central

Nagle, D L; Martin-DeLeon, P; Hough, R B; Bućan, M

1994-01-01

We are studying the chromosomal structure of three developmental mutations, dominant spotting (W), patch (Ph), and rump white (Rw) on mouse chromosome 5. These mutations are clustered in a region containing three genes encoding tyrosine kinase receptors (Kit, Pdgfra, and Flk1). Using probes for these genes and for a closely linked locus, D5Mn125, we established a high-resolution physical map covering approximately 2.8 Mb. The entire chromosomal segment mapped in this study is deleted in the W19H mutation. The map indicates the position of the Ph deletion, which encompasses not more than 400 kb around and including the Pdgfra gene. The map also places the distal breakpoint of the Rw inversion to a limited chromosomal segment between Kit and Pdgfra. In light of the structure of the Ph-W-Rw region, we interpret the previously published complementation analyses as indicating that the pigmentation defect in Rw/+ heterozygotes could be due to the disruption of Kit and/or Pdgfra regulatory sequences, whereas the gene(s) responsible for the recessive lethality of Rw/Rw embryos is not closely linked to the Ph and W loci and maps proximally to the W19H deletion. The structural analysis of chromosomal rearrangements associated with W19H, Ph, and Rw combined with the high-resolution physical mapping points the way toward the definition of these mutations in molecular terms and isolation of homologous genes on human chromosome 4. Images PMID:8041773

A population of deletion mutants and an integrated mapping and Exome-seq pipeline for gene discovery in maize

USDA-ARS?s Scientific Manuscript database

To better understand maize endosperm filling and maturation, we developed a novel functional genomics platform that combined Bulked Segregant RNA and Exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. Using gamma-irradiation of B73 maize to...

High-resolution mapping of genotype-phenotype relationships in cridu chat syndrome using array comparative genomic hybridization

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

Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard

2007-07-03

We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology tomore » 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.« less

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

PubMed Central

Wenzl, Peter; Li, Haobing; Carling, Jason; Zhou, Meixue; Raman, Harsh; Paul, Edie; Hearnden, Phillippa; Maier, Christina; Xia, Ling; Caig, Vanessa; Ovesná, Jaroslava; Cakir, Mehmet; Poulsen, David; Wang, Junping; Raman, Rosy; Smith, Kevin P; Muehlbauer, Gary J; Chalmers, Ken J; Kleinhofs, Andris; Huttner, Eric; Kilian, Andrzej

2006-01-01

Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations. PMID:16904008

QTL mapping for Mediterranean corn borer resistance in European flint germplasm using recombinant inbred lines

PubMed Central

2010-01-01

Background Ostrinia nubilalis (ECB) and Sesamia nonagrioides (MCB) are two maize stem borers which cause important losses in temperate maize production, but QTL analyses for corn borer resistance were mostly restricted to ECB resistance and maize materials genetically related (mapping populations derived from B73). Therefore, the objective of this work was to identify and characterize QTLs for MCB resistance and agronomic traits in a RILs population derived from European flint inbreds. Results Three QTLs were detected for stalk tunnel length at bins 1.02, 3.05 and 8.05 which explained 7.5% of the RILs genotypic variance. The QTL at bin 3.05 was co-located to a QTL related to plant height and grain humidity and the QTL at bin 8.05 was located near a QTL related to yield. Conclusions Our results, when compared with results from other authors, suggest the presence of genes involved in cell wall biosynthesis or fortification with effects on resistance to different corn borer species and digestibility for dairy cattle. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling in the region 3.05. However, the small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulating MCB resistance and we conclude that MAS seems not promising for this trait. Two QTLs detected for stalk tunnelling overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes affecting resistance and agronomic traits. PMID:20230603

Conditional poliovirus mutants made by random deletion mutagenesis of infectious cDNA.

PubMed Central

Kirkegaard, K; Nelsen, B

1990-01-01

Small deletions were introduced into DNA plasmids bearing cDNA copies of Mahoney type 1 poliovirus RNA. The procedure used was similar to that of P. Hearing and T. Shenk (J. Mol. Biol. 167:809-822, 1983), with modifications designed to introduce only one lesion randomly into each DNA molecule. Methods to map small deletions in either large DNA or RNA molecules were employed. Two poliovirus mutants, VP1-101 and VP1-102, were selected from mutagenized populations on the basis of their host range phenotype, showing a large reduction in the relative numbers of plaques on CV1 and HeLa cells compared with wild-type virus. The deletions borne by the mutant genomes were mapped to the region encoding the amino terminus of VP1. That these lesions were responsible for the mutant phenotypes was substantiated by reintroduction of the sequenced lesions into a wild-type poliovirus cDNA by deoxyoligonucleotide-directed mutagenesis. The deletion of nucleotides encoding amino acids 8 and 9 of VP1 was responsible for the VP1-101 phenotype; the VP1-102 defect was caused by the deletion of the sequences encoding the first four amino acids of VP1. The peptide sequence at the VP1-VP3 proteolytic cleavage site was altered from glutamine-glycine to glutamine-methionine in VP1-102; this apparently did not alter the proteolytic cleavage pattern. The biochemical defects resulting from these mutations are discussed in the accompanying report. Images PMID:2152811

High-Resolution Regional Biomass Map of Siberia from Glas, Palsar L-Band Radar and Landsat Vcf Data

NASA Astrophysics Data System (ADS)

Sun, G.; Ranson, K.; Montesano, P.; Zhang, Z.; Kharuk, V.

2015-12-01

The Arctic-Boreal zone is known be warming at an accelerated rate relative to other biomes. The taiga or boreal forest covers over 16 x106 km2 of Arctic North America, Scandinavia, and Eurasia. A large part of the northern Boreal forests are in Russia's Siberia, as area with recent accelerated climate warming. During the last two decades we have been working on characterization of boreal forests in north-central Siberia using field and satellite measurements. We have published results of circumpolar biomass using field plots, airborne (PALS, ACTM) and spaceborne (GLAS) lidar data with ASTER DEM, LANDSAT and MODIS land cover classification, MODIS burned area and WWF's ecoregion map. Researchers from ESA and Russia have also been working on biomass (or growing stock) mapping in Siberia. For example, they developed a pan-boreal growing stock volume map at 1-kilometer scale using hyper-temporal ENVISAT ASAR ScanSAR backscatter data. Using the annual PALSAR mosaics from 2007 to 2010 growing stock volume maps were retrieved based on a supervised random forest regression approach. This method is being used in the ESA/Russia ZAPAS project for Central Siberia Biomass mapping. Spatially specific biomass maps of this region at higher resolution are desired for carbon cycle and climate change studies. In this study, our work focused on improving resolution ( 50 m) of a biomass map based on PALSAR L-band data and Landsat Vegetation Canopy Fraction products. GLAS data were carefully processed and screened using land cover classification, local slope, and acquisition dates. The biomass at remaining footprints was estimated using a model developed from field measurements at GLAS footprints. The GLAS biomass samples were then aggregated into 1 Mg/ha bins of biomass and mean VCF and PALSAR backscatter and textures were calculated for each of these biomass bins. The resulted biomass/signature data was used to train a random forest model for biomass mapping of entire region from 50oN to 75oN, and 80oE to 145oE. The spatial patterns of the new biomass map is much better than the previous maps due to spatially specific mapping in high resolution. The uncertainties of field/GLAS and GLAS/imagery models were investigated using bootstrap procedure, and the final biomass map was compared with previous maps.

Elucidation of the mechanism of homozygous deletion of 3p12-13 in the U2020 cell line reveals the unexpected involvement of other chromosomes.

PubMed

Heppell-Parton, A C; Nacheva, E; Carter, N P; Bergh, J; Ogilvie, D; Rabbitts, P H

1999-06-01

Homozygous deletions in tumor cells have been useful in the localization and validation of tumor suppressor genes. We have described a homozygous deletion in a lung cancer cell line (U2020) which is located within the most proximal of the three regions on the short arm of chromosome 3 believed to be lost in lung cancer development. Construction of a YAC contig map indicates that the deletion spans around 8 Mb, but no large deletion was apparent on conventional cytogenetic analysis of the cell line. To investigate this paradox, whole chromosome, arm-specific, and regional paints have been used. This analysis has revealed that genetic loss has occurred by complex rearrangements of chromosomes 3, rather than simple interstitial deletion. These studies emphasize the power of molecular cytogenetics to disclose unsuspected tumor-specific translocations within the extremely complex karyotypes characteristic of solid tumors.

3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

PubMed

Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

2015-06-01

Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π-π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (ϕ, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ≤ ϕ < -155°; -205° ≤ ψ < -160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ(1)/χ(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ(1)/χ(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. © 2015 Wiley Periodicals, Inc.

QTL mapping of stalk bending strength in a recombinant inbred line maize population.

PubMed

Hu, Haixiao; Liu, Wenxin; Fu, Zhiyi; Homann, Linda; Technow, Frank; Wang, Hongwu; Song, Chengliang; Li, Shitu; Melchinger, Albrecht E; Chen, Shaojiang

2013-09-01

Stalk bending strength (SBS) is a reliable indicator for evaluating stalk lodging resistance of maize plants. Based on biomechanical considerations, the maximum load exerted to breaking (F max), the breaking moment (M max) and critical stress (σ max) are three important parameters to characterize SBS. We investigated the genetic architecture of SBS by phenotyping F max, M max and σ max of the fourth internode of maize plants in a population of 216 recombinant inbred lines derived from the cross B73 × Ce03005 evaluated in four environments. Heritability of F max, M max and σ max was 0.81, 0.79 and 0.75, respectively. F max and σ max were positively correlated with several other stalk characters. By using a linkage map with 129 SSR markers, we detected two, three and two quantitative trait loci (QTL) explaining 22.4, 26.1 and 17.2 % of the genotypic variance for F max, M max and σ max, respectively. The QTL for F max, M max and σ max located in adjacent bins 5.02 and 5.03 as well as in bin 10.04 for F max were detected with high frequencies in cross-validation. As our QTL mapping results suggested a complex polygenic inheritance for SBS-related traits, we also evaluated the prediction accuracy of two genomic prediction methods (GBLUP and BayesB). In general, we found that both explained considerably higher proportions of the genetic variance than the values obtained in QTL mapping with cross-validation. Nevertheless, the identified QTL regions could be used as a starting point for fine mapping and gene cloning.

Prior-Based Quantization Bin Matching for Cloud Storage of JPEG Images.

PubMed

Liu, Xianming; Cheung, Gene; Lin, Chia-Wen; Zhao, Debin; Gao, Wen

2018-07-01

Millions of user-generated images are uploaded to social media sites like Facebook daily, which translate to a large storage cost. However, there exists an asymmetry in upload and download data: only a fraction of the uploaded images are subsequently retrieved for viewing. In this paper, we propose a cloud storage system that reduces the storage cost of all uploaded JPEG photos, at the expense of a controlled increase in computation mainly during download of requested image subset. Specifically, the system first selectively re-encodes code blocks of uploaded JPEG images using coarser quantization parameters for smaller storage sizes. Then during download, the system exploits known signal priors-sparsity prior and graph-signal smoothness prior-for reverse mapping to recover original fine quantization bin indices, with either deterministic guarantee (lossless mode) or statistical guarantee (near-lossless mode). For fast reverse mapping, we use small dictionaries and sparse graphs that are tailored for specific clusters of similar blocks, which are classified via tree-structured vector quantizer. During image upload, cluster indices identifying the appropriate dictionaries and graphs for the re-quantized blocks are encoded as side information using a differential distributed source coding scheme to facilitate reverse mapping during image download. Experimental results show that our system can reap significant storage savings (up to 12.05%) at roughly the same image PSNR (within 0.18 dB).

Mapping TES Aerobreaking Data of The Martian Polar Caps

NASA Astrophysics Data System (ADS)

Altunaiji, E. S.; Edwards, C. S.; Smith, M. D.; AlShamsi, M. R.; AlJanaahi, A. A.

2016-12-01

The purpose of this paper is to create maps of the north and south Mars polar caps using Thermal Emission Spectrometer (TES) aerobreaking surface temperature data in south and north as well as Lambert albedo data in the south. TES is an instrument on board the Mars Global Surveyor (MGS) spacecraft. It has six detectors arranged in a 2x3 array with a nominal spot size of 3 × 6 km; however, given the elliptical nature of the orbit during aerobreaking the footprint can be significantly larger (10s of km), especially over the southern hemisphere. TES is a Fourier transform infrared spectrometer designed to study the Martian surface and atmosphere using thermal infrared emission spectroscopy. It is composed of 2 separate channels, a broadband visible/near-infrared bolometer and hyperspectral thermal infrared spectrometer with a broadband thermal infrared bolometer. TES aerobraking spectra were taken between Mars Year 23, Ls=180° and Mars Year 24, Ls=30°. To determine the footprint location on the surface, geometry is calculated using the Spacecraft Planet Instrument Camera Matrix and Event (SPICE) Toolkit. These data were then binned and mapped to surface in polar stereographic projection. While some early studies focused on these data, we have expanded upon the ranges, generated time-/seasonally-binned data, and re-examined this largely underutilized set of data from TES ultimately extending the record of polar science on Mars.

Chromosome 22q11.2 deletion in a boy with Opitz (G/BBB) syndrome

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

Fryburg, J.S.; Lin, K.Y.; Golden, W.L.

This report is on a 14-month-old boy with manifestations of Opitz (G/BBB) syndrome in whom a 22q11.2 deletion was found. Deletion analysis was requested because of some findings in this patient reminiscent of velocardiofacial (VCF) syndrome. The extent of aspiration and of respiratory symptoms in this child is not usually seen in VCF syndrome. Opitz syndrome maps to at least two loci, one on Xp, the other on 22q11.2. 12 refs., 2 figs.

Temporal and spectral manipulations of correlated photons using a time lens

NASA Astrophysics Data System (ADS)

Mittal, Sunil; Orre, Venkata Vikram; Restelli, Alessandro; Salem, Reza; Goldschmidt, Elizabeth A.; Hafezi, Mohammad

2017-10-01

A common challenge in quantum information processing with photons is the limited ability to manipulate and measure correlated states. An example is the inability to measure picosecond-scale temporal correlations of a multiphoton state, given state-of-the-art detectors have a temporal resolution of about 100 ps. Here, we demonstrate temporal magnification of time-bin-entangled two-photon states using a time lens and measure their temporal correlation function, which is otherwise not accessible because of the limited temporal resolution of single-photon detectors. Furthermore, we show that the time lens maps temporal correlations of photons to frequency correlations and could be used to manipulate frequency-bin-entangled photons. This demonstration opens a new avenue to manipulate and analyze spectral and temporal wave functions of many-photon states.

Homozygous deletions at 3p12 in breast and lung cancer.

PubMed

Sundaresan, V; Chung, G; Heppell-Parton, A; Xiong, J; Grundy, C; Roberts, I; James, L; Cahn, A; Bench, A; Douglas, J; Minna, J; Sekido, Y; Lerman, M; Latif, F; Bergh, J; Li, H; Lowe, N; Ogilvie, D; Rabbitts, P

1998-10-01

We have constructed a physical map of the region homozygously deleted in the U2020 cell line at 3p12, including the location of putative CpG islands. Adjacent to one of these islands, we have identified and cloned a new gene (DUTT1) and used probes from this gene to detect two other homozygous deletions occurring in lung and breast carcinomas: the smallest deletion is within the gene itself and would result in a truncated protein. The DUTT1 gene is a member of the neural cell adhesion molecule family, although its widespread expression suggests it plays a less specialized role compared to other members of the family.

Cosmological parameters, shear maps and power spectra from CFHTLenS using Bayesian hierarchical inference

NASA Astrophysics Data System (ADS)

Alsing, Justin; Heavens, Alan; Jaffe, Andrew H.

2017-04-01

We apply two Bayesian hierarchical inference schemes to infer shear power spectra, shear maps and cosmological parameters from the Canada-France-Hawaii Telescope (CFHTLenS) weak lensing survey - the first application of this method to data. In the first approach, we sample the joint posterior distribution of the shear maps and power spectra by Gibbs sampling, with minimal model assumptions. In the second approach, we sample the joint posterior of the shear maps and cosmological parameters, providing a new, accurate and principled approach to cosmological parameter inference from cosmic shear data. As a first demonstration on data, we perform a two-bin tomographic analysis to constrain cosmological parameters and investigate the possibility of photometric redshift bias in the CFHTLenS data. Under the baseline ΛCDM (Λ cold dark matter) model, we constrain S_8 = σ _8(Ω _m/0.3)^{0.5} = 0.67+0.03-0.03 (68 per cent), consistent with previous CFHTLenS analyses but in tension with Planck. Adding neutrino mass as a free parameter, we are able to constrain ∑mν < 4.6 eV (95 per cent) using CFHTLenS data alone. Including a linear redshift-dependent photo-z bias Δz = p2(z - p1), we find p_1=-0.25+0.53-0.60 and p_2 = -0.15+0.17-0.15, and tension with Planck is only alleviated under very conservative prior assumptions. Neither the non-minimal neutrino mass nor photo-z bias models are significantly preferred by the CFHTLenS (two-bin tomography) data.

Construction of the physical map of the gpa7 locus reveals that a large segment was deleted during rice domestication.

PubMed

Li, Xianran; Tian, Feng; Huang, Haiyan; Tan, Lubin; Zhu, Zuofeng; Hu, Songnian; Sun, Chuanqing

2008-06-01

To facilitate cloning gene(s) underlying gpa7, a deep-coverage BAC library was constructed for an isolate of common wild rice (Oryza rufipogon Griff.) collected from Dongxiang, Jiangxi Province, China (DXCWR). gpa7, a quantitative trait locus corresponding to grain number per panicle, is positioned in the short arm of chromosome 7. The BAC library containing 96,768 clones represents approximate 18 haploid genome equivalents. The contig spanning DXCWR gpa7 was constructed with a series of ordered markers. The putative physical map near the gpa7 locus of another accession of O. rufipogon (Accession: IRGC 105491) was also isolated in silico. Analysis of the physical maps of gpa7 indicated that a segment of about 150 kb was deleted during domestication of common wild rice.

Glimpse: Sparsity based weak lensing mass-mapping tool

NASA Astrophysics Data System (ADS)

Lanusse, F.; Starck, J.-L.; Leonard, A.; Pires, S.

2018-02-01

Glimpse, also known as Glimpse2D, is a weak lensing mass-mapping tool that relies on a robust sparsity-based regularization scheme to recover high resolution convergence from either gravitational shear alone or from a combination of shear and flexion. Including flexion allows the supplementation of the shear on small scales in order to increase the sensitivity to substructures and the overall resolution of the convergence map. To preserve all available small scale information, Glimpse avoids any binning of the irregularly sampled input shear and flexion fields and treats the mass-mapping problem as a general ill-posed inverse problem, regularized using a multi-scale wavelet sparsity prior. The resulting algorithm incorporates redshift, reduced shear, and reduced flexion measurements for individual galaxies and is made highly efficient by the use of fast Fourier estimators.

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

PubMed Central

Parker, Heidi G.; Kukekova, Anna V.; Akey, Dayna T.; Goldstein, Orly; Kirkness, Ewen F.; Baysac, Kathleen C.; Mosher, Dana S.; Aguirre, Gustavo D.; Acland, Gregory M.; Ostrander, Elaine A.

2007-01-01

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. PMID:17916641

Error Correcting Optical Mapping Data.

PubMed

Mukherjee, Kingshuk; Washimkar, Darshan; Muggli, Martin D; Salmela, Leena; Boucher, Christina

2018-05-26

Optical mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome [21]. Recently it has been used for scaffolding contigs and assembly validation for large-scale sequencing projects, including the maize [32], goat [6], and amborella [4] genomes. However, a major impediment in the use of this data is the variety and quantity of errors in the raw optical mapping data, which are called Rmaps. The challenges associated with using Rmap data are analogous to dealing with insertions and deletions in the alignment of long reads. Moreover, they are arguably harder to tackle since the data is numerical and susceptible to inaccuracy. We develop cOMET to error correct Rmap data, which to the best of our knowledge is the only optical mapping error correction method. Our experimental results demonstrate that cOMET has high prevision and corrects 82.49% of insertion errors and 77.38% of deletion errors in Rmap data generated from the E. coli K-12 reference genome. Out of the deletion errors corrected, 98.26% are true errors. Similarly, out of the insertion errors corrected, 82.19% are true errors. It also successfully scales to large genomes, improving the quality of 78% and 99% of the Rmaps in the plum and goat genomes, respectively. Lastly, we show the utility of error correction by demonstrating how it improves the assembly of Rmap data. Error corrected Rmap data results in an assembly that is more contiguous, and covers a larger fraction of the genome.

Dark Energy Survey Year 1 results: curved-sky weak lensing mass map

NASA Astrophysics Data System (ADS)

Chang, C.; Pujol, A.; Mawdsley, B.; Bacon, D.; Elvin-Poole, J.; Melchior, P.; Kovács, A.; Jain, B.; Leistedt, B.; Giannantonio, T.; Alarcon, A.; Baxter, E.; Bechtol, K.; Becker, M. R.; Benoit-Lévy, A.; Bernstein, G. M.; Bonnett, C.; Busha, M. T.; Rosell, A. Carnero; Castander, F. J.; Cawthon, R.; da Costa, L. N.; Davis, C.; De Vicente, J.; DeRose, J.; Drlica-Wagner, A.; Fosalba, P.; Gatti, M.; Gaztanaga, E.; Gruen, D.; Gschwend, J.; Hartley, W. G.; Hoyle, B.; Huff, E. M.; Jarvis, M.; Jeffrey, N.; Kacprzak, T.; Lin, H.; MacCrann, N.; Maia, M. A. G.; Ogando, R. L. C.; Prat, J.; Rau, M. M.; Rollins, R. P.; Roodman, A.; Rozo, E.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Sevilla-Noarbe, I.; Sheldon, E.; Troxel, M. A.; Varga, T. N.; Vielzeuf, P.; Vikram, V.; Wechsler, R. H.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Kind, M. Carrasco; Carretero, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Estrada, J.; Neto, A. Fausti; Fernandez, E.; Flaugher, B.; Frieman, J.; García-Bellido, J.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Kent, S.; Kirk, D.; Krause, E.; Kuehn, K.; Kuhlmann, S.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Menanteau, F.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nichol, R. C.; Petravick, D.; Plazas, A. A.; Romer, A. K.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Tarle, G.; Thomas, D.; Tucker, D. L.; Walker, A. R.; Wester, W.; Zhang, Y.

2018-04-01

We construct the largest curved-sky galaxy weak lensing mass map to date from the DES first-year (DES Y1) data. The map, about 10 times larger than the previous work, is constructed over a contiguous ≈1500 deg2, covering a comoving volume of ≈10 Gpc3. The effects of masking, sampling, and noise are tested using simulations. We generate weak lensing maps from two DES Y1 shear catalogues, METACALIBRATION and IM3SHAPE, with sources at redshift 0.2 < z < 1.3, and in each of four bins in this range. In the highest signal-to-noise map, the ratio between the mean signal to noise in the E-mode map and the B-mode map is ˜1.5 (˜2) when smoothed with a Gaussian filter of σG = 30 (80) arcmin. The second and third moments of the convergence κ in the maps are in agreement with simulations. We also find no significant correlation of κ with maps of potential systematic contaminants. Finally, we demonstrate two applications of the mass maps: (1) cross-correlation

Performance analysis of different database in new internet mapping system

NASA Astrophysics Data System (ADS)

Yao, Xing; Su, Wei; Gao, Shuai

2017-03-01

In the Mapping System of New Internet, Massive mapping entries between AID and RID need to be stored, added, updated, and deleted. In order to better deal with the problem when facing a large number of mapping entries update and query request, the Mapping System of New Internet must use high-performance database. In this paper, we focus on the performance of Redis, SQLite, and MySQL these three typical databases, and the results show that the Mapping System based on different databases can adapt to different needs according to the actual situation.

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

Schuffenhauer, S.; Daumer-Haas, C.; Murken, J.

Karyotypes with an interstitial deletion and a marker chromosome formed from the deleted segment are rare. We identified such a rearrangement in a newborn infant, who presented with macrocephaly, asymmetric square skull, minor facial anomalies, omphalocele, inguinal hernias, hypospadias, and club feet. The karyotype 46,XY,del(5)(pter{r_arrow}p13::cen{r_arrow}qter)/47,XY,+dicr(5)(:p13{r_arrow}cen::p13{r_arrow}cen),del(5)(pter{r_arrow}p13::cen{r_arrow}qter) was identified by banding studies and FISH analysis in the peripheral lymphocytes. One breakpoint on the del(5) maps distal to GDNF, and FISH analysis using an {alpha}-satellite probe suggests that the proximal breakpoint maps within the centromere. The dicentric r(5) consists of two copies of the segment deleted in the del(5), resulting in trisomy ofmore » proximal 5p (5p13-cen). The phenotype of the propositus is compared with other trisomy 5p cases and possible mechanisms for the generation of this unique chromosomal rearrangement are discussed. 27 refs., 3 figs.« less

Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.

PubMed

Sardiu, Mihaela E; Gilmore, Joshua M; Carrozza, Michael J; Li, Bing; Workman, Jerry L; Florens, Laurence; Washburn, Michael P

2009-10-06

Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex.

Deletion mapping of 22q11 in CATCH22 syndrome: Identification of a second critical region

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

Kurahashi, Hiroki; Nakayama, Takahiro; Nishisho, Isamu

1996-06-01

The deletion at 22q11.2 implicates a variety of congenital anomaly syndromes, for which the acronym CATCH22 has been proposed . Most patients with these syndromes share the common large deletion spanning 1-2 Mb, while the phenotypic variability of the patients does not seem to correlate with the extent of the deletions. On the basis of the deletions of rare cases with unbalanced translocation, the shortest region of overlap (SRO) had been identified in the most-centromeric region of the common large deletion. One patient (ADU) has been reported to carry a balanced translocation with the breakpoint located in the SRO. Recently,more » three transcripts were identified at or very close to the ADU breakpoint (ADUBP), making them strong candidates for CATCH22 syndrome. Here, we describe one patient with a unique deletion at 22q11.2 revealed by quantitative hybridization and/or FISH with six DNA markers in the common large deletion. The patient was dizygous at loci within the SRO and hemizygous only at the most-telomeric locus in the common large deletion. This finding suggests that there must be another critical region in the common large deletion besides the breakpoint of the ADU and that haploinsufficiency of genes in this deletion may also play a major role in CATCH22 pathogenesis. 15 refs., 3 figs.« less

Investigation of tumor suppressor genes apart from VHL on 3p by deletion mapping in sporadic clear cell renal cell carcinoma (cRCC).

PubMed

Singh, Rashmi Bhat; Amare Kadam, Pratibha S

2013-10-01

To investigate the most recurrent deletion loci on 3p12-p26 by deletion mapping studies by PCR-LOH and BAC array-FISH in sporadic conventional renal cell carcinoma (cRCC) and further, to evaluate the their clinicopathologic significance in cRCC. Comparative allelotyping studies in cRCC and major epithelial carcinomas (MEC) such as lung, breast, and bladder tumors were also carried out to investigate the specificity of the targeted loci in cRCC. A total of 40 c-RCC patients were enrolled in this study, categorized in to 2 groups: group I comprises of patients of stages I and II and group II includes patients at stages III and IV. Loss of heterozygosity (LOH) studies were performed by PCR using 15 microsatellite markers of region 3p12-p26 on paired normal-tumor tissues. The recurrent LOH loci found in 27 cRCC tumors were further validated by BAC array-FISH using 23 serially mapped BAC clones. Simultaneously, the allelic deletion status of fragile histidine triad (FHIT) gene was studied by FISH in cRCC and major epithelial carcinoma (MEC) tumors. The numerical aberrations of chromosome 3 were also studied using the centromere enumeration probe (CEP) probe for chromosome 3 to validate the observed allelic losses by BAC array-FISH in cRCC as well as MECs. Our study revealed 3 affected regions of LOH on 3p in cRCC: 3p12.2-p14.1, 3p14.2-p21.1, and 3p24.2-p26.1 in both group I (stages I and II) and group II (stage III and IV). Comparative allelotyping studies revealed that except for LOH loci D3S2406 (20%), D3S1766 (14%), and D3S1560 (20%), remaining affected loci revealed retention of heterozygosity (ROH) in breast carcinomas. Lung and bladder tumors revealed ROH at all affected LOH loci. FISH with FHIT gene probe revealed deletions in cRCC (88%), breast (30%), and lung tumors (10%). FHIT gene deletions frequency was almost equal in both groups I and II (>70%), whereas a locus 3p13 (D3S2454) revealed the highest LOH in group II (83%) patients in comparison to group I (16%). BAC array-FISH studies in cRCC identified 15 recurrent deletion loci at crucial regions, 3p12.2, 3p14.2, 3p21.3, and 3p24.2-p26 with long continuous deletion of 3p14.1-p26.1 exclusively in patients of stages III and IV. Validation of LOH loci in breast carcinomas by BAC array-FISH with BAC clones mapped at these loci revealed comparatively lower deletion frequency for RP11-59E22 (3p12.2) (30%), RP11-759B7(3p21.1) (12%), and RP11-57D6 (3p25.2, proximal to VHL) (15%) than cRCC. Molecular cytogenetic studies by BAC array-FISH was found to be more sensitive over LOH. Deletion patterns on 3p explored that deletion of FHIT and flanking loci may occur as an initiating event followed by deletions at 3p12.2, 3p21.31-3p21.32, and 3p24.2-3p26.1 in the initial stage of development of disease, while continuous large deletions of 3p21.3-3p26.1 and 3p14.1-3p26.1 occur as progressive deletion due to genetic instability. Lack of VHL along with flanking loci in 50% cRCC patients that included both groups I and II supported the hypothesis of both VHL dependent and VHL independent pathways in cRCC tumorigenesis. Comparative allelotyping studies in cRCC and MECs indicated association of specific targeted loci including VHL in cRCC. Further expansion of these studies with characterization of the genes at targeted loci and correlation with clinical outcome will explore the prognostic significance and also provide an insight into the mechanisms of tumor suppressive pathways in genitourinary cancers such as CRCC. Copyright © 2013 Elsevier Inc. All rights reserved.

76 FR 13994 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-15

... received which result in a contrary determination. ADDRESSES: You may submit comments, identified by dock... of Defense. Deletion: K700.03 Manpower and Personnel System (MAPS) (February 22, 1993, 58 FR 10562). Reason: Manpower and Personnel System (MAPS) has been replaced with Open Source Corporate Management...

Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284.

PubMed

Nsabiyera, Vallence; Bariana, Harbans S; Qureshi, Naeela; Wong, Debbie; Hayden, Matthew J; Bansal, Urmil K

2018-07-01

A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S. A recombinant inbred line (RIL) population comprising 121 lines was developed and tested in the field at three locations in 2016 and two in 2017 crop seasons. Monogenic segregation for adult plant stripe rust response was observed among the Aus27284/Avocet S RIL population and the underlying locus was temporarily designated YrAW11. Bulked-segregant analysis using the Infinium iSelect 90K SNP wheat array placed YrAW11 in chromosome 3B. Kompetitive allele specific PCR (KASP) primers were designed for the linked SNPs and YrAW11 was flanked by KASP_65624 and KASP_53292 (3 cM) proximally and KASP_53113 (4.9 cM) distally. A partial linkage map of the genomic region carrying YrAW11 comprised nine KASP and two SSR markers. The physical position of KASP markers in the pseudomolecule of chromosome 3B placed YrAW11 in the long arm and the location of markers gwm108 and gwm376 in the deletion bin 3BL2-0.22 supported this conclusion. As no other stripe rust resistance locus has been reported in chromosome 3BL, YrAW11 was formally designated Yr80. Marker KASP_ 53113 was polymorphic among 94% of 81 Australian wheat cultivars used for validation.

Verification of QTL for Grain Starch Content and Its Genetic Correlation with Oil Content Using Two Connected RIL Populations in High-Oil Maize

PubMed Central

Yang, Guohu; Dong, Yongbin; Li, Yuling; Wang, Qilei; Shi, Qingling; Zhou, Qiang

2013-01-01

Grain oil content is negatively correlated with starch content in maize in general. In this study, 282 and 263 recombinant inbred lines (RIL) developed from two crosses between one high-oil maize inbred and two normal dent maize inbreds were evaluated for grain starch content and its correlation with oil content under four environments. Single-trait QTL for starch content in single-population and joint-population analysis, and multiple-trait QTL for both starch and oil content were detected, and compared with the result obtained in the two related F2∶3 populations. Totally, 20 single-population QTL for grain starch content were detected. No QTL was simultaneously detected across all ten cases. QTL at bins 5.03 and 9.03 were all detected in both populations and in 4 and 5 cases, respectively. Only 2 of the 16 joint-population QTL had significant effects in both populations. Three single-population QTL and 8 joint-population QTL at bins 1.03, 1.04–1.05, 3.05, 8.04–8.05, 9.03, and 9.05 could be considered as fine-mapped. Common QTL across F2∶3 and RIL generations were observed at bins 5.04, 8.04 and 8.05 in population 1 (Pop.1), and at bin 5.03 in population 2 (Pop.2). QTL at bins 3.02–3.03, 3.05, 8.04–8.05 and 9.03 should be focused in high-starch maize breeding. In multiple-trait QTL analysis, 17 starch-oil QTL were detected, 10 in Pop.1 and 7 in Pop.2. And 22 single-trait QTL failed to show significance in multiple-trait analysis, 13 QTL for starch content and 9 QTL for oil content. However, QTL at bins 1.03, 6.03–6.04 and 8.03–8.04 might increase grain starch content and/or grain oil content without reduction in another trait. Further research should be conducted to validate the effect of these QTL in the simultaneous improvement of grain starch and oil content in maize. PMID:23320103

High-resolution mapping of Martian water ice clouds using Mars Express OMEGA observations - Derivation of the diurnal cloud life cycle

NASA Astrophysics Data System (ADS)

Szantai, Andre; Audouard, Joachim; Madeleine, Jean-Baptiste; Forget, Francois; Pottier, Alizée; Millour, Ehouarn; Gondet, Brigitte; Langevin, Yves; Bibring, Jean-Pierre

2016-10-01

The mapping in space and time of water ice clouds can help to explain the Martian water cycle and atmospheric circulation. For this purpose, an ice cloud index (ICI) corresponding to the depth of a water ice absorption band at 3.4 microns is derived from a series of OMEGA images (spectels) covering 5 Martian years. The ICI values for the corresponding pixels are then binned on a high-resolution regular grid (1° longitude x 1° latitude x 5° Ls x 1 h local time) and averaged. Inside each bin, the cloud cover is calculated by dividing the number of pixels considered as cloudy (after comparison to a threshold) to the number of all (valid) pixelsWe compare the maps of clouds obtained around local time 14:00 with collocated TES cloud observations (which were only obtained around this time of the day). A good agreement is found.Averaged ICI compared to the water ice column variable from the Martian Climate Database (MCD) show a correct correlation (~0.5) , which increases when values limited to the tropics only are compared.The number of gridpoints containing ICI values is small ( ~1%), but by taking several neighbor gridpoints and over longer periods, we can observe a cloud life cycle during daytime. An example in the the tropics, around the northern summer solstice, shows a decrease of cloudiness in the morning followed by an increase in the afternoon.

Big Bangs in Galaxy Clusters: Using X-ray Temperature Maps to Trace Merger Histories in Clusters with Radio Halos/Relics

NASA Astrophysics Data System (ADS)

Burns, Jack O.; Datta, Abhirup; Hallman, Eric J.

2016-06-01

Galaxy clusters are assembled through large and small mergers which are the most energetic events ("bangs") since the Big Bang. Cluster mergers "stir" the intracluster medium (ICM) creating shocks and turbulence which are illuminated by ~Mpc-sized radio features called relics and halos. These shocks heat the ICM and are detected in x-rays via thermal emission. Disturbed morphologies in x-ray surface brightness and temperatures are direct evidence for cluster mergers. In the radio, relics (in the outskirts of the clusters) and halos (located near the cluster core) are also clear signposts of recent mergers. Our recent ENZO cosmological simulations suggest that around a merger event, radio emission peaks very sharply (and briefly) while the x-ray emission rises and decays slowly. Hence, a sample of galaxy clusters that shows both luminous x-ray emission and radio relics/halos are good candidates for very recent mergers. We are in the early stages of analyzing a unique sample of 48 galaxy clusters with (i) known radio relics and/or halos and (ii) significant archival x-ray observations (>50 ksec) from Chandra and/or XMM. We have developed a new x-ray data analysis pipeline, implemented on parallel processor supercomputers, to create x-ray surface brightness, high fidelity temperature, and pressure maps of these clusters in order to study merging activity. The temperature maps are made using three different map-making techniques: Weighted Voronoi Tessellation, Adaptive Circular Binning, and Contour Binning. In this talk, we will show preliminary results for several clusters, including Abell 2744 and the Bullet cluster. This work is supported by NASA ADAP grant NNX15AE17G.

AutoMap User’s Guide

DTIC Science & Technology

2006-10-01

Hierarchy of Pre-Processing Techniques 3. NLP (Natural Language Processing) Utilities 3.1 Named-Entity Recognition 3.1.1 Example for Named-Entity... Recognition 3.2 Symbol RemovalN-Gram Identification: Bi-Grams 4. Stemming 4.1 Stemming Example 5. Delete List 5.1 Open a Delete List 5.1.1 Small...iterative and involves several key processes: • Named-Entity Recognition Named-Entity Recognition is an Automap feature that allows you to

Topography of the Duchenne muscular dystrophy (DMD) gene: FIGE and cDNA analysis of 194 cases reveals 115 deletions and 13 duplications.

PubMed Central

Den Dunnen, J T; Grootscholten, P M; Bakker, E; Blonden, L A; Ginjaar, H B; Wapenaar, M C; van Paassen, H M; van Broeckhoven, C; Pearson, P L; van Ommen, G J

1989-01-01

We have studied 34 Becker and 160 Duchenne muscular dystrophy (DMD) patients with the dystrophin cDNA, using conventional blots and FIGE analysis. One hundred twenty-eight mutations (65%) were found, 115 deletions and 13 duplications, of which 106 deletions and 11 duplications could be precisely mapped in relation to both the mRNA and the major and minor mutation hot spots. Junction fragments, ideal markers for carrier detection, were found in 23 (17%) of the 128 cases. We identified eight new cDNA RFLPs within the DMD gene. With the use of cDNA probes we have completed the long-range map of the DMD gene, by the identification of a 680-kb SfiI fragment containing the gene's 3' end. The size of the DMD gene is now determined to be about 2.3 million basepairs. The combination of cDNA hybridizations with long-range analysis of deletion and duplication patients yields a global picture of the exon spacing within the dystrophin gene. The gene shows a large variability of intron size, ranging from only a few kilobases to 160-180 kb for the P20 intron. Images Figure 1 Figure 4 PMID:2573997

Comparative sequence analysis of a region on human chromosome 13q14, frequently deleted in B-cell chronic lymphocytic leukemia, and its homologous region on mouse chromosome 14.

PubMed

Kapanadze, B; Makeeva, N; Corcoran, M; Jareborg, N; Hammarsund, M; Baranova, A; Zabarovsky, E; Vorontsova, O; Merup, M; Gahrton, G; Jansson, M; Yankovsky, N; Einhorn, S; Oscier, D; Grandér, D; Sangfelt, O

2000-12-15

Previous studies have indicated the presence of a putative tumor suppressor gene on human chromosome 13q14, commonly deleted in patients with B-cell chronic lymphocytic leukemia (B-CLL). We have recently identified a minimally deleted region encompassing parts of two adjacent genes, termed LEU1 and LEU2 (leukemia-associated genes 1 and 2), and several additional transcripts. In addition, 50 kb centromeric to this region we have identified another gene, LEU5/RFP2. To elucidate further the complex genomic organization of this region, we have identified, mapped, and sequenced the homologous region in the mouse. Fluorescence in situ hybridization analysis demonstrated that the region maps to mouse chromosome 14. The overall organization and gene order in this region were found to be highly conserved in the mouse. Sequence comparison between the human deletion hotspot region and its homologous mouse region revealed a high degree of sequence conservation with an overall score of 74%. However, our data also show that in terms of transcribed sequences, only two of those, human LEU2 and LEU5/RFP2, are clearly conserved, strengthening the case for these genes as putative candidate B-CLL tumor suppressor genes.

Deletion analysis of male sterility effects of t-haplotypes in the mouse.

PubMed

Bennett, D; Artzt, K

1990-01-01

We present data on the effects of three chromosome 17 deletions on transmission ratio distortion (TRD) and sterility of several t-haplotypes. All three deletions have similar effects on male TRD: that is, Tdel/tcomplete genotypes all transmit their t-haplotype in very high proportion. However, each deletion has different effects on sterility of heterozygous males, with TOr/t being fertile, Thp/t less fertile, and TOrl/t still less fertile. These data suggest that wild-type genes on chromosomes homologous to t-haplotypes can be important regulators of both TRD and fertility in males, and that the wild-type genes concerned with TRD and fertility are at least to some extent different. The data also provide a rough map of the positions of these genes.

ECK, a human EPH-related gene, maps to 1p36.1, a common region of alteration in human cancers

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

Sulman, E.P.; Brodeur, G.M.; Ikegaki, N.

1997-03-01

Mouse eck, a member of the EPH gene family, has been mapped to mouse chromosome 4. The syntenic relationship between this chromosome and human chromosome 1 suggests that the human ECK gene maps to the distal short arm of human chromosome 1 (1p). Since this region is frequently deleted or altered in certain tumors of neuroectodermal origin, it is important to define the specific chromosomal localization of the human ECK gene. PCR screening of a rodent-human somatic cell hybrid panel by ECK-specific primers showed that ECK is indeed localized to human chromosome 1. Additional PCR screening of a regional screeningmore » panel for chromosome 1p indicated that ECK is localized to 1p36, distal to FUCA1. Furthermore, fluorescence in situ hybridization analysis with an ECK-specific P1 clone showed that ECK maps proximal to genetic marker D1S228. Taken together, the data suggest that ECK maps to 1p36.1, a region that is frequently deleted in neuroblastoma, melanoma, and other neuroectodermal tumors. 23 refs., 3 figs.« less

No clustering for linkage map based on low-copy and undermethylated microsatellites.

PubMed

Zhou, Yi; Gwaze, David P; Reyes-Valdés, M Humberto; Bui, Thomas; Williams, Claire G

2003-10-01

Clustering has been reported for conifer genetic maps based on hypomethylated or low-copy molecular markers, resulting in uneven marker distribution. To test this, a framework genetic map was constructed from three types of microsatellites: low-copy, undermethylated, and genomic. These Pinus taeda L. microsatellites were mapped using a three-generation pedigree with 118 progeny. The microsatellites were highly informative; of the 32 markers in intercross configuration, 29 were segregating for three or four alleles in the progeny. The sex-averaged map placed 51 of the 95 markers in 15 linkage groups at LOD > 4.0. No clustering or uneven distribution across the genome was observed. The three types of P. taeda microsatellites were randomly dispersed within each linkage group. The 51 microsatellites covered a map distance of 795 cM, an average distance of 21.8 cM between markers, roughly half of the estimated total map length. The minimum and maximum distances between any two bins was 4.4 and 45.3 cM, respectively. These microsatellites provided anchor points for framework mapping for polymorphism in P. taeda and other closely related hard pines.

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng

2014-06-04

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Galaxy bias from the Dark Energy Survey Science Verification data: Combining galaxy density maps and weak lensing maps

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

Chang, C.; Pujol, A.; Gaztañaga, E.

We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg 2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars inmore » four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues by including shape noise, photo-z errors, and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Moreover, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.« less

Galaxy bias from the Dark Energy Survey Science Verification data: Combining galaxy density maps and weak lensing maps

DOE PAGES

Chang, C.; Pujol, A.; Gaztañaga, E.; ...

2016-04-15

We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg 2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars inmore » four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues by including shape noise, photo-z errors, and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Moreover, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.« less

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

PubMed

Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

2015-10-16

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.

Identifying allelic loss and homozygous deletions in pancreatic cancer without matched normals using high-density single-nucleotide polymorphism arrays.

PubMed

Calhoun, Eric S; Hucl, Tomas; Gallmeier, Eike; West, Kristen M; Arking, Dan E; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Chakravarti, Aravinda; Hruban, Ralph H; Kern, Scott E

2006-08-15

Recent advances in oligonucleotide arrays and whole-genome complexity reduction data analysis now permit the evaluation of tens of thousands of single-nucleotide polymorphisms simultaneously for a genome-wide analysis of allelic status. Using these arrays, we created high-resolution allelotype maps of 26 pancreatic cancer cell lines. The areas of heterozygosity implicitly served to reveal regions of allelic loss. The array-derived maps were verified by a panel of 317 microsatellite markers used in a subset of seven samples, showing a 97.1% concordance between heterozygous calls. Three matched tumor/normal pairs were used to estimate the false-negative and potential false-positive rates for identifying loss of heterozygosity: 3.6 regions (average minimal region of loss, 720,228 bp) and 2.3 regions (average heterozygous gap distance, 4,434,994 bp) per genome, respectively. Genomic fractional allelic loss calculations showed that cumulative levels of allelic loss ranged widely from 17.1% to 79.9% of the haploid genome length. Regional increases in "NoCall" frequencies combined with copy number loss estimates were used to identify 41 homozygous deletions (19 first reports), implicating an additional 13 regions disrupted in pancreatic cancer. Unexpectedly, 23 of these occurred in just two lines (BxPc3 and MiaPaCa2), suggesting the existence of at least two subclasses of chromosomal instability (CIN) patterns, distinguished here by allelic loss and copy number changes (original CIN) and those also highly enriched in the genomic "holes" of homozygous deletions (holey CIN). This study provides previously unavailable high-resolution allelotype and deletion breakpoint maps in widely shared pancreatic cancer cell lines and effectively eliminates the need for matched normal tissue to define informative loci.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

PubMed Central

Mosbæk, Freya; Kjeldal, Henrik; Mulat, Daniel G; Albertsen, Mads; Ward, Alastair J; Feilberg, Anders; Nielsen, Jeppe L

2016-01-01

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of 13C-labeled CO2 and CH4 were detected immediately following incubation with [U-13C]acetate, indicating high turnover rate of acetate. The identified 13C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways. PMID:27128991

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics.

PubMed

Mosbæk, Freya; Kjeldal, Henrik; Mulat, Daniel G; Albertsen, Mads; Ward, Alastair J; Feilberg, Anders; Nielsen, Jeppe L

2016-10-01

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

Dark Energy Survey Year 1 Results: Curved-Sky Weak Lensing Mass Map

DOE PAGES

Chang, C.; Sheldon, E.; Pujol, A.; ...

2018-01-04

We construct the largest curved-sky galaxy weak lensing mass map to date from the DES firstyear (DES Y1) data. The map, about 10 times larger than previous work, is constructed over a contiguous ≈1;500 deg 2, covering a comoving volume of ≈10 Gpc 3. The effects of masking, sampling, and noise are tested using simulations. We generate weak lensing maps from two DES Y1 shear catalogs, METACALIBRATION and IM3SHAPE, with sources at redshift 0:2 < z < 1:3; and in each of four bins in this range. In the highest signal-to-noise map, the ratio between the mean signal-to-noise in themore » E-mode and the B-mode map is ~1.5 (~2) when smoothed with a Gaussian filter of sG =30 (80) arcminutes. The second and third moments of the convergence k in the maps are in agreement with simulations. We also find no significant correlation of k with maps of potential systematic contaminants. Finally, we demonstrate two applications of the mass maps: (1) cross-correlation with different foreground tracers of mass and (2) exploration of the largest peaks and voids in the maps.« less

Dark Energy Survey Year 1 Results: Curved-Sky Weak Lensing Mass Map

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

Chang, C.; Sheldon, E.; Pujol, A.

We construct the largest curved-sky galaxy weak lensing mass map to date from the DES firstyear (DES Y1) data. The map, about 10 times larger than previous work, is constructed over a contiguous ≈1;500 deg 2, covering a comoving volume of ≈10 Gpc 3. The effects of masking, sampling, and noise are tested using simulations. We generate weak lensing maps from two DES Y1 shear catalogs, METACALIBRATION and IM3SHAPE, with sources at redshift 0:2 < z < 1:3; and in each of four bins in this range. In the highest signal-to-noise map, the ratio between the mean signal-to-noise in themore » E-mode and the B-mode map is ~1.5 (~2) when smoothed with a Gaussian filter of sG =30 (80) arcminutes. The second and third moments of the convergence k in the maps are in agreement with simulations. We also find no significant correlation of k with maps of potential systematic contaminants. Finally, we demonstrate two applications of the mass maps: (1) cross-correlation with different foreground tracers of mass and (2) exploration of the largest peaks and voids in the maps.« less

Recurrent Deletions and Reciprocal Duplications of 10q11.21q11.23 Including CHAT and SLC18A3 are Likely Mediated by Complex Low-Copy Repeats

PubMed Central

Stankiewicz, Paweł; Kulkarni, Shashikant; Dharmadhikari, Avinash V.; Sampath, Srirangan; Bhatt, Samarth S.; Shaikh, Tamim H.; Xia, Zhilian; Pursley, Amber N.; Cooper, M. Lance; Shinawi, Marwan; Paciorkowski, Alex R.; Grange, Dorothy K.; Noetzel, Michael J.; Saunders, Scott; Simons, Paul; Summar, Marshall; Lee, Brendan; Scaglia, Fernando; Fellmann, Florence; Martinet, Danielle; Beckmann, Jacques S.; Asamoah, Alexander; Platky, Kathryn; Sparks, Susan; Martin, Ann S.; Madan-Khetarpal, Suneeta; Hoover, Jacqueline; Medne, Livija; Bonnemann, Carsten G.; Moeschler, John B.; Vallee, Stephanie E.; Parikh, Sumit; Irwin, Polly; Dalzell, Victoria P.; Smith, Wendy E.; Banks, Valerie C.; Flannery, David B.; Lovell, Carolyn M.; Bellus, Gary A.; Golden-Grant, Kathryn; Gorski, Jerome L.; Kussmann, Jennifer L.; McGregor, Tracy L.; Hamid, Rizwan; Pfotenhauer, Jean; Ballif, Blake C.; Shaw, Chad A.; Kang, Sung-Hae L.; Bacino, Carlos A.; Patel, Ankita; Rosenfeld, Jill A.; Cheung, Sau Wai; Shaffer, Lisa G.

2013-01-01

We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers. PMID:21948486

Homozygous hereditary C3 deficiency due to a partial gene deletion.

PubMed Central

Botto, M; Fong, K Y; So, A K; Barlow, R; Routier, R; Morley, B J; Walport, M J

1992-01-01

The molecular mechanism of C3 deficiency in an Afrikaans patient with recurrent pyogenic infections was studied. Restriction enzyme analysis showed a gene deletion of 800 base pairs (bp) mapping to the alpha chain of C3. Amplification of genomic DNA, using the PCR, demonstrated that the deletion included exons 22 and 23 of the C3 gene. Truncated mRNA was shown in an Epstein-Barr virus-transformed B-cell line by PCR amplification of first-strand cDNA. A consequence of this deletion was that the RNA transcribed 3' to the deletion was out of frame, resulting in formation of a stop codon 19 bp downstream from the deletion. The molecular basis of the deletion was compatible with homologous recombination between two Alu sequences located in introns 21 and 23. An unrelated nonconsanguineous relative and two of a sample of 174 Afrikaans-speaking individuals were heterozygous carriers of the same gene deletion. The wide prevalence of this null allele in this population is probably due to the effects of a small founder population. The presence of this deletion in the C3 gene is not compatible with production of any functional C3, supporting the idea that study of such patients offers a valid model for understanding physiological activities of C3 in vivo in humans. Images PMID:1350678

Chromosomal DNA Deletions Explain Phenotypic Characteristics of Two Antigenic Variants, Phase II and RSA 514 (Crazy), of the Coxiella burnetii Nine Mile Strain†

PubMed Central

Hoover, T. A.; Culp, D. W.; Vodkin, M. H.; Williams, J. C.; Thompson, H. A.

2002-01-01

After repeated passages through embyronated eggs, the Nine Mile strain of Coxiella burnetii exhibits antigenic variation, a loss of virulence characteristics, and transition to a truncated lipopolysaccharide (LPS) structure. In two independently derived strains, Nine Mile phase II and RSA 514, these phenotypic changes were accompanied by a large chromosomal deletion (M. H. Vodkin and J. C. Williams, J. Gen. Microbiol. 132:2587-2594, 1986). In the work reported here, additional screening of a cosmid bank prepared from the wild-type strain was used to map the deletion termini of both mutant strains and to accumulate all the segments of DNA that comprise the two deletions. The corresponding DNAs were then sequenced and annotated. The Nine Mile phase II deletion was completely nested within the deletion of the RSA 514 strain. Basic alignment and homology studies indicated that a large group of LPS biosynthetic genes, arranged in an apparent O-antigen cluster, was deleted in both variants. Database homologies identified, in particular, mannose pathway genes and genes encoding sugar methylases and nucleotide sugar epimerase-dehydratase proteins. Candidate genes for addition of sugar units to the core oligosaccharide for synthesis of the rare sugar 6-deoxy-3-C-methylgulose (virenose) were identified in the deleted region. Repeats, redundancies, paralogous genes, and two regions with reduced G+C contents were found within the deletions. PMID:12438347

PAR1 deletions downstream of SHOX are the most frequent defect in a Spanish cohort of Léri-Weill dyschondrosteosis (LWD) probands.

PubMed

Benito-Sanz, Sara; del Blanco, Darya Gorbenko; Aza-Carmona, Miriam; Magano, Luis F; Lapunzina, Pablo; Argente, Jesús; Campos-Barros, Angel; Heath, Karen E

2006-10-01

Léri-Weill dyschondrosteosis (LWD) is a skeletal dysplasia characterized by disproportionate short stature and Madelung deformity. Mutations or deletions of the SHOX gene have been previously identified as the main cause of LWD. We recently identified the existence of a second class of pseudoautosomal region 1 (PAR1) deletions which do not include SHOX, implicated in the etiopathogenesis of LWD. The deletions map at least 30-250 kb downstream of SHOX, are variable in size and clearly cosegregate with the LWD phenotype. In order to determine the frequency of this new type of deletions in the Spanish population we analyzed the distribution of PAR1 defects, including the screening of SHOX deletions, mutations, and PAR1 deletions downstream of SHOX, in a total of 26 LWD probands by a combination of MLPA, microsatellite analysis, SNP genotyping, dHPLC, and DNA sequencing. A molecular defect was identified in 16/26 LWD patients (61.5%): 10 PAR1 deletions downstream of SHOX, four SHOX encompassing deletions, and two SHOX mutations. No apparent phenotypic differences were observed between patients with SHOX defects and those with PAR1 deletions downstream of SHOX. In the examined cohort of Spanish LWD probands, PAR1 deletions downstream of SHOX represent the highest proportion of identified mutations (38%) compared to SHOX deletions (15%) and mutations (8%). As a consequence of our findings, the screening of this region should be included in the routine genetic testing of LWD. Also, LWD patients who tested negative for SHOX defects should be re-evaluated for PAR1 deletions downstream of SHOX.

A 20-year collection of sub-surface salinity and temperature observations for the Australian shelf seas

NASA Astrophysics Data System (ADS)

Proctor, R.; Mancini, S.; Hoenner, X.; Tattersall, K.; Pasquer, B.; Galibert, G.; Moltmann, T.

2016-02-01

Salinity and temperature measurements from different sources have been assembled into a common data structure in a relational database. Quality Control flags have been mapped to a common scheme and associated to each measurement. For datasets like gliders, moorings or ship underway which are sampled at high temporal resolution (e.g. data every second) a binning and sub-sampling approach has been applied to some datasets in order to reduce the number of measurements to hourly sampling. After averaging approximately 25 Million measurements are available in this dataset collection. A national shelf and coastal data atlas has been created using all the temperature and salinity measurements that pass various quality control checks. These observations have been binned spatially on a horizontal grid of ¼ degree with standard vertical levels (every 10 meters from the surface to 500m depth) and temporally on a monthly time range over the period January 1995 to December 2014. The number of observations in each bin has been determined and additional statistics, the mean, the standard deviation, minimum and maximum values, have been calculated, enabling a degree of uncertainty to be associated with any measurement. The data atlas is available as a Web Feature Service.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

Monoamine oxidase deficiency in males with an X chromosome deletion.

PubMed

Sims, K B; de la Chapelle, A; Norio, R; Sankila, E M; Hsu, Y P; Rinehart, W B; Corey, T J; Ozelius, L; Powell, J F; Bruns, G

1989-01-01

Mapping of the human MAOA gene to chromosomal region Xp21-p11 prompted our study of two affected males in a family previously reported to have Norrie disease resulting from a submicroscopic deletion in this chromosomal region. In this investigation we demonstrate in these cousins deletion of the MAOA gene, undetectable levels of MAO-A and MAO-B activities in their fibroblasts and platelets, respectively, loss of mRNA for MAO-A in fibroblasts, and substantial alterations in urinary catecholamine metabolites. The present study documents that a marked deficiency of MAO activity is compatible with life and that genes for MAO-A and MAO-B are near each other in this Xp chromosomal region. Some of the clinical features of these MAO deletion patients may help to identify X-linked MAO deficiency diseases in humans.

Mapping the binding domain of the F18 fimbrial adhesin.

PubMed

Smeds, A; Pertovaara, M; Timonen, T; Pohjanvirta, T; Pelkonen, S; Palva, A

2003-04-01

F18 fimbrial Esherichia coli strains are associated with porcine postweaning diarrhea and pig edema disease. Recently, the FedF subunit was identified as the adhesin of the F18 fimbriae. In this study, adhesion domains of FedF were further studied by constructing deletions within the fedF gene and expressing FedF proteins with deletions either together with the other F18 fimbrial subunits or as fusion proteins tagged with maltose binding protein. The region essential for adhesion to porcine intestinal epithelial cells was mapped between amino acid residues 60 and 109 of FedF. To map the binding domain even more closely, all eight charged amino acid residues within this region were independently replaced by alanine. Three of these single point mutants expressing F18 fimbriae exhibited significantly diminished capabilities to adhere to porcine epithelial cells in vitro. In addition, a triple point mutation and a double point mutation completely abolished receptor adhesiveness. The result further confirmed that the region between amino acid residues 60 and 109 is essential for the binding of F18 fimbriae to their receptor. In addition, the adhesion capability of the binding domain was eliminated after treatment with iodoacetamide, suggesting the formation of a disulfide bridge between Cys-63 and Cys-83, whereas Cys-111 and Cys-116 could be deleted without affecting the binding ability of FedF.

Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

PubMed

Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

2015-07-28

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

Snake River Plain Geothermal Play Fairway Analysis - Phase 1 Raster Files

DOE Data Explorer

John Shervais

2015-10-09

Snake River Plain Play Fairway Analysis - Phase 1 CRS Raster Files. This dataset contains raster files created in ArcGIS. These raster images depict Common Risk Segment (CRS) maps for HEAT, PERMEABILITY, AND SEAL, as well as selected maps of Evidence Layers. These evidence layers consist of either Bayesian krige functions or kernel density functions, and include: (1) HEAT: Heat flow (Bayesian krige map), Heat flow standard error on the krige function (data confidence), volcanic vent distribution as function of age and size, groundwater temperature (equivalue interval and natural breaks bins), and groundwater T standard error. (2) PERMEABILTY: Fault and lineament maps, both as mapped and as kernel density functions, processed for both dilational tendency (TD) and slip tendency (ST), along with data confidence maps for each data type. Data types include mapped surface faults from USGS and Idaho Geological Survey data bases, as well as unpublished mapping; lineations derived from maximum gradients in magnetic, deep gravity, and intermediate depth gravity anomalies. (3) SEAL: Seal maps based on presence and thickness of lacustrine sediments and base of SRP aquifer. Raster size is 2 km. All files generated in ArcGIS.

Consistency Check for the Bin Packing Constraint Revisited

NASA Astrophysics Data System (ADS)

Dupuis, Julien; Schaus, Pierre; Deville, Yves

The bin packing problem (BP) consists in finding the minimum number of bins necessary to pack a set of items so that the total size of the items in each bin does not exceed the bin capacity C. The bin capacity is common for all the bins.

The histidine permease gene (HIP1) of Saccharomyces cerevisiae.

PubMed

Tanaka, J; Fink, G R

1985-01-01

The histidine-specific permease gene (HIP1) of Saccharomyces cerevisiae has been mapped, cloned, and sequenced. The HIP1 gene maps to the right arm of chromosome VII, approx. 11 cM distal to the ADE3 gene. The gene was isolated as an 8.6-kb BamHI-Sau3A fragment by complementation of the histidine-specific permease deficiency in recipient yeast cells. We sequenced a 2.4-kb subfragment of this BamHI-Sau3A fragment containing the HIP1 gene and identified a 1596-bp open reading frame (ORF). We confirmed the assignment of the 1596-bp ORF as the HIP1 coding sequence by sequencing a hip1 nonsense mutation. Analysis of the amino acid (aa) sequence of the HIP1 gene reveals several hydrophobic stretches, but shows no obvious N-terminal signal peptide. We have constructed a deletion of the HIP1 gene in vitro and replaced the wild-type copy of the gene with this deletion. The hip1 deletion mutant can grow when it is supplemented with 30 mM histidine, 50 times the amount required for the growth of HIP1 cells. Revertants of this deletion mutant able to grow on a normal level of histidine arise by mutation in unlinked genes. Both these observations suggest that there are additional, low-affinity pathways for histidine uptake.

Identification of novel deletions of 15q11q13 in Angelman syndrome by array-CGH: molecular characterization and genotype-phenotype correlations.

PubMed

Sahoo, Trilochan; Bacino, Carlos A; German, Jennifer R; Shaw, Chad A; Bird, Lynne M; Kimonis, Virginia; Anselm, Irinia; Waisbren, Susan; Beaudet, Arthur L; Peters, Sarika U

2007-09-01

Angelman syndrome (AS) is a neurodevelopmental disorder characterized by mental retardation, absent speech, ataxia, and a happy disposition. Deletions of the 15q11q13 region are found in approximately 70% of AS patients. The deletions are sub-classified into class I and class II based on their sizes of approximately 6.8 and approximately 6.0, respectively, with two different proximal breakpoints and a common distal breakpoint. Utilizing a chromosome 15-specific comparative genomic hybridization genomic microarray (array-CGH), we have identified, determined the deletion sizes, and mapped the breakpoints in a cohort of 44 cases, to relate those breakpoints to the genomic architecture and derive more precise genotype-phenotype correlations. Interestingly four patients of the 44 studied (9.1%) had novel and unusually large deletions, and are reported here. This is the first report of very large deletions of 15q11q13 resulting in AS; the largest deletion being >10.6 Mb. These novel deletions involve three different distal breakpoints, two of which have been earlier shown to be involved in the generation of isodicentric 15q chromosomes (idic15). Additionally, precise determination of the deletion breakpoints reveals the presence of directly oriented low-copy repeats (LCRs) flanking the recurrent and novel breakpoints. The LCRs are adequate in size, orientation, and homology to enable abnormal recombination events leading to deletions and duplications. This genomic organization provides evidence for a common mechanism for the generation of both common and rare deletion types. Larger deletions result in a loss of several genes outside the common Angelman syndrome-Prader-Willi syndrome (AS-PWS) critical interval, and a more severe phenotype.

First CRISM Observations of Mars

NASA Astrophysics Data System (ADS)

Murchie, S.; Arvidson, R.; Bedini, P.; Beisser, K.; Bibring, J.; Bishop, J.; Brown, A.; Boldt, J.; Cavender, P.; Choo, T.; Clancy, R. T.; Darlington, E. H.; Des Marais, D.; Espiritu, R.; Fort, D.; Green, R.; Guinness, E.; Hayes, J.; Hash, C.; Heffernan, K.; Humm, D.; Hutcheson, J.; Izenberg, N.; Lees, J.; Malaret, E.; Martin, T.; McGovern, J. A.; McGuire, P.; Morris, R.; Mustard, J.; Pelkey, S.; Robinson, M.; Roush, T.; Seelos, F.; Seelos, K.; Slavney, S.; Smith, M.; Shyong, W. J.; Strohbehn, K.; Taylor, H.; Wirzburger, M.; Wolff, M.

2006-12-01

CRISM will make its first observations of Mars from MRO in late September 2006, and regular science observations begin in early November. CRISM is a gimbaled, hyperspectral imager whose objectives are (1) to map the entire surface using a subset of bands to characterize crustal mineralogy, (2) to map the mineralogy of key areas at high spectral and spatial resolution, and (3) to measure spatial and seasonal variations in the atmosphere. These objectives are addressed using three major types of observations. In the multispectral survey, with the gimbal pointed at planet nadir, data are collected at a subset of 72 wavelengths covering key mineralogic absorptions, and binned to pixel footprints of 100 or 200 m per pixel. Nearly the entire planet will be mapped in this fashion. In targeted orservations, the gimbal is scanned to remove most along-track motion, and a region of interest is mapped at full spatial and spectral resolution (15-19 m per pixel, 362-3920 nm at 6.55 nm per channel). Ten additional abbreviated, spatially-binned images are taken before and after the main image, providing an emission phase function (EPF) of the site for atmospheric study and correction of surface spectra for atmospheric effects. In atmospheric mode, only the EPF is acquired. Global grids of the resulting lower data volume observations are taken repeatedly throughout the Martian year to measure seasonal variations in atmospheric properties. Raw, calibrated, and map-projected data are delivered to the community with a spectral library to aid in interpretation. CRISM has undergone calibrations during its cruise to Mars using internal sources, including a closed loop controlled integrating sphere that serves as a radiometric reference. On 26 September a protective lens cover will be deployed. First data from Mars will focus on targeted observations of Phoenix and MER, targeted observations of sulfate- and phyllosilicate-containing sites identified by Mars Express per OMEGA, acquisition of initial EPF grids, and multispectral survey of the northern plains. Our presentation will discuss first results from targeted observations and multispectral mapping. Data processing and first analysis of EPFs will be discussed in companion abstracts.

[Genetic study of bacteriophage phi81. I. Isolation, study of complementation and preliminary mapping of amber-mutants of bacteriophage phi81].

PubMed

Sineokiĭ, S P; Pogosov, V Z; Iankovskiĭ, N K; Krylov, V N

1976-01-01

123 Amber mutants of lambdoid bacteriophage phi81 are isolated and distributed into 19 complementation groups. Deletion mapping made possible to locate 5 gene groups on the genetic map of bacteriophage phi81 and to determine a region of possible location of mm' sticky ends on the prophage genetic map. A gene of phage phi81 is localized, which controls the adsorption specificity, and which functional similarity to a respective gene of phage phi80 is demonstrated.

Comparison of recycling outcomes in three types of recycling collection units.

PubMed

Andrews, Ashley; Gregoire, Mary; Rasmussen, Heather; Witowich, Gretchen

2013-03-01

Commercial institutions have many factors to consider when implementing an effective recycling program. This study examined the effectiveness of three different types of recycling bins on recycling accuracy by determining the percent weight of recyclable material placed in the recycling bins, comparing the percent weight of recyclable material by type of container used, and examining whether a change in signage increased recycling accuracy. Data were collected over 6 weeks totaling 30 days from 3 different recycling bin types at a Midwest University medical center. Five bin locations for each bin type were used. Bags from these bins were collected, sorted into recyclable and non-recyclable material, and weighed. The percent recyclable material was calculated using these weights. Common contaminates found in the bins were napkins and paper towels, plastic food wrapping, plastic bags, and coffee cups. The results showed a significant difference in percent recyclable material between bin types and bin locations. Bin type 2 was found to have one bin location to be statistically different (p=0.048), which may have been due to lack of a trash bin next to the recycling bin in that location. Bin type 3 had significantly lower percent recyclable material (p<0.001), which may have been due to lack of a trash bin next to the recycling bin and increased contamination due to the combination of commingled and paper into one bag. There was no significant change in percent recyclable material in recycling bins post signage change. These results suggest a signage change may not be an effective way, when used alone, to increase recycling compliance and accuracy. This study showed two or three-compartment bins located next to a trash bin may be the best bin type for recycling accuracy. Copyright © 2012 Elsevier Ltd. All rights reserved.

A universal method for automated gene mapping

PubMed Central

Zipperlen, Peder; Nairz, Knud; Rimann, Ivo; Basler, Konrad; Hafen, Ernst; Hengartner, Michael; Hajnal, Alex

2005-01-01

Small insertions or deletions (InDels) constitute a ubiquituous class of sequence polymorphisms found in eukaryotic genomes. Here, we present an automated high-throughput genotyping method that relies on the detection of fragment-length polymorphisms (FLPs) caused by InDels. The protocol utilizes standard sequencers and genotyping software. We have established genome-wide FLP maps for both Caenorhabditis elegans and Drosophila melanogaster that facilitate genetic mapping with a minimum of manual input and at comparatively low cost. PMID:15693948

Dynamic bin packing problem

NASA Technical Reports Server (NTRS)

Dikshit, Piyush; Guimaraes, Katia; Ramamurthy, Maya; Agrawala, Ashok K.; Larsen, Ronald L.

1989-01-01

In a previous work we have defined a general architecture model for autonomous systems, which can be mapped easily to describe the functions of any automated system (SDAG-86-01). In this note, we use the model to describe the problem of thermal management in space stations. First we briefly review the architecture, then we present the environment of our application, and finally we detail the specific function for each functional block of the architecture for that environment.

Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation

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

Nussbaum, R.L.; Lesko, J.G.; Lewis, R.A.

1987-09-01

Choroideremia, an X-chromosome linked retinal dystrophy of unknown pathogenesis, causes progressive nightblindness and eventual central blindness in affected males by the third to fourth decade of life. Choroideremia has been mapped to Xq13-21 by tight linkage to restriction fragment length polymorphism loci. The authors have recently identified two families in which choroideremia is inherited with mental retardation and deafness. In family XL-62, an interstitial deletion Xq21 is visible by cytogenetic analysis and two linked anonymous DNA markers, DXYS1 and DXS72, are deleted. In the second family, XL-45, an interstitial deletion was suspected on phenotypic grounds but could not be confirmedmore » by high-resolution cytogenetic analysis. They used phenol-enhanced reassociation of 48,XXXX DNA in competition with excess XL-45 DNA to generate a library of cloned DNA enriched for sequences that might be deleted in XL-45. Two of the first 83 sequences characterized from the library were found to be deleted in probands from family XL-45 as well as from family XL-62. Isolation of these sequences proves that XL-45 does contain a submicroscopic deletion and provides a starting point for identifying overlapping genomic sequences that span the XL-45 deletion. Each overlapping sequence will be studied to identify exons from the choroideremia locus.« less

The mouse-human anatomy ontology mapping project.

PubMed

Hayamizu, Terry F; de Coronado, Sherri; Fragoso, Gilberto; Sioutos, Nicholas; Kadin, James A; Ringwald, Martin

2012-01-01

The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

Mental retardation in a boy with an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1: Implication for the MRX locus

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

Muroya, Koji; Ogata, Tsutomu; Natsuo, Nobutake

Although genotype-phenotype correlations in male patients with various types of nullisomy for Xp22.3 have assigned a locus for X-linked mental retardation (MRX) to an approximately 3-Mb region between DXS31 and STS, the precise location has not been determined. In this paper, we describe a 14 7/12 year old Japanese boy with mental retardation and an interstitial deletion at Xp22.3 involving STS, KAL1, and OA1, and compare the deletion map with that of previously reported three familial male patients with low-normal intelligence and a similar interstitial deletion at Xp22.3. The results suggest that the MRX gene is further localized to themore » roughly 1.5-Mb region between DXS1060 and DXS1139. 31 refs., 4 figs.« less

Web-based CERES Clouds QC Property Viewing Tool

NASA Astrophysics Data System (ADS)

Smith, R. A.; Chu, C.; Sun-Mack, S.; Chen, Y.; Heckert, E.; Minnis, P.

2014-12-01

This presentation will display the capabilities of a web-based CERES cloud property viewer. Terra data will be chosen for examples. It will demonstrate viewing of cloud properties in gridded global maps, histograms, time series displays, latitudinal zonal images, binned data charts, data frequency graphs, and ISCCP plots. Images can be manipulated by the user to narrow boundaries of the map as well as color bars and value ranges, compare datasets, view data values, and more. Other atmospheric studies groups will be encouraged to put their data into the underlying NetCDF data format and view their data with the tool. A laptop will hopefully be available to allow conference attendees to try navigating the tool.

A single-base deletion in soybean flavonol synthase gene is associated with magenta flower color.

PubMed

Takahashi, Ryoji; Githiri, Stephen M; Hatayama, Kouta; Dubouzet, Emilyn G; Shimada, Norimoto; Aoki, Toshio; Ayabe, Shin-ichi; Iwashina, Tsukasa; Toda, Kyoko; Matsumura, Hisakazu

2007-01-01

The Wm locus of soybean [Glycine max (L.) Merr.] controls flower color. Dominant Wm and recessive wm allele of the locus produce purple and magenta flower, respectively. A putative full-length cDNA of flavonol synthase (FLS), gmfls1 was isolated by 5' RACE and end-to-end PCR from a cultivar Harosoy with purple flower (WmWm). Sequence analysis revealed that gmfls1 consisted of 1,208 nucleotides encoding 334 amino acids. It had 59-72% homology with FLS proteins of other plant species. Conserved dioxygenase domains A and B were found in the deduced polypeptide. Sequence comparison between Harosoy and Harosoy-wm (magenta flower mutant of Harosoy; wmwm) revealed that they differed by a single G deletion in the coding region of Harosoy-wm. The deletion changed the subsequent reading frame resulting in a truncated polypeptide consisting of 37 amino acids that lacked the dioxygenase domains A and B. Extracts of E. coli cells expressing gmfls1 of Harosoy catalyzed the formation of quercetin from dihydroquercetin, whereas cell extracts expressing gmfls1 of Harosoy-wm had no FLS activity. Genomic Southern analysis suggested the existence of three to four copies of the FLS gene in the soybean genome. CAPS analysis was performed to detect the single-base deletion. Harosoy and Clark (WmWm) exhibited longer fragments, while Harosoy-wm had shorter fragments due to the single-base deletion. The CAPS marker co-segregated with genotypes at Wm locus in a F(2) population segregating for the locus. Linkage mapping using SSR markers revealed that the Wm and gmfls1 were mapped at similar position in the molecular linkage group F. The above results strongly suggest that gmfls1 represents the Wm gene and that the single-base deletion may be responsible for magenta flower color.

Molecular characterization of deletion breakpoints in adults with 22q11 deletion syndrome

PubMed Central

Stachon, Andrea C.; Squire, Jeremy A.; Moldovan, Laura; Bayani, Jane; Meyn, Stephen; Chow, Eva; Bassett, Anne S.

2011-01-01

22q11 Deletion syndrome (22q11DS) is a common microdeletion syndrome with variable expression, including congenital and later onset conditions such as schizophrenia. Most studies indicate that expression does not appear to be related to length of the deletion but there is limited information on the endpoints of even the common deletion breakpoint regions in adults. We used a real-time quantitative PCR (qPCR) approach to fine map 22q11.2 deletions in 44 adults with 22q11DS, 22 with schizophrenia (SZ; 12 M, 10 F; mean age 35.7 SD 8.0 years) and 22 with no history of psychosis (NP; 8 M, 14 F; mean age 27.1 SD 8.6 years). QPCR data were consistent with clinical FISH results using the TUPLE1 or N25 probes. Two subjects (one SZ, one NP) negative for clinical FISH had atypical 22q11.2 deletions confirmed by FISH using the RP11-138C22 probe. Most (n = 34; 18 SZ, 16 NP) subjects shared a common 3 Mb hemizygous 22q11.2 deletion. However, eight subjects showed breakpoint variability: a more telomeric proximal breakpoint (n = 2), or more centromeric (n = 3) or more telomeric distal breakpoint (n = 3). One NP subject had a proximal nested 1.4 Mb deletion. COMT and TBX1 were deleted in all 44 subjects, and PRODH in 40 subjects (19 SZ, 21 NP). The results delineate proximal and distal breakpoint variants in 22q11DS. Neither deletion extent nor PRODH haploinsufficiency appeared to explain the clinical expression of schizophrenia in the present study. Further studies are needed to elucidate the molecular basis of schizophrenia and clinical heterogeneity in 22q11DS. PMID:17028864

Microdeletion syndromes, balanced translocations, and gene mapping.

PubMed Central

Schinzel, A

1988-01-01

High resolution prometaphase chromosome banding has allowed the detection of discrete chromosome aberrations which escaped earlier metaphase examinations. Consistent tiny deletions have been detected in some well established malformation syndromes: an interstitial deletion in 15q11/12 in the majority of patients with the Prader-Willi syndrome and in a minority of patients with the Angelman (happy puppet) syndrome; a terminal deletion of 17p13.3 in most patients examined with the Miller-Dieker syndrome; an interstitial deletion of 8q23.3/24.1 in a large majority of patients with the Giedion-Langer syndrome; an interstitial deletion of 11p13 in virtually all patients with the WAGR (Wilms' tumour-aniridia-gonadoblastoma-retardation) syndrome; and an interstitial deletion in 22q11 in about one third of patients with the DiGeorge sequence. In addition, a combination of chromosome prometaphase banding and DNA marker studies has allowed the localisation of the genes for retinoblastoma and for Wilms' tumour and the clarification of both the autosomal recessive nature of the mutation and the possible somatic mutations by which the normal allele can be lost in retina and kidney cells. After a number of X linked genes had been mapped, discrete deletions in the X chromosome were detected by prometaphase banding with specific attention paid to the sites of the gene(s) in males who had from one to up to four different X linked disorders plus mental retardation. Furthermore, the detection of balanced translocations in probands with disorders caused by autosomal dominant or X linked genes has allowed a better insight into the localisation of these genes. In some females with X linked disorders, balanced X; autosomal translocations have allowed the localisation of X linked genes at the breakpoint on the X chromosome. Balanced autosome; autosome translocations segregating with autosomal dominant conditions have provided some clues to the gene location of these conditions. In two conditions, Greig cephalopolysyndactyly and dominant aniridia, two translocation families with one common breakpoint have allowed quite a confident location of the genes at the common breakpoint at 7p13 and 11p13, respectively. PMID:3050093

Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM

PubMed Central

Barrick, Doug

2011-01-01

Mapping the stability distributions of proteins in their native folded states provides a critical link between structure, thermodynamics, and function. Linear repeat proteins have proven more amenable to this kind of mapping than globular proteins. C-terminal deletion studies of YopM, a large, linear leucine-rich repeat (LRR) protein, show that stability is distributed quite heterogeneously, yet a high level of cooperativity is maintained [1]. Key components of this distribution are three interfaces that strongly stabilize adjacent sequences, thereby maintaining structural integrity and promoting cooperativity. To better understand the distribution of interaction energy around these critical interfaces, we studied internal (rather than terminal) deletions of three LRRs in this region, including one of these stabilizing interfaces. Contrary to our expectation that deletion of structured repeats should be destabilizing, we find that internal deletion of folded repeats can actually stabilize the native state, suggesting that these repeats are destabilizing, although paradoxically, they are folded in the native state. We identified two residues within this destabilizing segment that deviate from the consensus sequence at a position that normally forms a stacked leucine ladder in the hydrophobic core. Replacement of these nonconsensus residues with leucine is stabilizing. This stability enhancement can be reproduced in the context of nonnative interfaces, but it requires an extended hydrophobic core. Our results demonstrate that different LRRs vary widely in their contribution to stability, and that this variation is context-dependent. These two factors are likely to determine the types of rearrangements that lead to folded, functional proteins, and in turn, are likely to restrict the pathways available for the evolution of linear repeat proteins. PMID:21764506

Unmasking an autosomal recessive disorder by a deletion in the DiGeorge/Velo-cardio-facial chromosome region (DGCR) in 22q11.2

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

Budarf, M.L.; Michaud, D.; Emanuel, B.

Unmasking an autosomal recessive disorder by constitutional hemizygosity is well documented for the embryonal tumors RB and WAGR, where the second hit is a somatic event. Few deletion-mediated recessive conditions have been reported in patients with germline mutations. The major platelet receptor for von Willebrand factor, Glycoprotein Ib (GpIb), is a complex of two plasma membrane glycoproteins, Ib{alpha} and Ib{beta}, covalently linked by disulfide bonds. Defects in this receptor have been associated with the rare congenital autosomal recessive bleeding disorder, Bernard-Soulier syndrome (BSS). BSS is characterized by prolonged bleeding times, thrombocytopenia and very large platelets. The GpIb{beta} gene has beenmore » cloned and we have mapped it within the DGCR. We have identified a patient with phenotypic features of both BSS and VCFS. The patient was referred for 22q11-deletion FISH studies because of a conventricular VSD and mild dysmorphia. FISH with the N25 DiGeorge cosmid demonstrated a deletion in 22q11.2. Western blot analysis of the patient`s platelet proteins demonstrates a complete absence of GpIb{beta}. We suggest that haploinsufficiency for the DGCR in this patient unmasks a mutation in the remaining GpIb{beta} allele, resulting in manifestations of BSS. This mechanism, haploinsufficiency coupled with a mutation of the {open_quotes}normal{close_quotes} chromosome, might explain some of the phenotypic variability seen amongst patients with 22q11.2 microdeletions. These results further suggest that patients with contiguous gene deletion syndromes are at increased risk for autosomal recessive disorders and that they provide the opportunity to {open_quotes}map{close_quotes}disease loci.« less

Flow behaviour of supercritical CO2 and brine in Berea sandstone during drainage and imbibition revealed by medical X-ray CT images

NASA Astrophysics Data System (ADS)

Zhang, Yi; Nishizawa, Osamu; Kiyama, Tamotsu; Chiyonobu, Shun; Xue, Ziqiu

2014-06-01

We injected Berea sandstone with supercritical CO2 and imaged the results with a medical X-ray computed tomography (CT) scanner. The images were acquired by injecting CO2 into a core of brine-saturated sandstone (drainage), and additional images were acquired during reinjection of brine (imbibition) after drainage. We then analysed the temporal variations of CO2 saturation maps obtained from the CT images. The experiments were performed under a confining pressure of 12 MPa, a pore pressure of 10 MPa and a temperature of 40 °C. Porosity and CO2 saturation were calculated for each image voxel of the rock on the basis of the Hounsfield unit values (CT numbers) measured at three states of saturation: dry, full brine saturation and full CO2 saturation. The saturation maps indicated that the distributions of CO2 and brine were controlled by the sub-core-scale heterogeneities which consisted of a laminated structure (bedding) with high- and low-porosity layers. During drainage, CO2 preferentially flowed through the high-porosity layers where most of the CO2 was entrapped during low flow-rate imbibition. The entrapped CO2 was flushed out when high flow-rate imbibition commenced. Plots of the voxel's CT number against porosity revealed the relationship between fluid replacement and porosity. By reference to the CT numbers at the full brine-saturated stage, differential CT numbers were classified into three bins corresponding to voxel porosity: high, medium and low porosity. Distributions of the differential CT number for the three porosity bins were bimodal and in order with respect to the porosity bins during both drainage and imbibitions; however, the order differed between the two stages. This difference suggested that different replacement mechanisms operated for the two processes. Spatial autocorrelation of CO2 saturation maps on sections perpendicular to the flow direction revealed remarkable changes during passage of the replacement fronts during both drainage and imbibition, changes reflecting the interfingering pattern across the replacement fronts. Although the permeability differences between high- and low-porosity layers were not sufficiently large to disturb the uniform flow of brine, the CO2 concentration in the high-porosity layers may have been caused by the differences of capillary pressure between wide and narrow pore throats, perhaps enhanced by an invasion percolation mechanism in flow-path networks.

Limited-angle effect compensation for respiratory binned cardiac SPECT

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

Qi, Wenyuan; Yang, Yongyi, E-mail: yy@ece.iit.edu; Wernick, Miles N.

Purpose: In cardiac single photon emission computed tomography (SPECT), respiratory-binned study is used to combat the motion blur associated with respiratory motion. However, owing to the variability in respiratory patterns during data acquisition, the acquired data counts can vary significantly both among respiratory bins and among projection angles within individual bins. If not properly accounted for, such variation could lead to artifacts similar to limited-angle effect in image reconstruction. In this work, the authors aim to investigate several reconstruction strategies for compensating the limited-angle effect in respiratory binned data for the purpose of reducing the image artifacts. Methods: The authorsmore » first consider a model based correction approach, in which the variation in acquisition time is directly incorporated into the imaging model, such that the data statistics are accurately described among both the projection angles and respiratory bins. Afterward, the authors consider an approximation approach, in which the acquired data are rescaled to accommodate the variation in acquisition time among different projection angles while the imaging model is kept unchanged. In addition, the authors also consider the use of a smoothing prior in reconstruction for suppressing the artifacts associated with limited-angle effect. In our evaluation study, the authors first used Monte Carlo simulated imaging with 4D NCAT phantom wherein the ground truth is known for quantitative comparison. The authors evaluated the accuracy of the reconstructed myocardium using a number of metrics, including regional and overall accuracy of the myocardium, uniformity and spatial resolution of the left ventricle (LV) wall, and detectability of perfusion defect using a channelized Hotelling observer. As a preliminary demonstration, the authors also tested the different approaches on five sets of clinical acquisitions. Results: The quantitative evaluation results show that the three compensation methods could all, but to different extents, reduce the reconstruction artifacts over no compensation. In particular, the model based approach reduced the mean-squared-error of the reconstructed myocardium by as much as 40%. Compared to the approach of data rescaling, the model based approach further improved both the overall and regional accuracy of the myocardium; it also further improved the lesion detectability and the uniformity of the LV wall. When ML reconstruction was used, the model based approach was notably more effective for improving the LV wall; when MAP reconstruction was used, the smoothing prior could reduce the noise level and artifacts with little or no increase in bias, but at the cost of a slight resolution loss of the LV wall. The improvements in image quality by the different compensation methods were also observed in the clinical acquisitions. Conclusions: Compensating for the uneven distribution of acquisition time among both projection angles and respiratory bins can effectively reduce the limited-angle artifacts in respiratory-binned cardiac SPECT reconstruction. Direct incorporation of the time variation into the imaging model together with a smoothing prior in reconstruction can lead to the most improvement in the accuracy of the reconstructed myocardium.« less

Genetics Home Reference: Y chromosome infertility

MedlinePlus

... deletions" of the human Y chromosome and their relationship with male infertility. J Genet Genomics. 2008 Apr; ... for Links Data Files & API Site Map Subscribe Customer Support USA.gov Copyright Privacy Accessibility FOIA Viewers & ...

Performance Evaluation of a Radar by Computer

DTIC Science & Technology

1992-09-01

spatial-resolution map (0.25 nmi x 2.80 ) is employed to select the appropriate threshold values for the ground clutter; a doppler weighting that...seconds with approximately 16 mi’ x 3-Doppler-bin resolution. The second filter integrates over 5 seconds and covers within 20 miles of radar and within 3...also includes receiver matching loss , beamshape loss , and the signal processing loss. D, can be written as D,=D, (n) MLL,= -f- (3.2) where x

Military Review: The Professional Journal of the U.S. Army. January-February 2002

DTIC Science & Technology

2002-02-01

Internet.”9 He accuses bin Laden of hiding maps and photos of targets and of posting instructions on sports chat rooms, porno - graphic bulletin boards...anything unusual. Messages can be hidden in audio, video , or still image files, with information stored in the least significant bits of a digitized file...steganography, embedding secret messages in other messages to prevent observers from suspecting anything unusual. Messages can be hidden in audio, video , or

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance

PubMed Central

Hawkins, Leigh K.; Mylroie, J. Erik; Oliveira, Dafne A.; Smith, J. Spencer; Ozkan, Seval; Windham, Gary L.; Williams, W. Paul; Warburton, Marilyn L.

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait. PMID:26090679

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance.

PubMed

Hawkins, Leigh K; Mylroie, J Erik; Oliveira, Dafne A; Smith, J Spencer; Ozkan, Seval; Windham, Gary L; Williams, W Paul; Warburton, Marilyn L

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait.

Inflammatory peeling skin syndrome caused by homozygous genomic deletion in the PSORS1 region encompassing the CDSN gene.

PubMed

Ishida-Yamamoto, Akemi; Furio, Laetitia; Igawa, Satomi; Honma, Masaru; Tron, Elodie; Malan, Valerie; Murakami, Masamoto; Hovnanian, Alain

2014-01-01

Peeling skin syndrome (PSS) type B is a rare recessive genodermatosis characterized by lifelong widespread, reddish peeling of the skin with pruritus. The disease is caused by small-scale mutations in the Corneodesmosin gene (CDSN) leading to premature termination codons. We report for the first time a Japanese case resulting from complete deletion of CDSN. Corneodesmosin was undetectable in the epidermis, and CDSN was unamplifiable by PCR. QMPSF analysis demonstrated deletion of CDSN exons inherited from each parent. Deletion mapping using microsatellite haplotyping, CGH array and PCR analysis established that the genomic deletion spanned 49-72 kb between HCG22 and TCF19, removing CDSN as well as five other genes within the psoriasis susceptibility region 1 (PSORS1) on 6p21.33. This observation widens the spectrum of molecular defects underlying PSS type B and shows that loss of these five genes from the PSORS1 region does not result in an additional cutaneous phenotype. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Octree Bin-to-Bin Fractional-NTC Collisions

DTIC Science & Technology

2015-09-17

Briefing Charts 3. DATES COVERED (From - To) 24 August 2015 – 17 September 2015 4. TITLE AND SUBTITLE Octree bin-to-bin fractional -NTC collisions...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 OCTREE BIN-TO-BIN FRACTIONAL -NTC COLLISIONS Robert Martin ERC INC., SPACECRAFT PROPULSION...AFTC/PA clearance No. TBD ROBERT MARTIN (AFRL/RQRS) DISTRIBUTION A: APPROVED FOR PUBLIC RELEASE 1 / 15 OUTLINE 1 BACKGROUND 2 FRACTIONAL COLLISIONS 3 BIN

Isolation of a transcription factor expressed in neural crest from the region of 22q11 deleted in DiGeorge syndrome

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

Wadey, R.; Roberts, C.; Daw, S.

1994-09-01

Deletions within chromosome 22q11 cause a wide variety of birth defects including DiGeorge syndrome and Shprintzen syndrome. We have defined a commonly deleted region of over 2 Mb, and a critical region of 300 kb. A gene, TUPLE1, has been isolated from this critical region encoding a transcriptional regulator similar to the yeast HIR1 histone regulator gene. Since it has been suggested that DGS results from a defective neural crest, the expression of Tuple1 was examined in whole mouse and chick embryos, tissue sections and neural tube explants: Tuple1 is expressed in a dynamic pattern with high levels in regionsmore » containing migrating crest. Prior to crest migration Tuple1 is expressed in a rhombomere-specific expression pattern. Later Tuple1 is expressed in discrete domains within the developing neural tube. A remarkable feature of the experiments was the detection of a similar dynamic pattern with sense probe; i.e., there is an antisense Tuple1 transcript. This was confirmed using RPA. Tuple1 is being screened for mutations in non-deletion patients and constructs assembled for homologous recombination in ES cells. Tuple1 maps to MMU16 extending the homology of linkage with human chromosome 22. From these data we predict that the human homologue of the murine scid mutation maps to 22q11.« less

Sub-hectare crop area mapped wall-to-wall in Tigray Ethiopia with HEC processing of WorldView sub-meter panchromatic image texture

NASA Astrophysics Data System (ADS)

Neigh, C. S. R.; Carroll, M.; Wooten, M.; McCarty, J. L.; Powell, B.; Husak, G. J.; Enenkel, M.; Hain, C.

2017-12-01

Global food production in the developing world occurs within sub-hectare fields that are difficult to identify with moderate resolution satellite imagery. Knowledge about the distribution of these fields is critical in food security programs. We developed a semi-automated image segmentation approach using wall-to-wall sub-meter imagery with high-end computing (HEC) to map crop area (CA) throughout Tigray, Ethiopia that encompasses over 41,000 km2. Our approach tested multiple HEC processing streams to reduce processing time and minimize mapping error. We applied multiple resolution smoothing kernels to capture differences in land surface texture associated to CA. Typically, very-small fields (mean < 2 ha) have a smooth image roughness compared to natural scrub/shrub woody vegetation at the 1 m scale and these features can be segmented in panchromatic imagery with multi-level histogram thresholding. We found multi-temporal very-high resolution (VHR) panchromatic imagery with multi-spectral VHR and moderate resolution imagery are sufficient in extracting critical CA information needed in food security programs. We produced a 2011 ‒ 2015 CA map using over 3,000 WorldView-1 panchromatic images wall-to-wall in 1/2° mosaics for Tigray, Ethiopia in 1 week. We evaluated CA estimates with nearly 3,000 WorldView-2 2 m multispectral 250 × 250 m image subsets, with seven expert interpretations, and with in-situ global positioning system (GPS) photography. Our CA estimates ranged from 32 to 41% in sub-regions of Tigray with median maximum per bin commission and omission errors of 11% and 1% respectively, with most of the error occurring in bins less than 15%. This empirical, simple, and low direct cost approach via U.S. government license agreement and HEC could be a viable big-data methodology to extract wall-to-wall CA for other regions of the world that have very-small agriculture fields with similar image texture.

Will it Blend? Visualization and Accuracy Evaluation of High-Resolution Fuzzy Vegetation Maps

NASA Astrophysics Data System (ADS)

Zlinszky, A.; Kania, A.

2016-06-01

Instead of assigning every map pixel to a single class, fuzzy classification includes information on the class assigned to each pixel but also the certainty of this class and the alternative possible classes based on fuzzy set theory. The advantages of fuzzy classification for vegetation mapping are well recognized, but the accuracy and uncertainty of fuzzy maps cannot be directly quantified with indices developed for hard-boundary categorizations. The rich information in such a map is impossible to convey with a single map product or accuracy figure. Here we introduce a suite of evaluation indices and visualization products for fuzzy maps generated with ensemble classifiers. We also propose a way of evaluating classwise prediction certainty with "dominance profiles" visualizing the number of pixels in bins according to the probability of the dominant class, also showing the probability of all the other classes. Together, these data products allow a quantitative understanding of the rich information in a fuzzy raster map both for individual classes and in terms of variability in space, and also establish the connection between spatially explicit class certainty and traditional accuracy metrics. These map products are directly comparable to widely used hard boundary evaluation procedures, support active learning-based iterative classification and can be applied for operational use.

Real-time autocorrelator for fluorescence correlation spectroscopy based on graphical-processor-unit architecture: method, implementation, and comparative studies

NASA Astrophysics Data System (ADS)

Laracuente, Nicholas; Grossman, Carl

2013-03-01

We developed an algorithm and software to calculate autocorrelation functions from real-time photon-counting data using the fast, parallel capabilities of graphical processor units (GPUs). Recent developments in hardware and software have allowed for general purpose computing with inexpensive GPU hardware. These devices are more suited for emulating hardware autocorrelators than traditional CPU-based software applications by emphasizing parallel throughput over sequential speed. Incoming data are binned in a standard multi-tau scheme with configurable points-per-bin size and are mapped into a GPU memory pattern to reduce time-expensive memory access. Applications include dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS) experiments. We ran the software on a 64-core graphics pci card in a 3.2 GHz Intel i5 CPU based computer running Linux. FCS measurements were made on Alexa-546 and Texas Red dyes in a standard buffer (PBS). Software correlations were compared to hardware correlator measurements on the same signals. Supported by HHMI and Swarthmore College

The Atacama Cosmology Telescope: Detection or Sunyaev-Zel'Dovich Decrement in Groups and Clusters Associated with Luminous Red Galaxies

NASA Technical Reports Server (NTRS)

Hand, Nick; Appel, John William; Battaglia, Nick; Bond, J. Richard; Das, Sudeep; Devlin, Mark J.; Dunkley, Joanna; Dunner, Rolando; Essinger-Hileman, Thomas; Fowler, Joseph W.;

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

Design and Validation of a New MLPA-Based Assay for the Detection of RS1 Gene Deletions and Application in a Large Family with X-Linked Juvenile Retinoschisis.

PubMed

Nicoletti, Annalisa; Ziccardi, Lucia; Maltese, Paolo Enrico; Benedetti, Sabrina; Palumbo, Orazio; Rendina, Michelina; D'Agruma, Leonardo; Falsini, Benedetto; Wang, Xinjing; Bertelli, Matteo

2017-02-01

X-linked juvenile retinoschisis (XLRS) is a severe ocular disorder that can evolve to blindness. More than 200 different disease-causing mutations have been reported in the RS1 gene and approximately 10% of these are deletions. Since transmission is X-linked, males are always affected and females are usually carriers. The identification of female carriers is always important and poses a technical challenge. Therefore, we sought to develop a multiplex ligation dependent probe amplification (MLPA)-based method to identify deletions or duplications in this gene. We then used our assay to study a large XLRS family. We designed six probes specific for each RS1 exon and then optimized and validated our method using control samples with known gene deletions. In the XLRS family, RS1 gene copy number variation was assessed by "home-made" MLPA analysis and by single nucleotide polymorphism (SNP) array analysis using the CytoScan HD Array. Direct sequencing was used for deletion breakpoint mapping. Our assay detected all deletions in control samples. All affected males of the family were positive for a deletion of exon 2 of the RS1 gene (RS1:NM_000330:c.53-?_78+?del). Carrier females were also identified. Our method is easily replicated, reliable, and inexpensive and allows female carriers to be detected. This is the first report of deep characterization of a whole exon deletion in the RS1 gene.

A novel class of Pseudoautosomal region 1 deletions downstream of SHOX is associated with Leri-Weill dyschondrosteosis.

PubMed

Benito-Sanz, Sara; Thomas, N Simon; Huber, Céline; Huber, Celine; Gorbenko del Blanco, Darya; Del Blanco, Darya Gorbenko; Aza-Carmona, Miriam; Crolla, John A; Maloney, Vivienne; Rappold, Gudrun; Argente, Jesús; Argente, Jesus; Campos-Barros, Angel; Cormier-Daire, Valérie; Cormier-Daire, Valerie; Heath, Karen E

2005-10-01

Leri-Weill dyschondrosteosis (LWD) is a pseudoautosomal dominant disorder characterized by disproportionate short stature and a characteristic curving of the radius, known as the "Madelung deformity." SHOX mutations resulting in SHOX haploinsufficiency have been found in LWD and in a variable proportion of patients with idiopathic short stature (ISS), whereas homozygous loss of SHOX results in the more severe Langer mesomelic dysplasia (LMD). Defects in SHOX have been identified in approximately 60% of LWD cases, whereas, in the remaining approximately 40%, the molecular basis is unknown. This suggests either genetic heterogeneity or the presence of mutations in unanalyzed regions of SHOX, such as the upstream, intragenic, or downstream regulatory sequences. Therefore, the pseudoautosomal region 1 (PAR1) of 80 patients with LWD, in whom SHOX deletions and mutations had been excluded, was screened for deletions by use of a new panel of microsatellite markers. We identified 12 patients with LWD who presented with a novel class of PAR1 deletions that did not include SHOX. The deletions were of variable size and mapped at least approximately 30-530 kb downstream of SHOX. In our cohort, this type of deletion accounted for 15% of cases. In all cases, the deletions cosegregated with the phenotype. No apparent phenotypic differences were observed between patients with SHOX deletions and those with this new class of PAR1 deletions. Thus, we present here the identification of a second PAR1 region implicated in the etiopathogenesis of LWD. Our findings suggest the presence of distal regulatory elements of SHOX transcription in PAR1 or, alternatively, the existence of an additional locus apparently involved in the control of skeletal development. Deletion analysis of this newly identified region should be included in the mutation screening of patients with LWD, LMD, and ISS.

Pleiotropy in microdeletion syndromes: Neurologic and spermatogenic abnormalities in mice homozygous for the p{sup 6H} deletion are likely due to dysfunction of a single gene

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

Rinchik, E.M.; Carpenter, D.A.; Handel, M.A.

1995-07-03

Variability and complexity of phenotypes observed in microdeletion syndromes can be due to deletion of a single gene whose product participates in several aspects of development or can be due to the deletion of a number of tightly linked genes, each adding its own effect to the syndrome. The p{sup 6H} deletion in mouse chromosome 7 presents a good model with which to address this question of multigene vs. single-gene pleiotropy. Mice homozygous for the p{sup 6H} deletion are diluted in pigmentation, are smaller than their littermates, and manifest a nervous jerky-gait phenotype. Male homozygotes are sterile and exhibit profoundmore » abnormalities in spermiogenesis. By using N-ethyl-N-nitrosourea (EtNU) mutagenesis and a breeding protocol designed to recover recessive mutations expressed hemizygously opposite a large p-locus deletion, we have generated three noncomplementing mutations that map to the p{sup 6H} deletion. Each of these EtNU-induced mutations has adverse effects on the size, nervous behavior, and progression of spermiogenesis that characterize p{sup 6H} deletion homozygotes. Because etNU is thought to induce primarily intragenic (point) mutations in mouse stem-cell spermatogonia, we propose that the trio of phenotypes (runtiness, nervous jerky gait, and male sterility) expressed in p{sup 6H} deletion homozygotes is the result of deletion of a single highly pleiotropic gene. We also predict that a homologous single locus, quite possibly tightly linked and distal to the D15S12 (P) locus in human chromosome 15q11-q13, may be associated with similar developmental abnormalities in humans. 29 refs., 3 figs., 1 tab.« less

Thorough analysis of unorthodox ABO deletions called by the 1000 Genomes project.

PubMed

Möller, M; Hellberg, Å; Olsson, M L

2018-02-01

ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G. DNA samples from selected 1000G donors and African blood donors were examined by allele-specific PCR and Sanger sequencing to characterize predicted deletions. A 5821-bp deletion encompassing exons 5-7 was called in twenty 1000G individuals, predominantly Africans. This allele was confirmed and its exact deletion point defined by bioinformatic analyses and in vitro experiments. A PCR assay was developed, and screening of African samples revealed three donors heterozygous for this deletion, which was thereby phenotypically established as an O allele. Analysis of upstream genetic markers indicated an ancestral origin from ABO*O.01.02. We estimate this deletion as the 3rd most common mechanism behind O alleles. A 24-bp deletion was called in nine individuals and showed greater diversity regarding ethnic distribution and allelic background. It could neither be confirmed by in silico nor in vitro experiments. A previously uncharacterized ABO deletion among Africans was comprehensively mapped and a genotyping strategy devised. The false prediction of another deletion emphasizes the need for cautious interpretation of NGS data and calls for strict validation routines. © 2017 International Society of Blood Transfusion.

GPU-Based Interactive Exploration and Online Probability Maps Calculation for Visualizing Assimilated Ocean Ensembles Data

NASA Astrophysics Data System (ADS)

Hoteit, I.; Hollt, T.; Hadwiger, M.; Knio, O. M.; Gopalakrishnan, G.; Zhan, P.

2016-02-01

Ocean reanalyses and forecasts are nowadays generated by combining ensemble simulations with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. Tracking behavior over time, such as all possible paths of a particle in an ensemble vector field, becomes very difficult, as the number of combinations rises exponentially with the number of assimilation cycles. In general a single possible path is not of interest but only the probabilities that any point in space might be reached by a particle at some point in time. We present an approach using probability-weighted piecewise particle trajectories to allow for interactive probability mapping. This is achieved by binning the domain and splitting up the tracing process into the individual assimilation cycles, so that particles that fall into the same bin after a cycle can be treated as a single particle with a larger probability as input for the next cycle. As a result we loose the possibility to track individual particles, but can create probability maps for any desired seed at interactive rates. The technique is integrated in an interactive visualization system that enables the visual analysis of the particle traces side by side with other forecast variables, such as the sea surface height, and their corresponding behavior over time. By harnessing the power of modern graphics processing units (GPUs) for visualization as well as computation, our system allows the user to browse through the simulation ensembles in real-time, view specific parameter settings or simulation models and move between different spatial or temporal regions without delay. In addition our system provides advanced visualizations to highlight the uncertainty, or show the complete distribution of the simulations at user-defined positions over the complete time series of the domain.

VNTR internal structure mapping at the {alpha}-globin 3{prime}HVR locus reveals a hierachy of related lineages in oceania

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

Martinson, J.J.; Clegg, J.B.; Boyce, A.J.

1994-09-01

Analysis of the {alpha}-globin gene complex in Oceania has revealed many different rearrangements which remove one of the adult globin genes. Frequencies of these deletion chromosomes are elevated by malarial resistance conferred by the resulting {alpha}-thalassaemia. One particular deletion chromosome, designated -{alpha}{sup 3.7}III, is found at high levels in Melanesia and Polynesia: RFLP haplotype analysis shows that this deletion is always found on chromosomes bearing the IIIa haplotype and is likely to be the product of one single rearrangement event. A subset of the -{alpha}{sup 3.7}III chromosomes carries a more recent mutation which generates the haemoglobin variant HbJ{sup Tongariki}. Wemore » have characterized the allelic variation at the 3{prime}HVR VNTR locus located 6 kb from the globin genes in each of these groups of chromosomes. We have determined the internal structure of these alleles by RFLP mapping of PCR-amplified DNA: within each group, the allelic diversity results from the insertion and/or deletion of small {open_quotes}motifs{close_quotes} of up to 6 adjacent repeats. Mapping of 3{prime}HVR alleles associated with other haplotypes reveals that these are composed of repeat arrays that are substantially different to those derived from IIIa chromosomes, indicating that interchromosomal recombination between heterologous haplotypes does not account for any of the diversity seen to date. We have recently shown that allelic size variation at the two VNTR loci flanking the {alpha}-globin complex is very closely linked to the haplotypes known to be present at this locus. Here we show that, within a haplotype, VNTR alleles are very closely related to each other on the basis of internal structure and demonstrate that intrachromosomal mutation processes involving small numbers of tandem repeats are the main cause of variation at this locus.« less

Genetics Home Reference: proximal 18q deletion syndrome

MedlinePlus

... Feenstra I, Vissers LE, Orsel M, van Kessel AG, Brunner HG, Veltman JA, van Ravenswaaij-Arts CM. ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Mutations in ABCA12 Underlie the Severe Congenital Skin Disease Harlequin Ichthyosis

PubMed Central

Kelsell, David P.; Norgett, Elizabeth E.; Unsworth, Harriet; Teh, Muy-Teck; Cullup, Thomas; Mein, Charles A.; Dopping-Hepenstal, Patricia J.; Dale, Beverly A.; Tadini, Gianluca; Fleckman, Philip; Stephens, Karen G.; Sybert, Virginia P.; Mallory, Susan B.; North, Bernard V.; Witt, David R.; Sprecher, Eli; E. M. Taylor, Aileen; Ilchyshyn, Andrew; Kennedy, Cameron T.; Goodyear, Helen; Moss, Celia; Paige, David; Harper, John I.; Young, Bryan D.; Leigh, Irene M.; Eady, Robin A. J.; O’Toole, Edel A.

2005-01-01

Harlequin ichthyosis (HI) is the most severe and frequently lethal form of recessive congenital ichthyosis. Although defects in lipid transport, protein phosphatase activity, and differentiation have been described, the genetic basis underlying the clinical and cellular phenotypes of HI has yet to be determined. By use of single-nucleotide–polymorphism chip technology and homozygosity mapping, a common region of homozygosity was observed in five patients with HI in the chromosomal region 2q35. Sequencing of the ABCA12 gene, which maps within the minimal region defined by homozygosity mapping, revealed disease-associated mutations, including large intragenic deletions and frameshift deletions in 11 of the 12 screened individuals with HI. Since HI epidermis displays abnormal lamellar granule formation, ABCA12 may play a critical role in the formation of lamellar granules and the discharge of lipids into the intercellular spaces, which would explain the epidermal barrier defect seen in this disorder. This finding paves the way for early prenatal diagnosis. In addition, functional studies of ABCA12 will lead to a better understanding of epidermal differentiation and barrier formation. PMID:15756637

A candidate region for Nevoid Basal Cell Carcinoma Syndrome defined by genetic and physical mapping

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

Wainwright, B.; Negus, K.; Berkman, J.

1994-09-01

Nevoid Basal Cell Carcinoma Syndrome (NBCCS, or Gorlin`s syndrome) is a cancer predisposition syndrome charcterized by multiple basal cell carcinomas (BCCs) and diverse developmental defects. The gene responsible for NBCCS, which is most likely to be a tumor suppressor gene, has previously been mapped to 9q22.3-q31 in a 12 cM interval between the microsatellite marker loci D9S12 and D9S109. Combined multipoint and haplotype analyses of Australian pedigrees has further refined the localization to a 2 cM interval between markers D9S196 and D9S180. Our loss of heterozygosity (LOH) studies from sporadic (n= 58) and familial (n=41) BCCs indicate that 50% havemore » deletions within the NBCCS candidate region. All LOH is consistent with the genetic mapping of the NBCCS locus. Additionally, one sporadic tumor indicates that the smallest region of overlap in the deletions is within the interval D9S287 (proximal) and D9S180 (distal). A series of YAC clones from within this region has been mapped by FISH to examine chimerism. These clones, which have been mapped with respect to one another, form a contig which encompasses the candidate region from D9S196 to D9S180.« less

Genetic mapping and predictive testing for multiple endocrine neoplasia type 1 (MEN1)

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

Pandit, S.D.; Read, C.; Liu, L.

1994-09-01

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder with an estimated prevalance of 20-200 per million persons. It is characterized by the combined occurence of tumors involving two or more endocrine glands, namely the parathyroid glands, the endocrine pancreas and the anterior pituitary. This disorder affects virtually all age groups with an average range of 20-60 years. Linkage analysis mapped the MEN1 locus to 11q13 near the human muscle glycogen phosphorylase (PYGM) locus. Additional genetic mapping and deletion analysis studies have refined the region containing the MEN1 locus to a 3 cM interval flanked by markers PYGMmore » and D11S146/D11S97, a physical distance of approximately 1.5 Mb. We have identified 8 large families segregating MEN1 (71 affected from a population of 389 individuals). A high resolution reference map for the 11q13 region has been constructed using four new microsatellite markers, the CEPH reference (40 family) pedigree resource, and the CRI-MAP program package. Subsequent analyses using the LINKAGE program package and 8 MEN 1 families placed the MEN1 locus within the context of the microsatellite map. This map was used to develop a linkage-based predictive test. These markers have also been used to further refine the interval containing the MEN1 locus from the study of chromosome deletions (loss of heterozygosity, LOH studies) in paired sets of tumor and germline DNA from 87 MEN 1 affected individuals.« less

Combined pituitary hormone deficiency due to gross deletions in the POU1F1 (PIT-1) and PROP1 genes.

PubMed

Bertko, Eleonore; Klammt, Jürgen; Dusatkova, Petra; Bahceci, Mithat; Gonc, Nazli; Ten Have, Louise; Kandemir, Nurgun; Mansmann, Georg; Obermannova, Barbora; Oostdijk, Wilma; Pfäffle, Heike; Rockstroh-Lippold, Denise; Schlicke, Marina; Tuzcu, Alpaslan Kemal; Pfäffle, Roland

2017-08-01

Pituitary development depends on a complex cascade of interacting transcription factors and signaling molecules. Lesions in this cascade lead to isolated or combined pituitary hormone deficiency (CPHD). The aim of this study was to identify copy number variants (CNVs) in genes known to cause CPHD and to determine their structure. We analyzed 70 CPHD patients from 64 families. Deletions were found in three Turkish families and one family from northern Iraq. In one family we identified a 4.96 kb deletion that comprises the first two exons of POU1F1. In three families a homozygous 15.9 kb deletion including complete PROP1 was discovered. Breakpoints map within highly homologous AluY sequences. Haplotype analysis revealed a shared haplotype of 350 kb among PROP1 deletion carriers. For the first time we were able to assign the boundaries of a previously reported PROP1 deletion. This gross deletion shows strong evidence to originate from a common ancestor in patients with Kurdish descent. No CNVs within LHX3, LHX4, HESX1, GH1 and GHRHR were found. Our data prove multiplex ligation-dependent probe amplification to be a valuable tool for the detection of CNVs as cause of pituitary insufficiencies and should be considered as an analytical method particularly in Kurdish patients.

Combined pituitary hormone deficiency due to gross deletions in the POU1F1 (PIT-1) and PROP1 genes

PubMed Central

Bertko, Eleonore; Klammt, Jürgen; Dusatkova, Petra; Bahceci, Mithat; Gonc, Nazli; ten Have, Louise; Kandemir, Nurgun; Mansmann, Georg; Obermannova, Barbora; Oostdijk, Wilma; Pfäffle, Heike; Rockstroh-Lippold, Denise; Schlicke, Marina; Tuzcu, Alpaslan Kemal; Pfäffle, Roland

2017-01-01

Pituitary development depends on a complex cascade of interacting transcription factors and signaling molecules. Lesions in this cascade lead to isolated or combined pituitary hormone deficiency (CPHD). The aim of this study was to identify copy number variants (CNVs) in genes known to cause CPHD and to determine their structure. We analyzed 70 CPHD patients from 64 families. Deletions were found in three Turkish families and one family from northern Iraq. In one family we identified a 4.96 kb deletion that comprises the first two exons of POU1F1. In three families a homozygous 15.9 kb deletion including complete PROP1 was discovered. Breakpoints map within highly homologous AluY sequences. Haplotype analysis revealed a shared haplotype of 350 kb among PROP1 deletion carriers. For the first time we were able to assign the boundaries of a previously reported PROP1 deletion. This gross deletion shows strong evidence to originate from a common ancestor in patients with Kurdish descent. No CNVs within LHX3, LHX4, HESX1, GH1 and GHRHR were found. Our data prove multiplex ligation-dependent probe amplification to be a valuable tool for the detection of CNVs as cause of pituitary insufficiencies and should be considered as an analytical method particularly in Kurdish patients. PMID:28356564

optBINS: Optimal Binning for histograms

NASA Astrophysics Data System (ADS)

Knuth, Kevin H.

2018-03-01

optBINS (optimal binning) determines the optimal number of bins in a uniform bin-width histogram by deriving the posterior probability for the number of bins in a piecewise-constant density model after assigning a multinomial likelihood and a non-informative prior. The maximum of the posterior probability occurs at a point where the prior probability and the the joint likelihood are balanced. The interplay between these opposing factors effectively implements Occam's razor by selecting the most simple model that best describes the data.

Edge map analysis in chest X-rays for automatic pulmonary abnormality screening.

PubMed

Santosh, K C; Vajda, Szilárd; Antani, Sameer; Thoma, George R

2016-09-01

Our particular motivator is the need for screening HIV+ populations in resource-constrained regions for the evidence of tuberculosis, using posteroanterior chest radiographs (CXRs). The proposed method is motivated by the observation that abnormal CXRs tend to exhibit corrupted and/or deformed thoracic edge maps. We study histograms of thoracic edges for all possible orientations of gradients in the range [Formula: see text] at different numbers of bins and different pyramid levels, using five different regions-of-interest selection. We have used two CXR benchmark collections made available by the U.S. National Library of Medicine and have achieved a maximum abnormality detection accuracy (ACC) of 86.36 % and area under the ROC curve (AUC) of 0.93 at 1 s per image, on average. We have presented an automatic method for screening pulmonary abnormalities using thoracic edge map in CXR images. The proposed method outperforms previously reported state-of-the-art results.

Familial interstitial deletion of the short arm of chromosome 4 (p15.33-p16.3) characterized by molecular cytogenetic analysis.

PubMed

Basinko, Audrey; Douet-Guilbert, Nathalie; Parent, Philippe; Blondin, Gilles; Mingam, M; Monot, Françoise; Morel, Frédéric; Le Bris, Marie-Josée; De Braekeleer, Marc

2008-04-01

This 15-month boy was expressed at the cytogenetic laboratory because of psychomotor development delay. He was tall and had plagiocephaly, micrognathia, high nasal bridge, anteverted nostrils and pectus excavatum. A 46,XY,del(4)(p16.1p16.3) karyotype was found using high-resolution R-banding technique. FISH studies using the LSI Wolf-Hirschhorn dual color 4p16.3 and the TelVysion 4p probes showed no deletion. Using BACs, the distal breakpoint was located in 4p16.3, between RP11-165K4 and RP11-717M10 and the proximal breakpoint in 4p15.33, between RP11-74M11 and RP11-1J7; therefore, approximately 7.96 Mb of the short arm were deleted. The maternal karyotype showed the same deletion, but in a mosaic status. Two distinct phenotypes have been recognized on the basis of the chromosomal bands involved in 4p deletion: the Wolf-Hirschhorn syndrome (WHS) and a proximal 4p deletion syndrome (4p15.2-p15.32). Our observation confirms that the basic WHS phenotype maps distally to this region. Copyright 2008 Wiley-Liss, Inc.

Thalamic reticular impairment underlies attention deficit in Ptchd1(Y/-) mice.

PubMed

Wells, Michael F; Wimmer, Ralf D; Schmitt, L Ian; Feng, Guoping; Halassa, Michael M

2016-04-07

Developmental disabilities, including attention-deficit hyperactivity disorder (ADHD), intellectual disability (ID), and autism spectrum disorders (ASD), affect one in six children in the USA. Recently, gene mutations in patched domain containing 1 (PTCHD1) have been found in ~1% of patients with ID and ASD. Individuals with PTCHD1 deletion show symptoms of ADHD, sleep disruption, hypotonia, aggression, ASD, and ID. Although PTCHD1 is probably critical for normal development, the connection between its deletion and the ensuing behavioural defects is poorly understood. Here we report that during early post-natal development, mouse Ptchd1 is selectively expressed in the thalamic reticular nucleus (TRN), a group of GABAergic neurons that regulate thalamocortical transmission, sleep rhythms, and attention. Ptchd1 deletion attenuates TRN activity through mechanisms involving small conductance calcium-dependent potassium currents (SK). TRN-restricted deletion of Ptchd1 leads to attention deficits and hyperactivity, both of which are rescued by pharmacological augmentation of SK channel activity. Global Ptchd1 deletion recapitulates learning impairment, hyper-aggression, and motor defects, all of which are insensitive to SK pharmacological targeting and not found in the TRN-restricted deletion mouse. This study maps clinically relevant behavioural phenotypes onto TRN dysfunction in a human disease model, while also identifying molecular and circuit targets for intervention.

Testing the parton evolution with the use of two-body final states

NASA Astrophysics Data System (ADS)

Baranov, S. P.; Jung, H.; Lipatov, A. V.; Malyshev, M. A.

2017-01-01

We consider the production of b{bar{b}} quarks and Drell-Yan lepton pairs under LHC conditions focusing attention on the total transverse momentum of the produced pair and on the azimuthal angle between the momenta of the outgoing particles. Plotting the corresponding distributions in bins of the final-state invariant mass, one can reconstruct the full map of the transverse momentum dependent parton densities in a proton. We give examples of how these distributions can look like at the LHC energies.

Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line

PubMed Central

Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

2015-01-01

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs. PMID:26225967

Disrupted Membrane Structure and Intracellular Ca2+ Signaling in Adult Skeletal Muscle with Acute Knockdown of Bin1

PubMed Central

Tjondrokoesoemo, Andoria; Park, Ki Ho; Ferrante, Christopher; Komazaki, Shinji; Lesniak, Sebastian; Brotto, Marco; Ko, Jae-Kyun; Zhou, Jingsong; Weisleder, Noah; Ma, Jianjie

2011-01-01

Efficient intracellular Ca2+ ([Ca2+]i) homeostasis in skeletal muscle requires intact triad junctional complexes comprised of t-tubule invaginations of plasma membrane and terminal cisternae of sarcoplasmic reticulum. Bin1 consists of a specialized BAR domain that is associated with t-tubule development in skeletal muscle and involved in tethering the dihydropyridine receptors (DHPR) to the t-tubule. Here, we show that Bin1 is important for Ca2+ homeostasis in adult skeletal muscle. Since systemic ablation of Bin1 in mice results in postnatal lethality, in vivo electroporation mediated transfection method was used to deliver RFP-tagged plasmid that produced short –hairpin (sh)RNA targeting Bin1 (shRNA-Bin1) to study the effect of Bin1 knockdown in adult mouse FDB skeletal muscle. Upon confirming the reduction of endogenous Bin1 expression, we showed that shRNA-Bin1 muscle displayed swollen t-tubule structures, indicating that Bin1 is required for the maintenance of intact membrane structure in adult skeletal muscle. Reduced Bin1 expression led to disruption of t-tubule structure that was linked with alterations to intracellular Ca2+ release. Voltage-induced Ca2+ released in isolated single muscle fibers of shRNA-Bin1 showed that both the mean amplitude of Ca2+ current and SR Ca2+ transient were reduced when compared to the shRNA-control, indicating compromised coupling between DHPR and ryanodine receptor 1. The mean frequency of osmotic stress induced Ca2+ sparks was reduced in shRNA-Bin1, indicating compromised DHPR activation. ShRNA-Bin1 fibers also displayed reduced Ca2+ sparks' amplitude that was attributed to decreased total Ca2+ stores in the shRNA-Bin1 fibers. Human mutation of Bin1 is associated with centronuclear myopathy and SH3 domain of Bin1 is important for sarcomeric protein organization in skeletal muscle. Our study showing the importance of Bin1 in the maintenance of intact t-tubule structure and ([Ca2+]i) homeostasis in adult skeletal muscle could provide mechanistic insight on the potential role of Bin1 in skeletal muscle contractility and pathology of myopathy. PMID:21984944

VarBin, a novel method for classifying true and false positive variants in NGS data

PubMed Central

2013-01-01

Background Variant discovery for rare genetic diseases using Illumina genome or exome sequencing involves screening of up to millions of variants to find only the one or few causative variant(s). Sequencing or alignment errors create "false positive" variants, which are often retained in the variant screening process. Methods to remove false positive variants often retain many false positive variants. This report presents VarBin, a method to prioritize variants based on a false positive variant likelihood prediction. Methods VarBin uses the Genome Analysis Toolkit variant calling software to calculate the variant-to-wild type genotype likelihood ratio at each variant change and position divided by read depth. The resulting Phred-scaled, likelihood-ratio by depth (PLRD) was used to segregate variants into 4 Bins with Bin 1 variants most likely true and Bin 4 most likely false positive. PLRD values were calculated for a proband of interest and 41 additional Illumina HiSeq, exome and whole genome samples (proband's family or unrelated samples). At variant sites without apparent sequencing or alignment error, wild type/non-variant calls cluster near -3 PLRD and variant calls typically cluster above 10 PLRD. Sites with systematic variant calling problems (evident by variant quality scores and biases as well as displayed on the iGV viewer) tend to have higher and more variable wild type/non-variant PLRD values. Depending on the separation of a proband's variant PLRD value from the cluster of wild type/non-variant PLRD values for background samples at the same variant change and position, the VarBin method's classification is assigned to each proband variant (Bin 1 to Bin 4). Results To assess VarBin performance, Sanger sequencing was performed on 98 variants in the proband and background samples. True variants were confirmed in 97% of Bin 1 variants, 30% of Bin 2, and 0% of Bin 3/Bin 4. Conclusions These data indicate that VarBin correctly classifies the majority of true variants as Bin 1 and Bin 3/4 contained only false positive variants. The "uncertain" Bin 2 contained both true and false positive variants. Future work will further differentiate the variants in Bin 2. PMID:24266885

SPHINX--an algorithm for taxonomic binning of metagenomic sequences.

PubMed

Mohammed, Monzoorul Haque; Ghosh, Tarini Shankar; Singh, Nitin Kumar; Mande, Sharmila S

2011-01-01

Compared with composition-based binning algorithms, the binning accuracy and specificity of alignment-based binning algorithms is significantly higher. However, being alignment-based, the latter class of algorithms require enormous amount of time and computing resources for binning huge metagenomic datasets. The motivation was to develop a binning approach that can analyze metagenomic datasets as rapidly as composition-based approaches, but nevertheless has the accuracy and specificity of alignment-based algorithms. This article describes a hybrid binning approach (SPHINX) that achieves high binning efficiency by utilizing the principles of both 'composition'- and 'alignment'-based binning algorithms. Validation results with simulated sequence datasets indicate that SPHINX is able to analyze metagenomic sequences as rapidly as composition-based algorithms. Furthermore, the binning efficiency (in terms of accuracy and specificity of assignments) of SPHINX is observed to be comparable with results obtained using alignment-based algorithms. A web server for the SPHINX algorithm is available at http://metagenomics.atc.tcs.com/SPHINX/.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

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

Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W.

The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here, we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning amore » single sample as well as comparing the microbial community composition between different sampling environments. Availability and implementation: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license. Supplementary information: Supplementary data are available at Bioinformatics online.« less

Clinical comparison of overlapping deletions of 19p13.3.

PubMed

Risheg, Hiba; Pasion, Romela; Sacharow, Stephanie; Proud, Virginia; Immken, LaDonna; Schwartz, Stuart; Tepperberg, Jim H; Papenhausen, Peter; Tan, Tiong Y; Andrieux, Joris; Plessis, Ghislaine; Amor, David J; Keitges, Elisabeth A

2013-05-01

We present three patients with overlapping interstitial deletions of 19p13.3 identified by high resolution SNP microarray analysis. All three had a similar phenotype characterized by intellectual disability or developmental delay, structural heart abnormalities, large head relative to height and weight or macrocephaly, and minor facial anomalies. Deletion sizes ranged from 792 Kb to 1.0 Mb and included a common region arr [hg19] 19p13.3 (3,814,392-4,136,989), containing eight genes: ZFR2, ATCAY, NMRK2, DAPK3, EEF2, PIAS4, ZBTB7A, MAP2K2, and two non-coding RNA's MIR637 and SNORDU37. The patient phenotypes were compared with three previous single patient reports with similar interstitial 19p13.3 deletions and six additional patients from the DECIPHER and ISCA databases to determine if a common haploinsufficient phenotype for the region can be established. Copyright © 2013 Wiley Periodicals, Inc.

Prader-Willi syndrome: genetic tests and clinical findings.

PubMed

Fridman, C; Varela, M C; Kok, F; Setian, N; Koiffmann, C P

2000-01-01

Here we describe the genetic studies performed in 53 patients with the suspected diagnosis of Prader-Willi syndrome (PWS). PWS is characterized by neonatal hypotonia, hypogonadism, delayed psychomotor development, hyperphagia, obesity, short stature, small hands and feet, learning disabilities, and obsessive-compulsive behavior. Through the methylation analysis of the SNRPN gene, microsatellite studies of loci mapped within and outside the PWS/AS region, and fluorescence in situ hybridization (FISH) study, we confirmed the diagnosis in 35 patients: 27 with a paternal deletion, and 8 with maternal uniparental disomy (UPD). The clinical comparisons between deleted and UPD patients indicated that there were no major phenotype differences, except for a lower birth length observed in the UPD children. Our sample was composed of more girls than boys; UPD patients were diagnosed earlier than the deleted cohort (2(10/12) s. 7(9/12) years); and, in the deleted group, the boys were diagnosed earlier than the girls (5(2/12) vs. 7(8/12) years, respectively).

A Nonlinearity Minimization-Oriented Resource-Saving Time-to-Digital Converter Implemented in a 28 nm Xilinx FPGA

NASA Astrophysics Data System (ADS)

Wang, Yonggang; Liu, Chong

2015-10-01

Because large nonlinearity errors exist in the current tapped-delay line (TDL) style field programmable gate array (FPGA)-based time-to-digital converters (TDC), bin-by-bin calibration techniques have to be resorted for gaining a high measurement resolution. If the TDL in selected FPGAs is significantly affected by changes in ambient temperature, the bin-by-bin calibration table has to be updated as frequently as possible. The on-line calibration and calibration table updating increase the TDC design complexity and limit the system performance to some extent. This paper proposes a method to minimize the nonlinearity errors of TDC bins, so that the bin-by-bin calibration may not be needed while maintaining a reasonably high time resolution. The method is a two pass approach: By a bin realignment, the large number of wasted zero-width bins in the original TDL is reused and the granularity of the bins is improved; by a bin decimation, the bin size and its uniformity is traded-off, and the time interpolation by the delay line turns more precise so that the bin-by-bin calibration is not necessary. Using Xilinx 28 nm FPGAs, in which the TDL property is not very sensitive to ambient temperature, the proposed TDC achieves approximately 15 ps root-mean-square (RMS) time resolution by dual-channel measurements of time-intervals over the range of operating temperature. Because of removing the calibration and less logic resources required for the data post-processing, the method has bigger multi-channel capability.

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

PubMed Central

2012-01-01

Background Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. Results We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2 progeny from a very large F2 family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. Conclusions The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment. PMID:23157543

Plume Tracker: A New Toolkit for the Mapping of Volcanic Plumes with Multispectral Thermal Infrared Remote Sensing

NASA Astrophysics Data System (ADS)

Realmuto, V. J.; Baxter, S.; Webley, P. W.

2011-12-01

Plume Tracker is the next generation of interactive plume mapping tools pioneered by MAP_SO2. First developed in 1995, MAP_SO2 has been used to study plumes at a number of volcanoes worldwide with data acquired by both airborne and space-borne instruments. The foundation of these tools is a radiative transfer (RT) model, based on MODTRAN, which we use as the forward model for our estimation of ground temperature and sulfur dioxide concentration. Plume Tracker retains the main functions of MAP_SO2, providing interactive tools to input radiance measurements and ancillary data, such as profiles of atmospheric temperature and humidity, to the retrieval procedure, generating the retrievals, and visualizing the resulting retrievals. Plume Tracker improves upon MAP_SO2 in the following areas: (1) an RT model based on an updated version of MODTRAN, (2) a retrieval procedure based on maximizing the vector projection of model spectra onto observed spectra, rather than minimizing the least-squares misfit between the model and observed spectra, (3) an ability to input ozone profiles to the RT model, (4) increased control over the vertical distribution of the atmospheric gas species used in the model, (5) a standard programmatic interface to the RT model code, based on the Component Object Model (COM) interface, which will provide access to any programming language that conforms to the COM standard, and (6) a new binning algorithm that decreases running time by exploiting spatial redundancy in the radiance data. Based on our initial testing, the binning algorithm can reduce running time by an order of magnitude. The Plume Tracker project is a collaborative effort between the Jet Propulsion Laboratory and Geophysical Institute (GI) of the University of Alaska-Fairbanks. Plume Tracker is integrated into the GI's operational plume dispersion modeling system and will ingest temperature and humidity profiles generated by the Weather Research and Forecasting model, together with plume height estimates from the Puff model. The access to timely forecasts of atmospheric conditions, together with the reductions in running time, will increase the utility of Plume Tracker in the Alaska Volcano Observatory's mission to mitigate volcanic hazards in Alaska and the Northern Pacific region.

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

Molecular Mapping of the ROSY Locus in DROSOPHILA MELANOGASTER

PubMed Central

Coté, Babette; Bender, Welcome; Curtis, Daniel; Chovnick, Arthur

1986-01-01

The DNA from the chromosomal region of the Drosophila rosy locus has been examined in 83 rosy mutant strains. Several spontaneous and radiation-induced alleles were associated with insertions and deletions, respectively. The lesions are clustered in a 4-kb region. Some of the alleles identified on the DNA map have been located on the genetic map by fine-structure recombination experiments. The genetic and molecular maps are collinear, and the alignment identifies the DNA location of the rosy control region. A rosy RNA of 4.5 kb has been identified; its 5' end lies in or near the control region. PMID:2420682

6q deletion detected by fluorescence in situ hybridization using bacterial artificial chromosome in chronic lymphocytic leukemia.

PubMed

Dalsass, Alessia; Mestichelli, Francesca; Ruggieri, Miriana; Gaspari, Paola; Pezzoni, Valerio; Vagnoni, Davide; Angelini, Mario; Angelini, Stefano; Bigazzi, Catia; Falcioni, Sadia; Troiani, Emanuela; Alesiani, Francesco; Catarini, Massimo; Attolico, Immacolata; Scortechini, Ilaria; Discepoli, Giancarlo; Galieni, Piero

2013-07-01

Deletions of the long arm of chromosome 6 are known to occur at relatively low frequency (3-6%) in chronic lymphocytic leukemia (CLL), and they are more frequently observed in 6q21. Few data have been reported regarding other bands on 6q involved by cytogenetic alterations in CLL. The cytogenetic study was performed in nuclei and metaphases obtained after stimulation with a combination of CpG-oligonucleotide DSP30 and interleukin-2. Four bacterial artificial chromosome (BAC) clones mapping regions in bands 6q16, 6q23, 6q25, 6q27 were used as probes for fluorescence in situ hybridization in 107 CLL cases in order to analyze the occurrence and localization of 6q aberrations. We identified 11 cases (10.2%) with 6q deletion of 107 patients studied with CLL. The trends of survival curves and the treatment-free intervals (TFI) of patients with deletion suggest a better outcome than the other cytogenetic risk groups. We observed two subgroups with 6q deletion as the sole anomaly: two cases with 6q16 deletion, and three cases with 6q25.2-27 deletion. There were differences of age, stage, and TFI between both subgroups. By using BAC probes, we observed that 6q deletion has a higher frequency in CLL and is linked with a good prognosis. In addition, it was observed that the deletion in 6q16 appears to be the most frequent and, if present as the only abnormality, it could be associated with a most widespread disease. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Aberrant interchromosomal exchanges are the predominant cause of the 22q11.2 deletion

PubMed Central

Saitta, Sulagna C.; Harris, Stacy E.; Gaeth, Ann P.; Driscoll, Deborah A.; McDonald-McGinn, Donna M.; Maisenbacher, Melissa K.; Yersak, Jill M.; Chakraborty, Prabir K.; Hacker, April M.; Zackai, Elaine H.; Ashley, Terry; Emanuel, Beverly S.

2010-01-01

Chromosome 22q11.2 deletions are found in almost 90% of patients with DiGeorge/velocardiofacial syndrome (DGS/VCFS). Large, chromosome-specific low copy repeats (LCRs), flanking and within the deletion interval, are presumed to lead to misalignment and aberrant recombination in meiosis resulting in this frequent microdeletion syndrome. We traced the grandparental origin of regions flanking de novo 3 Mb deletions in 20 informative three-generation families. Haplotype reconstruction showed an unexpectedly high number of proximal interchromosomal exchanges between homologs, occurring in 19/20 families. Instead, the normal chromosome 22 in these probands showed interchromosomal exchanges in 2/15 informative meioses, a rate consistent with the genetic distance. Meiotic exchanges, visualized as MLH1 foci, localize to the distal long arm of chromosome 22 in 75% of human spermatocytes tested, also reflecting the genetic map. Additionally, we found no effect of proband gender or parental age on the crossover frequency. Parental origin studies in 65 de novo 3 Mb deletions (including these 20 patients) demonstrated no bias. Unlike Williams syndrome, we found no chromosomal inversions flanked by LCRs in 22 sets of parents of 22q11 deleted patients, or in eight non-deleted patients with a DGS/VCFS phenotype using FISH. Our data are consistent with significant aberrant interchromosomal exchange events during meiosis I in the proximal region of the affected chromosome 22 as the likely etiology for the deletion. This type of exchange occurs more often than is described for deletions of chromosomes 7q11, 15q11, 17p11 and 17q11, implying a difference in the meiotic behavior of chromosome 22. PMID:14681306

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

PubMed Central

Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Iso-Touru, Terhi; Vilkki, Johanna; De Koning, Dirk-Jan; Boichard, Didier; Lund, Mogens Sandø; Sahana, Goutam

2018-01-01

Abstract Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle. PMID:28985340

Molecular analyses of 17p11.2 deletions in 62 Smith-Magenis syndrome patients

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

Juyal, R.C.; Figuera, L.E.; Hauge, X.

1996-05-01

Smith-Magenis syndrome (SMS) is a clinically recognizable, multiple congenital anomalies/mental retardation syndrome caused by an interstitial deletion involving band p11.2 of chromosome 17. Toward the molecular definition of the interval defining this microdeletion syndrome, 62 unrelated SMS patients in conjunction with 70 available unaffected parents were molecularly analyzed with respect to the presence or absence of 14 loci in the proximal region of the short arm of chromosome 17. A multifaceted approach was used to determine deletion status at the various loci that combined (1) FISH analysis, (2) PCR and Southern analysis of somatic cell hybrids retaining the deleted chromosomemore » 17 from selected patients, and (3) genotype determination of patients for whom a parent(s) was available at four microsatellite marker loci and at four loci with associated RFLPs. The relative order of two novel anonymous markers and a new microsatellite marker was determined in 17p11.2. The results confirmed that the proximal deletion breakpoint in the majority of SMS patients is located between markers D17S58 (EW301) and D17S446 (FG1) within the 17p11.1-17p11.2 region. The common distal breakpoint was mapped between markers cCI17-638, which lies distal to D17S71, and cCI17-498, which lies proximal to the Charcot Marie-Tooth disease type 1A locus. The locus D17S258 was found to be deleted in all 62 patients, and probes from this region can be used for diagnosis of the SMS deletion by FISH. Ten patients demonstrated molecularly distinct deletions; of these, two patients had smaller deletions and will enable the definition of the critical interval for SMS. 49 refs.« less

Brassinosteroids regulate pavement cell growth by mediating BIN2-induced microtubule stabilization.

PubMed

Liu, Xiaolei; Yang, Qin; Wang, Yuan; Wang, Linhai; Fu, Ying; Wang, Xuelu

2018-02-23

Brassinosteroids (BRs), a group of plant steroid hormones, play important roles in regulating plant development. The cytoskeleton also affects key developmental processes and a deficiency in BR biosynthesis or signaling leads to abnormal phenotypes similar to those of microtubule-defective mutants. However, how BRs regulate microtubule and cell morphology remains unknown. Here, using liquid chromatography-tandem mass spectrometry, we identified tubulin proteins that interact with Arabidopsis BRASSINOSTEROID INSENSITIVE2 (BIN2), a negative regulator of BR responses in plants. In vitro and in vivo pull-down assays confirmed that BIN2 interacts with tubulin proteins. High-speed co-sedimentation assays demonstrated that BIN2 also binds microtubules. The Arabidopsis genome also encodes two BIN2 homologs, BIN2-LIKE 1 (BIL1) and BIL2, which function redundantly with BIN2. In the bin2-3 bil1 bil2 triple mutant, cortical microtubules were more sensitive to treatment with the microtubule-disrupting drug oryzalin than in wild-type, whereas in the BIN2 gain-of-function mutant bin2-1, cortical microtubules were insensitive to oryzalin treatment. These results provide important insight into how BR regulates plant pavement cell and leaf growth by mediating the stabilization of microtubules by BIN2.

Optimizing 4DCBCT projection allocation to respiratory bins.

PubMed

O'Brien, Ricky T; Kipritidis, John; Shieh, Chun-Chien; Keall, Paul J

2014-10-07

4D cone beam computed tomography (4DCBCT) is an emerging image guidance strategy used in radiotherapy where projections acquired during a scan are sorted into respiratory bins based on the respiratory phase or displacement. 4DCBCT reduces the motion blur caused by respiratory motion but increases streaking artefacts due to projection under-sampling as a result of the irregular nature of patient breathing and the binning algorithms used. For displacement binning the streak artefacts are so severe that displacement binning is rarely used clinically. The purpose of this study is to investigate if sharing projections between respiratory bins and adjusting the location of respiratory bins in an optimal manner can reduce or eliminate streak artefacts in 4DCBCT images. We introduce a mathematical optimization framework and a heuristic solution method, which we will call the optimized projection allocation algorithm, to determine where to position the respiratory bins and which projections to source from neighbouring respiratory bins. Five 4DCBCT datasets from three patients were used to reconstruct 4DCBCT images. Projections were sorted into respiratory bins using equispaced, equal density and optimized projection allocation. The standard deviation of the angular separation between projections was used to assess streaking and the consistency of the segmented volume of a fiducial gold marker was used to assess motion blur. The standard deviation of the angular separation between projections using displacement binning and optimized projection allocation was 30%-50% smaller than conventional phase based binning and 59%-76% smaller than conventional displacement binning indicating more uniformly spaced projections and fewer streaking artefacts. The standard deviation in the marker volume was 20%-90% smaller when using optimized projection allocation than using conventional phase based binning suggesting more uniform marker segmentation and less motion blur. Images reconstructed using displacement binning and the optimized projection allocation algorithm were clearer, contained visibly fewer streak artefacts and produced more consistent marker segmentation than those reconstructed with either equispaced or equal-density binning. The optimized projection allocation algorithm significantly improves image quality in 4DCBCT images and provides, for the first time, a method to consistently generate high quality displacement binned 4DCBCT images in clinical applications.

Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant

PubMed Central

Hannes, F D; Sharp, A J; Mefford, H C; de Ravel, T; Ruivenkamp, C A; Breuning, M H; Fryns, J-P; Devriendt, K; Van Buggenhout, G; Vogels, A; Stewart, H; Hennekam, R C; Cooper, G M; Regan, R; Knight, S J L; Eichler, E E; Vermeesch, J R

2009-01-01

Background: Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. Methods and Results: A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). Conclusion: These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients’ phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical relevance of the deletion and the duplication causes a paradigm shift in (cyto)genetic counselling. PMID:18550696

Deletions spanning the neurofibromatosis I gene: Identification and phenotype of five patients

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

Kayes, L.M.; Burke, W.; Bennett, R.

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder characterized by marked variation in clinical severity. To investigate the contribution to variability by genes either contiguous to or contained within the NF1 gene, the authors screened six NF1 patients with mild facial dysmorphology, mental retardation, and/or learning disabilities, for DNA rearrangement of the NF1 region. Five of the six patients had NF1 gene deletions on the basis of quantitative densitometry, locus hemizygosity, and analysis of somatic cell hybrid lines. Analysis of hybrid lines carrying each of the patient's chromosomes 17, with 15 regional DNA markers, demonstrated that each of themore » five patients carried a deletion >700 kb in size. Minimally, each of the deletions involved the entire 350-kb NF1 gene; the three genes - EVI2A, EVI2B, and OMG-that are contained within an NF1 intron; and considerable flanking DNA. For four of the patients, the deletions mapped to the same interval; the deletion in the fifth patient was larger, extending farther in both directions. The remaining NF1 allele presumably produced functional neurofibromin; no gene rearrangements were detected, and RNA-PCR demonstrated that it was transcribed. These data provide compelling evidence that the NF1 disorder results from haploid insufficiency of neurofibromin. Of the three documented de novo deletion cases, two involved the paternal NF1 allele and one the maternal allele. The parental origin of the single remaining expresses NF1 allele had no dramatic effect on patient phenotype. The deletion patients exhibited a variable number of physical anomalies that were not correlated with the extent of their deletion. All five patients with deletions were remarkable for exhibiting a large number of neurfibromas for their age, suggesting that deletion of an unknown gene in the NF1 region may affect tumor initiation or development. 69 refs., 5 figs., 1 tab.« less

Weak D caused by a founder deletion in the RHD gene.

PubMed

Fichou, Yann; Chen, Jian-Min; Le Maréchal, Cédric; Jamet, Déborah; Dupont, Isabelle; Chuteau, Claude; Durousseau, Cécile; Loirat, Marie-Jeanne; Bailly, Pascal; Férec, Claude

2012-11-01

The RhD blood group system exemplifies a genotype-phenotype correlation by virtue of its highly polymorphic and immunogenic nature. Weak D phenotypes are generally thought to result from missense mutations leading to quantitative change of the D antigen in the red blood cell membrane or intracellularly. Different sets of polymerase chain reaction primers were designed to map and clone a deletion involving RHD Exon 10, which was found in approximately 3% of approximately 2000 RHD hemizygous subjects with D phenotype ambiguity. D antigen density was measured by flow cytometry. Transcript analysis was carried out by 3'-rapid amplification of complementary DNA ends. Haplotype analysis was performed by microsatellite genotyping. A 5405-bp deletion that removed nearly two-thirds of Intron 9 and almost all of Exon 10 of the RHD gene was characterized. It is predicted to result in the replacement of the last eight amino acids of the wild-type RhD protein by another four amino acids. The mean RhD antigen density from two deletion carriers was determined to be only 30. A consensus haplotype could be deduced from the deletion carriers based on the microsatellite genotyping data. The currently reported deletion was derived from a common founder. This deletion appears to represent not only the first large deletion associated with weak D but also the weakest of weak D alleles so far reported. This highly unusual genotype-phenotype relationship may be attributable to the additive effect of three distinct mechanisms that affect mRNA formation, mRNA stability, and RhD/ankyrin-R interaction, respectively. © 2012 American Association of Blood Banks.

A large homozygous deletion in the SAMHD1 gene causes atypical Aicardi–Goutiéres syndrome associated with mtDNA deletions

PubMed Central

Leshinsky-Silver, Esther; Malinger, Gustavo; Ben-Sira, Liat; Kidron, Dvora; Cohen, Sarit; Inbar, Shani; Bezaleli, Tali; Levine, Arie; Vinkler, Chana; Lev, Dorit; Lerman-Sagie, Tally

2011-01-01

Aicardi–Goutiéres syndrome (AGS) is a genetic neurodegenerative disorder with clinical symptoms mimicking a congenital viral infection. Five causative genes have been described: three prime repair exonuclease1 (TREX1), ribonucleases H2A, B and C, and most recently SAM domain and HD domain 1 (SAMHD1). We performed a detailed clinical and molecular characterization of a family with autosomal recessive neurodegenerative disorder showing white matter destruction and calcifications, presenting in utero and associated with multiple mtDNA deletions. A muscle biopsy was normal and did not show any evidence of respiratory chain dysfunction. Southern blot analysis of tissue from a living child and affected fetuses demonstrated multiple mtDNA deletions. Molecular analysis of genes involved in mtDNA synthesis and maintenance (POLGα, POLGβ, Twinkle, ANT1, TK2, SUCLA1 and DGOUK) revealed normal sequences. Sequencing of TREX1 and ribonucleases H2A, B and C failed to reveal any mutations. Whole-genome homozygosity mapping revealed a candidate region containing the SAMHD1 gene. Sequencing of the gene in the affected child and two affected fetuses revealed a large deletion (9 kb), spanning the promoter, exon1 and intron 1. The parents were found to be heterozygous for this deletion. The identification of a homozygous large deletion in the SAMHD1 gene causing atypical AGS with multiple mtDNA deletions may add information regarding the involvement of mitochondria in self-activation of innate immunity by cell intrinsic components. PMID:21102625

Dandy-Walker malformation and Wisconsin syndrome: novel cases add further insight into the genotype-phenotype correlations of 3q23q25 deletions.

PubMed

Ferraris, Alessandro; Bernardini, Laura; Sabolic Avramovska, Vesna; Zanni, Ginevra; Loddo, Sara; Sukarova-Angelovska, Elena; Parisi, Valentina; Capalbo, Anna; Tumini, Stefano; Travaglini, Lorena; Mancini, Francesca; Duma, Filip; Barresi, Sabina; Novelli, Antonio; Mercuri, Eugenio; Tarani, Luigi; Bertini, Enrico; Dallapiccola, Bruno; Valente, Enza Maria

2013-05-16

The Dandy-Walker malformation (DWM) is one of the commonest congenital cerebellar defects, and can be associated with multiple congenital anomalies and chromosomal syndromes. The occurrence of overlapping 3q deletions including the ZIC1 and ZIC4 genes in few patients, along with data from mouse models, have implicated both genes in the pathogenesis of DWM. Using a SNP-array approach, we recently identified three novel patients carrying heterozygous 3q deletions encompassing ZIC1 and ZIC4. Magnetic resonance imaging showed that only two had a typical DWM, while the third did not present any defect of the DWM spectrum. SNP-array analysis in further eleven children diagnosed with DWM failed to identify deletions of ZIC1-ZIC4. The clinical phenotype of the three 3q deleted patients included multiple congenital anomalies and peculiar facial appearance, related to the localization and extension of each deletion. In particular, phenotypes resulted from the variable combination of three recognizable patterns: DWM (with incomplete penetrance); blepharophimosis, ptosis, and epicanthus inversus syndrome; and Wisconsin syndrome (WS), recently mapped to 3q. Our data indicate that the 3q deletion is a rare defect associated with DWM, and suggest that the hemizygosity of ZIC1-ZIC4 genes is neither necessary nor sufficient per se to cause this condition. Furthermore, based on a detailed comparison of clinical features and molecular data from 3q deleted patients, we propose clinical diagnostic criteria and refine the critical region for WS.

Subtelomeric deletions of chromosome 6p: molecular and cytogenetic characterization of three new cases with phenotypic overlap with Ritscher-Schinzel (3C) syndrome.

PubMed

Descipio, Cheryl; Schneider, Lori; Young, Terri L; Wasserman, Nora; Yaeger, Dinah; Lu, Fengmin; Wheeler, Patricia G; Williams, Marc S; Bason, Lynn; Jukofsky, Lori; Menon, Ammini; Geschwindt, Ryan; Chudley, Albert E; Saraiva, Jorge; Schinzel, Albert A G L; Guichet, Agnes; Dobyns, William E; Toutain, Annick; Spinner, Nancy B; Krantz, Ian D

2005-04-01

We have identified six children in three families with subtelomeric deletions of 6p25 and a recognizable phenotype consisting of ptosis, posterior embryotoxon, optic nerve abnormalities, mild glaucoma, Dandy-Walker malformation, hydrocephalus, atrial septal defect, patent ductus arteriosus, and mild mental retardation. There is considerable clinical overlap between these children and individuals with the Ritscher-Schinzel (or cranio-cerebello-cardiac (3C)) syndrome (OMIM #220210). Clinical features of 3C syndrome include craniofacial anomalies (macrocephaly, prominent forehead and occiput, foramina parietalia, hypertelorism, down-slanting palpebral fissures, ocular colobomas, depressed nasal bridge, narrow or cleft palate, and low-set ears), cerebellar malformations (variable manifestations of a Dandy-Walker malformation with moderate mental retardation), and cardiac defects (primarily septal defects). Since the original report, over 25 patients with 3C syndrome have been reported. Recessive inheritance has been postulated based on recurrence in siblings born to unaffected parents and parental consanguinity in two familial cases. Molecular and cytogenetic mapping of the 6p deletions in these three families with subtelomeric deletions of chromosome 6p have defined a 1.3 Mb minimally deleted critical region. To determine if 6p deletions are common in 3C syndrome, we analyzed seven unrelated individuals with 3C syndrome for deletions of this region. Three forkhead genes (FOXF1 and FOXQ1 from within the critical region, and FOXC1 proximal to this region) were evaluated as potential candidate disease genes for this disorder. No deletions or disease-causing mutations were identified.

Dandy-Walker malformation and Wisconsin syndrome: novel cases add further insight into the genotype-phenotype correlations of 3q23q25 deletions

PubMed Central

2013-01-01

Background The Dandy-Walker malformation (DWM) is one of the commonest congenital cerebellar defects, and can be associated with multiple congenital anomalies and chromosomal syndromes. The occurrence of overlapping 3q deletions including the ZIC1 and ZIC4 genes in few patients, along with data from mouse models, have implicated both genes in the pathogenesis of DWM. Methods and results Using a SNP-array approach, we recently identified three novel patients carrying heterozygous 3q deletions encompassing ZIC1 and ZIC4. Magnetic resonance imaging showed that only two had a typical DWM, while the third did not present any defect of the DWM spectrum. SNP-array analysis in further eleven children diagnosed with DWM failed to identify deletions of ZIC1-ZIC4. The clinical phenotype of the three 3q deleted patients included multiple congenital anomalies and peculiar facial appearance, related to the localization and extension of each deletion. In particular, phenotypes resulted from the variable combination of three recognizable patterns: DWM (with incomplete penetrance); blepharophimosis, ptosis, and epicanthus inversus syndrome; and Wisconsin syndrome (WS), recently mapped to 3q. Conclusions Our data indicate that the 3q deletion is a rare defect associated with DWM, and suggest that the hemizygosity of ZIC1-ZIC4 genes is neither necessary nor sufficient per se to cause this condition. Furthermore, based on a detailed comparison of clinical features and molecular data from 3q deleted patients, we propose clinical diagnostic criteria and refine the critical region for WS. PMID:23679990

Design and Validation of a New MLPA-Based Assay for the Detection of RS1 Gene Deletions and Application in a Large Family with X-Linked Juvenile Retinoschisis

PubMed Central

Nicoletti, Annalisa; Ziccardi, Lucia; Benedetti, Sabrina; Palumbo, Orazio; Rendina, Michelina; D'Agruma, Leonardo; Falsini, Benedetto; Wang, Xinjing; Bertelli, Matteo

2017-01-01

Aims: X-linked juvenile retinoschisis (XLRS) is a severe ocular disorder that can evolve to blindness. More than 200 different disease-causing mutations have been reported in the RS1 gene and approximately 10% of these are deletions. Since transmission is X-linked, males are always affected and females are usually carriers. The identification of female carriers is always important and poses a technical challenge. Therefore, we sought to develop a multiplex ligation dependent probe amplification (MLPA)-based method to identify deletions or duplications in this gene. We then used our assay to study a large XLRS family. Methods: We designed six probes specific for each RS1 exon and then optimized and validated our method using control samples with known gene deletions. In the XLRS family, RS1 gene copy number variation was assessed by “home-made” MLPA analysis and by single nucleotide polymorphism (SNP) array analysis using the CytoScan HD Array. Direct sequencing was used for deletion breakpoint mapping. Results: Our assay detected all deletions in control samples. All affected males of the family were positive for a deletion of exon 2 of the RS1 gene (RS1:NM_000330:c.53-?_78+?del). Carrier females were also identified. Conclusion: Our method is easily replicated, reliable, and inexpensive and allows female carriers to be detected. This is the first report of deep characterization of a whole exon deletion in the RS1 gene. PMID:27997221

On the nosology and pathogenesis of Wolf-Hirschhorn syndrome: genotype-phenotype correlation analysis of 80 patients and literature review.

PubMed

Zollino, Marcella; Murdolo, Marina; Marangi, Giuseppe; Pecile, Vanna; Galasso, Cinzia; Mazzanti, Laura; Neri, Giovanni

2008-11-15

Based on genotype-phenotype correlation analysis of 80 Wolf-Hirschhorn syndrome (WHS) patients, as well as on review of relevant literature, we add further insights to the following aspects of WHS: (1) clinical delineation and phenotypic categories; (2) characterization of the basic genomic defect, mechanisms of origin and familiarity; (3) identification of prognostic factors for mental retardation; (4) chromosome mapping of the distinctive clinical signs, in an effort to identify pathogenic genes. Clinically, we consider that minimal diagnostic criteria for WHS, defining a "core" phenotype, are typical facial appearance, mental retardation, growth delay and seizures (or EEG anomalies). Three different categories of the WHS phenotype were defined, generally correlating with the extent of the 4p deletion. The first one comprises a small deletion not exceeding 3.5 Mb, that is usually associated with a mild phenotype, lacking major malformations. This category is likely under-diagnosed. The second and by far the more frequent category is identified by large deletions, averaging between 5 and 18 Mb, and causes the widely recognizable WHS phenotype. The third clinical category results from a very large deletion exceeding 22-25 Mb causing a severe phenotype, that can hardly be defined as typical WHS. Genetically, de novo chromosome abnormalities in WHS include pure deletions but also complex rearrangements, mainly unbalanced translocations. With the exception of t(4p;8p), WHS-associated chromosome abnormalities are neither mediated by segmental duplications, nor associated with a parental inversion polymorphism on 4p16.3. Factors involved in prediction of prognosis include the extent of the deletion, the occurrence of complex chromosome anomalies, and the severity of seizures. We found that the core phenotype maps within the terminal 1.9 Mb region of chromosome 4p. Therefore, WHSCR-2 should be considered the critical region for this condition. We also confirmed that the pathogenesis of WHS is multigenic. Specific and independent chromosome regions were characterized for growth delay and seizures, as well as for the additional clinical signs that characterize this condition. With the exception of parental balanced translocations, familial recurrence is uncommon.

Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

PubMed Central

He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

2012-01-01

Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

PubMed

Harraghy, Niamh; Homerova, Dagmar; Herrmann, Mathias; Kormanec, Jan

2008-01-01

Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

LPmerge: an R package for merging genetic maps by linear programming.

PubMed

Endelman, Jeffrey B; Plomion, Christophe

2014-06-01

Consensus genetic maps constructed from multiple populations are an important resource for both basic and applied research, including genome-wide association analysis, genome sequence assembly and studies of evolution. The LPmerge software uses linear programming to efficiently minimize the mean absolute error between the consensus map and the linkage maps from each population. This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved. When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts. LPmerge is on CRAN at http://cran.r-project.org/web/packages/LPmerge. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A recombination outside the BB deletion refines the location of the X-linked retinitis pigmentosa locus RP3

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

Fujita, R.; Bingham, E.; Forsythe, P.

1996-07-01

Genetic loci for X-linked retinitis pigmentosa (XLRP) have been mapped between Xp11.22 and Xp22.13 (RP2, RP3, RP6, and RP15). The RP3 gene, which is responsible for the predominant form of XLRP in most Caucasian populations, has been localized to Xp21.1 by linkage analysis and the map positions of chromosomal deletions associated with the disease. Previous linkage studies have suggested that RP3 is flanked by the markers DXS1110 (distal) and OTC (proximal). Patient BB was though to have RP because of a lesion at the RP3 locus, in addition to chronic granulomatous disease, Duchenne muscular dystrophy (DMD), mild mental retardation, andmore » the McLeod phenotype. This patient carried a deletion extending {approximately}3 Mb from DMD in Xp21.3 to Xp21.1, with the proximal breakpoint located {approximately}40 kb centromeric to DXS1110. The RP3 gene, therefore, is believed to reside between DXS1110 and the proximal breakpoint of the BB deletion. In order to refine the location of RP3 and to ascertain patients with RP3, we have been analyzing several XLRP families for linkage to Xp markers. Linkage analysis in an American family of 27 individuals demonstrates segregation of XLRP with markers in Xp21.1, consistent with the RP3 subtype. One affected male shows a recombination event proximal to DXS1110. Additional markers within the DXS1110-OTC interval show that the crossover is between two novel polymorphic markers, DXS8349 and M6, both of which are present in BB DNA and lie centromeric to the proximal breakpoint. This recombination places the XLRP mutation in this family outside the BB deletion and redefines the location of RP3. 22 refs., 3 figs., 2 tabs.« less

Stereotactic probability and variability of speech arrest and anomia sites during stimulation mapping of the language dominant hemisphere.

PubMed

Chang, Edward F; Breshears, Jonathan D; Raygor, Kunal P; Lau, Darryl; Molinaro, Annette M; Berger, Mitchel S

2017-01-01

OBJECTIVE Functional mapping using direct cortical stimulation is the gold standard for the prevention of postoperative morbidity during resective surgery in dominant-hemisphere perisylvian regions. Its role is necessitated by the significant interindividual variability that has been observed for essential language sites. The aim in this study was to determine the statistical probability distribution of eliciting aphasic errors for any given stereotactically based cortical position in a patient cohort and to quantify the variability at each cortical site. METHODS Patients undergoing awake craniotomy for dominant-hemisphere primary brain tumor resection between 1999 and 2014 at the authors' institution were included in this study, which included counting and picture-naming tasks during dense speech mapping via cortical stimulation. Positive and negative stimulation sites were collected using an intraoperative frameless stereotactic neuronavigation system and were converted to Montreal Neurological Institute coordinates. Data were iteratively resampled to create mean and standard deviation probability maps for speech arrest and anomia. Patients were divided into groups with a "classic" or an "atypical" location of speech function, based on the resultant probability maps. Patient and clinical factors were then assessed for their association with an atypical location of speech sites by univariate and multivariate analysis. RESULTS Across 102 patients undergoing speech mapping, the overall probabilities of speech arrest and anomia were 0.51 and 0.33, respectively. Speech arrest was most likely to occur with stimulation of the posterior inferior frontal gyrus (maximum probability from individual bin = 0.025), and variance was highest in the dorsal premotor cortex and the posterior superior temporal gyrus. In contrast, stimulation within the posterior perisylvian cortex resulted in the maximum mean probability of anomia (maximum probability = 0.012), with large variance in the regions surrounding the posterior superior temporal gyrus, including the posterior middle temporal, angular, and supramarginal gyri. Patients with atypical speech localization were far more likely to have tumors in canonical Broca's or Wernicke's areas (OR 7.21, 95% CI 1.67-31.09, p < 0.01) or to have multilobar tumors (OR 12.58, 95% CI 2.22-71.42, p < 0.01), than were patients with classic speech localization. CONCLUSIONS This study provides statistical probability distribution maps for aphasic errors during cortical stimulation mapping in a patient cohort. Thus, the authors provide an expected probability of inducing speech arrest and anomia from specific 10-mm 2 cortical bins in an individual patient. In addition, they highlight key regions of interindividual mapping variability that should be considered preoperatively. They believe these results will aid surgeons in their preoperative planning of eloquent cortex resection.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

Shuttle car loading system

NASA Technical Reports Server (NTRS)

Collins, E. R., Jr. (Inventor)

1985-01-01

A system is described for loading newly mined material such as coal, into a shuttle car, at a location near the mine face where there is only a limited height available for a loading system. The system includes a storage bin having several telescoping bin sections and a shuttle car having a bottom wall that can move under the bin. With the bin in an extended position and filled with coal the bin sections can be telescoped to allow the coal to drop out of the bin sections and into the shuttle car, to quickly load the car. The bin sections can then be extended, so they can be slowly filled with more while waiting another shuttle car.

Detection of a megabase deletion in a patient with brachio-oto-renal syndrome (BOR) and tricho-rhino-phalangeal syndrome (TRPS): Implications for mapping and cloning the BOR gene

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

Gu, J.Z.; Wells, D.E.; Wagner, M.J.

Genetic linkage analysis has previously mapped the locus for the autosomal dominant disorder branchio-oto-renal syndrome (BOR) to the pericentric region of chromosome 8q. A YAC contig spanning the putative BOR region, from D8S543 to D8S541, was constructed and confirmed by sequence-tagged site content mapping using microsatellite markers and by DNA hybridization analysis. YACs spanning the BOR interval were used as fluorescence in situ hybridization probes on a cell line from a patient with BO and tricho-rhino-phalangeal syndrome I that involves a chromosome 8q rearrangement. In addition to the cytogenetically defined direct insertion of material from 8q13.3-q21.13 into 8q24.11, a previouslymore » unidentified deletion of just under one megabase was found in 8q13.3. These data narrowed the most likely location of the BOR gene to a region corresponding to the proximal two-thirds of YAC 869E10 between D8S543 and D8S279. 23 refs., 3 figs.« less

Physical mapping of chromosome 17p13.3 in the region of a putative tumor suppressor gene important in medulloblastoma

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

McDonald, J.D.; Daneshvar, L.; Willert, J.R.

1994-09-01

Deletion mapping of a medulloblastoma tumor panel revealed loss of distal chromosome 17p13.3 sequences in tumors from 14 of 32 patients (44%). Of the 14 tumors showing loss of heterozygosity by restriction fragment length polymorphism analysis, 14 of 14 (100%) displayed loss of the telomeric marker p144-D6 (D17S34), while a probe for the ABR gene on 17p13.3 was lost in 7 of 8 (88%) informative cases. Using pulsed-field gel electrophoresis, we localized the polymorphic marker (VNTR-A) of the ABR gene locus to within 220 kb of the p144-D6 locus. A cosmid contig constructed in this region was used to demonstratemore » by fluorescence in situ hybridization that the ABR gene is oriented transcriptionally 5{prime} to 3{prime} toward the telomere. This report provides new physical mapping data for the ABR gene, which has not been previously shown to be deleted in medulloblastoma. These results provide further evidence for the existence of a second tumor suppressor gene distinct from p53 on distal chromosome 17p. 12 refs., 3 figs.« less

Overcoming imatinib resistance conferred by the BIM deletion polymorphism in chronic myeloid leukemia with splice-switching antisense oligonucleotides

PubMed Central

Liu, Jun; Bhadra, Malini; Sinnakannu, Joanna Rajeswary; Yue, Wan Lin; Tan, Cheryl Weiqi; Rigo, Frank; Ong, S.Tiong; Roca, Xavier

2017-01-01

Many tyrosine kinase-driven cancers, including chronic myeloid leukemia (CML), are characterized by high response rates to specific tyrosine kinase inhibitors (TKIs) like imatinib. In East Asians, primary imatinib resistance is caused by a deletion polymorphism in Intron 2 of the BIM gene, whose product is required for TKI-induced apoptosis. The deletion biases BIM splicing from exon 4 to exon 3, generating splice isoforms lacking the exon 4-encoded pro-apoptotic BH3 domain, which impairs the ability of TKIs to induce apoptosis. We sought to identify splice-switching antisense oligonucleotides (ASOs) that block exon 3 but enhance exon 4 splicing, and thereby resensitize BIM deletion-containing cancers to imatinib. First, we mapped multiple cis-acting splicing elements around BIM exon 3 by minigene mutations, and found an exonic splicing enhancer acting via SRSF1. Second, by a systematic ASO walk, we isolated ASOs that corrected the aberrant BIM splicing. Eight of 67 ASOs increased exon 4 levels in BIM deletion-containing cells, and restored imatinib-induced apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by BIM deletion polymorphism can be resensitized to imatinib via splice-switching BIM ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine adjuvant treatment for BIM-polymorphism-associated TKI-resistant CML and other cancers. PMID:29100409

Overcoming imatinib resistance conferred by the BIM deletion polymorphism in chronic myeloid leukemia with splice-switching antisense oligonucleotides.

PubMed

Liu, Jun; Bhadra, Malini; Sinnakannu, Joanna Rajeswary; Yue, Wan Lin; Tan, Cheryl Weiqi; Rigo, Frank; Ong, S Tiong; Roca, Xavier

2017-09-29

Many tyrosine kinase-driven cancers, including chronic myeloid leukemia (CML), are characterized by high response rates to specific tyrosine kinase inhibitors (TKIs) like imatinib. In East Asians, primary imatinib resistance is caused by a deletion polymorphism in Intron 2 of the BIM gene, whose product is required for TKI-induced apoptosis. The deletion biases BIM splicing from exon 4 to exon 3, generating splice isoforms lacking the exon 4-encoded pro-apoptotic BH3 domain, which impairs the ability of TKIs to induce apoptosis. We sought to identify splice-switching antisense oligonucleotides (ASOs) that block exon 3 but enhance exon 4 splicing, and thereby resensitize BIM deletion-containing cancers to imatinib. First, we mapped multiple cis -acting splicing elements around BIM exon 3 by minigene mutations, and found an exonic splicing enhancer acting via SRSF1. Second, by a systematic ASO walk, we isolated ASOs that corrected the aberrant BIM splicing. Eight of 67 ASOs increased exon 4 levels in BIM deletion-containing cells, and restored imatinib-induced apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by BIM deletion polymorphism can be resensitized to imatinib via splice-switching BIM ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine adjuvant treatment for BIM -polymorphism-associated TKI-resistant CML and other cancers.

Genetic studies of Prader-Willi patients provide evidence for conservation of genomic architecture in proximal chromosome 15q.

PubMed

Hou, Aihua; Lin, Shuan-Pei; Ho, Shi Yun; Chen, Chi-Fung Jennifer; Lin, Hsiang-Yu; Chen, Yen-Juin; Huang, Chi-Yu; Chiu, Huei-Ching; Chuang, Chih-Kuang; Chen, Ken-Shiung

2011-03-01

Prader-Willi syndrome (PWS) is a neurogenetic disorder associated with recurrent genomic recombination involving low copy repeats (LCRs) located in the human chromosome 15q11-q13. Previous studies of PWS patients from Asia suggested that there is a higher incidence of deletion and lower incidence of maternal uniparental disomy (mUPD) compared to that of Western populations. In this report, we present genetic etiology of 28 PWS patients from Taiwan. Consistent with the genetic etiology findings from Western populations, the type II deletion appears to be the most common deletion subtype. Furthermore, the ratio of the two most common deletion subtypes and the ratio of the maternal heterodisomy to isodisomy cases observed from this study are in agreement with previous findings from Western populations. In addition, we identified and further mapped the deletion breakpoints in two patients with atypical deletions using array CGH (comparative genomic hybridization). Despite the relatively small numbers of patients in each subgroup, our findings suggest that the genomic architecture responsible for the recurrent recombination in PWS is conserved in Taiwanese of the Han Chinese heritage and Western populations, thereby predisposing chromosome 15q11-q13 to a similar risk of rearrangements. © 2010 The Authors Annals of Human Genetics © 2010 Blackwell Publishing Ltd/University College London.

A Novel Class of Pseudoautosomal Region 1 Deletions Downstream of SHOX Is Associated with Léri-Weill Dyschondrosteosis

PubMed Central

Benito-Sanz, Sara; Thomas, N. Simon; Huber, Céline; del Blanco, Darya Gorbenko; Aza-Carmona, Miriam; Crolla, John A.; Maloney, Vivienne; Argente, Jesús; Campos-Barros, Ángel; Cormier-Daire, Valérie; Heath, Karen E.

2005-01-01

Léri-Weill dyschondrosteosis (LWD) is a pseudoautosomal dominant disorder characterized by disproportionate short stature and a characteristic curving of the radius, known as the “Madelung deformity.” SHOX mutations resulting in SHOX haploinsufficiency have been found in LWD and in a variable proportion of patients with idiopathic short stature (ISS), whereas homozygous loss of SHOX results in the more severe Langer mesomelic dysplasia (LMD). Defects in SHOX have been identified in ∼60% of LWD cases, whereas, in the remaining ∼40%, the molecular basis is unknown. This suggests either genetic heterogeneity or the presence of mutations in unanalyzed regions of SHOX, such as the upstream, intragenic, or downstream regulatory sequences. Therefore, the pseudoautosomal region 1 (PAR1) of 80 patients with LWD, in whom SHOX deletions and mutations had been excluded, was screened for deletions by use of a new panel of microsatellite markers. We identified 12 patients with LWD who presented with a novel class of PAR1 deletions that did not include SHOX. The deletions were of variable size and mapped at least ∼30–530 kb downstream of SHOX. In our cohort, this type of deletion accounted for 15% of cases. In all cases, the deletions cosegregated with the phenotype. No apparent phenotypic differences were observed between patients with SHOX deletions and those with this new class of PAR1 deletions. Thus, we present here the identification of a second PAR1 region implicated in the etiopathogenesis of LWD. Our findings suggest the presence of distal regulatory elements of SHOX transcription in PAR1 or, alternatively, the existence of an additional locus apparently involved in the control of skeletal development. Deletion analysis of this newly identified region should be included in the mutation screening of patients with LWD, LMD, and ISS. PMID:16175500

Spectral multiplexing for scalable quantum photonics using an atomic frequency comb quantum memory and feed-forward control.

PubMed

Sinclair, Neil; Saglamyurek, Erhan; Mallahzadeh, Hassan; Slater, Joshua A; George, Mathew; Ricken, Raimund; Hedges, Morgan P; Oblak, Daniel; Simon, Christoph; Sohler, Wolfgang; Tittel, Wolfgang

2014-08-01

Future multiphoton applications of quantum optics and quantum information science require quantum memories that simultaneously store many photon states, each encoded into a different optical mode, and enable one to select the mapping between any input and a specific retrieved mode during storage. Here we show, with the example of a quantum repeater, how to employ spectrally multiplexed states and memories with fixed storage times that allow such mapping between spectral modes. Furthermore, using a Ti:Tm:LiNbO_{3} waveguide cooled to 3 K, a phase modulator, and a spectral filter, we demonstrate storage followed by the required feed-forward-controlled frequency manipulation with time-bin qubits encoded into up to 26 multiplexed spectral modes and 97% fidelity.

ActionMap: A web-based software that automates loci assignments to framework maps.

PubMed

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-07-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

ActionMap: a web-based software that automates loci assignments to framework maps

PubMed Central

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-01-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/). PMID:12824426

Defective interfering particles of poliovirus: mapping of the deletion and evidence that the deletions in the genomes of DI(1), (2), and (3) are located in the same region

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

Nomoto, A.; Jacobson, A.; Lee, Y.F.

1979-01-01

The deletions in RNAs of three defective interfering (DI) particles of poliovirus type 1 have been located and their approximate extent determined by three methods. (1) Digestion with RNase III of DI RNAs yields the same 3'-terminal fragments as digestion wth RNase III of standard virus RNA. The longest 3'-terminal located in the 5'-terminal half of the polio genome. (2) Fingerprints of RNase T/sub 1/-resistant oligonucleotides of all three DI RNAs are identical and lack four large oligonucleotides as compared to the fingerprints of standard virus, an observation suggesting that the deletions in all three DI RNAs are located inmore » the same reregion of the viral genome. The deletion-specific oligonucleotides have also been shown to be within the 5'-terminal half of the viral genome by alkali fragmentation of the RNA and fingerprinting poly(A)-linked (3'-terminal) fragments of decreasing size. (3) Virion RNA of DI(2) particles was annealed with denatured double-stranded RNA (RF) of standard virus and the hybrid heteroduplex molcules examined in the electron microscope. A single loop, approximately 900 nucleotides long and 20% from one end of the molecules, was observed. Both the size and extent of individual deletions is somewhat variable in different hetereoduplex molecules, an observation suggesting heterogeneity in the size of the deletion in RNA of the DI(2) population. Our data show that the DI RNAs of poliovirus contain an internal deletion in that region of the viral genome known to specify the capsid polypeptides. This result provides an explanation as to why poliovirus DI particles are unable to synthesize viral coat proteins.« less

Effect of various binning methods and ROI sizes on the accuracy of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of texture features at HRCT

NASA Astrophysics Data System (ADS)

Kim, Namkug; Seo, Joon Beom; Sung, Yu Sub; Park, Bum-Woo; Lee, Youngjoo; Park, Seong Hoon; Lee, Young Kyung; Kang, Suk-Ho

2008-03-01

To find optimal binning, variable binning size linear binning (LB) and non-linear binning (NLB) methods were tested. In case of small binning size (Q <= 10), NLB shows significant better accuracy than the LB. K-means NLB (Q = 26) is statistically significant better than every LB. To find optimal binning method and ROI size of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of textural analysis at HRCT Six-hundred circular regions of interest (ROI) with 10, 20, and 30 pixel diameter, comprising of each 100 ROIs representing six regional disease patterns (normal, NL; ground-glass opacity, GGO; reticular opacity, RO; honeycombing, HC; emphysema, EMPH; and consolidation, CONS) were marked by an experienced radiologist from HRCT images. Histogram (mean) and co-occurrence matrix (mean and SD of angular second moment, contrast, correlation, entropy, and inverse difference momentum) features were employed to test binning and ROI effects. To find optimal binning, variable binning size LB (bin size Q: 4~30, 32, 64, 128, 144, 196, 256, 384) and NLB (Q: 4~30) methods (K-means, and Fuzzy C-means clustering) were tested. For automated classification, a SVM classifier was implemented. To assess cross-validation of the system, a five-folding method was used. Each test was repeatedly performed twenty times. Overall accuracies with every combination of variable ROIs, and binning sizes were statistically compared. In case of small binning size (Q <= 10), NLB shows significant better accuracy than the LB. K-means NLB (Q = 26) is statistically significant better than every LB. In case of 30x30 ROI size and most of binning size, the K-means method showed better than other NLB and LB methods. When optimal binning and other parameters were set, overall sensitivity of the classifier was 92.85%. The sensitivity and specificity of the system for each class were as follows: NL, 95%, 97.9%; GGO, 80%, 98.9%; RO 85%, 96.9%; HC, 94.7%, 97%; EMPH, 100%, 100%; and CONS, 100%, 100%, respectively. We determined the optimal binning method and ROI size of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of texture features at HRCT.

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.

PubMed

Herath, Damayanthi; Tang, Sen-Lin; Tandon, Kshitij; Ackland, David; Halgamuge, Saman Kumara

2017-12-28

In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains. Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome. The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.

Mental maps and travel behaviour: meanings and models

NASA Astrophysics Data System (ADS)

Hannes, Els; Kusumastuti, Diana; Espinosa, Maikel León; Janssens, Davy; Vanhoof, Koen; Wets, Geert

2012-04-01

In this paper, the " mental map" concept is positioned with regard to individual travel behaviour to start with. Based on Ogden and Richards' triangle of meaning (The meaning of meaning: a study of the influence of language upon thought and of the science of symbolism. International library of psychology, philosophy and scientific method. Routledge and Kegan Paul, London, 1966) distinct thoughts, referents and symbols originating from different scientific disciplines are identified and explained in order to clear up the notion's fuzziness. Next, the use of this concept in two major areas of research relevant to travel demand modelling is indicated and discussed in detail: spatial cognition and decision-making. The relevance of these constructs to understand and model individual travel behaviour is explained and current research efforts to implement these concepts in travel demand models are addressed. Furthermore, these mental map notions are specified in two types of computational models, i.e. a Bayesian Inference Network (BIN) and a Fuzzy Cognitive Map (FCM). Both models are explained, and a numerical and a real-life example are provided. Both approaches yield a detailed quantitative representation of the mental map of decision-making problems in travel behaviour.

Cosmic microwave background reconstruction from WMAP and Planck PR2 data

NASA Astrophysics Data System (ADS)

Bobin, J.; Sureau, F.; Starck, J.-L.

2016-06-01

We describe a new estimate of the cosmic microwave background (CMB) intensity map reconstructed by a joint analysis of the full Planck 2015 data (PR2) and nine years of WMAP data. The proposed map provides more than a mere update of the CMB map introduced in a previous paper since it benefits from an improvement of the component separation method L-GMCA (Local-Generalized Morphological Component Analysis), which facilitates efficient separation of correlated components. Based on the most recent CMB data, we further confirm previous results showing that the proposed CMB map estimate exhibits appealing characteristics for astrophysical and cosmological applications: I) it is a full-sky map as it did not require any inpainting or interpolation postprocessing; II) foreground contamination is very low even on the galactic center; and III) the map does not exhibit any detectable trace of thermal Sunyaev-Zel'dovich contamination. We show that its power spectrum is in good agreement with the Planck PR2 official theoretical best-fit power spectrum. Finally, following the principle of reproducible research, we provide the codes to reproduce the L-GMCA, which makes it the only reproducible CMB map. The reconstructed CMB map and the code are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/591/A50

Assessment of Performance of the Industrial Process of Bulk Vacuum Packaging of Raw Meat with Nondestructive Optical Oxygen Sensing Systems.

PubMed

Kelly, Caroline A; Cruz-Romero, Malco; Kerry, Joseph P; Papkovsky, Dmitri P

2018-05-02

The commercially-available optical oxygen-sensing system Optech-O₂ Platinum was applied to nondestructively assess the in situ performance of bulk, vacuum-packaged raw beef in three ~300 kg containers. Twenty sensors were attached to the inner surface of the standard bin-contained laminate bag (10 on the front and back sides), such that after filling with meat and sealing under vacuum, the sensors were accessible for optical interrogation with the external reader device. After filling and sealing each bag, the sensors were measured repetitively and nondestructively over a 15-day storage period at 1 °C, thus tracking residual oxygen distribution in the bag and changes during storage. The sensors revealed a number of unidentified meat quality and processing issues, and helped to improve the packaging process by pouring flakes of dry ice into the bag. Sensor utility in mapping the distribution of residual O₂ in sealed bulk containers and optimising and improving the packaging process, including handling and storage of bulk vacuum-packaged meat bins, was evident.

Are there tumor suppressor genes on chromosome 4p in sporadic colorectal carcinoma?

PubMed

Zheng, Hai-Tao; Jiang, Li-Xin; Lv, Zhong-Chuan; Li, Da-Peng; Zhou, Chong-Zhi; Gao, Jian-Jun; He, Lin; Peng, Zhi-Hai

2008-01-07

To study the candidate tumor suppressor genes (TSG) on chromosome 4p by detecting the high frequency of loss of heterozygosity (LOH) in sporadic colorectal carcinoma in Chinese patients. Seven fluorescent labeled polymorphic microsatellite markers were analyzed in 83 cases of colorectal carcinoma and matched normal tissue DNA by PCR. PCR products were electrophoresed on an ABI 377 DNA sequencer. Genescan 3.7 and Genotype 3.7 software were used for LOH scanning and analysis. The same procedure was performed by the other six microsatellite markers spanning D4S3013 locus to make further detailed deletion mapping. Comparison between LOH frequency and clinicopathological factors was performed by c2 test. Data were collected from all informative loci. The average LOH frequency on 4p was 24.25%, and 42.3% and 35.62% on D4S405 and D4S3013 locus, respectively. Adjacent markers of D4S3013 displayed a low LOH frequency (< 30%) by detailed deletion mapping. Significant opposite difference was observed between LOH frequency and tumor diameter on D4S412 and D4S1546 locus (0% vs 16.67%, P = 0.041; 54.55% vs 11.11%, P = 0.034, respectively). On D4S403 locus, LOH was significantly associated with tumor gross pattern (11.11%, 0, 33.33%, P = 0.030). No relationship was detected on other loci compared with clinicopathological features. By deletion mapping, two obvious high frequency LOH regions spanning D4S3013 (4p15.2) and D4S405 (4p14) locus are detected. Candidate TSG, which is involved in carcinogenesis and progression of sporadic colorectal carcinoma on chromosome 4p, may be located between D4S3017 and D4S2933 (about 1.7 cm).

Substantial prevalence of microdeletions of the Y-chromosome in infertile men with idiopathic azoospermia and oligozoospermia detected using a sequence-tagged site-based mapping strategy

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

Najmabadi, H.; Huang, V.; Bhasin, D.

1996-04-01

Genes on the long arm of Y (Yq), particularly within interval 6, are believed to play a critical role in human spermatogenesis. Cytogenetically detectable deletions of this region are associated with azoospermia in men, but are relatively uncommon. The objective of this study was to validate a sequence-tagged site (STS)-mapping strategy for the detection of Yq microdeletions and to use this method to determine the proportion of men with idiopathic azoospermia or severe oligozoospermia who carry microdeletions in Yq. STS mapping of a sufficiently large sample of infertile men should also help further localize the putative gene(s) involved in themore » pathogenesis of male infertility. Genomic DNA was extracted from peripheral leukocytes of 16 normal fertile men, 7 normal fertile women, 60 infertile men, and 15 patients with the X-linked disorder, ichthyosis. PCR primers were synthesized for 26 STSs that span Yq interval 6. None of the 16 normal men of known fertility had microdeletions. Seven normal fertile women failed to amplify any of the 26 STSs, providing evidence of their Y specificity. No microdeletions were detected in any of the 15 patients with ichthyosis. Of the 60 infertile men typed with 26 STSs, 11 (18%; 10 azoospermic and 1 oligozoospermic) failed to amplify 1 or more STS. Interestingly, 4 of the 11 patients had microdeletions in a region that is outside the Yq region from which the DAZ (deleted in azoospermia gene region) gene was cloned. In an additional 3 patients, microdeletions were present both inside and outside the DAZ region. The physical locations of these microdeletions provide further support for the concept that a gene(s) on Yq deletion interval 6 plays an important role in spermatogenesis. The presence of deletions that do not overlap with the DAZ region suggests that genes other than the DAZ gene may also be implicated in the pathogenesis of some subsets of male infertility. 48 refs., 2 figs., 2 tabs.« less

Plains South of Valles Marineris

NASA Image and Video Library

2017-03-28

This enhanced-color sample reveals the incredible diversity of landforms on some Martian plains that appear bland and uniform at larger scales. Here we see layers, small channels suggesting water flow, craters, and indurated sand dunes. The map is projected here at a scale of 25 centimeters (9.8 inches) per pixel. [The original image scale is 25.7 centimeters (10.1 inches) per pixel (with 1 x 1 binning); objects on the order of 77 centimeters (30.3 inches) across are resolved.] North is up. http://photojournal.jpl.nasa.gov/catalog/PIA21573

A molecular deletion of distal chromosome 4p in two families with a satellited chromosome 4 lacking the Wolf-Hirschhorn syndrome phenotype.

PubMed

Estabrooks, L L; Lamb, A N; Kirkman, H N; Callanan, N P; Rao, K W

1992-11-01

We report two families with a satellited chromosome 4 short arm (4ps). Satellites and stalks normally occur on the short arms of acrocentric chromosomes; however, the literature cites several reports of satellited nonacrocentric chromosomes, which presumably result from a translocation with an acrocentric chromosome. This is the first report of 4ps chromosomes. Our families are remarkable in that both unaffected and affected individuals carry the 4ps chromosome. The phenotypes observed in affected individuals, although dissimilar, were sufficient to encourage a search for a deletion of chromosome 4p. By Southern blot analysis and fluorescence in situ hybridization, a deletion of material mapping approximately 150 kb from chromosome 4pter was discovered. This deletion is notable because it does not result in the Wolf-Hirschhorn syndrome and can result in an apparently normal phenotype. We speculate that homology between subterminal repeat sequences on 4p and sequences on the acrocentric short arms may explain the origin of the rearrangement and that position effect may play a role in the expression of the abnormal phenotype.

Subcellular Changes in Bridging Integrator 1 Protein Expression in the Cerebral Cortex During the Progression of Alzheimer Disease Pathology.

PubMed

Adams, Stephanie L; Tilton, Kathy; Kozubek, James A; Seshadri, Sudha; Delalle, Ivana

2016-08-01

Genome-wide association studies have established BIN1 (Bridging Integrator 1) as the most significant late-onset Alzheimer disease (AD) susceptibility locus after APOE We analyzed BIN1 protein expression using automated immunohistochemistry on the hippocampal CA1 region in 19 patients with either no, mild, or moderate-to-marked AD pathology, who had been assessed by Clinical Dementia Rating and CERAD scores. We also examined the amygdala, prefrontal, temporal, and occipital regions in a subset of these patients. In non-demented controls without AD pathology, BIN1 protein was expressed in white matter, glia, particularly oligodendrocytes, and in the neuropil in which the BIN1 signal decorated axons. With increasing severity of AD, BIN1 in the CA1 region showed: 1) sustained expression in glial cells, 2) decreased areas of neuropil expression, and 3) increased cytoplasmic neuronal expression that did not correlate with neurofibrillary tangle load. In patients with AD, both the prefrontal cortex and CA1 showed a decrease in BIN1-immunoreactive (BIN1-ir) neuropil areas and increases in numbers of BIN1-ir neurons. The numbers of CA1 BIN1-ir pyramidal neurons correlated with hippocampal CERAD neuritic plaque scores; BIN1 neuropil signal was absent in neuritic plaques. Our data provide novel insight into the relationship between BIN1 protein expression and the progression of AD-associated pathology and its diagnostic hallmarks. © 2016 American Association of Neuropathologists, Inc. All rights reserved.

Bin Ratio-Based Histogram Distances and Their Application to Image Classification.

PubMed

Hu, Weiming; Xie, Nianhua; Hu, Ruiguang; Ling, Haibin; Chen, Qiang; Yan, Shuicheng; Maybank, Stephen

2014-12-01

Large variations in image background may cause partial matching and normalization problems for histogram-based representations, i.e., the histograms of the same category may have bins which are significantly different, and normalization may produce large changes in the differences between corresponding bins. In this paper, we deal with this problem by using the ratios between bin values of histograms, rather than bin values' differences which are used in the traditional histogram distances. We propose a bin ratio-based histogram distance (BRD), which is an intra-cross-bin distance, in contrast with previous bin-to-bin distances and cross-bin distances. The BRD is robust to partial matching and histogram normalization, and captures correlations between bins with only a linear computational complexity. We combine the BRD with the ℓ1 histogram distance and the χ(2) histogram distance to generate the ℓ1 BRD and the χ(2) BRD, respectively. These combinations exploit and benefit from the robustness of the BRD under partial matching and the robustness of the ℓ1 and χ(2) distances to small noise. We propose a method for assessing the robustness of histogram distances to partial matching. The BRDs and logistic regression-based histogram fusion are applied to image classification. The experimental results on synthetic data sets show the robustness of the BRDs to partial matching, and the experiments on seven benchmark data sets demonstrate promising results of the BRDs for image classification.

Analysis of induced pluripotent stem cells carrying 22q11.2 deletion.

PubMed

Toyoshima, M; Akamatsu, W; Okada, Y; Ohnishi, T; Balan, S; Hisano, Y; Iwayama, Y; Toyota, T; Matsumoto, T; Itasaka, N; Sugiyama, S; Tanaka, M; Yano, M; Dean, B; Okano, H; Yoshikawa, T

2016-11-01

Given the complexity and heterogeneity of the genomic architecture underlying schizophrenia, molecular analyses of these patients with defined and large effect-size genomic defects could provide valuable clues. We established human-induced pluripotent stem cells from two schizophrenia patients with the 22q11.2 deletion (two cell lines from each subject, total of four cell lines) and three controls (total of four cell lines). Neurosphere size, neural differentiation efficiency, neurite outgrowth, cellular migration and the neurogenic-to-gliogenic competence ratio were significantly reduced in patient-derived cells. As an underlying mechanism, we focused on the role of DGCR8, a key gene for microRNA (miRNA) processing and mapped in the deleted region. In mice, Dgcr8 hetero-knockout is known to show a similar phenotype of reduced neurosphere size (Ouchi et al., 2013). The miRNA profiling detected reduced expression levels of miRNAs belonging to miR-17/92 cluster and miR-106a/b in the patient-derived neurospheres. Those miRNAs are reported to target p38α, and conformingly the levels of p38α were upregulated in the patient-derived cells. p38α is known to drive gliogenic differentiation. The inhibition of p38 activity by SB203580 in patient-derived neurospheres partially restored neurogenic competence. Furthermore, we detected elevated expression of GFAP, a gliogenic (astrocyte) marker, in postmortem brains from schizophrenia patients without the 22q11.2 deletion, whereas inflammation markers (IL1B and IL6) remained unchanged. In contrast, a neuronal marker, MAP2 expressions were decreased in schizophrenia brains. These results suggest that a dysregulated balance of neurogenic-to-gliogenic competence may underlie neurodevelopmental disorders such as schizophrenia.

Cri du Chat syndrome

PubMed Central

Cerruti Mainardi, Paola

2006-01-01

The Cri du Chat syndrome (CdCS) is a genetic disease resulting from a deletion of variable size occurring on the short arm of chromosome 5 (5p-). The incidence ranges from 1:15,000 to 1:50,000 live-born infants. The main clinical features are a high-pitched monochromatic cry, microcephaly, broad nasal bridge, epicanthal folds, micrognathia, abnormal dermatoglyphics, and severe psychomotor and mental retardation. Malformations, although not very frequent, may be present: cardiac, neurological and renal abnormalities, preauricular tags, syndactyly, hypospadias, and cryptorchidism. Molecular cytogenetic analysis has allowed a cytogenetic and phenotypic map of 5p to be defined, even if results from the studies reported up to now are not completely in agreement. Genotype-phenotype correlation studies showed a clinical and cytogenetic variability. The identification of phenotypic subsets associated with a specific size and type of deletion is of diagnostic and prognostic relevance. Specific growth and psychomotor development charts have been established. Two genes, Semaphorin F (SEMAF) and δ-catenin (CTNND2), which have been mapped to the "critical regions", are potentially involved in cerebral development and their deletion may be associated with mental retardation in CdCS patients. Deletion of the telomerase reverse transcriptase (hTERT) gene, localised to 5p15.33, could contribute to the phenotypic changes in CdCS. The critical regions were recently refined by using array comparative genomic hybridisation. The cat-like cry critical region was further narrowed using quantitative polymerase chain reaction (PCR) and three candidate genes were characterised in this region. The diagnosis is based on typical clinical manifestations. Karyotype analysis and, in doubtful cases, FISH analysis will confirm the diagnosis. There is no specific therapy for CdCS but early rehabilitative and educational interventions improve the prognosis and considerable progress has been made in the social adjustment of CdCS patients. PMID:16953888

Chromosomal microarray testing identifies a 4p terminal region associated with seizures in Wolf–Hirschhorn syndrome

PubMed Central

South, Sarah T; Lortz, Amanda; Hensel, Charles H; Sdano, Mallory R; Vanzo, Rena J; Martin, Megan M; Peiffer, Andreas; Lambert, Christophe G; Calhoun, Amy; Carey, John C; Battaglia, Agatino

2016-01-01

Background Wolf–Hirschhorn syndrome (WHS) is a contiguous gene deletion syndrome involving variable size deletions of the 4p16.3 region. Seizures are frequently, but not always, associated with WHS. We hypothesised that the size and location of the deleted region may correlate with seizure presentation. Methods Using chromosomal microarray analysis, we finely mapped the breakpoints of copy number variants (CNVs) in 48 individuals with WHS. Seizure phenotype data were collected through parent-reported answers to a comprehensive questionnaire and supplemented with available medical records. Results We observed a significant correlation between the presence of an interstitial 4p deletion and lack of a seizure phenotype (Fisher's exact test p=3.59e-6). In our cohort, there were five individuals with interstitial deletions with a distal breakpoint at least 751 kbp proximal to the 4p terminus. Four of these individuals have never had an observable seizure, and the fifth individual had a single febrile seizure at the age of 1.5 years. All other individuals in our cohort whose deletions encompass the terminal 751 kbp region report having seizures typical of WHS. Additional examples from the literature corroborate these observations and further refine the candidate seizure susceptibility region to a region 197 kbp in size, starting 368 kbp from the terminus of chromosome 4. Conclusions We identify a small terminal region of chromosome 4p that represents a seizure susceptibility region. Deletion of this region in the context of WHS is sufficient for seizure occurrence. PMID:26747863

Potential fitting biases resulting from grouping data into variable width bins

NASA Astrophysics Data System (ADS)

Towers, S.

2014-07-01

When reading peer-reviewed scientific literature describing any analysis of empirical data, it is natural and correct to proceed with the underlying assumption that experiments have made good faith efforts to ensure that their analyses yield unbiased results. However, particle physics experiments are expensive and time consuming to carry out, thus if an analysis has inherent bias (even if unintentional), much money and effort can be wasted trying to replicate or understand the results, particularly if the analysis is fundamental to our understanding of the universe. In this note we discuss the significant biases that can result from data binning schemes. As we will show, if data are binned such that they provide the best comparison to a particular (but incorrect) model, the resulting model parameter estimates when fitting to the binned data can be significantly biased, leading us to too often accept the model hypothesis when it is not in fact true. When using binned likelihood or least squares methods there is of course no a priori requirement that data bin sizes need to be constant, but we show that fitting to data grouped into variable width bins is particularly prone to produce biased results if the bin boundaries are chosen to optimize the comparison of the binned data to a wrong model. The degree of bias that can be achieved simply with variable binning can be surprisingly large. Fitting the data with an unbinned likelihood method, when possible to do so, is the best way for researchers to show that their analyses are not biased by binning effects. Failing that, equal bin widths should be employed as a cross-check of the fitting analysis whenever possible.

Transcriptional enhancer from milk protein genes

DOEpatents

Casperson, Gerald F.; Schmidhauser, Christian T.; Bissell, Mina J.

1999-01-01

The invention relates to novel enhancer nucleotide sequences which stimulate transcription of heterologous DNA in cells in culture. The enhancers are derived from major milk protein genes by the process of deletion mapping and functional analysis. The invention also relates to expression vectors containing the novel enhancers.

High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population.

PubMed

Yang, Yi; Shen, Yusen; Li, Shunda; Ge, Xianhong; Li, Zaiyun

2017-01-01

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed ( Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses ( B. rapa ssp. chinesis × O. violaceus ) × B. napus . In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs ( cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09 , and cqSL.C09 ) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

Positional cloning of disease genes on chromosome 16

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

Doggett, N.; Bruening, M.; Callen, D.

1996-04-01

The project seeks to elucidate the molecular basis of an important genetic disease (Batten`s disease) by molecular cloning of the affected gene by utilizing an overlapping clone map of chromosome 16. Batten disease (also known as juvenile neuronal ceroid lipofuscinosis) is a recessively inherited neurodegenerative disorder of childhood characterized by progressive loss of vision, seizures, and psychomoter disturbances. The Batten disease gene was genetically mapped to the chromosome region 16p 12.1 in close linkage with the genetic markers D16S299 and D16S298. Exon amplification of a cosmid containing D16S298 yielded a candidate gene that was disrupted by a 1 kb genomicmore » deletion in all patients containing the most common haplotype for the disease. Two separate deletions and a point mutation altering a splice site in three unrelated families have confirmed the gene as the Batten disease gene. The disease gene encodes a novel 438 amino acid membrane binding protein of unknown function.« less

Targeted Deletion of ERK5 MAP Kinase in the Developing Nervous System Impairs Development of GABAergic Interneurons in the Main Olfactory Bulb and Behavioral Discrimination between Structurally Similar Odorants

PubMed Central

Zou, Junhui; Pan, Yung-Wei; Wang, Zhenshan; Chang, Shih-Yu; Wang, Wenbin; Wang, Xin; Tournier, Cathy; Storm, Daniel R.; Xia, Zhengui

2012-01-01

ERK5 MAP kinase is highly expressed in the developing nervous system and has been implicated in promoting the survival of immature neurons in culture. However, its role in the development and function of the mammalian nervous system has not been established in vivo. Here, we report that conditional deletion of the erk5 gene in mouse neural stem cells during development reduces the number of GABAergic interneurons in the main olfactory bulb (OB). Our data suggest that this is due to a decrease in proliferation and an increase in apoptosis in the subventricular zone (SVZ) and rostral migratory stream (RMS) of ERK5 mutant mice. Interestingly, ERK5 mutant mice have smaller OB and are impaired in odor discrimination between structurally similar odorants. We conclude that ERK5 is a novel signaling pathway regulating developmental OB neurogenesis and olfactory behavior. PMID:22442076

45. VIEW OF UPPER LEVEL CRUSHER ADDITION FROM CRUSHED OXIDIZED ...

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

45. VIEW OF UPPER LEVEL CRUSHER ADDITION FROM CRUSHED OXIDIZED ORE BIN. 18 INCH BELT CONVEYOR BIN FEED, LOWER CENTER, WITH STEPHENS-ADAMSON 25 TON/HR ELEVATOR SPLIT DISCHARGE (OXIDIZED/UNOXIDIZED) IN CENTER. CRUDE ORE BINS AND MACHINE SHOP BEYOND. NOTE TOP OF CRUSHED OXIDIZED ORE BIN IS BELOW TOP OF CRUDE ORE BINS. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Effects of Mixtures on Liquid and Solid Fragment Size Distributions

DTIC Science & Technology

2016-05-01

bins, too few size bins, fixed bin widths, or inadequately- varying bin widths. Overpopulated bins – which typically occur for smaller fragments...2010 C. V. B. Cunningham, The Kuz-Ram Fragmentation Model – 20 Years On, In R. Holmberg et. al., Editors, Proceedings of the 3 rd World ...1992 P. K. Sahoo and T. Riedel, Mean Value Theorems and Functional Equations, World Scientific, 1998 K. A. Sallam, C. Aalburg, G.M. Faeth

Updates to Enhanced Geothermal System Resource Potential Estimate

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

Augustine, Chad

The deep EGS electricity generation resource potential estimate maintained by the National Renewable Energy Laboratory was updated using the most recent temperature-at-depth maps available from the Southern Methodist University Geothermal Laboratory. The previous study dates back to 2011 and was developed using the original temperature-at-depth maps showcased in the 2006 MIT Future of Geothermal Energy report. The methodology used to update the deep EGS resource potential is the same as in the previous study and is summarized in the paper. The updated deep EGS resource potential estimate was calculated for depths between 3 and 7 km and is binned inmore » 25 degrees C increments. The updated deep EGS electricity generation resource potential estimate is 4,349 GWe. A comparison of the estimates from the previous and updated studies shows a net increase of 117 GWe in the 3-7 km depth range, due mainly to increases in the underlying temperature-at-depth estimates from the updated maps.« less

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

PubMed

Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

2017-03-01

With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize ( Zea mays ) recombinant inbred line population ( n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

PubMed Central

Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

2017-01-01

With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

Update to Enhanced Geothermal System Resource Potential Estimate: Preprint

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

Augustine, Chad

2016-10-01

The deep EGS electricity generation resource potential estimate maintained by the National Renewable Energy Laboratory was updated using the most recent temperature-at-depth maps available from the Southern Methodist University Geothermal Laboratory. The previous study dates back to 2011 and was developed using the original temperature-at-depth maps showcased in the 2006 MIT Future of Geothermal Energy report. The methodology used to update the deep EGS resource potential is the same as in the previous study and is summarized in the paper. The updated deep EGS resource potential estimate was calculated for depths between 3 and 7 km and is binned inmore » 25 degrees C increments. The updated deep EGS electricity generation resource potential estimate is 4,349 GWe. A comparison of the estimates from the previous and updated studies shows a net increase of 117 GWe in the 3-7 km depth range, due mainly to increases in the underlying temperature-at-depth estimates from the updated maps.« less

BIN1 is reduced and Cav1.2 trafficking is impaired in human failing cardiomyocytes.

PubMed

Hong, Ting-Ting; Smyth, James W; Chu, Kevin Y; Vogan, Jacob M; Fong, Tina S; Jensen, Brian C; Fang, Kun; Halushka, Marc K; Russell, Stuart D; Colecraft, Henry; Hoopes, Charles W; Ocorr, Karen; Chi, Neil C; Shaw, Robin M

2012-05-01

Heart failure is a growing epidemic, and a typical aspect of heart failure pathophysiology is altered calcium transients. Normal cardiac calcium transients are initiated by Cav1.2 channels at cardiac T tubules. Bridging integrator 1 (BIN1) is a membrane scaffolding protein that causes Cav1.2 to traffic to T tubules in healthy hearts. The mechanisms of Cav1.2 trafficking in heart failure are not known. To study BIN1 expression and its effect on Cav1.2 trafficking in failing hearts. Intact myocardium and freshly isolated cardiomyocytes from nonfailing and end-stage failing human hearts were used to study BIN1 expression and Cav1.2 localization. To confirm Cav1.2 surface expression dependence on BIN1, patch-clamp recordings were performed of Cav1.2 current in cell lines with and without trafficking-competent BIN1. Also, in adult mouse cardiomyocytes, surface Cav1.2 and calcium transients were studied after small hairpin RNA-mediated knockdown of BIN1. For a functional readout in intact heart, calcium transients and cardiac contractility were analyzed in a zebrafish model with morpholino-mediated knockdown of BIN1. BIN1 expression is significantly decreased in failing cardiomyocytes at both mRNA (30% down) and protein (36% down) levels. Peripheral Cav1.2 is reduced to 42% by imaging, and a biochemical T-tubule fraction of Cav1.2 is reduced to 68%. The total calcium current is reduced to 41% in a cell line expressing a nontrafficking BIN1 mutant. In mouse cardiomyocytes, BIN1 knockdown decreases surface Cav1.2 and impairs calcium transients. In zebrafish hearts, BIN1 knockdown causes a 75% reduction in calcium transients and severe ventricular contractile dysfunction. The data indicate that BIN1 is significantly reduced in human heart failure, and this reduction impairs Cav1.2 trafficking, calcium transients, and contractility. Copyright © 2012 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

BIN1 is Reduced and Cav1.2 Trafficking is Impaired in Human Failing Cardiomyocytes

PubMed Central

Hong, Ting-Ting; Smyth, James W.; Chu, Kevin Y.; Vogan, Jacob M.; Fong, Tina S.; Jensen, Brian C.; Fang, Kun; Halushka, Marc K.; Russell, Stuart D.; Colecraft, Henry; Hoopes, Charles W.; Ocorr, Karen; Chi, Neil C.; Shaw, Robin M.

2011-01-01

Background Heart failure is a growing epidemic and a typical aspect of heart failure pathophysiology is altered calcium transients. Normal cardiac calcium transients are initiated by Cav1.2 channels at cardiac T-tubules. BIN1 is a membrane scaffolding protein that causes Cav1.2 to traffic to T-tubules in healthy hearts. The mechanisms of Cav1.2 trafficking in heart failure are not known. Objective To study BIN1 expression and its effect on Cav1.2 trafficking in failing hearts. Methods Intact myocardium and freshly isolated cardiomyocytes from non-failing and end-stage failing human hearts were used to study BIN1 expression and Cav1.2 localization. To confirm Cav1.2 surface expression dependence on BIN1, patch clamp recordings were performed of Cav1.2 current in cell lines with and without trafficking competent BIN1. Also, in adult mouse cardiomyocytes, surface Cav1.2 and calcium transients were studied after shRNA mediated knockdown of BIN1. For a functional readout in intact heart, calcium transients and cardiac contractility were analyzed in a zebrafish model with morpholino mediated knockdown of BIN1. Results BIN1 expression is significantly decreased in failing cardiomyocytes at both mRNA (30% down) and protein (36% down) levels. Peripheral Cav1.2 is reduced 42% by imaging and biochemical T-tubule fraction of Cav1.2 is reduced 68%. Total calcium current is reduced 41% in a cell line expressing non-trafficking BIN1 mutant. In mouse cardiomyocytes, BIN1 knockdown decreases surface Cav1.2 and impairs calcium transients. In zebrafish hearts, BIN1 knockdown causes a 75% reduction in calcium transients and severe ventricular contractile dysfunction. Conclusions The data indicate that BIN1 is significantly reduced in human heart failure, and this reduction impairs Cav1.2 trafficking, calcium transients, and contractility. PMID:22138472

Mapping of herpes simplex virus-1 neurovirulence to. gamma. sub 1 34. 5, a gene nonessential for growth in culture

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

Chou, J.; Roizman, B.; Kern, E.R.

1990-11-30

The gene designated {gamma}{sub 1}34.5 maps in the inverted repeats flanking the long unique sequence of herpes simplex virus-1 (HSV-1) DNA, and therefore it is present in two copies per genome. This gene is not essential for viral growth in cell culture. Four recombinant viruses were genetically engineered to test the function of this gene. These were (i) a virus from which both copies of the gene were deleted, (ii) a virus containing a stop codon in both copies of the gene, (iii) a virus containing after the first codon an insert encoding a 16-amino acid epitope known to reactmore » with a specific monoclonal antibody, and (iv) a virus in which the deleted sequences were restored. The viruses from which the gene was deleted or which carried stop codons were avirulent on intracerebral inoculation of mice. The virus with the gene tagged by the sequence encoding the epitope was moderately virulent, whereas the restored virus reacquired the phenotype of the parent virus. Significant amounts of virus were recovered only from brains of animals inoculated with virulent viruses. Inasmuch as the product of the {gamma}{sub 1}34.5 gene extended the host range of the virus by enabling it to replicate and destroy brain cells, it is a viral neurovirulence factor.« less

15. NORTH ELEVATION OF UPPER ORE BIN, CHUTE, AND JAW ...

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

15. NORTH ELEVATION OF UPPER ORE BIN, CHUTE, AND JAW CRUSHER, LOOKING SOUTH FROM END OF CONVEYOR PLATFORM. NOTICE THE THREE ORE BIN CONTROL DOORS, CORRESPONDING TO SEPARATE COMPARTMENTS OF THE BIN. - Skidoo Mine, Park Route 38 (Skidoo Road), Death Valley Junction, Inyo County, CA

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

PubMed Central

Kiefer, Christina; Fehlmann, Tobias; Backes, Christina

2017-01-01

Abstract Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02–95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee. PMID:28472498

Characteristic face: a key indicator for direct diagnosis of 22q11.2 deletions in Chinese velocardiofacial syndrome patients.

PubMed

Wu, Dandan; Chen, Yang; Xu, Chen; Wang, Ke; Wang, Huijun; Zheng, Fengyun; Ma, Duan; Wang, Guomin

2013-01-01

Velocardiofacial syndrome (VCFS) is a disease in human with an expansive phenotypic spectrum and diverse genetic mechanisms mainly associated with copy number variations (CNVs) on 22q11.2 or other chromosomes. However, the correlations between CNVs and phenotypes remain ambiguous. This study aims to analyze the types and sizes of CNVs in VCFS patients, to define whether correlations exist between CNVs and clinical manifestations in Chinese VCFS patients. In total, 55 clinically suspected Chinese VCFS patients and 100 normal controls were detected by multiplex ligation-dependent probe amplification (MLPA). The data from MLPA and all the detailed clinical features of the objects were documented and analyzed. A total of 44 patients (80.0%) were diagnosed with CNVs on 22q11.2. Among them, 43 (78.2%) presented with 22q11.2 heterozygous deletions, of whom 40 (93.0%) had typical 3-Mb deletion, and 3 (7.0%) exhibited proximal 1.5-Mb deletion; no patient was found with atypical deletion on 22q11.2. One patient (1.8%) presented with a 3-Mb duplication mapping to the typical 3-Mb region on 22q11.2, while none of the chromosomal abnormalities in the MLPA kit were found in the other 11 patients and 100 normal controls. All the 43 patients with 22q11.2 deletions displayed characteristic face and palatal anomalies; 37 of them (86.0%) had cognitive or behavioral disorders, and 23 (53.5%) suffered from immune deficiencies; 10 patients (23.3%) manifested congenital heart diseases. Interestingly, all patients with the characteristic face had 22q11.2 heterozygous deletions, but no difference in phenotypic spectrum was observed between 3-Mb and 1.5-Mb deletions. Our data suggest that the characteristic face can be used as a key indicator for direct diagnosis of 22q11.2 deletions in Chinese VCFS patients.

Investigation of recurrent deletion loci specific to conventional renal cell carcinoma by comparative allelotyping in major epithelial carcinomas

PubMed Central

Bhat (Singh), Rashmi R.; Amare (Kadam), Pratibha S.

2012-01-01

Objective: Loss of heterozygosity (LOH) studies were undertaken to investigate the consistently deleted loci/? tumor suppressor gene loci (TSG) on 3p in conventional renal cell carcinoma (cRCC). Materials and Methods: LOH studies were performed by polymerase chain reaction (PCR) using 15 micro satellite markers mapped in region 3p12-p26 on 40 paired cRCC tumors and normal kidney at Stages I-IV. Simultaneously, fluorescent in-situ hybridization (FISH) studies were performed to investigate the allelic deletion of fragile histidine triad (FHIT). Results: Our studies revealed three affected regions; 3p12.2-p14.1, 3p14.2-p21.1, and 3p24.2-p26.1 with differential frequencies in Group I (Stage I and II) and Group II (Stage III and IV). Incidence for D3S1234 (FHIT locus) and D3S2454 (3p13) was 75% and 83% in Group I and II, respectively. Comparative allelotyping in epithelial malignancies like lung, bladder, and breast tumors revealed LOH (frequency 14–20%) only in breast tumors for D3S2406, D3S1766 (distal to FHIT), and D3S1560 (distal to VHL, Von-Hippal Lindau). FISH using FHIT gene probe revealed deletions in cRCC (88%), breast (30%), and lung tumors (10%) with no deletions in bladder tumors and leukemias, signifying the importance of FHIT in the pathogenesis of tumors of epithelial origin. Conclusion: Our findings suggested FHIT deletion as an early and VHL deletion as an early and/or late event in cRCC. Additionally, studies also disclosed the recurrent deletions of flanking loci to FHIT and VHL in cRCC. The dilemma of interstitial or continuous deletion on 3p needs to be resolved by implementation of latest sensitive molecular techniques that would further help to narrow down search for TSG loci specific to cRCC, other than VHL and FHIT. PMID:22557717

Investigation of recurrent deletion loci specific to conventional renal cell carcinoma by comparative allelotyping in major epithelial carcinomas.

PubMed

Bhat Singh, Rashmi R; Amare Kadam, Pratibha S

2012-01-01

Loss of heterozygosity (LOH) studies were undertaken to investigate the consistently deleted loci/? tumor suppressor gene loci (TSG) on 3p in conventional renal cell carcinoma (cRCC). LOH studies were performed by polymerase chain reaction (PCR) using 15 micro satellite markers mapped in region 3p12-p26 on 40 paired cRCC tumors and normal kidney at Stages I-IV. Simultaneously, fluorescent in-situ hybridization (FISH) studies were performed to investigate the allelic deletion of fragile histidine triad (FHIT). Our studies revealed three affected regions; 3p12.2-p14.1, 3p14.2-p21.1, and 3p24.2-p26.1 with differential frequencies in Group I (Stage I and II) and Group II (Stage III and IV). Incidence for D3S1234 (FHIT locus) and D3S2454 (3p13) was 75% and 83% in Group I and II, respectively. Comparative allelotyping in epithelial malignancies like lung, bladder, and breast tumors revealed LOH (frequency 14-20%) only in breast tumors for D3S2406, D3S1766 (distal to FHIT), and D3S1560 (distal to VHL, Von-Hippal Lindau). FISH using FHIT gene probe revealed deletions in cRCC (88%), breast (30%), and lung tumors (10%) with no deletions in bladder tumors and leukemias, signifying the importance of FHIT in the pathogenesis of tumors of epithelial origin. Our findings suggested FHIT deletion as an early and VHL deletion as an early and/or late event in cRCC. Additionally, studies also disclosed the recurrent deletions of flanking loci to FHIT and VHL in cRCC. The dilemma of interstitial or continuous deletion on 3p needs to be resolved by implementation of latest sensitive molecular techniques that would further help to narrow down search for TSG loci specific to cRCC, other than VHL and FHIT.

Validation of consensus quantitative trait loci associated with resistance to multiple foliar pathogens of maize.

PubMed

Asea, Godfrey; Vivek, Bindiganavile S; Bigirwa, George; Lipps, Patrick E; Pratt, Richard C

2009-05-01

Maize production in sub-Saharan Africa incurs serious losses to epiphytotics of foliar diseases. Quantitative trait loci conditioning partial resistance (rQTL) to infection by causal agents of gray leaf spot (GLS), northern corn leaf blight (NCLB), and maize streak have been reported. Our objectives were to identify simple-sequence repeat (SSR) molecular markers linked to consensus rQTL and one recently identified rQTL associated with GLS, and to determine their suitability as tools for selection of improved host resistance. We conducted evaluations of disease severity phenotypes in separate field nurseries, each containing 410 F2:3 families derived from a cross between maize inbred CML202 (NCLB and maize streak resistant) and VP31 (a GLS-resistant breeding line) that possess complimentary rQTL. F2:3 families were selected for resistance based on genotypic (SSR marker), phenotypic, or combined data and the selected F3:4 families were reevaluated. Phenotypic values associated with SSR markers for consensus rQTL in bins 4.08 for GLS, 5.04 for NCLB, and 1.04 for maize streak significantly reduced disease severity in both generations based on single-factor analysis of variance and marker-interval analysis. These results were consistent with the presence of homozygous resistant parent alleles, except in bin 8.06, where markers were contributed by the NCLB-susceptible parent. Only one marker associated with resistance could be confirmed in bins 2.09 (GLS) and 3.06 (NCLB), illustrating the need for more robust rQTL discovery, fine-mapping, and validation prior to undertaking marker-based selection.

Environmental diversity as a surrogate for species representation.

PubMed

Beier, Paul; de Albuquerque, Fábio Suzart

2015-10-01

Because many species have not been described and most species ranges have not been mapped, conservation planners often use surrogates for conservation planning, but evidence for surrogate effectiveness is weak. Surrogates are well-mapped features such as soil types, landforms, occurrences of an easily observed taxon (discrete surrogates), and well-mapped environmental conditions (continuous surrogate). In the context of reserve selection, the idea is that a set of sites selected to span diversity in the surrogate will efficiently represent most species. Environmental diversity (ED) is a rarely used surrogate that selects sites to efficiently span multivariate ordination space. Because it selects across continuous environmental space, ED should perform better than discrete surrogates (which necessarily ignore within-bin and between-bin heterogeneity). Despite this theoretical advantage, ED appears to have performed poorly in previous tests of its ability to identify 50 × 50 km cells that represented vertebrates in Western Europe. Using an improved implementation of ED, we retested ED on Western European birds, mammals, reptiles, amphibians, and combined terrestrial vertebrates. We also tested ED on data sets for plants of Zimbabwe, birds of Spain, and birds of Arizona (United States). Sites selected using ED represented European mammals no better than randomly selected cells, but they represented species in the other 7 data sets with 20% to 84% effectiveness. This far exceeds the performance in previous tests of ED, and exceeds the performance of most discrete surrogates. We believe ED performed poorly in previous tests because those tests considered only a few candidate explanatory variables and used suboptimal forms of ED's selection algorithm. We suggest future work on ED focus on analyses at finer grain sizes more relevant to conservation decisions, explore the effect of selecting the explanatory variables most associated with species turnover, and investigate whether nonclimate abiotic variables can provide useful surrogates in an ED framework. © 2015 Society for Conservation Biology.

Assessment of dosimetric impact of system specific geometric distortion in an MRI only based radiotherapy workflow for prostate

NASA Astrophysics Data System (ADS)

Gustafsson, C.; Nordström, F.; Persson, E.; Brynolfsson, J.; Olsson, L. E.

2017-04-01

Dosimetric errors in a magnetic resonance imaging (MRI) only radiotherapy workflow may be caused by system specific geometric distortion from MRI. The aim of this study was to evaluate the impact on planned dose distribution and delineated structures for prostate patients, originating from this distortion. A method was developed, in which computer tomography (CT) images were distorted using the MRI distortion field. The displacement map for an optimized MRI treatment planning sequence was measured using a dedicated phantom in a 3 T MRI system. To simulate the distortion aspects of a synthetic CT (electron density derived from MR images), the displacement map was applied to CT images, referred to as distorted CT images. A volumetric modulated arc prostate treatment plan was applied to the original CT and the distorted CT, creating a reference and a distorted CT dose distribution. By applying the inverse of the displacement map to the distorted CT dose distribution, a dose distribution in the same geometry as the original CT images was created. For 10 prostate cancer patients, the dose difference between the reference dose distribution and inverse distorted CT dose distribution was analyzed in isodose level bins. The mean magnitude of the geometric distortion was 1.97 mm for the radial distance of 200-250 mm from isocenter. The mean percentage dose differences for all isodose level bins, were  ⩽0.02% and the radiotherapy structure mean volume deviations were  <0.2%. The method developed can quantify the dosimetric effects of MRI system specific distortion in a prostate MRI only radiotherapy workflow, separated from dosimetric effects originating from synthetic CT generation. No clinically relevant dose difference or structure deformation was found when 3D distortion correction and high acquisition bandwidth was used. The method could be used for any MRI sequence together with any anatomy of interest.

Assessment of dosimetric impact of system specific geometric distortion in an MRI only based radiotherapy workflow for prostate.

PubMed

Gustafsson, C; Nordström, F; Persson, E; Brynolfsson, J; Olsson, L E

2017-04-21

Dosimetric errors in a magnetic resonance imaging (MRI) only radiotherapy workflow may be caused by system specific geometric distortion from MRI. The aim of this study was to evaluate the impact on planned dose distribution and delineated structures for prostate patients, originating from this distortion. A method was developed, in which computer tomography (CT) images were distorted using the MRI distortion field. The displacement map for an optimized MRI treatment planning sequence was measured using a dedicated phantom in a 3 T MRI system. To simulate the distortion aspects of a synthetic CT (electron density derived from MR images), the displacement map was applied to CT images, referred to as distorted CT images. A volumetric modulated arc prostate treatment plan was applied to the original CT and the distorted CT, creating a reference and a distorted CT dose distribution. By applying the inverse of the displacement map to the distorted CT dose distribution, a dose distribution in the same geometry as the original CT images was created. For 10 prostate cancer patients, the dose difference between the reference dose distribution and inverse distorted CT dose distribution was analyzed in isodose level bins. The mean magnitude of the geometric distortion was 1.97 mm for the radial distance of 200-250 mm from isocenter. The mean percentage dose differences for all isodose level bins, were  ⩽0.02% and the radiotherapy structure mean volume deviations were  <0.2%. The method developed can quantify the dosimetric effects of MRI system specific distortion in a prostate MRI only radiotherapy workflow, separated from dosimetric effects originating from synthetic CT generation. No clinically relevant dose difference or structure deformation was found when 3D distortion correction and high acquisition bandwidth was used. The method could be used for any MRI sequence together with any anatomy of interest.

A roadmap for functional structural variants in the soybean genome

USDA-ARS?s Scientific Manuscript database

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean accessions serving as parents in a soybean nested association mapping population for deletions and duplications in over 53...

Adenovirus sequences required for replication in vivo.

PubMed Central

Wang, K; Pearson, G D

1985-01-01

We have studied the in vivo replication properties of plasmids carrying deletion mutations within cloned adenovirus terminal sequences. Deletion mapping located the adenovirus DNA replication origin entirely within the first 67 bp of the adenovirus inverted terminal repeat. This region could be further subdivided into two functional domains: a minimal replication origin and an adjacent auxillary region which boosted the efficiency of replication by more than 100-fold. The minimal origin occupies the first 18 to 21 bp and includes sequences conserved between all adenovirus serotypes. The adjacent auxillary region extends past nucleotide 36 but not past nucleotide 67 and contains the binding site for nuclear factor I. Images PMID:2991857

The Voronoi spatio-temporal data structure

NASA Astrophysics Data System (ADS)

Mioc, Darka

2002-04-01

Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal information. This formal model of spatio-temporal change representation is currently applied to retroactive map updates and visualization of map evolution. It offers new possibilities in the domains of temporal GIS, transaction processing, spatio-temporal queries, spatio-temporal analysis, map animation and map visualization.

Global Mapping of the Yeast Genetic Interaction Network

NASA Astrophysics Data System (ADS)

Tong, Amy Hin Yan; Lesage, Guillaume; Bader, Gary D.; Ding, Huiming; Xu, Hong; Xin, Xiaofeng; Young, James; Berriz, Gabriel F.; Brost, Renee L.; Chang, Michael; Chen, YiQun; Cheng, Xin; Chua, Gordon; Friesen, Helena; Goldberg, Debra S.; Haynes, Jennifer; Humphries, Christine; He, Grace; Hussein, Shamiza; Ke, Lizhu; Krogan, Nevan; Li, Zhijian; Levinson, Joshua N.; Lu, Hong; Ménard, Patrice; Munyana, Christella; Parsons, Ainslie B.; Ryan, Owen; Tonikian, Raffi; Roberts, Tania; Sdicu, Anne-Marie; Shapiro, Jesse; Sheikh, Bilal; Suter, Bernhard; Wong, Sharyl L.; Zhang, Lan V.; Zhu, Hongwei; Burd, Christopher G.; Munro, Sean; Sander, Chris; Rine, Jasper; Greenblatt, Jack; Peter, Matthias; Bretscher, Anthony; Bell, Graham; Roth, Frederick P.; Brown, Grant W.; Andrews, Brenda; Bussey, Howard; Boone, Charles

2004-02-01

A genetic interaction network containing ~1000 genes and ~4000 interactions was mapped by crossing mutations in 132 different query genes into a set of ~4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

A Measurement of the Galaxy Group-Thermal Sunyaev-Zel’dovich Effect Cross-Correlation Function

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

Vikram, Vinu; Lidz, Adam; Jain, Bhuvnesh

2017-01-09

Stacking cosmic microwave background maps around known galaxy clusters and groups provides a powerful probe of the distribution of hot gas in these systems via the Sunyaev-Zel'dovich (SZ) effect. A stacking analysis allows one to detect the average SZ signal around low-mass haloes, to extend measurements out to large scales and measure the redshift dependence of the SZ background. Motivated by these exciting prospects, we measure the two-point cross-correlation function between similar to 380 000 galaxy groups (at z = 0.01-0.2) from the Sloan Digital Sky Survey and Compton-y parameter maps constructed by the Planck collaboration. We find statistically significantmore » correlations in each of six separate mass bins, with halo masses ranging from 1011.5 to 1015.5 M(circle dot)h(-1). We compare with halo models of the SZ signal, which describe the stacked measurement in terms of one-halo and two-halo contributions. The onehalo term quantifies the average pressure profile around the groups in a mass bin, while the two-halo term describes the contribution of correlated neighbouring haloes. For the massive groups, we find clear evidence for the one-and two-halo regimes, while groups with mass below 1013M(circle dot)h(-1) are dominated by the two-halo term, given the resolution of Planck data. We use the signal in the two-halo regime to determine the bias-weighted electron pressure of the Universe: < bPe > = 1.50 +/- 0.226 x 10(-7) keV cm(-3) (sigma) at z approximate to 0.15.« less

A Measurement of the Galaxy Group-Thermal Sunyaev-Zel'dovich Effect Cross-Correlation Function

NASA Astrophysics Data System (ADS)

Vikram, Vinu; Lidz, Adam; Jain, Bhuvnesh

2017-05-01

Stacking cosmic microwave background maps around known galaxy clusters and groups provides a powerful probe of the distribution of hot gas in these systems via the Sunyaev-Zel'dovich (SZ) effect. A stacking analysis allows one to detect the average SZ signal around low-mass haloes, to extend measurements out to large scales and measure the redshift dependence of the SZ background. Motivated by these exciting prospects, we measure the two-point cross-correlation function between ˜380 000 galaxy groups (at z = 0.01-0.2) from the Sloan Digital Sky Survey and Compton-y parameter maps constructed by the Planck collaboration. We find statistically significant correlations in each of six separate mass bins, with halo masses ranging from 1011.5 to 1015.5 M⊙ h-1. We compare with halo models of the SZ signal, which describe the stacked measurement in terms of one-halo and two-halo contributions. The one-halo term quantifies the average pressure profile around the groups in a mass bin, while the two-halo term describes the contribution of correlated neighbouring haloes. For the massive groups, we find clear evidence for the one- and two-halo regimes, while groups with mass below 1013 M⊙ h-1 are dominated by the two-halo term, given the resolution of Planck data. We use the signal in the two-halo regime to determine the bias-weighted electron pressure of the Universe: = 1.50 ± 0.226 × 10-7 keV cm-3 (1σ) at z ≈ 0.15.

Benefits of a 4th Ice Class in the Simulated Radar Reflectivities of Convective Systems Using a Bulk Microphysics Scheme

NASA Technical Reports Server (NTRS)

Lang, Stephen E.; Tao, Wei-Kuo; Chern, Jiun-Dar; Wu, Di; Li, Xiaowen

2015-01-01

Numerous cloud microphysical schemes designed for cloud and mesoscale models are currently in use, ranging from simple bulk to multi-moment, multi-class to explicit bin schemes. This study details the benefits of adding a 4th ice class (hail) to an already improved 3-class ice bulk microphysics scheme developed for the Goddard Cumulus Ensemble model based on Rutledge and Hobbs (1983,1984). Besides the addition and modification of several hail processes from Lin et al. (1983), further modifications were made to the 3-ice processes, including allowing greater ice super saturation and mitigating spurious evaporationsublimation in the saturation adjustment scheme, allowing graupelhail to become snow via vapor growth and hail to become graupel via riming, and the inclusion of a rain evaporation correction and vapor diffusivity factor. The improved 3-ice snowgraupel size-mapping schemes were adjusted to be more stable at higher mixing rations and to increase the aggregation effect for snow. A snow density mapping was also added. The new scheme was applied to an intense continental squall line and a weaker, loosely-organized continental case using three different hail intercepts. Peak simulated reflectivities agree well with radar for both the intense and weaker case and were better than earlier 3-ice versions when using a moderate and large intercept for hail, respectively. Simulated reflectivity distributions versus height were also improved versus radar in both cases compared to earlier 3-ice versions. The bin-based rain evaporation correction affected the squall line case more but did not change the overall agreement in reflectivity distributions.

Web-based CERES Clouds QC Property Viewing Tool

NASA Astrophysics Data System (ADS)

Smith, R. A.

2015-12-01

Churngwei Chu1, Rita Smith1, Sunny Sun-Mack1, Yan Chen1, Elizabeth Heckert1, Patrick Minnis21 Science Systems and Applications, Inc., Hampton, Virginia2 NASA Langley Research Center, Hampton, Virginia This presentation will display the capabilities of a web-based CERES cloud property viewer. Aqua/Terra/NPP data will be chosen for examples. It will demonstrate viewing of cloud properties in gridded global maps, histograms, time series displays, latitudinal zonal images, binned data charts, data frequency graphs, and ISCCP plots. Images can be manipulated by the user to narrow boundaries of the map as well as color bars and value ranges, compare datasets, view data values, and more. Other atmospheric studies groups will be encouraged to put their data into the underlying NetCDF data format and view their data with the tool.

30 CFR 57.16002 - Bins, hoppers, silos, tanks, and surge piles.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Bins, hoppers, silos, tanks, and surge piles... NONMETAL MINES Materials Storage and Handling § 57.16002 Bins, hoppers, silos, tanks, and surge piles. (a) Bins, hoppers, silos, tanks, and surge piles, where loose unconsolidated materials are stored, handled...

30 CFR 56.16002 - Bins, hoppers, silos, tanks, and surge piles.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Bins, hoppers, silos, tanks, and surge piles... MINES Materials Storage and Handling § 56.16002 Bins, hoppers, silos, tanks, and surge piles. (a) Bins, hoppers, silos, tanks, and surge piles, where loose unconsolidated materials are stored, handled or...

Pack Factor Measurementss for Corn in Grain Storage Bins

USDA-ARS?s Scientific Manuscript database

Grain is commonly stored commercially in tall bins, which often are as deep as 35 m (114.8 ft) for tall and narrow concrete bins and about 32 m (105 ft) in diameter for large corrugated steel bins. Grain can support the great pressure without crushing, but it yields somewhat to compaction under its ...

19. VIEW OF CRUDE ORE BINS FROM EAST. EAST CRUDE ...

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

19. VIEW OF CRUDE ORE BINS FROM EAST. EAST CRUDE ORE BIN IN FOREGROUND WITH DISCHARGE TO GRIZZLY AT BOTTOM OF VIEW. CONCRETE RETAINING WALL TO LEFT (SOUTH) AND BOTTOM (EAST EDGE OF EAST BIN). - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Radio Frequency Identification (RFID) and communication technologies for solid waste bin and truck monitoring system.

PubMed

Hannan, M A; Arebey, Maher; Begum, R A; Basri, Hassan

2011-12-01

This paper deals with a system of integration of Radio Frequency Identification (RFID) and communication technologies for solid waste bin and truck monitoring system. RFID, GPS, GPRS and GIS along with camera technologies have been integrated and developed the bin and truck intelligent monitoring system. A new kind of integrated theoretical framework, hardware architecture and interface algorithm has been introduced between the technologies for the successful implementation of the proposed system. In this system, bin and truck database have been developed such a way that the information of bin and truck ID, date and time of waste collection, bin status, amount of waste and bin and truck GPS coordinates etc. are complied and stored for monitoring and management activities. The results showed that the real-time image processing, histogram analysis, waste estimation and other bin information have been displayed in the GUI of the monitoring system. The real-time test and experimental results showed that the performance of the developed system was stable and satisfied the monitoring system with high practicability and validity. Copyright © 2011 Elsevier Ltd. All rights reserved.

MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects.

PubMed

Wang, Ying; Hu, Haiyan; Li, Xiaoman

2016-08-01

Metagenomics is a next-generation omics field currently impacting postgenomic life sciences and medicine. Binning metagenomic reads is essential for the understanding of microbial function, compositions, and interactions in given environments. Despite the existence of dozens of computational methods for metagenomic read binning, it is still very challenging to bin reads. This is especially true for reads from unknown species, from species with similar abundance, and/or from low-abundance species in environmental samples. In this study, we developed a novel taxonomy-dependent and alignment-free approach called MBMC (Metagenomic Binning by Markov Chains). Different from all existing methods, MBMC bins reads by measuring the similarity of reads to the trained Markov chains for different taxa instead of directly comparing reads with known genomic sequences. By testing on more than 24 simulated and experimental datasets with species of similar abundance, species of low abundance, and/or unknown species, we report here that MBMC reliably grouped reads from different species into separate bins. Compared with four existing approaches, we demonstrated that the performance of MBMC was comparable with existing approaches when binning reads from sequenced species, and superior to existing approaches when binning reads from unknown species. MBMC is a pivotal tool for binning metagenomic reads in the current era of Big Data and postgenomic integrative biology. The MBMC software can be freely downloaded at http://hulab.ucf.edu/research/projects/metagenomics/MBMC.html .

Bin-Hash Indexing: A Parallel Method for Fast Query Processing

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

Bethel, Edward W; Gosink, Luke J.; Wu, Kesheng

2008-06-27

This paper presents a new parallel indexing data structure for answering queries. The index, called Bin-Hash, offers extremely high levels of concurrency, and is therefore well-suited for the emerging commodity of parallel processors, such as multi-cores, cell processors, and general purpose graphics processing units (GPU). The Bin-Hash approach first bins the base data, and then partitions and separately stores the values in each bin as a perfect spatial hash table. To answer a query, we first determine whether or not a record satisfies the query conditions based on the bin boundaries. For the bins with records that can not bemore » resolved, we examine the spatial hash tables. The procedures for examining the bin numbers and the spatial hash tables offer the maximum possible level of concurrency; all records are able to be evaluated by our procedure independently in parallel. Additionally, our Bin-Hash procedures access much smaller amounts of data than similar parallel methods, such as the projection index. This smaller data footprint is critical for certain parallel processors, like GPUs, where memory resources are limited. To demonstrate the effectiveness of Bin-Hash, we implement it on a GPU using the data-parallel programming language CUDA. The concurrency offered by the Bin-Hash index allows us to fully utilize the GPU's massive parallelism in our work; over 12,000 records can be simultaneously evaluated at any one time. We show that our new query processing method is an order of magnitude faster than current state-of-the-art CPU-based indexing technologies. Additionally, we compare our performance to existing GPU-based projection index strategies.« less

SU-F-J-135: Tumor Displacement-Based Binning for Respiratory-Gated Time-Independent 5DCT Treatment Planning

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

Yang, L; O’Connell, D; Lee, P

2016-06-15

Purpose: A published 5DCT breathing motion model enables image reconstruction at any user-selected breathing phase, defined by the model as a specific amplitude (v) and rate (f). Generation of reconstructed phase-specific CT scans will be required for time-independent radiation dose distribution simulations. This work answers the question: how many amplitude and rate bins are required to describe the tumor motion with a specific spatial resolution? Methods: 19 lung-cancer patients with 21 tumors were scanned using a free-breathing 5DCT protocol, employing an abdominally positioned pneumatic-bellows breathing surrogate and yielding voxel-specific motion model parameters α and β corresponding to motion as amore » function of amplitude and rate, respectively. Tumor GTVs were contoured on the first (reference) of 25 successive free-breathing fast helical CT image sets. The tumor displacements were binned into widths of 1mm to 5mm in 1mm steps and the total required number of bins recorded. The simulation evaluated the number of bins needed to encompass 100% of the breathing-amplitude and between the 5th and 95th percentile amplitudes to exclude breathing outliers. Results: The mean respiration-induced tumor motion was 9.90mm ± 7.86mm with a maximum of 25mm. The number of bins required was a strong function of the spatial resolution and varied widely between patients. For example, for 2mm bins, between 1–13 amplitude bins and 1–9 rate bins were required to encompass 100% of the breathing amplitude, while 1–6 amplitude bins and 1–3 rate bins were required to encompass 90% of the breathing amplitude. Conclusion: The strong relationship between number of bins and spatial resolution as well as the large variation between patients implies that time-independent radiation dose distribution simulations should be conducted using patient-specific data and that the breathing conditions will have to be carefully considered. This work will lead to the assessment of the dosimetric impact of binning resolution. This study is supported by Siemens Healthcare.« less

Data-driven optimal binning for respiratory motion management in PET.

PubMed

Kesner, Adam L; Meier, Joseph G; Burckhardt, Darrell D; Schwartz, Jazmin; Lynch, David A

2018-01-01

Respiratory gating has been used in PET imaging to reduce the amount of image blurring caused by patient motion. Optimal binning is an approach for using the motion-characterized data by binning it into a single, easy to understand/use, optimal bin. To date, optimal binning protocols have utilized externally driven motion characterization strategies that have been tuned with population-derived assumptions and parameters. In this work, we are proposing a new strategy with which to characterize motion directly from a patient's gated scan, and use that signal to create a patient/instance-specific optimal bin image. Two hundred and nineteen phase-gated FDG PET scans, acquired using data-driven gating as described previously, were used as the input for this study. For each scan, a phase-amplitude motion characterization was generated and normalized using principle component analysis. A patient-specific "optimal bin" window was derived using this characterization, via methods that mirror traditional optimal window binning strategies. The resulting optimal bin images were validated by correlating quantitative and qualitative measurements in the population of PET scans. In 53% (n = 115) of the image population, the optimal bin was determined to include 100% of the image statistics. In the remaining images, the optimal binning windows averaged 60% of the statistics and ranged between 20% and 90%. Tuning the algorithm, through a single acceptance window parameter, allowed for adjustments of the algorithm's performance in the population toward conservation of motion or reduced noise-enabling users to incorporate their definition of optimal. In the population of images that were deemed appropriate for segregation, average lesion SUV max were 7.9, 8.5, and 9.0 for nongated images, optimal bin, and gated images, respectively. The Pearson correlation of FWHM measurements between optimal bin images and gated images were better than with nongated images, 0.89 and 0.85, respectively. Generally, optimal bin images had better resolution than the nongated images and better noise characteristics than the gated images. We extended the concept of optimal binning to a data-driven form, updating a traditionally one-size-fits-all approach to a conformal one that supports adaptive imaging. This automated strategy was implemented easily within a large population and encapsulated motion information in an easy to use 3D image. Its simplicity and practicality may make this, or similar approaches ideal for use in clinical settings. © 2017 American Association of Physicists in Medicine.

Deletion of tumor progression locus 2 attenuates alcohol induced hepatic inflammation

USDA-ARS?s Scientific Manuscript database

BACKGROUND: The pathogenesis of alcoholic liver disease (ALD) involves the interaction of several inflammatory signaling pathways. Tumor progression locus 2 (TPL2), also known as Cancer Osaka Thyroid (COT) and MAP3K8, is a serine threonine kinase that functions as a critical regulator of inflammator...

Construction of a YAC contig and STS map spanning 2.5 Mbp in Xq25, the critical region for the X-linked lymphoproliferative (XLP) gene

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

Lanyi, A.; Li, B.F.; Li, S.

1994-09-01

X-linked lymphoproliferative disease (XLP) is characterized by a marked vulnerability in Epstein-Barr virus (EBV) infection. Infection of XLP patients with EBV invariably results in fatal mononucleosis, agammaglobulinemia or B-cell lymphoma. The XLP gene lies within a 10 cM region in Xq25 between DXS42 and DXS10. Initial chromosome studies revealed an interstitial, cytogenetically visible deletion in Xq25 in one XLP family (43-004). We estimated the size of the Xq25 deletion by dual laser flow karyotyping to involve 2% of the X chromosome, or approximately 3 Mbp of DNA sequences. To further delineate the deletion we performed a series of pulsed fieldmore » gel electrophoresis (PFGE) analyses which showed that DXS6 and DXS100, two Xq25-specific markers, are missing from 45-004 DNA. Five yeast artificial chromosomes (YACs) from a chromosome X specific YAC library containing sequences deleted in patient`s 43-004 DNA were isolated. These five YACs did not overlap, and their end fragments were used to screen the CEPH MegaYAC library. Seven YACs were isolated from the CEPH MegaYAC library. They could be arranged into a contig which spans between DXS6 and DXS100. The contig contains a minimum of 2.5 Mbp of human DNA. A total of 12 YAC end clone, lambda subclones and STS probes have been used to order clones within the contig. These reagents were also used in Southern blot and patients showed interstitial deletions in Xq25. The size of these deletions range between 0.5 and 2.5 Mbp. The shortest deletion probably represents the critical region for the XLP gene.« less

Chromosomal microarray testing identifies a 4p terminal region associated with seizures in Wolf-Hirschhorn syndrome.

PubMed

Ho, Karen S; South, Sarah T; Lortz, Amanda; Hensel, Charles H; Sdano, Mallory R; Vanzo, Rena J; Martin, Megan M; Peiffer, Andreas; Lambert, Christophe G; Calhoun, Amy; Carey, John C; Battaglia, Agatino

2016-04-01

Wolf-Hirschhorn syndrome (WHS) is a contiguous gene deletion syndrome involving variable size deletions of the 4p16.3 region. Seizures are frequently, but not always, associated with WHS. We hypothesised that the size and location of the deleted region may correlate with seizure presentation. Using chromosomal microarray analysis, we finely mapped the breakpoints of copy number variants (CNVs) in 48 individuals with WHS. Seizure phenotype data were collected through parent-reported answers to a comprehensive questionnaire and supplemented with available medical records. We observed a significant correlation between the presence of an interstitial 4p deletion and lack of a seizure phenotype (Fisher's exact test p=3.59e-6). In our cohort, there were five individuals with interstitial deletions with a distal breakpoint at least 751 kbp proximal to the 4p terminus. Four of these individuals have never had an observable seizure, and the fifth individual had a single febrile seizure at the age of 1.5 years. All other individuals in our cohort whose deletions encompass the terminal 751 kbp region report having seizures typical of WHS. Additional examples from the literature corroborate these observations and further refine the candidate seizure susceptibility region to a region 197 kbp in size, starting 368 kbp from the terminus of chromosome 4. We identify a small terminal region of chromosome 4p that represents a seizure susceptibility region. Deletion of this region in the context of WHS is sufficient for seizure occurrence. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

14 CFR 125.183 - Carriage of cargo in passenger compartments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... emergency landing conditions applicable to the passenger seats of the airplane in which the bin is installed... bin. (3) The bin may not impose any load on the floor or other structure of the airplane that exceeds the load limitations of that structure. (4) The bin must be attached to the seat tracks or to the...

18. VIEW OF CRUDE ORE BINS FROM WEST. WEST CRUDE ...

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

18. VIEW OF CRUDE ORE BINS FROM WEST. WEST CRUDE ORE BIN AND TRESTLE FROM TWO JOHNS TRAMLINE TO SOUTH, CRUDE ORE BIN IN FOREGROUND. MACHINE SHOP IN BACKGROUND. THE TRAM TO PORTLAND PASSED TO NORTH OF MACHINE SHOP. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

4. TROJAN MILL, DETAIL OF CRUDE ORE BINS FROM NORTH, ...

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

4. TROJAN MILL, DETAIL OF CRUDE ORE BINS FROM NORTH, c. 1912. SHOWS TIMBER FRAMING UNDER CONSTRUCTION FOR EAST AND WEST CRUDE ORE BINS AT PREVIOUS LOCATION OF CRUSHER HOUSE, AND SNOW SHED PRESENT OVER SOUTH CRUDE ORE BIN WITH PHASE CHANGE IN SNOW SHED CONSTRUCTION INDICATED AT EAST END OF EAST CRUDE ORE BIN. THIS PHOTOGRAPH IS THE FIRST IMAGE OF THE MACHINE SHOP, UPPER LEFT CORNER. CREDIT JW. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.

PubMed

Wang, Linhai; Xia, Qiuju; Zhang, Yanxin; Zhu, Xiaodong; Zhu, Xiaofeng; Li, Donghua; Ni, Xuemei; Gao, Yuan; Xiang, Haitao; Wei, Xin; Yu, Jingyin; Quan, Zhiwu; Zhang, Xiurong

2016-01-05

Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3-24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3-46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies.

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

PubMed Central

Heidelberg, John F.; Tully, Benjamin J.

2017-01-01

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes. PMID:28289564

9. 5TH FLOOR, INTERIOR DETAIL TO EAST OF SOAP BIN ...

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

9. 5TH FLOOR, INTERIOR DETAIL TO EAST OF SOAP BIN No. 4: UPPER SCREWS MOVED SOAP CHIPS HORIZONTALLY FROM BIN TO BIN; LOWER LEFT-AND RIGHT-HAND SCREWS MOVED CHIPS TO CHUTE LEADING TO 3RD FLOOR SOAP MILLS - Colgate & Company Jersey City Plant, Building No. B-14, 54-58 Grand Street, Jersey City, Hudson County, NJ

13. OBLIQUE VIEW OF UPPER ORE BIN, LOOKING WEST NORTHWEST. ...

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

13. OBLIQUE VIEW OF UPPER ORE BIN, LOOKING WEST NORTHWEST. THIS ORE BIN WAS ADDED IN THE LATE 1930'S. IT IS TRAPAZOIDAL IN SHAPE, WIDER AT THE REAR THAN THE FRONT, AND DIVIDED INTO THREE BINS, EACH WITH ITS OWN CONTROL DOOR (SEE CA-290-15). - Skidoo Mine, Park Route 38 (Skidoo Road), Death Valley Junction, Inyo County, CA

3. EAGLE MILL, DETAIL OF CRUDE ORE BIN FROM NORTH, ...

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

3. EAGLE MILL, DETAIL OF CRUDE ORE BIN FROM NORTH, c. 1908-10. SHOWS EXPOSED CRUSHER HOUSE IN FRONT OF (SOUTH) CRUDE ORE BIN AND SNOW SHED ADDED OVER TRAM TRACKS. NOTE LACK OF EAST OR WEST CRUDE ORE BINS. CREDIT JW. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Deletion of a 760 kb region at 4p16 determines the prenatal and postnatal growth retardation characteristic of Wolf-Hirschhorn syndrome.

PubMed

Concolino, Daniela; Rossi, Elena; Strisciuglio, Pietro; Iembo, Maria Antonietta; Giorda, Roberto; Ciccone, Roberto; Tenconi, Romano; Zuffardi, Orsetta

2007-10-01

Recently the genotype/phenotype map of Wolf-Hirschhorn syndrome (WHS) has been refined, using small 4p deletions covering or flanking the critical region in patients showing only some of the WHS malformations. Accordingly, prenatal-onset growth retardation and failure to thrive have been found to result from haploinsufficiency for a 4p gene located between 0.4 and 1.3 Mb, whereas microcephaly results from haploinsufficiency of at least two different 4p regions, one of 2.2-2.38 Mb and a second one of 1.9-1.28 Mb. We defined the deletion size of a ring chromosome (r(4)) in a girl with prenatal onset growth retardation, severe failure to thrive and true microcephaly but without the WHS facial gestalt and mental retardation. A high-resolution comparative genome hybridisation array revealed a 760 kb 4p terminal deletion. This case, together with a familial 4p deletion involving the distal 400 kb reported in normal women, may narrow the critical region for short stature on 4p to 360-760 kb. This region is also likely to contain a gene for microcephaly. "In silico" analysis of all genes within the critical region failed to reveal any strikingly suggestive expression pattern; all genes remain candidates for short stature and microcephaly.

Functional Studies and Homology Modeling of Msh2-Msh3 Predict that Mispair Recognition Involves DNA Bending and Strand Separation▿ †

PubMed Central

Dowen, Jill M.; Putnam, Christopher D.; Kolodner, Richard D.

2010-01-01

The Msh2-Msh3 heterodimer recognizes various DNA mispairs, including loops of DNA ranging from 1 to 14 nucleotides and some base-base mispairs. Homology modeling of the mispair-binding domain (MBD) of Msh3 using the related Msh6 MBD revealed that mismatch recognition must be different, even though the MBD folds must be similar. Model-based point mutation alleles of Saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. One class caused defects in repair of both small and large insertion/deletion mispairs, whereas the second class caused defects only in the repair of small insertion/deletion mispairs; mutations of the first class also caused defects in the removal of nonhomologous tails present at the ends of double-strand breaks (DSBs) during DSB repair, whereas mutations of the second class did not cause defects in the removal of nonhomologous tails during DSB repair. Thus, recognition of small insertion/deletion mispairs by Msh3 appears to require a greater degree of interactions with the DNA conformations induced by small insertion/deletion mispairs than with those induced by large insertion/deletions that are intrinsically bent and strand separated. Mapping of the two classes of mutations onto the Msh3 MBD model appears to distinguish mispair recognition regions from DNA stabilization regions. PMID:20421420

Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation.

PubMed

Dowen, Jill M; Putnam, Christopher D; Kolodner, Richard D

2010-07-01

The Msh2-Msh3 heterodimer recognizes various DNA mispairs, including loops of DNA ranging from 1 to 14 nucleotides and some base-base mispairs. Homology modeling of the mispair-binding domain (MBD) of Msh3 using the related Msh6 MBD revealed that mismatch recognition must be different, even though the MBD folds must be similar. Model-based point mutation alleles of Saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. One class caused defects in repair of both small and large insertion/deletion mispairs, whereas the second class caused defects only in the repair of small insertion/deletion mispairs; mutations of the first class also caused defects in the removal of nonhomologous tails present at the ends of double-strand breaks (DSBs) during DSB repair, whereas mutations of the second class did not cause defects in the removal of nonhomologous tails during DSB repair. Thus, recognition of small insertion/deletion mispairs by Msh3 appears to require a greater degree of interactions with the DNA conformations induced by small insertion/deletion mispairs than with those induced by large insertion/deletions that are intrinsically bent and strand separated. Mapping of the two classes of mutations onto the Msh3 MBD model appears to distinguish mispair recognition regions from DNA stabilization regions.

VizieR Online Data Catalog: Extinction map towards the Galactic bulge (Chen+, 2013)

NASA Astrophysics Data System (ADS)

Chen, B.; Schultheis, M.; Jiang, B.; Gonzalez, O. A.; Robin, A. C.; Rejkuba, M.; Minniti, D.

2012-11-01

We combine the observations with the Besancon model of the Galaxy to investigate the variations of extinction along different lines of sight towards the inner Galactic bulge as a function of distance. The full results are listed in Table 1 and Table 2. These results will be also added into the BEAM calculator webpage (http://mill.astro.puc.cl/BEAM/calculator.php). For each position we give the E(J-Ks), E(H-Ks) as well as the corresponding sigma for each distance bin starting from 1 to 10kpc. (2 data files).

Loss of Bin1 Promotes the Propagation of Tau Pathology.

PubMed

Calafate, Sara; Flavin, William; Verstreken, Patrik; Moechars, Diederik

2016-10-18

Tau pathology propagates within synaptically connected neuronal circuits, but the underlying mechanisms are unclear. BIN1-amphiphysin2 is the second most prevalent genetic risk factor for late-onset Alzheimer's disease. In diseased brains, the BIN1-amphiphysin2 neuronal isoform is downregulated. Here, we show that lowering BIN1-amphiphysin2 levels in neurons promotes Tau pathology propagation whereas overexpression of neuronal BIN1-amphiphysin2 inhibits the process in two in vitro models. Increased Tau propagation is caused by increased endocytosis, given our finding that BIN1-amphiphysin2 negatively regulates endocytic flux. Furthermore, blocking endocytosis by inhibiting dynamin also reduces Tau pathology propagation. Using a galectin-3-binding assay, we show that internalized Tau aggregates damage the endosomal membrane, allowing internalized aggregates to leak into the cytoplasm to propagate pathology. Our work indicates that lower BIN1 levels promote the propagation of Tau pathology by efficiently increasing aggregate internalization by endocytosis and endosomal trafficking. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Mosquito larvicide BinAB revealed by de novo phasing with an X-ray laser

PubMed Central

Colletier, Jacques-Philippe; Sawaya, Michael R.; Gingery, Mari; Rodriguez, Jose A.; Cascio, Duilio; Brewster, Aaron S.; Michels-Clark, Tara; Hice, Robert H.; Coquelle, Nicolas; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; DePonte, Daniel P.; Sierra, Raymond G.; Laksmono, Hartawan; Koglin, Jason E.; Hunter, Mark S.; Park, Hyun-Woo; Uervirojnangkoorn, Monarin; Bideshi, Dennis K.; Brunger, Axel T.; Federici, Brian A.; Sauter, Nicholas K.; Eisenberg, David S.

2016-01-01

Summary BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally toxic oligomeric pores. The small size of the crystals, 50 unit cells per edge, on average, has impeded structural characterization by conventional means. Here, we report the structure of BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser (XFEL). The structure reveals tyrosine and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation. PMID:27680699

On the Mathematical Consequences of Binning Spike Trains.

PubMed

Cessac, Bruno; Le Ny, Arnaud; Löcherbach, Eva

2017-01-01

We initiate a mathematical analysis of hidden effects induced by binning spike trains of neurons. Assuming that the original spike train has been generated by a discrete Markov process, we show that binning generates a stochastic process that is no longer Markov but is instead a variable-length Markov chain (VLMC) with unbounded memory. We also show that the law of the binned raster is a Gibbs measure in the DLR (Dobrushin-Lanford-Ruelle) sense coined in mathematical statistical mechanics. This allows the derivation of several important consequences on statistical properties of binned spike trains. In particular, we introduce the DLR framework as a natural setting to mathematically formalize anticipation, that is, to tell "how good" our nervous system is at making predictions. In a probabilistic sense, this corresponds to condition a process by its future, and we discuss how binning may affect our conclusions on this ability. We finally comment on the possible consequences of binning in the detection of spurious phase transitions or in the detection of incorrect evidence of criticality.

A molecular deletion of distal chromosome 4p in two families with a satellited chromosome 4 lacking the Wolf-Hirschhorn syndrome phenotype.

PubMed Central

Estabrooks, L L; Lamb, A N; Kirkman, H N; Callanan, N P; Rao, K W

1992-01-01

We report two families with a satellited chromosome 4 short arm (4ps). Satellites and stalks normally occur on the short arms of acrocentric chromosomes; however, the literature cites several reports of satellited nonacrocentric chromosomes, which presumably result from a translocation with an acrocentric chromosome. This is the first report of 4ps chromosomes. Our families are remarkable in that both unaffected and affected individuals carry the 4ps chromosome. The phenotypes observed in affected individuals, although dissimilar, were sufficient to encourage a search for a deletion of chromosome 4p. By Southern blot analysis and fluorescence in situ hybridization, a deletion of material mapping approximately 150 kb from chromosome 4pter was discovered. This deletion is notable because it does not result in the Wolf-Hirschhorn syndrome and can result in an apparently normal phenotype. We speculate that homology between subterminal repeat sequences on 4p and sequences on the acrocentric short arms may explain the origin of the rearrangement and that position effect may play a role in the expression of the abnormal phenotype. Images Figure 2 Figure 3 PMID:1384329

Deletion of ameloblastin exon 6 is associated with amelogenesis imperfecta

PubMed Central

Poulter, James A.; Murillo, Gina; Brookes, Steven J.; Smith, Claire E. L.; Parry, David A.; Silva, Sandra; Kirkham, Jennifer; Inglehearn, Chris F.; Mighell, Alan J.

2014-01-01

Amelogenesis imperfecta (AI) describes a heterogeneous group of inherited dental enamel defects reflecting failure of normal amelogenesis. Ameloblastin (AMBN) is the second most abundant enamel matrix protein expressed during amelogenesis. The pivotal role of AMBN in amelogenesis has been confirmed experimentally using mouse models. However, no AMBN mutations have been associated with human AI. Using autozygosity mapping and exome sequencing, we identified genomic deletion of AMBN exon 6 in a second cousin consanguineous family with three of the six children having hypoplastic AI. The genomic deletion corresponds to an in-frame deletion of 79 amino acids, shortening the protein from 447 to 368 residues. Exfoliated primary teeth (unmatched to genotype) were available from family members. The most severely affected had thin, aprismatic enamel (similar to that reported in mice homozygous for Ambn lacking exons 5 and 6). Other teeth exhibited thicker but largely aprismatic enamel. One tooth had apparently normal enamel. It has been suggested that AMBN may function in bone development. No clinically obvious bone or other co-segregating health problems were identified in the family investigated. This study confirms for the first time that AMBN mutations cause non-syndromic human AI and that mouse models with disrupted Ambn function are valid. PMID:24858907

A recessive contiguous gene deletion causing infantile hyperinsulinism, enteropathy and deafness identifies the Usher type 1C gene.

PubMed

Bitner-Glindzicz, M; Lindley, K J; Rutland, P; Blaydon, D; Smith, V V; Milla, P J; Hussain, K; Furth-Lavi, J; Cosgrove, K E; Shepherd, R M; Barnes, P D; O'Brien, R E; Farndon, P A; Sowden, J; Liu, X Z; Scanlan, M J; Malcolm, S; Dunne, M J; Aynsley-Green, A; Glaser, B

2000-09-01

Usher syndrome type 1 describes the association of profound, congenital sensorineural deafness, vestibular hypofunction and childhood onset retinitis pigmentosa. It is an autosomal recessive condition and is subdivided on the basis of linkage analysis into types 1A through 1E. Usher type 1C maps to the region containing the genes ABCC8 and KCNJ11 (encoding components of ATP-sensitive K + (KATP) channels), which may be mutated in patients with hyperinsulinism. We identified three individuals from two consanguineous families with severe hyperinsulinism, profound congenital sensorineural deafness, enteropathy and renal tubular dysfunction. The molecular basis of the disorder is a homozygous 122-kb deletion of 11p14-15, which includes part of ABCC8 and overlaps with the locus for Usher syndrome type 1C and DFNB18. The centromeric boundary of this deletion includes part of a gene shown to be mutated in families with type 1C Usher syndrome, and is hence assigned the name USH1C. The pattern of expression of the USH1C protein is consistent with the clinical features exhibited by individuals with the contiguous gene deletion and with isolated Usher type 1C.

Association of deletion in the chromosomal 8p21.3-23 region with the development of invasive head & neck squamous cell carcinoma in Indian patients.

PubMed

Bhattacharya, N; Tripathi, A; Dasgupta, S; Sabbir, Md G; Roy, A; Sengupta, A; Roy, B; Roychowdhury, S; Panda, C K

2003-08-01

Deletions in chromosome 8 (chr.8) have been shown to be necessary for the development of head and neck squamous cell carcinoma (HNSCC). Attempts have been made in this study to detect the minimal deleted region in chr.8 associated with the development of HNSCC in Indian patients and to study the association of clinicopathological features with the progression of the disease. The deletion mapping of chr.8 was done in samples from 10 primary dysplastic lesions and 43 invasive squamous cell carcinomas from the head and neck region of Indian patients to detect allelic alterations (deletion or size alteration) using 12 highly polymorphic microsatellite markers. The association of the highly deleted region was correlated with the tumour node metastasis (TNM) stages, nodal involvement, tobacco habit and human papilloma virus (HPV) infection of the samples. High frequency (49%) of loss of heterozygosity (LOH) was seen within 13.12 megabase (Mb) region of chromosomal 8p21.3-23 region in the HNSCC samples, whereas the dysplastic samples did not show any allelic alterations in this region. The highest frequency (17%) of microsatellite size alterations (MA) was observed in the chr.8p22 region. The loss of short arm or normal copy of chr.8 and rare bi-allelic alterations were seen in the stage II-IV tumours (939, 5184, 2772, 1319 and 598) irrespective of their primary sites. The highly deleted region did not show any significant association with any of the clinical parameters. However, HPV infection was significantly associated (P < 0.05) with the differentiation grades and overall allelic alterations (LOH/MA) of the samples. Our data indicate that the 13.12 Mb deleted region in the chromosomal 8p21.3-23 region could harbour candidate tumour suppressor gene(s) (TSGs) associated with the progression anti invasion of HNSCC tumours in Indian patients.

Targeted Metagenomic Survey of the Fe-Cycling Microbial Community at Chocolate Pots Hot Springs, Yellowstone National Park

NASA Astrophysics Data System (ADS)

Fortney, N. W.; He, S.; Kulkarni, A.; Friedrich, M. W.; Boyd, E. S.; Roden, E. E.

2016-12-01

Chocolate Pots hot springs (CP) is a circumneutral pH, Fe-rich geothermal feature located in Yellowstone National Park. Fe-based metabolic processes are deeply rooted in the tree of life and studying environments like CP are important for us to study to gain insight into ancient Earth ecosystems. Recently identified features on Mars are indicative of near-surface hydrothermal environments and studies of modern Earth systems like CP allow us a glimpse into how life may have potentially arisen on other rocky worlds. Previous enrichment culture studies of the microbial community present at CP identified close relatives of dissimilatory Fe-reducing bacteria (DIRB), including Geobacter metallireducens and Melioribacter roseus. However, the question still remains as to the composition and activity of the microbial community in situ. Here we used 13C stable isotope probing to gain an understanding of the Fe cycling microbial community at CP. Fe-Si oxide sediments collected from near the hot spring vent were incubated under in situ conditions and amended with 13C-acetate or -bicarbonate to target DIRB and Fe-oxidizing bacteria, respectively. 16S rRNA gene amplicon libraries along with shotgun metagenomic libraries were obtained from both sets of incubations. Differential read coverage mapping of metagenomic reads identified a set of taxonomic bins that showed a response to the incubation treatments. We searched the Fe-reducing incubation bins for homologues of genes involved in known extracellular electron transfer (EET) systems such as Pcc and MtrAB, as well as putative porins proximal to multiheme cytochrome c genes. We also searched bins from the Fe-oxidizing incubations for these EET systems in addition to homologues of the outer membrane cytochrome c Cyc2. The Fe-oxidizing bins were also examined for genes encoding RuBisCo to identify potential chemolithoautotrophs. Our targeted metagenomic analysis will identify which organisms are likely to be part of an active Fe cycle and shed light on the potential for an internally coupled Fe and C cycle within the CP vent pool and sediments.

7. TROJAN MILL, EXTERIOR FROM NORTHWEST, c. 191828. ADDITIONS FOR ...

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

7. TROJAN MILL, EXTERIOR FROM NORTHWEST, c. 1918-28. ADDITIONS FOR PRIMARY THICKENERS No. 1 AND No. 2, SECONDARY THICKENERS No. 1, No. 2, AND No. 3, AGITATORS, AIR COMPRESSOR, AND PORTLAND FILTERS ARE SHOWN COMPLETE. STAIR ON NORTH SIDE OF CRUDE ORE BINS IS PRESENT AS IS THE LIME BIN ADJACENT TO THE WEST CRUDE ORE BIN, AND THE SNOW SHED ADDED OVER THE TRAMLINE SERVING THE EAST AND WEST CRUDE ORE BINS. ALSO PRESENT IS THE BABBITT HOUSE AND ROCK BIN. CREDIT JW. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome

PubMed Central

Ríos, Gabino; Naranjo, Miguel A; Iglesias, Domingo J; Ruiz-Rivero, Omar; Geraud, Marion; Usach, Antonio; Talón, Manuel

2008-01-01

Background Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Results Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. Conclusion In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement. PMID:18691431

Deletion of 7q31.1 supports involvement of FOXP2 in language impairment: clinical report and review.

PubMed

Lennon, P A; Cooper, M L; Peiffer, D A; Gunderson, K L; Patel, A; Peters, Sarika; Cheung, S W; Bacino, C A

2007-04-15

We report on a young male with moderate mental retardation, dysmorphic features, and language delay who is deleted for 7q31.1-7q31.31. His full karyotype is 46,XY,der(7)del(7)(q31.1q31.31)ins(10;7)(q24.3;q31.1q31.31)mat. This child had language impairment, including developmental verbal dyspraxia, but did not meet criteria for autism according to standardized ADOS testing. Our patient's deletion, which is the smallest reported deletion including FOXP2, adds to the body of evidence that supports the role of FOXP2 in speech and language impairment, but not in autism. A reported association between autism and deletions of WNT2, a gene also deleted in our patient, is likewise not supported by our case. Previously, fine mapping with microsatellites markers within in a large three-generation family, in which half the members had severe specific language impairment, aided the localization of the SPCH1 locus to 7q31 within markers D7S2459 (107.1 Mb) and D7S643 (120.5 Mb). Additionally, chromosome rearrangement of 7q31 and mutational analyses have supported the growing evidence that FOXP2, a gene within the SPCH1 region, is involved with speech and language development. It is unclear however whether the AUTS1 (autistic spectrum 1) locus, highly linked to 7q31, overlaps with the SPCH1 and FOXP2. Copyright 2007 Wiley-Liss, Inc.

A Catalog of Genes Homozygously Deleted in Human Lung Cancer and the Candidacy of PTPRD as a Tumor Suppressor Gene

PubMed Central

Kohno, Takashi; Otsuka, Ayaka; Girard, Luc; Sato, Masanori; Iwakawa, Reika; Ogiwara, Hideaki; Sanchez-Cespedes, Montse; Minna, John D.; Yokota, Jun

2010-01-01

A total of 176 genes homozygously deleted in human lung cancer were identified by DNA array-based whole genome scanning of 52 lung cancer cell lines and subsequent genomic PCR in 74 cell lines, including the 52 cell lines scanned. One or more exons of these genes were homozygously deleted in one (1%) to 20 (27%) cell lines. These genes included known tumor suppressor genes, e.g., CDKN2A/p16, RB1, and SMAD4, and candidate tumor suppressor genes whose hemizygous or homozygous deletions were reported in several types of human cancers, such as FHIT, KEAP1, and LRP1B/LRP-DIP. CDKN2A/p16 and p14ARF located in 9p21 were most frequently deleted (20/74, 27%). The PTPRD gene was most frequently deleted (8/74, 11%) among genes mapping to regions other than 9p21. Somatic mutations, including a nonsense mutation, of the PTPRD gene were detected in 8/74 (11%) of cell lines and 4/95 (4%) of surgical specimens of lung cancer. Reduced PTPRD expression was observed in the majority (>80%) of cell lines and surgical specimens of lung cancer. Therefore, PTPRD is a candidate tumor suppressor gene in lung cancer. Microarray-based expression profiling of 19 lung cancer cell lines also indicated that some of the 176 genes, such as KANK and ADAMTS1, are preferentially inactivated by epigenetic alterations. Genetic/epigenetic as well as functional studies of these 176 genes will increase our understanding of molecular mechanisms behind lung carcinogenesis. PMID:20073072

Association of Tissue-Specific DNA Methylation Alterations with α-Thalassemia Southeast Asian Deletion

PubMed Central

Pangeson, Tanapat; Sanguansermsri, Phanchana; Sanguansermsri, Torpong; Seeratanachot, Teerapat; Suwanakhon, Narutchala; Srikummool, Metawee; Kaewkong, Worasak; Mahingsa, Khwanruedee

2017-01-01

In the wild-type allele, DNA methylation levels of 10 consecutive CpG sites adjacent to the upstream 5′-breakpoint of α-thalassemia Southeast Asian (SEA) deletion are not different between placenta and leukocytes. However, no previous study has reported the map of DNA methylation in the SEA allele. This report aims to show that the SEA mutation is associated with DNA methylation changes, resulting in differential methylation between placenta and leukocytes. Methylation-sensitive high-resolution analysis was used to compare DNA methylation among placenta, leukocytes, and unmethylated control DNA. The result indicates that the DNA methylation between placenta and leukocyte DNA is different and shows that the CpG status of both is not fully unmethylated. Mapping of individual CpG sites was performed by targeted bisulfite sequencing. The DNA methylation level of the 10 consecutive CpG sites was different between placenta and leukocyte DNA. When the 10th CpG of the mutation allele was considered as a hallmark for comparing DNA methylation level, it was totally different from the unmethylated 10th CpG of the wild-type allele. Finally, the distinct DNA methylation patterns between both DNA were extracted. In total, 24 patterns were found in leukocyte samples and 9 patterns were found in placenta samples. This report shows that the large deletion is associated with DNA methylation change. In further studies for clinical application, the distinct DNA methylation pattern might be a potential marker for detecting cell-free fetal DNA. PMID:29162979

SU-F-T-253: Volumetric Comparison Between 4D CT Amplitude and Phase Binning Mode

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

Yang, G; Ma, R; Reyngold, M

2016-06-15

Purpose: Motion artifact in 4DCT images can affect radiation treatment quality. To identify the most robust and accurate binning method, we compare the volume difference between targets delineated on amplitude and phase binned 4DCT scans. Methods: Varian RPM system and CT scanner were used to acquire 4DCTs of a Quasar phantom with embedded cubic and spherical objects having superior-inferior motion. Eight patients’ respiration waveforms were used to drive the phantom. The 4DCT scan was reconstructed into 10 phase and 10 amplitude bins (2 mm slices). A scan of the static phantom was also acquired. For each waveform, sphere and cubemore » volumes were generated automatically on each phase using HU thresholding. Phase (amplitude) ITVs were the union of object volumes over all phase (amplitude) binned images. The sphere and cube volumes measured in the static phantom scan were V{sub sphere}=4.19cc and V{sub cube}=27.0cc. Volume difference (VD) and dice similarity coefficient (DSC) of the ITVs, and mean volume error (MVE) defined as the average target volume percentage difference between each phase image and the static image, were used to evaluate the performance of amplitude and phase binning. Results: Averaged over the eight breathing traces, the VD and DSC of the internal target volume (ITV) between amplitude and phase binning were 3.4%±3.2% (mean ± std) and 95.9%±2.1% for sphere; 2.1%±3.3% and 98.0% ±1.5% for cube, respectively.For all waveforms, the average sphere MVE of amplitude and phase binning was 6.5% ± 5.0% and 8.2%±6.3%, respectively; and the average cube MVE of amplitude and phase binning was 5.7%±3.5%and 12.9%±8.9%, respectively. Conclusion: ITV volume and spatial overlap as assessed by VD and DSC are similar between amplitude and phase binning. Compared to phase binning, amplitude binning results in lower MVE suggesting it is less susceptible to motion artifact.« less

A lifelong learning hyper-heuristic method for bin packing.

PubMed

Sim, Kevin; Hart, Emma; Paechter, Ben

2015-01-01

We describe a novel hyper-heuristic system that continuously learns over time to solve a combinatorial optimisation problem. The system continuously generates new heuristics and samples problems from its environment; and representative problems and heuristics are incorporated into a self-sustaining network of interacting entities inspired by methods in artificial immune systems. The network is plastic in both its structure and content, leading to the following properties: it exploits existing knowledge captured in the network to rapidly produce solutions; it can adapt to new problems with widely differing characteristics; and it is capable of generalising over the problem space. The system is tested on a large corpus of 3,968 new instances of 1D bin-packing problems as well as on 1,370 existing problems from the literature; it shows excellent performance in terms of the quality of solutions obtained across the datasets and in adapting to dynamically changing sets of problem instances compared to previous approaches. As the network self-adapts to sustain a minimal repertoire of both problems and heuristics that form a representative map of the problem space, the system is further shown to be computationally efficient and therefore scalable.

Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population.

PubMed

Balint-Kurti, P J; Krakowsky, M D; Jines, M P; Robertson, L A; Molnár, T L; Goodman, M M; Holl, J B

2006-10-01

ABSTRACT A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.

Nance-Horan syndrome: a contiguous gene syndrome involving deletion of the amelogenin gene? A case report and molecular analysis.

PubMed

Franco, E; Hodgson, S; Lench, N; Roberts, G J

1995-03-01

A case of Nance-Horan syndrome in a male is presented, with some features of the condition in his carrier mother and her mother. It is proposed that Nance-Horan syndrome might be a contiguous gene syndrome mapping to chromosome Xp21.2-p22.3. The proband had congenital cataract microphthalmia and dental abnormalities including screwdriver shaped incisors and evidence of enamel pitting hypoplasia. The region Xp21.2-p22.3 also contains the tooth enamel protein gene, amelogenin (AMGX). Using molecular genetic techniques, we have shown that there is no evidence that the AMGX gene is deleted in this case of the Nance-Horan syndrome.

Surface contamination of hazardous drug pharmacy storage bins and pharmacy distributor shipping containers.

PubMed

Redic, Kimberly A; Fang, Kayleen; Christen, Catherine; Chaffee, Bruce W

2018-03-01

Purpose This study was conducted to determine whether there is contamination on exterior drug packaging using shipping totes from the distributor and carousel storage bins as surrogate markers of external packaging contamination. Methods A two-part study was conducted to measure the presence of 5-fluorouracil, ifosfamide, cyclophosphamide, docetaxel and paclitaxel using surrogate markers for external drug packaging. In Part I, 10 drug distributor shipping totes designated for transport of hazardous drugs provided a snapshot view of contamination from regular use and transit in and out of the pharmacy. An additional two totes designated for transport of non-hazardous drugs served as controls. In Part II, old carousel storage bins (i.e. those in use pre-study) were wiped for snapshot view of hazardous drug contamination on storage bins. New carousel storage bins were then put into use for storage of the five tested drugs and used for routine storage and inventory maintenance activities. Carousel bins were wiped at time intervals 0, 8, 16 and 52 weeks to measure surface contamination. Results Two of the 10 hazardous shipping totes were contaminated. Three of the five-old carousel bins were contaminated with cyclophosphamide. One of the old carousel bins was also contaminated with ifosfamide. There were no detectable levels of hazardous drugs on any of the new storage bins at time 0, 8 or 16 weeks. However, at the Week 52, there was a detectable level of 5-FU present in the 5-FU carousel bin. Conclusions Contamination of the surrogate markers suggests that external packaging for hazardous drugs is contaminated, either during the manufacturing process or during routine chain of custody activities. These results demonstrate that occupational exposure may occur due to contamination from shipping totes and storage bins, and that handling practices including use of personal protective equipment is warranted.

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

Zhang, Yaping; Williams, Brent J.; Goldstein, Allen H.

Here, we present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arrangedmore » into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.« less

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

Islam, Md. Shafiqul, E-mail: shafique@eng.ukm.my; Hannan, M.A., E-mail: hannan@eng.ukm.my; Basri, Hassan

Highlights: • Solid waste bin level detection using Dynamic Time Warping (DTW). • Gabor wavelet filter is used to extract the solid waste image features. • Multi-Layer Perceptron classifier network is used for bin image classification. • The classification performance evaluated by ROC curve analysis. - Abstract: The increasing requirement for Solid Waste Management (SWM) has become a significant challenge for municipal authorities. A number of integrated systems and methods have introduced to overcome this challenge. Many researchers have aimed to develop an ideal SWM system, including approaches involving software-based routing, Geographic Information Systems (GIS), Radio-frequency Identification (RFID), or sensormore » intelligent bins. Image processing solutions for the Solid Waste (SW) collection have also been developed; however, during capturing the bin image, it is challenging to position the camera for getting a bin area centralized image. As yet, there is no ideal system which can correctly estimate the amount of SW. This paper briefly discusses an efficient image processing solution to overcome these problems. Dynamic Time Warping (DTW) was used for detecting and cropping the bin area and Gabor wavelet (GW) was introduced for feature extraction of the waste bin image. Image features were used to train the classifier. A Multi-Layer Perceptron (MLP) classifier was used to classify the waste bin level and estimate the amount of waste inside the bin. The area under the Receiver Operating Characteristic (ROC) curves was used to statistically evaluate classifier performance. The results of this developed system are comparable to previous image processing based system. The system demonstration using DTW with GW for feature extraction and an MLP classifier led to promising results with respect to the accuracy of waste level estimation (98.50%). The application can be used to optimize the routing of waste collection based on the estimated bin level.« less

The retrospective binning method improves the consistency of phase binning in respiratory-gated PET/CT

NASA Astrophysics Data System (ADS)

Didierlaurent, D.; Ribes, S.; Batatia, H.; Jaudet, C.; Dierickx, L. O.; Zerdoud, S.; Brillouet, S.; Caselles, O.; Courbon, F.

2012-12-01

This study assesses the accuracy of prospective phase-gated PET/CT data binning and presents a retrospective data binning method that improves image quality and consistency. Respiratory signals from 17 patients who underwent 4D PET/CT were analysed to evaluate the reproducibility of temporal triggers used for the standard phase-based gating method. Breathing signals were reprocessed to implement retrospective PET data binning. The mean and standard deviation of time lags between automatic triggers provided by the Real-time Position Management (RPM, Varian) gating device and inhalation peaks derived from respiratory curves were computed for each patient. The total number of respiratory cycles available for 4D PET/CT according to the binning mode (prospective versus retrospective) was compared. The maximum standardized uptake value (SUVmax), biological tumour volume (BTV) and tumour trajectory measures were determined from the PET/CT images of five patients. Compared to retrospective binning (RB), prospective gating approach led to (i) a significant loss in breathing cycles (15%) and (ii) the inconsistency of data binning due to temporal dispersion of triggers (average 396 ms). Consequently, tumour characterization could be impacted. In retrospective mode, SUVmax was up to 27% higher, where no significant difference appeared in BTV. In addition, prospective mode gave an inconsistent spatial location of the tumour throughout the bins. Improved consistency with breathing patterns and greater motion amplitude of the tumour centroid were observed with retrospective mode. The detection of the tumour motion and trajectory was improved also for small temporal dispersion of triggers. This study shows that the binning mode could have a significant impact on 4D PET images. The consistency of triggers with breathing signals should be checked before clinical use of gated PET/CT images, and our RB method improves 4D PET/CT image quantification.

Mapping the subgenomic RNA promoter of the Citrus leaf blotch virus coat protein gene by Agrobacterium-mediated inoculation.

PubMed

Renovell, Agueda; Gago, Selma; Ruiz-Ruiz, Susana; Velázquez, Karelia; Navarro, Luis; Moreno, Pedro; Vives, Mari Carmen; Guerri, José

2010-10-25

Citrus leaf blotch virus has a single-stranded positive-sense genomic RNA (gRNA) of 8747 nt organized in three open reading frames (ORFs). The ORF1, encoding a polyprotein involved in replication, is translated directly from the gRNA, whereas ORFs encoding the movement (MP) and coat (CP) proteins are expressed via 3' coterminal subgenomic RNAs (sgRNAs). We characterized the minimal promoter region critical for the CP-sgRNA expression in infected cells by deletion analyses using Agrobacterium-mediated infection of Nicotiana benthamiana plants. The minimal CP-sgRNA promoter was mapped between nucleotides -67 and +50 nt around the transcription start site. Surprisingly, larger deletions in the region between the CP-sgRNA transcription start site and the CP translation initiation codon resulted in increased CP-sgRNA accumulation, suggesting that this sequence could modulate the CP-sgRNA transcription. Site-specific mutational analysis of the transcription start site revealed that the +1 guanylate and the +2 adenylate are important for CP-sgRNA synthesis. Copyright © 2010 Elsevier Inc. All rights reserved.

Impaired hippocampal place cell dynamics in a mouse model of the 22q11.2 deletion

PubMed Central

Zaremba, Jeffrey D; Diamantopoulou, Anastasia; Danielson, Nathan B; Grosmark, Andres D; Kaifosh, Patrick W; Bowler, John C; Liao, Zhenrui; Sparks, Fraser T; Gogos, Joseph A; Losonczy, Attila

2018-01-01

Hippocampal place cells represent the cellular substrate of episodic memory. Place cell ensembles reorganize to support learning but must also maintain stable representations to facilitate memory recall. Despite extensive research, the learning-related role of place cell dynamics in health and disease remains elusive. Using chronic two-photon Ca2+ imaging in hippocampal area CA1 of wild-type and Df(16)A+/− mice, an animal model of 22q11.2 deletion syndrome, one of the most common genetic risk factors for cognitive dysfunction and schizophrenia, we found that goal-oriented learning in wild-type mice was supported by stable spatial maps and robust remapping of place fields toward the goal location. Df(16)A+/− mice showed a significant learning deficit accompanied by reduced spatial map stability and the absence of goal-directed place cell reorganization. These results expand our understanding of the hippocampal ensemble dynamics supporting cognitive flexibility and demonstrate their importance in a model of 22q11.2-associated cognitive dysfunction. PMID:28869582

A harmonic analysis of lunar topography

NASA Technical Reports Server (NTRS)

Bills, B. G.; Ferrari, A. J.

1977-01-01

A global lunar topographic map has been derived from existing earth-based and orbital observations supplemented in areas without data by a linear autocovariance predictor. Of 2592 bins, each 5 deg square, 1380 (64.7% by area) contain at least one measurement. A spherical harmonic analysis to degree 12 yields a mean radius of 1737.53 plus or minus 0.03 km (formal standard error) and an offset of the center of figure of 1.98 plus or minus 0.06 km toward (19 plus or minus 2) deg S, (194 plus or minus 1) deg E. A Bouguer gravity map, derived from a 12-degree free-air gravity model and the present topography data, is presented for an elevation of 100 km above the mean surface. It is confirmed that the low-degree gravity harmonics are determined primarily by surface height variations and only secondarily by lateral density variations.

Zika virus: Endemic and epidemic ranges of Aedes mosquito transmission.

PubMed

Attaway, David F; Waters, Nigel M; Geraghty, Estella M; Jacobsen, Kathryn H

As evidence linking Zika virus with serious health complications strengthens, public health officials and clinicians worldwide need to know which locations are likely to be at risk for autochthonous Zika infections. We created risk maps for epidemic and endemic Aedes-borne Zika virus infections globally using a predictive analysis method that draws on temperature, precipitation, elevation, land cover, and population density variables to identify locations suitable for mosquito activity seasonally or year-round. Aedes mosquitoes capable of transmitting Zika and other viruses are likely to live year-round across many tropical areas in the Americas, Africa, and Asia. Our map provides an enhanced global projection of where vector control initiatives may be most valuable for reducing the risk of Zika virus and other Aedes-borne infections. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

Compensation of PVT Variations in ToF Imagers with In-Pixel TDC

PubMed Central

Vornicu, Ion; Carmona-Galán, Ricardo; Rodríguez-Vázquez, Ángel

2017-01-01

The design of a direct time-of-flight complementary metal-oxide-semiconductor (CMOS) image sensor (dToF-CIS) based on a single-photon avalanche-diode (SPAD) array with an in-pixel time-to-digital converter (TDC) must contemplate system-level aspects that affect its overall performance. This paper provides a detailed analysis of the impact of process parameters, voltage supply, and temperature (PVT) variations on the time bin of the TDC array. Moreover, the design and characterization of a global compensation loop is presented. It is based on a phase locked loop (PLL) that is integrated on-chip. The main building block of the PLL is a voltage-controlled ring-oscillator (VCRO) that is identical to the ones employed for the in-pixel TDCs. The reference voltage that drives the master VCRO is distributed to the voltage control inputs of the slave VCROs such that their multiphase outputs become invariant to PVT changes. These outputs act as time interpolators for the TDCs. Therefore the compensation scheme prevents the time bin of the TDCs from drifting over time due to the aforementioned factors. Moreover, the same scheme is used to program different time resolutions of the direct time-of-flight (ToF) imager aimed at 3D ranging or depth map imaging. Experimental results that validate the analysis are provided as well. The compensation loop proves to be remarkably effective. The spreading of the TDCs time bin is lowered from: (i) 20% down to 2.4% while the temperature ranges from 0 °C to 100 °C; (ii) 27% down to 0.27%, when the voltage supply changes within ±10% of the nominal value; (iii) 5.2 ps to 2 ps standard deviation over 30 sample chips, due to process parameters’ variation. PMID:28486405

Compensation of PVT Variations in ToF Imagers with In-Pixel TDC.

PubMed

Vornicu, Ion; Carmona-Galán, Ricardo; Rodríguez-Vázquez, Ángel

2017-05-09

The design of a direct time-of-flight complementary metal-oxide-semiconductor (CMOS) image sensor (dToF-CIS) based on a single-photon avalanche-diode (SPAD) array with an in-pixel time-to-digital converter (TDC) must contemplate system-level aspects that affect its overall performance. This paper provides a detailed analysis of the impact of process parameters, voltage supply, and temperature (PVT) variations on the time bin of the TDC array. Moreover, the design and characterization of a global compensation loop is presented. It is based on a phase locked loop (PLL) that is integrated on-chip. The main building block of the PLL is a voltage-controlled ring-oscillator (VCRO) that is identical to the ones employed for the in-pixel TDCs. The reference voltage that drives the master VCRO is distributed to the voltage control inputs of the slave VCROs such that their multiphase outputs become invariant to PVT changes. These outputs act as time interpolators for the TDCs. Therefore the compensation scheme prevents the time bin of the TDCs from drifting over time due to the aforementioned factors. Moreover, the same scheme is used to program different time resolutions of the direct time-of-flight (ToF) imager aimed at 3D ranging or depth map imaging. Experimental results that validate the analysis are provided as well. The compensation loop proves to be remarkably effective. The spreading of the TDCs time bin is lowered from: (i) 20% down to 2.4% while the temperature ranges from 0 °C to 100 °C; (ii) 27% down to 0.27%, when the voltage supply changes within ±10% of the nominal value; (iii) 5.2 ps to 2 ps standard deviation over 30 sample chips, due to process parameters' variation.

16. Coke 'fines' bin at Furnace D. After delivery to ...

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

16. Coke 'fines' bin at Furnace D. After delivery to the trestle bins, the coke was screened and the coke 'fines' or breeze, were transported by conveyor to the coke fines bins where it was collected and leaded into dump trucks. The coke fines were then sold for fuel to a sinter plant in Lorain, Ohio. - Central Furnaces, 2650 Broadway, east bank of Cuyahoga River, Cleveland, Cuyahoga County, OH

Qatar: Background and U.S. Relations

DTIC Science & Technology

2014-11-04

Ahmed bin Abdullah bin Ziad Al Mahmoud Foreign Minister Khalid Bin Mohammed Al Attiyah Minister of Energy and Industry Mohammed bin Saleh al Sada...about voter franchise extension were resolved.5 The Advisory Council would have oversight authority over the Council of Ministers and would be able...Sunni armed groups in Syria has the potential to have a more lasting impact on the region, but has challenged the traditional Qatari preference for

Toward zero waste events: Reducing contamination in waste streams with volunteer assistance.

PubMed

Zelenika, Ivana; Moreau, Tara; Zhao, Jiaying

2018-06-01

Public festivals and events generate a tremendous amount of waste, especially when they involve food and drink. To reduce contamination across waste streams, we evaluated three types of interventions at a public event. In a randomized control trial, we examined the impact of volunteer staff assistance, bin tops, and sample 3D items with bin tops, on the amount of contamination and the weight of the organics, recyclable containers, paper, and garbage bins at a public event. The event was the annual Apple Festival held at the University of British Columbia, which was attended by around 10,000 visitors. We found that contamination was the lowest in the volunteer staff condition among all conditions. Specifically, volunteer staff reduced contamination by 96.1% on average in the organics bin, 96.9% in the recyclable containers bin, 97.0% in the paper bin, and 84.9% in the garbage bin. Our interventions did not influence the weight of the materials in the bins. This finding highlights the impact of volunteers on reducing contamination in waste streams at events, and provides suggestions and implications for waste management for event organizers to minimize contamination in all waste streams to achieve zero waste goals. Copyright © 2018. Published by Elsevier Ltd.

Improved Taxation Rate for Bin Packing Games

NASA Astrophysics Data System (ADS)

Kern, Walter; Qiu, Xian

A cooperative bin packing game is a N-person game, where the player set N consists of k bins of capacity 1 each and n items of sizes a 1, ⋯ ,a n . The value of a coalition of players is defined to be the maximum total size of items in the coalition that can be packed into the bins of the coalition. We present an alternative proof for the non-emptiness of the 1/3-core for all bin packing games and show how to improve this bound ɛ= 1/3 (slightly). We conjecture that the true best possible value is ɛ= 1/7.

[Clinical experience and academic thoughts of Professor LIU Feng-bin on case series of gastroesophageal reflux disease based on data mining].

PubMed

Hou, Zheng-Kun; Li, Ji-Ping; Chen, Zhuo-Qun; Liu, Feng-Bin

2018-03-01

To analyze and summarize Professor LIU Feng-bin's clinical experience and academic thoughts on gastroesophageal reflux disease (GERD), the study group adopted the retrospective study for case series and expert interview, extracted the retrospective data, including the herbs, diseases, syndrome type, medical expense and quantity of herbs of GERD patients attended the First Affiliated Hospital of Guangzhou University of Chinese Medicine. Statistical description and binary Logistic regression were used for the identification and modification of syndrome type and initial core herbs. After expert interviews were performed for the syndrome type and herbs, the final scheme were formed. A total of 112 GERD patients ages（48.97±13.13）y; male: 35 (31.3%), female: 77(68.7%) were enrolled. The numbers of patients with liver and stomach incoordination syndrome, heat stagnation of liver and stomach syndrome, syndrome of dual deficiency of Qi and Yin, syndrome of spleen deficiency and dampness-heat, spleen-stomach disharmony syndrome were 40, 26, 19, 17 and 10, respectively. The patients used totally 80 herbs, and 26 of them had significant differences among different syndrome groups. According to the logistic regression analysis on the 23 herbs used by 112 patients, the herbs scheme was modified for the second time. After the expert interviews and modification, the final consensus was reached. The main causes for GERD were dietary irregularities, moodiness, and weak constitution. The basic mechanism of GERD was spleen deficiency with Qi adverseness. The spleen-stomach disharmony syndrome was deleted by expert interviews. The 10 core herbs for GERD treatment were Taizishen(Pseudostellariae Radix), Fuling(Poria), Baizhu(Atractylodismacrocephalae Rhizoma), Gancao(Glycyrrhizae Radix Et Rhizoma), Zhebeimu(Fritillariae Thunbergii Bulbus), Haipiaoxiao(Sepiae Endoconcha), Zhiqiao(Aurantii Fructus), Chenxiang(Alosewood), Pugongying(Taraxaci Herba), Zhizitan(Cape Jasmine Fruit). The modification and psychological and diet interventions were also identified. This study summarized Professor LIU Feng-bin's clinical experience and academic thoughts of chronic atrophic gastritis based on data mining of case series and expert interviews. The quality of methodologies and report were both well. The results provide a foundation and ideas for further study on the complex intervention for GERD, and can be directly applied in clinical practice. Copyright© by the Chinese Pharmaceutical Association.

Genetic modulation of the iris transillumination defect: a systems genetics analysis using the expanded family of BXD glaucoma strains

PubMed Central

Swaminathan, Shankar; Lu, Hong; Williams, Robert W; Lu, Lu; Jablonski, Monica M

2013-01-01

We investigated the contributions of Tyrp1 and Gpnmb to the iris transillumination defect (TID) in five age cohorts of BXD mice. Using systems genetics, we also evaluated the role of other known pigmentation genes (PGs). Mapping studies indicate that Tyrp1 contributes to the phenotype at all ages, yet the TID maps to Gpnmb only in the oldest cohort. Composite interval mapping reveals secondary loci viz. Oca2, Myo5a, Prkcz, and Zbtb20 that modulate the phenotype in the age groups up to 10–13 months. The contributions of Tyrp1 and Gpnmb were highly significant in all age cohorts. Moreover, in young mice, all six gene candidates had substantial interactions in our model. Our model accounted for 71–88% of the explained variance of the TID phenotype across the age bins. These results demonstrate that along with Tyrp1 and Gpnmb, Oca2, Myo5a, Prkcz, and Zbtb20 modulate the TID in an age-dependent manner. PMID:23582180

Are there tumor suppressor genes on chromosome 4p in sporadic colorectal carcinoma?

PubMed Central

Zheng, Hai-Tao; Jiang, Li-Xin; Lv, Zhong-Chuan; Li, Da-Peng; Zhou, Chong-Zhi; Gao, Jian-Jun; He, Lin; Peng, Zhi-Hai

2008-01-01

AIM: To study the candidate tumor suppressor genes (TSG) on chromosome 4p by detecting the high frequency of loss of heterozygosity (LOH) in sporadic colorectal carcinoma in Chinese patients. METHODS: Seven fluorescent labeled polymorphic microsatellite markers were analyzed in 83 cases of colorectal carcinoma and matched normal tissue DNA by PCR. PCR products were eletrophoresed on an ABI 377 DNA sequencer. Genescan 3.7 and Genotype 3.7 software were used for LOH scanning and analysis. The same procedure was performed by the other six microsatellite markers spanning D4S3013 locus to make further detailed deletion mapping. Comparison between LOH frequency and clinicopathological factors was performed by χ2 test. RESULTS: Data were collected from all informative loci. The average LOH frequency on 4p was 24.25%, and 42.3% and 35.62% on D4S405 and D4S3013 locus, respectively. Adjacent markers of D4S3013 displayed a low LOH frequency (< 30%) by detailed deletion mapping. Significant opposite difference was observed between LOH frequency and tumor diameter on D4S412 and D4S1546 locus (0% vs 16.67%, P = 0.041; 54.55% vs 11.11%, P = 0.034, respectively). On D4S403 locus, LOH was significantly associated with tumor gross pattern (11.11%, 0, 33.33%, P = 0.030). No relationship was detected on other loci compared with clinicopathological features. CONCLUSION: By deletion mapping, two obvious high frequency LOH regions spanning D4S3013 (4p15.2) and D4S405 (4p14) locus are detected. Candidate TSG, which is involved in carcinogenesis and progression of sporadic colorectal carcinoma on chromosome 4p, may be located between D4S3017 and D4S2933 (about 1.7 cm). PMID:18176968

Mental retardation in a child with a {open_quotes}de novo{close_quotes} deletion of terminal 14q and a family history of dyslexia

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

Mak-Tam, E.; Capua, E.; Shugar, A.

1994-09-01

A couple presented for prenatal diagnosis for advanced maternal age. A review of the family history revealed that their elder daughter was mentally retarded while their second daughter was of normal intelligence. The father and his brother were both dyslexic. The paternal grandmother had lost three pregnancies, all female. The elder daughter had been fully assessed in the past, but no diagnosis had been made. During her first few years, she was frequently ill and failed to thrive. A developmental assessment at age 5 years concluded that she was moderately mentally retarded. She was minimally dysmorphic. DNA testing for fragilemore » X and urine amnio acids, organic acids and metabolic screen were negative. Chromosome and FISH analyses revealed a satellited 14q with a deletion of 14q32.3. Parents did not show the karyotypic changes, but FISH studies on them and the dyslexic uncle are pending. A molecular work-up of chromosome 14 in this family is also in progress. In this child, the phenotype is probably related to the cytogenetic findings. The information about 14q terminal deletions in the literature is limited but a fairly consistent phenotype, which is slightly different from ring 14, is emerging. This is more obvious in infants that in older children. The family history of dyslexia could be unrelated to our patient`s findings but it is also possible that there is a recessive gene for dyslexia in this family which maps to 14q32.3. The current molecular map of this area provides no answer to this question. Genes mapped to 14q3.3 include the alpha-1-antitrypsin gene, the brain component of creative kinase (CKB) and the immunoglobulin heavy chain genes. Loss of heterozygosity of 14q has been associated with end stage human neuroblastoma and colonic neoplasia.« less

Tomographic Imaging of the Fermi-LAT γ-Ray Sky through Cross-correlations: A Wider and Deeper Look

NASA Astrophysics Data System (ADS)

Cuoco, Alessandro; Bilicki, Maciej; Xia, Jun-Qing; Branchini, Enzo

2017-09-01

We investigate the nature of the extragalactic unresolved γ-ray background (UGRB) by cross-correlating several galaxy catalogs with sky maps of the UGRB built from 78 months of Pass 8 Fermi-Large Area Telescope data. This study updates and improves similar previous analyses in several aspects. First, the use of a larger γ-ray data set allows us to investigate the energy dependence of the cross-correlation in more detail, using up to eight energy bins over a wide energy range of [0.25,500] GeV. Second, we consider larger and deeper catalogs (2MASS Photometric Redshift catalog, 2MPZ; WISE × SuperCOSMOS, WI×SC and SDSS DR12 photometric redshift data set) in addition to the ones employed in the previous studies (NVSS and SDSS QSOs). Third, we exploit the redshift information available for the above catalogs to divide them into redshift bins and perform the cross-correlation separately in each of them. Our results confirm, with higher statistical significance, the detection of cross-correlation signals between the UGRB maps and all the catalogs considered, on angular scales smaller than 1°. Significances range from 16.3σ for NVSS, 7σ for SDSS DR12 and WI×SC, to 5σ for 2MPZ and 4σ for SDSS QSOs. Furthermore, including redshift tomography, the significance of the SDSS DR12 signal strikingly rises up to ˜ 12σ and that of WI×SC to ˜ 10.6σ . We offer a simple interpretation of the signal in the framework of the halo model. The precise redshift and energy information allows us to clearly detect a change over redshift in the spectral and clustering behavior of the γ-ray sources contributing to the UGRB.

8. EAST ELEVATION OF SKIDOO MILL AND UPPER ORE BIN, ...

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

8. EAST ELEVATION OF SKIDOO MILL AND UPPER ORE BIN, LOOKING WEST FROM ACCESS ROAD. THE ROADWAY ON THIS LEVEL (CENTER) WAS USED FOR UNLOADING ORE BROUGHT ON BURROWS INTO THE ORE BIN AT THE TOP LEVEL OF THE MILL. THE ORE BIN IN THE UPPER LEFT WAS ADDED LATER WHEN ORE WAS BROUGHT TO THE MILL BY TRUCKS. - Skidoo Mine, Park Route 38 (Skidoo Road), Death Valley Junction, Inyo County, CA

Effect of horizontal pick and place locations on shoulder kinematics.

PubMed

Könemann, R; Bosch, T; Kingma, I; Van Dieën, J H; De Looze, M P

2015-01-01

In this study the effects of horizontal bin locations in an order picking workstation on upper arm elevation, trunk inclination and hand use were investigated. Eight subjects moved (self-paced) light or heavy products (0.2 and 3.0 kg) from a central product bin to an inner or outer order bin (at 60 or 150 cm) on the left or right side of the workstation, while movements were recorded. The outer compared to inner bin location resulted in more upper arm elevation and trunk inclination per work cycle, both in terms of number of peak values and in terms of time integrals of angles (which is a dose measure over time). Considering the peak values and time integrals per minute (instead of per work cycle), these effects are reduced, due to the higher cycle times for outer bins. Hand use (left, right or both) was not affected by order bin locations.

Distribution of hybrid entanglement and hyperentanglement with time-bin for secure quantum channel under noise via weak cross-Kerr nonlinearity.

PubMed

Heo, Jino; Kang, Min-Sung; Hong, Chang-Ho; Yang, Hyung-Jin; Choi, Seong-Gon; Hong, Jong-Phil

2017-08-31

We design schemes to generate and distribute hybrid entanglement and hyperentanglement correlated with degrees of freedom (polarization and time-bin) via weak cross-Kerr nonlinearities (XKNLs) and linear optical devices (including time-bin encoders). In our scheme, the multi-photon gates (which consist of XKNLs, quantum bus [qubus] beams, and photon-number-resolving [PNR] measurement) with time-bin encoders can generate hyperentanglement or hybrid entanglement. And we can also purify the entangled state (polarization) of two photons using only linear optical devices and time-bin encoders under a noisy (bit-flip) channel. Subsequently, through local operations (using a multi-photon gate via XKNLs) and classical communications, it is possible to generate a four-qubit hybrid entangled state (polarization and time-bin). Finally, we discuss how the multi-photon gate using XKNLs, qubus beams, and PNR measurement can be reliably performed under the decoherence effect.

Selection of 3013 Containers for Field Surveillance. Fiscal Year 2016 Update

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

Kelly, Elizabeth J.; Berg, John M.; Cheadle, Jesse

2016-04-19

This update is the eighth in a series of reports that document the binning and sample selection of 3013 containers for the Field Surveillance program as part of the Integrated Surveillance Program. This report documents changes made to both the container binning assignments and the sample selection approach. Binning changes documented in this update are a result of changes to the prompt gamma calibration curves and the reassignment of a small number of Hanford items from the Pressure bin to the Pressure and Corrosion (P&C) bin. Field Surveillance sample selection changes are primarily a result of focusing future destructive examinationsmore » (DEs) on the potential for stress corrosion cracking in higher moisture containers in the P&C bin. The decision to focus the Field Surveillance program on higher moisture items is based on findings from both the Shelf-life testing program and DEs.« less

Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

PubMed Central

Higgins, M J; Turmel, C; Noolandi, J; Neumann, P E; Lalande, M

1990-01-01

Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis. Images PMID:1970636

Identification of genomic indels and structural variations using split reads

PubMed Central

2011-01-01

Background Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection. Results We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions vs. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs. Conclusions Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for deletions. Moreover, with the advent of the third-generation sequencing technologies that produce longer reads, we expect our method to be even more useful. PMID:21787423

Phenotypic consequences of deletion of the {gamma}{sub 3}, {alpha}{sub 5}, or {beta}{sub 3} subunit of the type A {gamma}-aminobutyric acid receptor in mice

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

Culia, C.T.; Stubbs, L.J.; Montgomery, C.S.

1994-03-29

Three genes (Gabrg3, Gabra5, and Gabrb3) encoding the {gamma}{sub 3}, {alpha}{sub 5}, and {beta}{sub 3} subunits of the type A {gamma}-aminobutyric acid receptor, respectively, are known to map near the pink-eyed dilution (p) locus in mouse chromosome 7. This region shares homology with a segment of human chromosome 15 that is implicated in Angelman syndrome, an inherited neurobehavioral disorder. By mapping Gabrg3-Gabra5-Gabrb3-telomere. Like Gabrb3, neither the Gabra5 nor Gabrg3 gene is functionally imprinted in adult mouse brain. Mice deleted for all three subunits die at birth with a cleft palate, although there are rare survivors ({approximately} 5%) that do notmore » have a cleft palate but do exhibit a neurological abnormality characterized by tremor, jerky gait, and runtiness. The authors have previously suggested that deficiency of the {beta}{sub 3} subunit may be responsible for the clefting defect. Most notably, however, in this report they describe mice carrying two overlapping, complementing p deletions that fail to express the {gamma}{sub 3} transcript, as well as mice from another line that express neither the {gamma}{sub 3} nor {alpha}{sub 5} transcripts. Surprisingly, mice from both of these lines are phenotypically normal and do not exhibit any of the neurological symptoms characteristic of the rare survivors that are deleted for all three ({gamma}{sub 3}, {alpha}{sub 5}, and {beta}{sub 3}) subunits. These mice therefore provide a whole-organism type A {gamma}-aminobutyric-acid receptor background that is devoid of any receptor subtypes that normally contain the {gamma}{sub 3} and/or {alpha}{sub 5} subunits. The absence of an overt neurological phenotype in mice lacking the {gamma}{sub 3} and/or {alpha}{sub 5} subunits also suggests that mutations in these genes are unlikely to provide useful animal models for Angelman syndrome in humans.« less

Fine-mapping, mutation analyses, and structural mapping of cerebrotendinous xanthomatosis in U.S. pedigrees.

PubMed

Lee, M H; Hazard, S; Carpten, J D; Yi, S; Cohen, J; Gerhardt, G T; Salen, G; Patel, S B

2001-02-01

Cerebrotendinous xanthomatosis (CTX) is a rare autosomal recessive disorder of bile acid biosynthesis. Clinically, CTX patients present with tendon xanthomas, juvenile cataracts, and progressive neurological dysfunction and can be diagnosed by the detection of elevated plasma cholestanol levels. CTX is caused by mutations affecting the sterol 27-hydroxylase gene (CYP27 ). CTX has been identified in a number of populations, but seems to have a higher prevalence in the Japanese, Sephardic Jewish, and Italian populations. We have assembled 12 previously unreported pedigrees from the United States. The CYP27 locus had been previously mapped to chromosome 2q33-qter. We performed linkage analyses and found no evidence of genetic heterogeneity. All CTX patients showed segregation with the CYP27 locus, and haplotype analysis and recombinant events allowed us to precisely map CYP27 to chromosome 2q35, between markers D2S1371 and D2S424. Twenty-three mutations were identified from 13 probands analyzed thus far; 11 were compound heterozygotes and 2 had homozygous mutations. Of these, five are novel mutations [Trp100Stop, Pro408Ser, Gln428Stop, a 10-base pair (bp) deletion in exon 1, and a 2-bp deletion in exon 6 of the CYP27 gene]. Three-dimensional structural modeling of sterol 27-hydroxylase showed that, while the majority of the missense mutations disrupt the heme-binding and adrenodoxin-binding domains critical for enzyme activity, two missense mutations (Arg94Trp/Gln and Lys226Arg) are clearly located outside these sites and may identify a potential substrate-binding or other protein contact site.

The cld mutation: narrowing the critical chromosomal region and selecting candidate genes.

PubMed

Péterfy, Miklós; Mao, Hui Z; Doolittle, Mark H

2006-10-01

Combined lipase deficiency (cld) is a recessive, lethal mutation specific to the tw73 haplotype on mouse Chromosome 17. While the cld mutation results in lipase proteins that are inactive, aggregated, and retained in the endoplasmic reticulum (ER), it maps separately from the lipase structural genes. We have narrowed the gene critical region by about 50% using the tw18 haplotype for deletion mapping and a recombinant chromosome used originally to map cld with respect to the phenotypic marker tf. The region now extends from 22 to 25.6 Mbp on the wild-type chromosome, currently containing 149 genes and 50 expressed sequence tags (ESTs). To identify the affected gene, we have selected candidates based on their known role in associated biological processes, cellular components, and molecular functions that best fit with the predicted function of the cld gene. A secondary approach was based on differences in mRNA levels between mutant (cld/cld) and unaffected (+/cld) cells. Using both approaches, we have identified seven functional candidates with an ER localization and/or an involvement in protein maturation and folding that could explain the lipase deficiency, and six expression candidates that exhibit large differences in mRNA levels between mutant and unaffected cells. Significantly, two genes were found to be candidates with regard to both function and expression, thus emerging as the strongest candidates for cld. We discuss the implications of our mapping results and our selection of candidates with respect to other genes, deletions, and mutations occurring in the cld critical region.

Untangling taxonomy: a DNA barcode reference library for Canadian spiders.

PubMed

Blagoev, Gergin A; deWaard, Jeremy R; Ratnasingham, Sujeevan; deWaard, Stephanie L; Lu, Liuqiong; Robertson, James; Telfer, Angela C; Hebert, Paul D N

2016-01-01

Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30-50% higher than currently recognized. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Binning in Gaussian Kernel Regularization

DTIC Science & Technology

2005-04-01

OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the SVM trained on 27,179 samples, but reduces the...71.40%) on 966 randomly sampled data. Using the OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the...the OSU-SVM Matlab package, the SVM trained on 966 bins has a comparable test classification rate as the SVM trained on 27,179 samples, and reduces

General Khalid Bin Waleed: Understanding the 7th Century Campaign against Sassanid Persian Empire from the Perspective of Operational Art

DTIC Science & Technology

2012-12-06

ABSTRACT This monograph investigates Khalid Bin Waleed’s seventh century (AD 633-634) campaign against the Sassanid Persian Empire in Mesopotamia to...Khalid Bin Waleed’s seventh century (AD 633-634) campaign against the Sassanid Persian Empire in Mesopotamia to trace the evidence that substantiates...Bin Waleed employed characteristics and elements of operational art to defeat the Persian forces in Mesopotamia . He established operational objectives

SeaWiFS technical report series. Volume 32: Level-3 SeaWiFS data products. Spatial and temporal binning algorithms

NASA Technical Reports Server (NTRS)

Hooker, Stanford B. (Editor); Firestone, Elaine R. (Editor); Acker, James G. (Editor); Campbell, Janet W.; Blaisdell, John M.; Darzi, Michael

1995-01-01

The level-3 data products from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) are statistical data sets derived from level-2 data. Each data set will be based on a fixed global grid of equal-area bins that are approximately 9 x 9 sq km. Statistics available for each bin include the sum and sum of squares of the natural logarithm of derived level-2 geophysical variables where sums are accumulated over a binning period. Operationally, products with binning periods of 1 day, 8 days, 1 month, and 1 year will be produced and archived. From these accumulated values and for each bin, estimates of the mean, standard deviation, median, and mode may be derived for each geophysical variable. This report contains two major parts: the first (Section 2) is intended as a users' guide for level-3 SeaWiFS data products. It contains an overview of level-0 to level-3 data processing, a discussion of important statistical considerations when using level-3 data, and details of how to use the level-3 data. The second part (Section 3) presents a comparative statistical study of several binning algorithms based on CZCS and moored fluorometer data. The operational binning algorithms were selected based on the results of this study.

WAGR(O?) syndrome and congenital ptosis caused by an unbalanced t(11;15)(p13;p11.2)dn demonstrating a 7 megabase deletion by FISH.

PubMed

Lennon, P A; Scott, D A; Lonsdorf, D; Wargowski, D S; Kirkpatrick, S; Patel, A; Cheung, S W

2006-06-01

Aniridia usually occurs in isolation, but may also occur as part of the WAGR contiguous gene deletion syndrome, which includes Wilms tumor, aniridia, genitourinary abnormalities, and mental retardation. The aniridia and predisposition for Wilms tumor seen in WAGR are caused by haploinsufficiency for PAX 6 and WT1, respectively. We present a female infant with aniridia, bilateral ptosis, bilateral posterior capsular cataracts, nystagmus, left-sided glaucoma, microcephaly, mild unilateral hydronephrosis, poor linear growth, and gross motor delay consistent with a clinical diagnosis of WAGR syndrome. In addition, weight-for-height ratio at 12 months is at the 94th centile, raising the possibility of a diagnosis of WAGRO (WAGR + Obesity). Chromosome analysis revealed a translocation (11;15)(p13;p11.2) which has not been previously associated with a diagnosis of WAGR. Subsequent clinical WAGR fluorescent in situ hybridization (FISH) analysis demonstrated a deletion of 11p13 including PAX6 and WT1. A complete FISH-mapping of the breakpoints on chromosome 11 revealed a 7 Mb deletion within 11p13-11p14. The patient is examined in light of other reported patients with deletions and/or translocations involving the regions between 11p12 --> 11p14 including patients with WAGR + obesity (WAGRO) as well as with other reported patients with aniridia and congenital ptosis. Copyright 2006 Wiley-Liss, Inc.

A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock

PubMed Central

Kadri, Naveen Kumar; Sahana, Goutam; Charlier, Carole; Iso-Touru, Terhi; Guldbrandtsen, Bernt; Karim, Latifa; Nielsen, Ulrik Sander; Panitz, Frank; Aamand, Gert Pedersen; Schulman, Nina; Georges, Michel; Vilkki, Johanna; Lund, Mogens Sandø; Druet, Tom

2014-01-01

In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated. PMID:24391517

Deletion mapping of the Aequorea victoria green fluorescent protein.

PubMed

Dopf, J; Horiagon, T M

1996-01-01

Aequorea victoria green fluorescent protein (GFP) is a promising fluorescent marker which is active in a diverse array of prokaryotic and eukaryotic organisms. A key feature underlying the versatility of GFP is its capacity to undergo heterocyclic chromophore formation by cyclization of a tripeptide present in its primary sequence and thereby acquiring fluorescent activity in a variety of intracellular environments. In order to define further the primary structure requirements for chromophore formation and fluorescence in GFP, a series of N- and C-terminal GFP deletion variant expression vectors were created using the polymerase chain reaction. Scanning spectrofluorometric analyses of crude soluble protein extracts derived from eleven GFP expression constructs revealed that amino acid (aa) residues 2-232, of a total of 238 aa in the native protein, were required for the characteristic emission and absorption spectra of native GFP. Heterocyclic chromophore formation was assayed by comparing the absorption spectrum of GFP deletion variants over the 300-500-nm range to the absorption spectra of full-length GFP and GFP deletion variants missing the chromophore substrate domain from the primary sequence. GFP deletion variants lacking fluorescent activity showed no evidence of heterocyclic ring structure formation when the soluble extracts of their bacterial expression hosts were studied at pH 7.9. These observations suggest that the primary structure requirements for the fluorescent activity of GFP are relatively extensive and are compatible with the view that much of the primary structure serves an autocatalytic function.

Deletion of an enhancer near DLX5 and DLX6 in a family with hearing loss, craniofacial defects, and an inv(7)(q21.3q35)

PubMed Central

Brown, Kerry K.; Reiss, Jacob A.; Crow, Kate; Ferguson, Heather L.; Kelly, Chantal; Fritzsch, Bernd; Morton, Cynthia C.

2010-01-01

Precisely regulated temporal and spatial patterns of gene expression are essential for proper human development. Cis-acting regulatory elements, some located at large distances from their corresponding genes, play a critical role in transcriptional control of key developmental genes and disruption of these regulatory elements can lead to disease. We report a three generation family with five affected members, all of whom have hearing loss, craniofacial defects, and a paracentric inversion of the long arm of chromosome 7, inv(7)(q21.3q35). High resolution mapping of the inversion showed that the 7q21.3 breakpoint is located 65 and 80 kb centromeric of DLX6 and DLX5, respectively. Further analysis revealed a 5115 bp deletion at the 7q21.3 breakpoint. While the breakpoint does not disrupt either DLX5 or DLX6, the syndrome present in the family is similar to that observed in Dlx5 knockout mice and includes a subset of the features observed in individuals with DLX5 and DLX6 deletions, implicating dysregulation of DLX5 and DLX6 in the family’s phenotype. Bioinformatic analysis indicates that the 5115 bp deletion at the 7q21.3 breakpoint could contain regulatory elements necessary for DLX5 and DLX6 expression. Using a transgenic mouse reporter assay, we show that the deleted sequence can drive expression in the ear and developing bones of E12.5 embryos. Consequently, the observed familial syndrome is likely caused by dysregulation of DLX5 and/or DLX6 in specific tissues due to deletion of an enhancer and possibly separation from other regulatory elements by the chromosomal inversion. PMID:19707792

Myotubular Myopathy in a girl with a deletion of Xq27-q28 and unbalanced X inactivation assigns the MTM1 gene to a 600-kb region

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

Dahl, N.; Mandel, J.L.; Chery, M.

1995-05-01

A young girl with a clinically moderate form of myotubular myopathy was found to carry a cytogenetically detectable deletion in Xq27-q28. The deletion had occurred de novo on the paternal X chromosome. It encompasses the fragile X (FRAXA) and Hunter syndrome (IDS) loci, and the DXS304 and DXS455 markers, in Xq27.3 and proximal Xq28. Other loci from the proximal half of Xq28 (DXS49, DXS256, DXS258, DXS305, and DXS497) were found intact. As the X-linked myotubular myopathy locus (MTM1) was previously mapped to Xq28 by linkage analysis, the present observation suggested that MTM1 is included in the deletion. However, a significantmore » clinical phenotype is unexpected in a female MTM1 carrier. Analysis of inactive X-specific methylation at the androgen receptor gene showed that the deleted X chromosome was active in {approximately}80% of leukocytes. Such unbalanced inactivation may account for the moderate MTM1 phenotype and for the mental retardation that later developed in the patient. This observation is discussed in relation to the hypothesis that a locus modulating X inactivation may lie in the region. Comparison of this deletion with that carried by a male patient with a severe Hunter syndrome phenotype but no myotubular myopathy, in light of recent linkage data on recombinant MTM1 families, led to a considerable refinement of the position of the MTM1 locus, to a region of {approximately}600 kb, between DXS304 and DXS497. 46 refs., 4 figs.« less

DNA Sequences Proximal to Human Mitochondrial DNA Deletion Breakpoints Prevalent in Human Disease Form G-quadruplexes, a Class of DNA Structures Inefficiently Unwound by the Mitochondrial Replicative Twinkle Helicase*

PubMed Central

Bharti, Sanjay Kumar; Sommers, Joshua A.; Zhou, Jun; Kaplan, Daniel L.; Spelbrink, Johannes N.; Mergny, Jean-Louis; Brosh, Robert M.

2014-01-01

Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the “Pattern Finder” G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase. PMID:25193669

A technique for rapid source apportionment applied to ambient organic aerosol measurements from a thermal desorption aerosol gas chromatograph (TAG)

DOE PAGES

Zhang, Yaping; Williams, Brent J.; Goldstein, Allen H.; ...

2016-11-25

Here, we present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arrangedmore » into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.« less

A technique for rapid source apportionment applied to ambient organic aerosol measurements from a thermal desorption aerosol gas chromatograph (TAG)

NASA Astrophysics Data System (ADS)

Zhang, Yaping; Williams, Brent J.; Goldstein, Allen H.; Docherty, Kenneth S.; Jimenez, Jose L.

2016-11-01

We present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography-mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arranged into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.

De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser

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

Colletier, Jacques -Philippe; Sawaya, Michael R.; Gingery, Mari

BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals—50 unit cells per edge, on average—has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contactsmore » acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Furthermore, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.« less

De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure [A potent binary mosquito larvicide revealed by de novo phasing with an X-ray free-electron laser

DOE PAGES

Colletier, Jacques -Philippe; Sawaya, Michael R.; Gingery, Mari; ...

2016-09-28

BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals—50 unit cells per edge, on average—has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contactsmore » acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Furthermore, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.« less

37. VIEW NORTH FROM EAST CRUDE ORE BIN TO CRUSHER ...

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

37. VIEW NORTH FROM EAST CRUDE ORE BIN TO CRUSHER ADDITION AND CRUSHED OXIDIZED ORE BIN. VISIBLE ARE DINGS MAGNETIC PULLEY (CENTER), THE 100-TON STEEL CRUSHED UNOXIDIZED ORE BIN, AND UPPER PORTION OF THE STEPHENS-ADAMSON 25 TON/HR BUCKET ELEVATOR. THE UPPER TAILINGS POND LIES BEYOND THE MILL WITH THE UPPER TAILINGS DAM UNDER THE GRAVEL ROAD IN THE UPPER RIGHT CORNER. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Angelman syndrome associated with an inversion of chromosome 15q11.2q24.3

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

Greger, V.; Knoll, J.H.M.; Wagstaff, J.

1997-03-01

Angelman syndrome (AS) most frequently results from large ({ge}5 Mb) de novo deletions of chromosome 15q11-q13. The deletions are exclusively of maternal origin, and a few cases of paternal uniparental disomy of chromosome 15 have been reported. The latter finding indicates that AS is caused by the absence of a maternal contribution to the imprinted 15q11-q13 region. Failure to inherit a paternal 15q11-q13 contribution results in the clinically distinct disorder of Prader-Willi syndrome. Cases of AS resulting from translocations or pericentric inversions have been observed to be associated with deletions, and there have been no confirmed reports of balanced rearrangementsmore » in AS. We report the first such case involving a paracentric inversion with a breakpoint located {approximately}25 kb proximal to the reference marker D15S10. This inversion has been inherited from a phenotypically normal mother. No deletion is evident by molecular analysis in this case, by use of cloned fragments mapped to within {approximately}1 kb of the inversion breakpoint. Several hypotheses are discussed to explain the relationship between the inversion and the AS phenotype. 47 refs., 3 figs.« less

Clinical, cytogenetic and molecular investigation in a fetus with Wolf-Hirschhorn syndrome with paternally derived 4p deletion. Case report and review of the literature.

PubMed

Dietze, Ilona; Fritz, Barbara; Huhle, Dagmar; Simoens, Wouter; Piecha, Ernestine; Rehder, Helga

2004-01-01

Wolf-Hirschhorn (4p-) syndrome (WHS), caused by partial deletion of the short arm of chromosome 4, has been extensively described in children and young adults. Knowledge on fetuses with WHS is still limited due to the small number of published cases. We report on a fetus with prenatally diagnosed severe intrauterine growth retardation, reduced thoracal diameter, clubfeet deformity and midface hypoplasia including slight microretrognathia indicative for fetal karyotyping. Chromosome analysis after amniocentesis revealed a de novo terminal deletion of chromosome 4p [karyotype: 46,XX,del(4) (p16)] which was confirmed by FISH. Analyses of a set of polymorphic markers mapping in 4pter->4p15.3 showed absence of paternal haplotypes. These observations corroborate the preferential paternal origin of the de novo 4p deletion in WHS patients. Furthermore, the distal breakpoint could be narrowed to band 4p16.1. At autopsy, the fetus showed typical craniofacial dysmorphic signs of WHS, severe IUGR and delayed bone age. This report suggests the possibility of recognising the particular phenotype of WHS in utero by prenatal ultrasound and emphasises the importance of karyotyping fetuses with severe IUGR, especially when the amount of amniotic fluid is normal. Copyright 2004 S. Karger AG, Basel

Deletion of ameloblastin exon 6 is associated with amelogenesis imperfecta.

PubMed

Poulter, James A; Murillo, Gina; Brookes, Steven J; Smith, Claire E L; Parry, David A; Silva, Sandra; Kirkham, Jennifer; Inglehearn, Chris F; Mighell, Alan J

2014-10-15

Amelogenesis imperfecta (AI) describes a heterogeneous group of inherited dental enamel defects reflecting failure of normal amelogenesis. Ameloblastin (AMBN) is the second most abundant enamel matrix protein expressed during amelogenesis. The pivotal role of AMBN in amelogenesis has been confirmed experimentally using mouse models. However, no AMBN mutations have been associated with human AI. Using autozygosity mapping and exome sequencing, we identified genomic deletion of AMBN exon 6 in a second cousin consanguineous family with three of the six children having hypoplastic AI. The genomic deletion corresponds to an in-frame deletion of 79 amino acids, shortening the protein from 447 to 368 residues. Exfoliated primary teeth (unmatched to genotype) were available from family members. The most severely affected had thin, aprismatic enamel (similar to that reported in mice homozygous for Ambn lacking exons 5 and 6). Other teeth exhibited thicker but largely aprismatic enamel. One tooth had apparently normal enamel. It has been suggested that AMBN may function in bone development. No clinically obvious bone or other co-segregating health problems were identified in the family investigated. This study confirms for the first time that AMBN mutations cause non-syndromic human AI and that mouse models with disrupted Ambn function are valid. © The Author 2014. Published by Oxford University Press.

Deletions of fetal and adult muscle cDNA in Duchenne and Becker muscular dystrophy patients.

PubMed Central

Cross, G S; Speer, A; Rosenthal, A; Forrest, S M; Smith, T J; Edwards, Y; Flint, T; Hill, D; Davies, K E

1987-01-01

We have isolated a cDNA molecule from a human adult muscle cDNA library which is deleted in several Duchenne muscular dystrophy patients. Patient deletions have been used to map the exons across the Xp21 region of the short arm of the X chromosome. We demonstrate that a very mildly affected 61 year old patient is deleted for at least nine exons of the adult cDNA. We find no evidence for differential exon usage between adult and fetal muscle in this region of the gene. There must therefore be less essential domains of the protein structure which can be removed without complete loss of function. The sequence of 2.0 kb of the adult cDNA shows no homology to any previously described protein listed in the data banks although sequence comparison at the amino acid level suggests that the protein has a structure not dissimilar to rod structures of cytoskeletal proteins such as lamin and myosin. There are single nucleotide differences in the DNA sequence between the adult and fetal cDNAs which result in amino acid changes but none that would be predicted to change the structure of the protein dramatically. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 7. PMID:3428261

An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations.

PubMed

Bohra, Abhishek; Saxena, Rachit K; Gnanesh, B N; Saxena, Kulbhushan; Byregowda, M; Rathore, Abhishek; Kavikishor, P B; Cook, Douglas R; Varshney, Rajeev K

2012-10-01

Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59-140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea.

Sensitivity of a Cloud-Resolving Model to the Bulk and Explicit Bin Microphysical Schemes. Part 1; Validations with a PRE-STORM Case

NASA Technical Reports Server (NTRS)

Li, Xiao-Wen; Tao, Wei-Kuo; Khain, Alexander P.; Simpson, Joanne; Johnson, Daniel E.

2004-01-01

A cloud-resolving model is used to study sensitivities of two different microphysical schemes, one is the bulk type, and the other is an explicit bin scheme, in simulating a mid-latitude squall line case (PRE-STORM, June 10-11, 1985). Simulations using different microphysical schemes are compared with each other and also with the observations. Both the bulk and bin models reproduce the general features during the developing and mature stage of the system. The leading convective zone, the trailing stratiform region, the horizontal wind flow patterns, pressure perturbation associated with the storm dynamics, and the cool pool in front of the system all agree well with the observations. Both the observations and the bulk scheme simulation serve as validations for the newly incorporated bin scheme. However, it is also shown that, the bulk and bin simulations have distinct differences, most notably in the stratiform region. Weak convective cells exist in the stratiform region in the bulk simulation, but not in the bin simulation. These weak convective cells in the stratiform region are remnants of the previous stronger convections at the leading edge of the system. The bin simulation, on the other hand, has a horizontally homogeneous stratiform cloud structure, which agrees better with the observations. Preliminary examinations of the downdraft core strength, the potential temperature perturbation, and the evaporative cooling rate show that the differences between the bulk and bin models are due mainly to the stronger low-level evaporative cooling in convective zone simulated in the bulk model. Further quantitative analysis and sensitivity tests for this case using both the bulk and bin models will be presented in a companion paper.

Isidis Basin Ejecta

NASA Image and Video Library

2017-03-02

This scene is a jumbled mess. There are blocks and smears of many different rocks types that appear to have been dumped into a pile. That's probably about what happened, as ejecta from the Isidis impact basin to the east. This pile of old rocks is an island surrounded by younger lava flows from Syrtis Major. The map is projected here at a scale of 25 centimeters (9.8 inches) per pixel. [The original image scale is 27.4 centimeters (10.8 inches) per pixel (with 1 x 1 binning); objects on the order of 82 centimeters (32.2 inches) across are resolved.] North is up. http://photojournal.jpl.nasa.gov/catalog/PIA21553

Is NF-1 gene deletion the molecular mechanism of neurofibromatosis type 1 with destinctive facies?

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

Leppig, K.A.; Stephens, K.G.; Viskochill, D.

We have studied a patient with neurofibromatosis type 1 and unusual facial features using fluorescence in situ hybridization (FISH) and found that the patient had a deletion that minimially encompasses exon 2-11 of the NF-1 gene. The patient was one of two individuals initially described by Kaplan and Rosenblatt who suggested that another condition aside from neurofibromatosis type 1 may account for the unusual facial features observed in these patients with neurofibromatosis type 1. FISH studies were performed using a P1 clone probe, P1-9, which contains exons 2-11 of the NF-1 gene on chromosomes prepared from the patients. In allmore » 20 metaphase cells analyzed, one of the chromosome 17 homologues was deleted for the P1-9 probe. Therefore, this patient had neurofibromatosis type 1 and unusual facial features as the result of a deletion which minimally includes exons 2-11 of the NF-1 gene. The extent of the deletion is being mapped by FISH and somatic cell hybrid analysis. The patient studied was a 7-year-old male with mild developmental delays, normal growth parameters, and physical findings consistent with neurofibromatosis type 1, including multiple cafe au lait spots, several curaneous neurofibroma, and speckling of the irises. In addition, his unusual facial features consisted of telecanthus, antimongoloid slant of the palpebral fissures, a broad base of the nose, low set and mildly posteriorly rotated ears, thick helices, high arched palate, short and pointed chin, and low posterior hairline. We propose that deletions of the NF-1 gene and/or contiguous genes are the etiology of neurofibromatosis type 1 and unusual facial features. This particular facial appearance was inherited from the patient`s mother and has been described in other individuals with neurofibromatosis type 1. We are using FISH to rapidly screen patients with this phenotype for large deletions involving the NF-1 gene and flanking DNA sequences.« less

Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis.

PubMed

Goettel, Wolfgang; Ramirez, Martha; Upchurch, Robert G; An, Yong-Qiang Charles

2016-08-01

Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.

DETAIL VIEW OF LOWER TRAM TERMINAL, SECONDARY ORE BIN, CRUSHER ...

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

DETAIL VIEW OF LOWER TRAM TERMINAL, SECONDARY ORE BIN, CRUSHER FOUNDATION, AND BALL MILL FOUNDATIONS, LOOKING NORTH NORTHWEST. ORE FROM THE MINES WAS DUMPED FROM THE TRAM BUCKETS INTO THE PRIMARY ORE BIN UNDER THE TRAM TERMINAL. A SLIDING CONTROL DOOR INTRODUCED THE INTO THE JAW CRUSHER (FOUNDATIONS,CENTER). THE CRUSHED ORE WAS THEN CONVEYED INTO THE SECONDARY ORE BIN AT CENTER LEFT. A HOLE IN THE FLOOR OF THE ORE BIN PASSED ORE ONTO ANOTHER CONVEYOR THAT BROUGHT IT OUT TO THE BALL MILL(FOUNDATIONS,CENTER BOTTOM). THIS SYSTEM IS MOST LIKELY NOT THE ORIGINAL SET UP, PROBABLY INSTALLED IN THE MINE'S LAST OCCUPATION IN THE EARLY 1940s. - Keane Wonder Mine, Park Route 4 (Daylight Pass Cutoff), Death Valley Junction, Inyo County, CA

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

PubMed

Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

2018-01-18

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Probabilistic, Seismically-Induced Landslide Hazard Mapping of Western Oregon

NASA Astrophysics Data System (ADS)

Olsen, M. J.; Sharifi Mood, M.; Gillins, D. T.; Mahalingam, R.

2015-12-01

Earthquake-induced landslides can generate significant damage within urban communities by damaging structures, obstructing lifeline connection routes and utilities, generating various environmental impacts, and possibly resulting in loss of life. Reliable hazard and risk maps are important to assist agencies in efficiently allocating and managing limited resources to prepare for such events. This research presents a new methodology in order to communicate site-specific landslide hazard assessments in a large-scale, regional map. Implementation of the proposed methodology results in seismic-induced landslide hazard maps that depict the probabilities of exceeding landslide displacement thresholds (e.g. 0.1, 0.3, 1.0 and 10 meters). These maps integrate a variety of data sources including: recent landslide inventories, LIDAR and photogrammetric topographic data, geology map, mapped NEHRP site classifications based on available shear wave velocity data in each geologic unit, and USGS probabilistic seismic hazard curves. Soil strength estimates were obtained by evaluating slopes present along landslide scarps and deposits for major geologic units. Code was then developed to integrate these layers to perform a rigid, sliding block analysis to determine the amount and associated probabilities of displacement based on each bin of peak ground acceleration in the seismic hazard curve at each pixel. The methodology was applied to western Oregon, which contains weak, weathered, and often wet soils at steep slopes. Such conditions have a high landslide hazard even without seismic events. A series of landslide hazard maps highlighting the probabilities of exceeding the aforementioned thresholds were generated for the study area. These output maps were then utilized in a performance based design framework enabling them to be analyzed in conjunction with other hazards for fully probabilistic-based hazard evaluation and risk assessment. a) School of Civil and Construction Engineering, Oregon State University, Corvallis, OR 97331, USA

Bovine Polledness – An Autosomal Dominant Trait with Allelic Heterogeneity

PubMed Central

Medugorac, Ivica; Seichter, Doris; Graf, Alexander; Russ, Ingolf; Blum, Helmut; Göpel, Karl Heinrich; Rothammer, Sophie; Förster, Martin; Krebs, Stefan

2012-01-01

The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a ∼381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations. PMID:22737241

The Norrie disease gene maps to a 150 kb region on chromosome Xp11.3.

PubMed

Sims, K B; Lebo, R V; Benson, G; Shalish, C; Schuback, D; Chen, Z Y; Bruns, G; Craig, I W; Golbus, M S; Breakefield, X O

1992-05-01

Norrie disease is a human X-linked recessive disorder of unknown etiology characterized by congenital blindness, sensory neural deafness and mental retardation. This disease gene was previously linked to the DXS7 (L1.28) locus and the MAO genes in band Xp11.3. We report here fine physical mapping of the obligate region containing the Norrie disease gene (NDP) defined by a recombination and by the smallest submicroscopic chromosomal deletion associated with Norrie disease identified to date. Analysis, using in addition two overlapping YAC clones from this region, allowed orientation of the MAOA and MAOB genes in a 5'-3'-3'-5' configuration. A recombination event between a (GT)n polymorphism in intron 2 of the MAOB gene and the NDP locus, in a family previously reported to have a recombination between DXS7 and NDP, delineates a flanking marker telomeric to this disease gene. An anonymous DNA probe, dc12, present in one of the YACs and in a patient with a submicroscopic deletion which includes MAOA and MAOB but not L1.28, serves as a flanking marker centromeric to the disease gene. An Alu-PCR fragment from the right arm of the MAO YAC (YMAO.AluR) is not deleted in this patient and also delineates the centromeric extent of the obligate disease region. The apparent order of these loci is telomere ... DXS7-MAOA-MAOB-NDP-dc12-YMAO.AluR ... centromere. Together these data define the obligate region containing the NDP gene to a chromosomal segment less than 150 kb.

25. DETAIL OF STRUCTURAL TIMBERS, ORE BIN, AND STAIRWAY TO ...

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

25. DETAIL OF STRUCTURAL TIMBERS, ORE BIN, AND STAIRWAY TO TOP FLOOR OF MILL, LOOKING SOUTH FROM SECOND FLOOR OF MILL. PORTION OF ORE BIN ON RIGHT, STAIRS ON LEFT. - Skidoo Mine, Park Route 38 (Skidoo Road), Death Valley Junction, Inyo County, CA

14. Interior view, grain tanks (bins). Barrel view of tunnel ...

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

14. Interior view, grain tanks (bins). Barrel view of tunnel for load-out belt conveyor system located below tanks. Square, numbered spouts gravity-feed grain from overhead bins onto belt. - Saint Anthony Elevator No. 3, 620 Malcom Avenue, Southeast, Minneapolis, Hennepin County, MN

Longitudinal structure of the equatorial ionosphere: Time evolution of the four-peaked EIA structure

NASA Astrophysics Data System (ADS)

Lin, C. H.; Hsiao, C. C.; Liu, J. Y.; Liu, C. H.

2007-12-01

Longitudinal structure of the equatorial ionosphere during the 24 h local time period is observed by the FORMOSAT-3/COSMIC (F3/C) satellite constellation. By binning the F3/C radio occultation observations during September and October 2006, global ionospheric total electron content (TEC) maps at a constant local time map (local time TEC map, referred as LT map) can be obtained to monitor the development and subsidence of the four-peaked longitudinal structure of the equatorial ionosphere. From LT maps, the four-peaked structure starts to develop at 0800-1000 LT and becomes most prominent at 1200-1600 LT. The longitudinal structure starts to subside after 2200-2400 LT and becomes indiscernible after 0400-0600 LT. In addition to TEC, ionospheric peak altitude also shows a four-peaked longitudinal structure with variation very similar to TEC during daytime. The four-peaked structure of the ionospheric peak altitude is indiscernible at night. With global local time maps of ionospheric TEC and peak altitude, we compare temporal variations of the longitudinal structure with variations of E × B drift from the empirical model. Our results indicate that the observations are consistent with the hypothesis that the four-peaked longitudinal structure is caused by the equatorial plasma fountain modulated by the E3 nonmigrating tide. Additionally, the four maximum regions show a tendency of moving eastward with propagation velocity of several 10 s m/s.

Exenatide once weekly versus daily basal insulin as add-on treatment to metformin with or without a sulfonylurea: a retrospective pooled analysis in patients with poor glycemic control.

PubMed

Grimm, Michael; Li, Yan; Brunell, Steven C; Blase, Erich

2013-09-01

Basal insulin (b-INS) is typically the add-on treatment of choice for patients with poor glycemic control (ie, glycated hemoglobin [HbA1c] level ≥ 8.5%), but it is unclear whether b-INS is the best option. In this post hoc analysis, the efficacy and tolerability of exenatide once weekly (EQW) were compared with those of b-INS in patients with type 2 diabetes mellitus and a baseline HbA1c level 8.5% who were undergoing treatment with metformin ± a sulfonylurea. Data were pooled from two 26-week, randomized, controlled trials (EQW vs insulin glargine and EQW vs insulin detemir [EQW, N = 137; b-INS, N = 126]). Treatment with either EQW or b-INS for 26 weeks was associated with significant improvements in HbA1c level compared with baseline, although patients treated with EQW experienced a significantly greater decrease in HbA1c level than those treated with b-INS (least squares [LS] mean ± SE: -2.0% ± 0.08% vs -1.6% ± 0.08%; P = 0.0008). Treatment with EQW was associated with a weight loss of 2.4 kg ± 0.23 kg (LS mean ± SE), whereas treatment with b-INS was associated with a weight gain of 2.0 kg ± 0.24 kg (LS mean difference between groups, -4.4 kg ± 0.33; P < 0.0001). Patients in the EQW group were significantly more likely to achieve the composite endpoint of an HbA1c level < 7.0%, no weight gain, and no hypoglycemic events (defined as a blood glucose level < 54 mg/dL requiring self-treatment or assistance to resolve) than patients in the b-INS group (33.6% vs 3.2%; P < 0.0001). The exposure-adjusted hypoglycemic event rates were 0.08 and 0.37 events per patient-year in the EQW and b-INS groups, respectively. Gastrointestinal adverse events occurred at a higher rate in patients who underwent EQW treatment than those who were treated with b-INS. These results show that EQW treatment was associated with significantly greater improvement in HbA1c level compared with b-INS treatment among patients with poor glycemic control, with the added benefits of weight loss (vs weight gain with b-INS therapy) and a lower incidence of hypoglycemic events. These results suggest that EQW is an alternative treatment to b-INS for patients with type 2 diabetes mellitus and a baseline HbA1c level ≥ 8.5%.

A Comprehensive Expedient Methods Field Manual.

DTIC Science & Technology

1984-09-01

structures. " Revetments may be constructed of sandbags, sod blocks , and other expedients [17:933." Bunkers are emplacements with overhead protective...Lapland Fence............................. 75 19. Hardening: Dimensional Timber (Soil Bin) Revetment ............................................. 76...20. Hardening: Log Bulkhead (Soil Bin) Revetment ... 77 21. Hardening: Landing Mat Bulkhead (Soil Bin) Revetment

Large-scale mapping of cortical alterations in 22q11.2 deletion syndrome: Convergence with idiopathic psychosis and effects of deletion size.

PubMed

Sun, Daqiang; Ching, Christopher R K; Lin, Amy; Forsyth, Jennifer K; Kushan, Leila; Vajdi, Ariana; Jalbrzikowski, Maria; Hansen, Laura; Villalon-Reina, Julio E; Qu, Xiaoping; Jonas, Rachel K; van Amelsvoort, Therese; Bakker, Geor; Kates, Wendy R; Antshel, Kevin M; Fremont, Wanda; Campbell, Linda E; McCabe, Kathryn L; Daly, Eileen; Gudbrandsen, Maria; Murphy, Clodagh M; Murphy, Declan; Craig, Michael; Vorstman, Jacob; Fiksinski, Ania; Koops, Sanne; Ruparel, Kosha; Roalf, David R; Gur, Raquel E; Schmitt, J Eric; Simon, Tony J; Goodrich-Hunsaker, Naomi J; Durdle, Courtney A; Bassett, Anne S; Chow, Eva W C; Butcher, Nancy J; Vila-Rodriguez, Fidel; Doherty, Joanne; Cunningham, Adam; van den Bree, Marianne B M; Linden, David E J; Moss, Hayley; Owen, Michael J; Murphy, Kieran C; McDonald-McGinn, Donna M; Emanuel, Beverly; van Erp, Theo G M; Turner, Jessica A; Thompson, Paul M; Bearden, Carrie E

2018-06-13

The 22q11.2 deletion (22q11DS) is a common chromosomal microdeletion and a potent risk factor for psychotic illness. Prior studies reported widespread cortical changes in 22q11DS, but were generally underpowered to characterize neuroanatomic abnormalities associated with psychosis in 22q11DS, and/or neuroanatomic effects of variability in deletion size. To address these issues, we developed the ENIGMA (Enhancing Neuro Imaging Genetics Through Meta-Analysis) 22q11.2 Working Group, representing the largest analysis of brain structural alterations in 22q11DS to date. The imaging data were collected from 10 centers worldwide, including 474 subjects with 22q11DS (age = 18.2 ± 8.6; 46.9% female) and 315 typically developing, matched controls (age = 18.0 ± 9.2; 45.9% female). Compared to controls, 22q11DS individuals showed thicker cortical gray matter overall (left/right hemispheres: Cohen's d = 0.61/0.65), but focal thickness reduction in temporal and cingulate cortex. Cortical surface area (SA), however, showed pervasive reductions in 22q11DS (left/right hemispheres: d = -1.01/-1.02). 22q11DS cases vs. controls were classified with 93.8% accuracy based on these neuroanatomic patterns. Comparison of 22q11DS-psychosis to idiopathic schizophrenia (ENIGMA-Schizophrenia Working Group) revealed significant convergence of affected brain regions, particularly in fronto-temporal cortex. Finally, cortical SA was significantly greater in 22q11DS cases with smaller 1.5 Mb deletions, relative to those with typical 3 Mb deletions. We found a robust neuroanatomic signature of 22q11DS, and the first evidence that deletion size impacts brain structure. Psychotic illness in this highly penetrant deletion was associated with similar neuroanatomic abnormalities to idiopathic schizophrenia. These consistent cross-site findings highlight the homogeneity of this single genetic etiology, and support the suitability of 22q11DS as a biological model of schizophrenia.

In silico mapping of quantitative trait loci in maize.

PubMed

Parisseaux, B; Bernardo, R

2004-08-01

Quantitative trait loci (QTL) are most often detected through designed mapping experiments. An alternative approach is in silico mapping, whereby genes are detected using existing phenotypic and genomic databases. We explored the usefulness of in silico mapping via a mixed-model approach in maize (Zea mays L.). Specifically, our objective was to determine if the procedure gave results that were repeatable across populations. Multilocation data were obtained from the 1995-2002 hybrid testing program of Limagrain Genetics in Europe. Nine heterotic patterns comprised 22,774 single crosses. These single crosses were made from 1,266 inbreds that had data for 96 simple sequence repeat (SSR) markers. By a mixed-model approach, we estimated the general combining ability effects associated with marker alleles in each heterotic pattern. The numbers of marker loci with significant effects--37 for plant height, 24 for smut [Ustilago maydis (DC.) Cda.] resistance, and 44 for grain moisture--were consistent with previous results from designed mapping experiments. Each trait had many loci with small effects and few loci with large effects. For smut resistance, a marker in bin 8.05 on chromosome 8 had a significant effect in seven (out of a maximum of 18) instances. For this major QTL, the maximum effect of an allele substitution ranged from 5.4% to 41.9%, with an average of 22.0%. We conclude that in silico mapping via a mixed-model approach can detect associations that are repeatable across different populations. We speculate that in silico mapping will be more useful for gene discovery than for selection in plant breeding programs. Copyright 2004 Springer-Verlag

Suppression of Prostate Tumor Progression by Bin 1

DTIC Science & Technology

2006-02-01

experiment). The full protocol was approved by IACUC review. Cohort A. Castration + Testostrone propionate s.c. + MNU i.v. Cohort B. Castration... Testostrone propionate s.c. + MNU i.v. + testosterone pellet Strain 1. mosaic Bin1 flox)/KO  Strain 2. Bin1 flox/+ (control for strain 1) Strain

Bioinformatics and Astrophysics Cluster (BinAc)

NASA Astrophysics Data System (ADS)

Krüger, Jens; Lutz, Volker; Bartusch, Felix; Dilling, Werner; Gorska, Anna; Schäfer, Christoph; Walter, Thomas

2017-09-01

BinAC provides central high performance computing capacities for bioinformaticians and astrophysicists from the state of Baden-Württemberg. The bwForCluster BinAC is part of the implementation concept for scientific computing for the universities in Baden-Württemberg. Community specific support is offered through the bwHPC-C5 project.

EFFECTS OF NUMBER AND LOCATION OF BINS ON PLASTIC RECYCLING AT A UNIVERSITY

PubMed Central

O'Connor, Ryan T; Lerman, Dorothea C; Fritz, Jennifer N; Hodde, Henry B

2010-01-01

The proportion of plastic bottles that consumers placed in appropriate recycling receptacles rather than trash bins was examined across 3 buildings on a university campus. We extended previous research on interventions to increase recycling by controlling the number of recycling receptacles across conditions and by examining receptacle location without the use of posted signs. Manipulating the appearance or number of recycling bins in common areas did not increase recycling. Consumers recycled substantially more plastic bottles when the recycling bins were located in classrooms. PMID:21541154

Effects of number and location of bins on plastic recycling at a university.

PubMed

O'Connor, Ryan T; Lerman, Dorothea C; Fritz, Jennifer N; Hodde, Henry B

2010-01-01

The proportion of plastic bottles that consumers placed in appropriate recycling receptacles rather than trash bins was examined across 3 buildings on a university campus. We extended previous research on interventions to increase recycling by controlling the number of recycling receptacles across conditions and by examining receptacle location without the use of posted signs. Manipulating the appearance or number of recycling bins in common areas did not increase recycling. Consumers recycled substantially more plastic bottles when the recycling bins were located in classrooms.

BinMag: Widget for comparing stellar observed with theoretical spectra

NASA Astrophysics Data System (ADS)

Kochukhov, O.

2018-05-01

BinMag examines theoretical stellar spectra computed with Synth/SynthMag/Synmast/Synth3/SME spectrum synthesis codes and compare them to observations. An IDL widget program, BinMag applies radial velocity shift and broadening to the theoretical spectra to account for the effects of stellar rotation, radial-tangential macroturbulence, instrumental smearing. The code can also simulate spectra of spectroscopic binary stars by appropriate coaddition of two synthetic spectra. Additionally, BinMag can be used to measure equivalent width, fit line profile shapes with analytical functions, and to automatically determine radial velocity and broadening parameters. BinMag interfaces with the Synth3 (ascl:1212.010) and SME (ascl:1202.013) codes, allowing the user to determine chemical abundances and stellar atmospheric parameters from the observed spectra.

Effects of empty bins on image upscaling in capsule endoscopy

NASA Astrophysics Data System (ADS)

Rukundo, Olivier

2017-07-01

This paper presents a preliminary study of the effect of empty bins on image upscaling in capsule endoscopy. The presented study was conducted based on results of existing contrast enhancement and interpolation methods. A low contrast enhancement method based on pixels consecutiveness and modified bilinear weighting scheme has been developed to distinguish between necessary empty bins and unnecessary empty bins in the effort to minimize the number of empty bins in the input image, before further processing. Linear interpolation methods have been used for upscaling input images with stretched histograms. Upscaling error differences and similarity indices between pairs of interpolation methods have been quantified using the mean squared error and feature similarity index techniques. Simulation results demonstrated more promising effects using the developed method than other contrast enhancement methods mentioned.

The volatile compound BinBase mass spectral database.

PubMed

Skogerson, Kirsten; Wohlgemuth, Gert; Barupal, Dinesh K; Fiehn, Oliver

2011-08-04

Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in chemical ecology in both plant and animal kingdoms. In past decades, sampling methods and instrumentation for the analysis of complex volatile mixtures have improved; however, design and implementation of database tools to process and store the complex datasets have lagged behind. The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu). The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://binbase.sourceforge.net/ under the LGPL 2.0 license agreement.

The volatile compound BinBase mass spectral database

PubMed Central

2011-01-01

Background Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in chemical ecology in both plant and animal kingdoms. In past decades, sampling methods and instrumentation for the analysis of complex volatile mixtures have improved; however, design and implementation of database tools to process and store the complex datasets have lagged behind. Description The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu). Conclusions The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://binbase.sourceforge.net/ under the LGPL 2.0 license agreement. PMID:21816034

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

PubMed Central

Perkins, J D; Heath, J D; Sharma, B R; Weinstock, G M

1992-01-01

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications. Images PMID:1312707

Towards isolation of the gene for X-linked retinitis pigmentosa (RP3)

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

Dry, K.L.; Aldred, M.A.; Hardwick, L.J.

1994-09-01

Until recently the region of interest containing the gene for X-linked retinitis pigmentosa (RP3) was thought to lie between CYBB (Xp21.1) and the proximal end of the deletion in patient BB (JBBprox). This region was thought to span 100-150 kb. Here we present new mapping data to show that the distance between the 5{prime} (most proximal) end of CYBB and JBBprox is only 50 kb. Recently Roux et al. (1994) have described the isolation of a gene within this region but this showed no disease-associated changes. Further evidence from mapping the deletion in patient NF (who suffered from McLead`s syndromemore » and CGD but not RP) and from linkage analysis of our RP3 families with a new dinucleotide repeat suggests that the gene must extend proximally from JBBprox. In order to extend the region of search we have constructed a YAC contig spanning 800 kb to OTC. We are continuing our search for the RP3 gene using a variety of strategies including exon trapping and cDNA enrichment as well as direct screening of cDNA libraries with subclones from this region.« less

cis-fumagillin, a new methionine aminopeptidase (type 2) inhibitor produced by Penicillium sp. F2757.

PubMed

Kwon, J Y; Jeong, H W; Kim, H K; Kang, K H; Chang, Y H; Bae, K S; Choi, J D; Lee, U C; Son, K H; Kwon, B M

2000-08-01

Selective inhibition against the yeast MetAP2 (methionine aminopeptidase type 2) was detected in the fermentation broth of a fungus F2757 that was later identified as Penicillium janczewskii. A new compound cis-fumagillin methyl ester (1) was isolated from the diazomethane treated fermentation extracts together with the known compound fumagillin methyl ester (2). The cis-fumagillin methyl ester, a stereoisomer of fumagillin methyl ester at the C2'-C3' position of the aliphatic side chain, selectively inhibited growth of the map1 mutant yeast strain (MetAP1 deletion strain) at a concentration as low as 1 ng. However, the wild type yeast w303 and the mutant map2 (MetAP2 deleted) strains were resistant up to 10 microg of the compound. In enzyme experiments, compound 1 inhibited the MetAP2 with an IC50 value of 6.3 nM, but it did not inhibit the MetAP1 (IC50 >200 microM). Compound 2 also inhibited the MetAP2 with an IC50 value of 9.2 nM and 105 microM against MetAP1.

FurA contributes to the oxidative stress response regulation of Mycobacterium avium ssp. paratuberculosis

PubMed Central

Eckelt, Elke; Meißner, Thorsten; Meens, Jochen; Laarmann, Kristin; Nerlich, Andreas; Jarek, Michael; Weiss, Siegfried; Gerlach, Gerald-F.; Goethe, Ralph

2015-01-01

The ferric uptake regulator A (FurA) is known to be involved in iron homeostasis and stress response in many bacteria. In mycobacteria the precise role of FurA is still unclear. In the presented study, we addressed the functional role of FurA in the ruminant pathogen Mycobacterium avium ssp. paratuberculosis (MAP) by construction of a furA deletion strain (MAPΔfurA). RNA deep sequencing revealed that the FurA regulon consists of repressed and activated genes associated to stress response or intracellular survival. Not a single gene related to metal homeostasis was affected by furA deletion. A decisive role of FurA during intracellular survival in macrophages was shown by significantly enhanced survival of MAPΔfurA compared to the wildtype, indicating that a principal task of mycobacterial FurA is oxidative stress response regulation in macrophages. This resistance was not associated with altered survival of mice after long term infection with MAP. Our results demonstrate for the first time, that mycobacterial FurA is not involved in the regulation of iron homeostasis. However, they provide strong evidence that FurA contributes to intracellular survival as an oxidative stress sensing regulator. PMID:25705205

FurA contributes to the oxidative stress response regulation of Mycobacterium avium ssp. paratuberculosis.

PubMed

Eckelt, Elke; Meißner, Thorsten; Meens, Jochen; Laarmann, Kristin; Nerlich, Andreas; Jarek, Michael; Weiss, Siegfried; Gerlach, Gerald-F; Goethe, Ralph

2015-01-01

The ferric uptake regulator A (FurA) is known to be involved in iron homeostasis and stress response in many bacteria. In mycobacteria the precise role of FurA is still unclear. In the presented study, we addressed the functional role of FurA in the ruminant pathogen Mycobacterium avium ssp. paratuberculosis (MAP) by construction of a furA deletion strain (MAPΔfurA). RNA deep sequencing revealed that the FurA regulon consists of repressed and activated genes associated to stress response or intracellular survival. Not a single gene related to metal homeostasis was affected by furA deletion. A decisive role of FurA during intracellular survival in macrophages was shown by significantly enhanced survival of MAPΔfurA compared to the wildtype, indicating that a principal task of mycobacterial FurA is oxidative stress response regulation in macrophages. This resistance was not associated with altered survival of mice after long term infection with MAP. Our results demonstrate for the first time, that mycobacterial FurA is not involved in the regulation of iron homeostasis. However, they provide strong evidence that FurA contributes to intracellular survival as an oxidative stress sensing regulator.

In Southern Africa, Brown Oculocutaneous Albinism (BOCA) Maps to the OCA2 Locus on Chromosome 15q: P-Gene Mutations Identified

PubMed Central

Manga, Prashiela; Kromberg, Jennifer G. R.; Turner, Angela; Jenkins, Trefor; Ramsay, Michele

2001-01-01

In southern Africa, brown oculocutaneous albinism (BOCA) is a distinct pigmentation phenotype. In at least two cases, it has occurred in the same families as tyrosinase-positive oculocutaneous albinism (OCA2), suggesting that it may be allelic, despite the fact that this phenotype was attributed to mutations in the TYRP1 gene in an American individual of mixed ancestry. Linkage analysis in five families mapped the BOCA locus to the same region as the OCA2 locus (maximum LOD 3.07; θ=0 using a six-marker haplotype). Mutation analysis of the human homologue of the mouse pink-eyed dilution gene (P), in 10 unrelated individuals with BOCA revealed that 9 had one copy of the 2.7-kb deletion. No other mutations were identified. Additional haplotype studies, based on closely linked markers (telomere to centromere: D15S1048, D15S1019, D15S1533, P-gene 2.7-kb deletion, D15S219, and D15S156) revealed several BOCA-associated P haplotypes. These could be divided into two core haplotypes, suggesting that a limited number of P-gene mutations give rise to this phenotype. PMID:11179026

Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles.

PubMed

Glaubitz, Ulrike; Li, Xia; Schaedel, Sandra; Erban, Alexander; Sulpice, Ronan; Kopka, Joachim; Hincha, Dirk K; Zuther, Ellen

2017-01-01

Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars. © 2016 John Wiley & Sons Ltd.

Optimization and quality control of genome-wide Hi-C library preparation.

PubMed

Zhang, Xiang-Yuan; He, Chao; Ye, Bing-Yu; Xie, De-Jian; Shi, Ming-Lei; Zhang, Yan; Shen, Wen-Long; Li, Ping; Zhao, Zhi-Hu

2017-09-20

Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells. After preliminary quality control by Sanger sequencing, the two replicates were high-throughput sequenced. The bioinformatics analysis of the raw sequencing data revealed the mapping-ability and pair-mate rate of the raw data were around 90% and 72%, respectively. Additionally, after removal of self-circular ligations and dangling-end products, more than 96% of the valid pairs were reached. Genome-wide interactome profiling shows clear topological associated domains (TADs), which is consistent with previous reports. Further correlation analysis showed that the two biological replicates strongly correlate with each other in terms of both bin coverage and all bin pairs. All these results indicated that the optimized Hi-C procedure is robust and stable, which will be very helpful for the wide applications of the Hi-C assay.

Planck/SDSS Cluster Mass and Gas Scaling Relations for a Volume-Complete redMaPPer Sample

NASA Astrophysics Data System (ADS)

Jimeno, Pablo; Diego, Jose M.; Broadhurst, Tom; De Martino, I.; Lazkoz, Ruth

2018-04-01

Using Planck satellite data, we construct Sunyaev-Zel'dovich (SZ) gas pressure profiles for a large, volume-complete sample of optically selected clusters. We have defined a sample of over 8,000 redMaPPer clusters from the Sloan Digital Sky Survey (SDSS), within the volume-complete redshift region 0.100 < z < 0.325, for which we construct SZ effect maps by stacking Planck data over the full range of richness. Dividing the sample into richness bins we simultaneously solve for the mean cluster mass in each bin together with the corresponding radial pressure profile parameters, employing an MCMC analysis. These profiles are well detected over a much wider range of cluster mass and radius than previous work, showing a clear trend towards larger break radius with increasing cluster mass. Our SZ-based masses fall ˜16% below the mass-richness relations from weak lensing, in a similar fashion as the "hydrostatic bias" related with X-ray derived masses. Finally, we derive a tight Y500-M500 relation over a wide range of cluster mass, with a power law slope equal to 1.70 ± 0.07, that agrees well with the independent slope obtained by the Planck team with an SZ-selected cluster sample, but extends to lower masses with higher precision.

Genomic Variation by Whole-Genome SNP Mapping Arrays Predicts Time-to-Event Outcome in Patients with Chronic Lymphocytic Leukemia

PubMed Central

Schweighofer, Carmen D.; Coombes, Kevin R.; Majewski, Tadeusz; Barron, Lynn L.; Lerner, Susan; Sargent, Rachel L.; O'Brien, Susan; Ferrajoli, Alessandra; Wierda, William G.; Czerniak, Bogdan A.; Medeiros, L. Jeffrey; Keating, Michael J.; Abruzzo, Lynne V.

2013-01-01

Genomic abnormalities, such as deletions in 11q22 or 17p13, are associated with poorer prognosis in patients with chronic lymphocytic leukemia (CLL). We hypothesized that unknown regions of copy number variation (CNV) affect clinical outcome and can be detected by array-based single-nucleotide polymorphism (SNP) genotyping. We compared SNP genotypes from 168 untreated patients with CLL with genotypes from 73 white HapMap controls. We identified 322 regions of recurrent CNV, 82 of which occurred significantly more often in CLL than in HapMap (CLL-specific CNV), including regions typically aberrant in CLL: deletions in 6q21, 11q22, 13q14, and 17p13 and trisomy 12. In univariate analyses, 35 of total and 11 of CLL-specific CNVs were associated with unfavorable time-to-event outcomes, including gains or losses in chromosomes 2p, 4p, 4q, 6p, 6q, 7q, 11p, 11q, and 17p. In multivariate analyses, six CNVs (ie, CLL-specific variations in 11p15.1-15.4 or 6q27) predicted time-to-treatment or overall survival independently of established markers of prognosis. Moreover, genotypic complexity (ie, the number of independent CNVs per patient) significantly predicted prognosis, with a median time-to-treatment of 64 months versus 23 months in patients with zero to one versus two or more CNVs, respectively (P = 3.3 × 10−8). In summary, a comparison of SNP genotypes from patients with CLL with HapMap controls allowed us to identify known and unknown recurrent CNVs and to determine regions and rates of CNV that predict poorer prognosis in patients with CLL. PMID:23273604

The Transcription Factor Ste12 Mediates the Regulatory Role of the Tmk1 MAP Kinase in Mycoparasitism and Vegetative Hyphal Fusion in the Filamentous Fungus Trichoderma atroviride

PubMed Central

Gruber, Sabine; Zeilinger, Susanne

2014-01-01

Mycoparasitic species of the fungal genus Trichoderma are potent antagonists able to combat plant pathogenic fungi by direct parasitism. An essential step in this mycoparasitic fungus-fungus interaction is the detection of the fungal host followed by activation of molecular weapons in the mycoparasite by host-derived signals. The Trichoderma atroviride MAP kinase Tmk1, a homolog of yeast Fus3/Kss1, plays an essential role in regulating the mycoparasitic host attack, aerial hyphae formation and conidiation. However, the transcription factors acting downstream of Tmk1 are hitherto unknown. Here we analyzed the functions of the T. atroviride Ste12 transcription factor whose orthologue in yeast is targeted by the Fus3 and Kss1 MAP kinases. Deletion of the ste12 gene in T. atroviride not only resulted in reduced mycoparasitic overgrowth and lysis of host fungi but also led to loss of hyphal avoidance in the colony periphery and a severe reduction in conidial anastomosis tube formation and vegetative hyphal fusion events. The transcription of several orthologues of Neurospora crassa hyphal fusion genes was reduced upon ste12 deletion; however, the Δste12 mutant showed enhanced expression of mycoparasitism-relevant chitinolytic and proteolytic enzymes and of the cell wall integrity MAP kinase Tmk2. Based on the comparative analyses of Δste12 and Δtmk1 mutants, an essential role of the Ste12 transcriptional regulator in mediating outcomes of the Tmk1 MAPK pathway such as regulation of the mycoparasitic activity, hyphal fusion and carbon source-dependent vegetative growth is suggested. Aerial hyphae formation and conidiation, in contrast, were found to be independent of Ste12. PMID:25356841

Functional characterization of the MKC1 gene of Candida albicans, which encodes a mitogen-activated protein kinase homolog related to cell integrity.

PubMed Central

Navarro-García, F; Sánchez, M; Pla, J; Nombela, C

1995-01-01

Mitogen-activated protein (MAP) kinases represent a group of serine/threonine protein kinases playing a central role in signal transduction processes in eukaryotic cells. Using a strategy based on the complementation of the thermosensitive autolytic phenotype of slt2 null mutants, we have isolated a Candida albicans homolog of Saccharomyces cerevisiae MAP kinase gene SLT2 (MPK1), which is involved in the recently outlined PKC1-controlled signalling pathway. The isolated gene, named MKC1 (MAP kinase from C. albicans), coded for a putative protein, Mkc1p, of 58,320 Da that displayed all the characteristic domains of MAP kinases and was 55% identical to S. cerevisiae Slt2p (Mpk1p). The MKC1 gene was deleted in a diploid Candida strain, and heterozygous and homozygous strains, in both Ura+ and Ura- backgrounds, were obtained to facilitate the analysis of the function of the gene. Deletion of the two alleles of the MKC1 gene gave rise to viable cells that grew at 28 and 37 degrees C but, nevertheless, displayed a variety of phenotypic traits under more stringent conditions. These included a low growth yield and a loss of viability in cultures grown at 42 degrees C, a high sensitivity to thermal shocks at 55 degrees C, an enhanced susceptibility to caffeine that was osmotically remediable, and the formation of a weak cell wall with a very low resistance to complex lytic enzyme preparations. The analysis of the functions downstream of the MKC1 gene should contribute to understanding of the connection of growth and morphogenesis in pathogenic fungi. PMID:7891715

The transcription factor Ste12 mediates the regulatory role of the Tmk1 MAP kinase in mycoparasitism and vegetative hyphal fusion in the filamentous fungus Trichoderma atroviride.

PubMed

Gruber, Sabine; Zeilinger, Susanne

2014-01-01

Mycoparasitic species of the fungal genus Trichoderma are potent antagonists able to combat plant pathogenic fungi by direct parasitism. An essential step in this mycoparasitic fungus-fungus interaction is the detection of the fungal host followed by activation of molecular weapons in the mycoparasite by host-derived signals. The Trichoderma atroviride MAP kinase Tmk1, a homolog of yeast Fus3/Kss1, plays an essential role in regulating the mycoparasitic host attack, aerial hyphae formation and conidiation. However, the transcription factors acting downstream of Tmk1 are hitherto unknown. Here we analyzed the functions of the T. atroviride Ste12 transcription factor whose orthologue in yeast is targeted by the Fus3 and Kss1 MAP kinases. Deletion of the ste12 gene in T. atroviride not only resulted in reduced mycoparasitic overgrowth and lysis of host fungi but also led to loss of hyphal avoidance in the colony periphery and a severe reduction in conidial anastomosis tube formation and vegetative hyphal fusion events. The transcription of several orthologues of Neurospora crassa hyphal fusion genes was reduced upon ste12 deletion; however, the Δste12 mutant showed enhanced expression of mycoparasitism-relevant chitinolytic and proteolytic enzymes and of the cell wall integrity MAP kinase Tmk2. Based on the comparative analyses of Δste12 and Δtmk1 mutants, an essential role of the Ste12 transcriptional regulator in mediating outcomes of the Tmk1 MAPK pathway such as regulation of the mycoparasitic activity, hyphal fusion and carbon source-dependent vegetative growth is suggested. Aerial hyphae formation and conidiation, in contrast, were found to be independent of Ste12.

The major resistance gene cluster in lettuce is highly duplicated and spans several megabases.

PubMed Central

Meyers, B C; Chin, D B; Shen, K A; Sivaramakrishnan, S; Lavelle, D O; Zhang, Z; Michelmore, R W

1998-01-01

At least 10 Dm genes conferring resistance to the oomycete downy mildew fungus Bremia lactucae map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana, which contains Dm3. A deletion breakpoint map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates (RGC2) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome clones were identified by using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion breakpoint map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes, including RGC2, in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over. PMID:9811791

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

van Heyningen, V.; Bickmore, W.A.; Seawright, A.

Detailed molecular definition of the WAGR region at chromosome 11p13 has been achieved by chromosome breakpoint analysis and long-range restriction mapping. Here the authors describe the molecular detection of a cytogenetically invisible 1-megabase deletion in an individual with aniridia, cryptorchidism, and hypospadias but no Wilms tumor (WT). The region of overlap between this deletion and one associated with WT and similar genital anomalies but no aniridia covers a region of 350-400 kilobases, which is coincident with the extent of homozygous deletion detected in tumor tissue from a sporadic WT. A candidate WT gene located within this region has recently beenmore » isolated, suggesting nonpenetrance for tumor expression in the first individual. The inclusion within the overlap region of a gene for WT predisposition and a gene for the best-documented WT-associated genitourinary malformations leads to suggest that both of these anomalies result from a loss-of-function mutation at the same locus. This in turn implies that the WT gene exerts pleiotropic effect on both kidney and genitourinary development, a possibility supported by the observed expression pattern of the WT candidate gene in developing kidney and gonads.« less

A stretch of residues within the protease-resistant core is not necessary for prion structure and infectivity

PubMed Central

Munoz-Montesino, Carola; Sizun, Christina; Moudjou, Mohammed; Herzog, Laetitia; Reine, Fabienne; Igel-Egalon, Angelique; Barbereau, Clément; Chapuis, Jérôme; Ciric, Danica; Laude, Hubert; Béringue, Vincent; Rezaei, Human; Dron, Michel

2017-01-01

ABSTRACT Mapping out regions of PrP influencing prion conversion remains a challenging issue complicated by the lack of prion structure. The portion of PrP associated with infectivity contains the α-helical domain of the correctly folded protein and turns into a β-sheet-rich insoluble core in prions. Deletions performed so far inside this segment essentially prevented the conversion. Recently we found that deletion of the last C-terminal residues of the helix H2 was fully compatible with prion conversion in the RK13-ovPrP cell culture model, using 3 different infecting strains. This was in agreement with preservation of the overall PrPC structure even after removal of up to one-third of this helix. Prions with internal deletion were infectious for cells and mice expressing the wild-type PrP and they retained prion strain-specific characteristics. We thus identified a piece of the prion domain that is neither necessary for the conformational transition of PrPC nor for the formation of a stable prion structure. PMID:28281924

A stretch of residues within the protease-resistant core is not necessary for prion structure and infectivity.

PubMed

Munoz-Montesino, Carola; Sizun, Christina; Moudjou, Mohammed; Herzog, Laetitia; Reine, Fabienne; Igel-Egalon, Angelique; Barbereau, Clément; Chapuis, Jérôme; Ciric, Danica; Laude, Hubert; Béringue, Vincent; Rezaei, Human; Dron, Michel

2017-01-02

Mapping out regions of PrP influencing prion conversion remains a challenging issue complicated by the lack of prion structure. The portion of PrP associated with infectivity contains the α-helical domain of the correctly folded protein and turns into a β-sheet-rich insoluble core in prions. Deletions performed so far inside this segment essentially prevented the conversion. Recently we found that deletion of the last C-terminal residues of the helix H2 was fully compatible with prion conversion in the RK13-ovPrP cell culture model, using 3 different infecting strains. This was in agreement with preservation of the overall PrP C structure even after removal of up to one-third of this helix. Prions with internal deletion were infectious for cells and mice expressing the wild-type PrP and they retained prion strain-specific characteristics. We thus identified a piece of the prion domain that is neither necessary for the conformational transition of PrP C nor for the formation of a stable prion structure.

Genome-Wide Mutational Signature of the Chemotherapeutic Agent Mitomycin C in Caenorhabditis elegans.

PubMed

Tam, Annie S; Chu, Jeffrey S C; Rose, Ann M

2015-11-12

Cancer therapy largely depends on chemotherapeutic agents that generate DNA lesions. However, our understanding of the nature of the resulting lesions as well as the mutational profiles of these chemotherapeutic agents is limited. Among these lesions, DNA interstrand crosslinks are among the more toxic types of DNA damage. Here, we have characterized the mutational spectrum of the commonly used DNA interstrand crosslinking agent mitomycin C (MMC). Using a combination of genetic mapping, whole genome sequencing, and genomic analysis, we have identified and confirmed several genomic lesions linked to MMC-induced DNA damage in Caenorhabditis elegans. Our data indicate that MMC predominantly causes deletions, with a 5'-CpG-3' sequence context prevalent in the deleted regions of DNA. Furthermore, we identified microhomology flanking the deletion junctions, indicative of DNA repair via nonhomologous end joining. Based on these results, we propose a general repair mechanism that is likely to be involved in the biological response to this highly toxic agent. In conclusion, the systematic study we have described provides insight into potential sequence specificity of MMC with DNA. Copyright © 2016 Tam et al.

SNR improvement for hyperspectral application using frame and pixel binning

NASA Astrophysics Data System (ADS)

Rehman, Sami Ur; Kumar, Ankush; Banerjee, Arup

2016-05-01

Hyperspectral imaging spectrometer systems are increasingly being used in the field of remote sensing for variety of civilian and military applications. The ability of such instruments in discriminating finer spectral features along with improved spatial and radiometric performance have made such instruments a powerful tool in the field of remote sensing. Design and development of spaceborne hyper spectral imaging spectrometers poses lot of technological challenges in terms of optics, dispersion element, detectors, electronics and mechanical systems. The main factors that define the type of detectors are the spectral region, SNR, dynamic range, pixel size, number of pixels, frame rate, operating temperature etc. Detectors with higher quantum efficiency and higher well depth are the preferred choice for such applications. CCD based Si detectors serves the requirement of high well depth for VNIR band spectrometers but suffers from smear. Smear can be controlled by using CMOS detectors. Si CMOS detectors with large format arrays are available. These detectors generally have smaller pitch and low well depth. Binning technique can be used with available CMOS detectors to meet the large swath, higher resolution and high SNR requirements. Availability of larger dwell time of satellite can be used to bin multiple frames to increase the signal collection even with lesser well depth detectors and ultimately increase the SNR. Lab measurements reveal that SNR improvement by frame binning is more in comparison to pixel binning. Effect of pixel binning as compared to the frame binning will be discussed and degradation of SNR as compared to theoretical value for pixel binning will be analyzed.

Generalized index for spatial data sets as a measure of complete spatial randomness

NASA Astrophysics Data System (ADS)

Hackett-Jones, Emily J.; Davies, Kale J.; Binder, Benjamin J.; Landman, Kerry A.

2012-06-01

Spatial data sets, generated from a wide range of physical systems can be analyzed by counting the number of objects in a set of bins. Previous work has been limited to equal-sized bins, which are inappropriate for some domains (e.g., circular). We consider a nonequal size bin configuration whereby overlapping or nonoverlapping bins cover the domain. A generalized index, defined in terms of a variance between bin counts, is developed to indicate whether or not a spatial data set, generated from exclusion or nonexclusion processes, is at the complete spatial randomness (CSR) state. Limiting values of the index are determined. Using examples, we investigate trends in the generalized index as a function of density and compare the results with those using equal size bins. The smallest bin size must be much larger than the mean size of the objects. We can determine whether a spatial data set is at the CSR state or not by comparing the values of a generalized index for different bin configurations—the values will be approximately the same if the data is at the CSR state, while the values will differ if the data set is not at the CSR state. In general, the generalized index is lower than the limiting value of the index, since objects do not have access to the entire region due to blocking by other objects. These methods are applied to two applications: (i) spatial data sets generated from a cellular automata model of cell aggregation in the enteric nervous system and (ii) a known plant data distribution.

Meta-analysis of 32 genome-wide linkage studies of schizophrenia

PubMed Central

Ng, MYM; Levinson, DF; Faraone, SV; Suarez, BK; DeLisi, LE; Arinami, T; Riley, B; Paunio, T; Pulver, AE; Irmansyah; Holmans, PA; Escamilla, M; Wildenauer, DB; Williams, NM; Laurent, C; Mowry, BJ; Brzustowicz, LM; Maziade, M; Sklar, P; Garver, DL; Abecasis, GR; Lerer, B; Fallin, MD; Gurling, HMD; Gejman, PV; Lindholm, E; Moises, HW; Byerley, W; Wijsman, EM; Forabosco, P; Tsuang, MT; Hwu, H-G; Okazaki, Y; Kendler, KS; Wormley, B; Fanous, A; Walsh, D; O’Neill, FA; Peltonen, L; Nestadt, G; Lasseter, VK; Liang, KY; Papadimitriou, GM; Dikeos, DG; Schwab, SG; Owen, MJ; O’Donovan, MC; Norton, N; Hare, E; Raventos, H; Nicolini, H; Albus, M; Maier, W; Nimgaonkar, VL; Terenius, L; Mallet, J; Jay, M; Godard, S; Nertney, D; Alexander, M; Crowe, RR; Silverman, JM; Bassett, AS; Roy, M-A; Mérette, C; Pato, CN; Pato, MT; Roos, J Louw; Kohn, Y; Amann-Zalcenstein, D; Kalsi, G; McQuillin, A; Curtis, D; Brynjolfson, J; Sigmundsson, T; Petursson, H; Sanders, AR; Duan, J; Jazin, E; Myles-Worsley, M; Karayiorgou, M; Lewis, CM

2009-01-01

A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (PSR) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for ‘aggregate’ genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies. PMID:19349958

Altered Splicing of the BIN1 Muscle-Specific Exon in Humans and Dogs with Highly Progressive Centronuclear Myopathy

PubMed Central

Böhm, Johann; Vasli, Nasim; Maurer, Marie; Cowling, Belinda; Shelton, G. Diane; Kress, Wolfram; Toussaint, Anne; Prokic, Ivana; Schara, Ulrike; Anderson, Thomas James; Weis, Joachim; Tiret, Laurent; Laporte, Jocelyn

2013-01-01

Amphiphysin 2, encoded by BIN1, is a key factor for membrane sensing and remodelling in different cell types. Homozygous BIN1 mutations in ubiquitously expressed exons are associated with autosomal recessive centronuclear myopathy (CNM), a mildly progressive muscle disorder typically showing abnormal nuclear centralization on biopsies. In addition, misregulation of BIN1 splicing partially accounts for the muscle defects in myotonic dystrophy (DM). However, the muscle-specific function of amphiphysin 2 and its pathogenicity in both muscle disorders are not well understood. In this study we identified and characterized the first mutation affecting the splicing of the muscle-specific BIN1 exon 11 in a consanguineous family with rapidly progressive and ultimately fatal centronuclear myopathy. In parallel, we discovered a mutation in the same BIN1 exon 11 acceptor splice site as the genetic cause of the canine Inherited Myopathy of Great Danes (IMGD). Analysis of RNA from patient muscle demonstrated complete skipping of exon 11 and BIN1 constructs without exon 11 were unable to promote membrane tubulation in differentiated myotubes. Comparative immunofluorescence and ultrastructural analyses of patient and canine biopsies revealed common structural defects, emphasizing the importance of amphiphysin 2 in membrane remodelling and maintenance of the skeletal muscle triad. Our data demonstrate that the alteration of the muscle-specific function of amphiphysin 2 is a common pathomechanism for centronuclear myopathy, myotonic dystrophy, and IMGD. The IMGD dog is the first faithful model for human BIN1-related CNM and represents a mammalian model available for preclinical trials of potential therapies. PMID:23754947

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

PubMed

Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

2017-05-12

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Deterministic Tectonic Origin Tsunami Hazard Analysis for the Eastern Mediterranean and its Connected Seas

NASA Astrophysics Data System (ADS)

Necmioglu, O.; Meral Ozel, N.

2014-12-01

Accurate earthquake source parameters are essential for any tsunami hazard assessment and mitigation, including early warning systems. Complex tectonic setting makes the a priori accurate assumptions of earthquake source parameters difficult and characterization of the faulting type is a challenge. Information on tsunamigenic sources is of crucial importance in the Eastern Mediterranean and its Connected Seas, especially considering the short arrival times and lack of offshore sea-level measurements. In addition, the scientific community have had to abandon the paradigm of a ''maximum earthquake'' predictable from simple tectonic parameters (Ruff and Kanamori, 1980) in the wake of the 2004 Sumatra event (Okal, 2010) and one of the lessons learnt from the 2011 Tohoku event was that tsunami hazard maps may need to be prepared for infrequent gigantic earthquakes as well as more frequent smaller-sized earthquakes (Satake, 2011). We have initiated an extensive modeling study to perform a deterministic Tsunami Hazard Analysis for the Eastern Mediterranean and its Connected Seas. Characteristic earthquake source parameters (strike, dip, rake, depth, Mwmax) at each 0.5° x 0.5° size bin for 0-40 km depth (total of 310 bins) and for 40-100 km depth (total of 92 bins) in the Eastern Mediterranean, Aegean and Black Sea region (30°N-48°N and 22°E-44°E) have been assigned from the harmonization of the available databases and previous studies. These parameters have been used as input parameters for the deterministic tsunami hazard modeling. Nested Tsunami simulations of 6h duration with a coarse (2 arc-min) and medium (1 arc-min) grid resolution have been simulated at EC-JRC premises for Black Sea and Eastern and Central Mediterranean (30°N-41.5°N and 8°E-37°E) for each source defined using shallow water finite-difference SWAN code (Mader, 2004) for the magnitude range of 6.5 - Mwmax defined for that bin with a Mw increment of 0.1. Results show that not only the earthquakes resembling the well-known historical earthquakes such as AD 365 or AD 1303 in the Hellenic Arc, but also earthquakes with lower magnitudes do constitute to the tsunami hazard in the study area.

Uncertainty in Modeling Dust Mass Balance and Radiative Forcing from Size Parameterization

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

Zhao, Chun; Chen, Siyu; Leung, Lai-Yung R.

2013-11-05

This study examines the uncertainties in simulating mass balance and radiative forcing of mineral dust due to biases in the aerosol size parameterization. Simulations are conducted quasi-globally (180oW-180oE and 60oS-70oN) using the WRF24 Chem model with three different approaches to represent aerosol size distribution (8-bin, 4-bin, and 3-mode). The biases in the 3-mode or 4-bin approaches against a relatively more accurate 8-bin approach in simulating dust mass balance and radiative forcing are identified. Compared to the 8-bin approach, the 4-bin approach simulates similar but coarser size distributions of dust particles in the atmosphere, while the 3-mode pproach retains more finemore » dust particles but fewer coarse dust particles due to its prescribed og of each mode. Although the 3-mode approach yields up to 10 days longer dust mass lifetime over the remote oceanic regions than the 8-bin approach, the three size approaches produce similar dust mass lifetime (3.2 days to 3.5 days) on quasi-global average, reflecting that the global dust mass lifetime is mainly determined by the dust mass lifetime near the dust source regions. With the same global dust emission (~6000 Tg yr-1), the 8-bin approach produces a dust mass loading of 39 Tg, while the 4-bin and 3-mode approaches produce 3% (40.2 Tg) and 25% (49.1 Tg) higher dust mass loading, respectively. The difference in dust mass loading between the 8-bin approach and the 4-bin or 3-mode approaches has large spatial variations, with generally smaller relative difference (<10%) near the surface over the dust source regions. The three size approaches also result in significantly different dry and wet deposition fluxes and number concentrations of dust. The difference in dust aerosol optical depth (AOD) (a factor of 3) among the three size approaches is much larger than their difference (25%) in dust mass loading. Compared to the 8-bin approach, the 4-bin approach yields stronger dust absorptivity, while the 3-mode approach yields weaker dust absorptivity. Overall, on quasi-global average, the three size parameterizations result in a significant difference of a factor of 2~3 in dust surface cooling (-1.02~-2.87 W m-2) and atmospheric warming (0.39~0.96 W m-2) and in a tremendous difference of a factor of ~10 in dust TOA cooling (-0.24~-2.20 W m-2). An uncertainty of a factor of 2 is quantified in dust emission estimation due to the different size parameterizations. This study also highlights the uncertainties in modeling dust mass and number loading, deposition fluxes, and radiative forcing resulting from different size parameterizations, and motivates further investigation of the impact of size parameterizations on modeling dust impacts on air quality, climate, and ecosystem.« less

Low-Temperature Effects on the Design and Performance of Composting of Explosives-Contaminated Soils

DTIC Science & Technology

1991-03-01

7 7. Aerated bins used in field composting tests on dairy manure ............................. 10 8. Typical temperature developed...during bin compostiag of dairy manure under conditions of constant airflow and optimum moisture ................. 10 9. Effect of agitation on the...temperature profile during bin composting of dairy manure

16 CFR 1301.6 - Test conditions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Test conditions. 1301.6 Section 1301.6... UNSTABLE REFUSE BINS § 1301.6 Test conditions. (a) The refuse bin shall be empty and have its lids or covers in a position which would most adversely affect the stability of the bin when tested. (b) The...

16 CFR 1301.6 - Test conditions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Test conditions. 1301.6 Section 1301.6... UNSTABLE REFUSE BINS § 1301.6 Test conditions. (a) The refuse bin shall be empty and have its lids or covers in a position which would most adversely affect the stability of the bin when tested. (b) The...

16 CFR 1301.6 - Test conditions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test conditions. 1301.6 Section 1301.6... UNSTABLE REFUSE BINS § 1301.6 Test conditions. (a) The refuse bin shall be empty and have its lids or covers in a position which would most adversely affect the stability of the bin when tested. (b) The...

90. Photographic copy of plan of bins, section of boot, ...

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

90. Photographic copy of plan of bins, section of boot, and photograph of construction originally published in Plans of Grain Elevators (Chicago; Grain Dealers Journal, 1918), p.53. PLAN OF BINS; SECTION OF BOOT; VIEW OF CONSTRUCTION LOOKING NORTHWEST - Northwestern Consolidated Elevator "A", 119 Fifth Avenue South, Minneapolis, Hennepin County, MN

Increasing donations to supermarket food-bank bins using proximal prompts.

PubMed

Farrimond, Samantha J; Leland, Louis S

2006-01-01

There has been little research into interventions to increase participation in donating items to food-bank bins. In New Zealand, there has been an increased demand from food banks (Stewart, 2002). This study demonstrated that point-of-sale prompts can be an effective method of increasing donations to a supermarket food-bank bin.

64. NORTH WALL OF CRUSHED OXIDIZED ORE BIN. THE PRIMARY ...

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

64. NORTH WALL OF CRUSHED OXIDIZED ORE BIN. THE PRIMARY MILL FEEDS AT BOTTOM. MILL SOLUTION TANKS WERE TO THE LEFT (EAST) AND BARREN SOLUTION TANK TO THE RIGHT (WEST) OR THE CRUSHED ORE BIN. - Bald Mountain Gold Mill, Nevada Gulch at head of False Bottom Creek, Lead, Lawrence County, SD

Identification of Candidate Genes Underlying an Iron Efficiency Quantitative Trait Locus in Soybean1

PubMed Central

Peiffer, Gregory A.; King, Keith E.; Severin, Andrew J.; May, Gregory D.; Cianzio, Silvia R.; Lin, Shun Fu; Lauter, Nicholas C.; Shoemaker, Randy C.

2012-01-01

Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean (Glycine max) commercial plantings, the identification and use of iron-efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency quantitative trait locus (QTL) explaining more than 70% of the phenotypic variation for the trait. In this research, we identified candidate genes underlying this QTL through molecular breeding, mapping, and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines in which a region located on soybean chromosome 3 required for iron efficiency was identified. The region corresponds to the previously reported iron efficiency QTL. The location was further confirmed through QTL mapping conducted in this study. Transcriptome sequencing and quantitative real-time-polymerase chain reaction identified two genes encoding transcription factors within the region that were significantly induced in soybean roots under iron stress. The two induced transcription factors were identified as homologs of the subgroup lb basic helix-loop-helix (bHLH) genes that are known to regulate the strategy I response in Arabidopsis (Arabidopsis thaliana). Resequencing of these differentially expressed genes unveiled a significant deletion within a predicted dimerization domain. We hypothesize that this deletion disrupts the Fe-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT)/bHLH heterodimer that has been shown to induce known iron acquisition genes. PMID:22319075

Detailed clinical and molecular study of 20 females with Xq deletions with special reference to menstruation and fertility.

PubMed

Mercer, Catherine L; Lachlan, Katherine; Karcanias, Alexandra; Affara, Nabeel; Huang, Shuwen; Jacobs, Patricia A; Thomas, N Simon

2013-01-01

Integrity of the long arm of the X chromosome is important for maintaining female fertility and several critical regions for normal ovarian function have been proposed. In order to understand further the importance of specific areas of the X chromosome, we describe a series of 20 previously unreported patients missing part of Xq in whom detailed phenotypic information has been gathered as well as precise chromosome mapping using array Comparative Genomic Hybridization. Features often associated with Turner syndrome were not common in our study and excluding puberty, menarche and menstruation, the phenotypes observed were present in only a minority of women and were not specific to the X chromosome. The most frequently occurring phenotypic features in our patients were abnormalities of menstruation and fertility. Larger terminal deletions were associated with a higher incidence of primary ovarian failure, occurring at a younger age; however patients with similar or even identical deletions had discordant menstrual phenotypes, making accurate genetic counselling difficult. Nevertheless, large deletions are likely to be associated with complete skewing of X inactivation so that the resulting phenotypes are relatively benign given the amount of genetic material missing, even in cases with unbalanced X;autosome translocations. Some degree of ovarian dysfunction is highly likely, especially for terminal deletions extending proximal to Xq27. In conjunction with patient data from the literature, our study suggests that loss of Xq26-Xq28 has the most significant effect on ovarian function. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

A map of copy number variations in Chinese populations.

PubMed

Lou, Haiyi; Li, Shilin; Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.

A Map of Copy Number Variations in Chinese Populations

PubMed Central

Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies. PMID:22087296

An 18-ps TDC using timing adjustment and bin realignment methods in a Cyclone-IV FPGA

NASA Astrophysics Data System (ADS)

Cao, Guiping; Xia, Haojie; Dong, Ning

2018-05-01

The method commonly used to produce a field-programmable gate array (FPGA)-based time-to-digital converter (TDC) creates a tapped delay line (TDL) for time interpolation to yield high time precision. We conduct timing adjustment and bin realignment to implement a TDC in the Altera Cyclone-IV FPGA. The former tunes the carry look-up table (LUT) cell delay by changing the LUT's function through low-level primitives according to timing analysis results, while the latter realigns bins according to the timing result obtained by timing adjustment so as to create a uniform TDL with bins of equivalent width. The differential nonlinearity and time resolution can be improved by realigning the bins. After calibration, the TDC has a 18 ps root-mean-square timing resolution and a 45 ps least-significant bit resolution.

Political orientation moderates worldview defense in response to Osama bin Laden’s death

PubMed Central

Chopik, William J.; Konrath, Sara H.

2016-01-01

The current study examines Americans’ psychological responses to Osama bin Laden’s death. We tracked changes in how different participants responded to dissimilar others from the night of bin Laden’s death for five weeks. Liberal participants reported lower worldview defense (i.e., a defensive reaction to uphold one’s cultural worldview) immediately after bin Laden’s death but then returned to similar levels as their conservative counterparts over time. Conservative participants reported greater worldview defense during each point of the study and did not significantly change over time. These temporal differences between liberals and conservatives were only present in the year of bin Laden’s death and not one year prior before. The current findings demonstrate that liberals and conservatives may react differently after major societal events in predictable ways considering their moral foundations. PMID:28239251

Genetic organization of the unc-22 IV gene and the adjacent region in Caenorhabditis elegans.

PubMed

Rogalski, T M; Baillie, D L

1985-01-01

The genetic organization of the region immediately adjacent to the unc-22 IV gene in Caenorhabditis elegans has been studied. We have identified twenty essential genes in this interval of approximately 1.5-map units on Linkage Group IV. The mutations that define these genes were positioned by recombination mapping and complementation with several deficiencies. With few exceptions, the positions obtained by these two methods agreed. Eight of the twenty essential genes identified are represented by more than one allele. Three possible internal deletions of the unc-22 gene have been located by intra-genic mapping. In addition, the right end point of a deficiency or an inversion affecting the adjacent genes let-56 and unc-22 has been positioned inside the unc-22 gene.

Use of nonpathogenic, green fluorescent protein-marked Escherichia coli Biotype I cultures to evaluate the self-cleansing capabilities of a commercial beef grinding system after a contamination event.

PubMed

Wages, Jennifer A; Williams, Jennifer; Adams, Jacquelyn; George, Bruce; Oxford, Eric; Zelenka, Dan

2014-11-01

Inoculated beef trim containing a cocktail of green fluorescent protein-marked Escherichia coli biotype I cultures as surrogates for E. coli O157:H7 was introduced into two large, commercial grinding facilities capable of producing 180,000 kg of ground product in 1 day. Three repetitions were performed over 3 days. Sampling occurred at three different points within the process: postprimary grind, postsecondary grind-blender, and postpackaging. Resulting data show that, as the inoculated meat passes through the system, the presence of the marked surrogate quickly diminishes. The depletion rates are directly related to the amount of product in kilograms (represented by time) that has passed through the system, but these rates vary with each step of the process. The primary grinder appears to rid itself of the contaminant the most quickly; in all repetitions, the contaminant was not detected within 5 min of introduction of the contaminated combo bin into the system, which in all cases, was prior to the introduction of a second combo bin and within 1,800 kg of product. After the blending step and subsequent secondary grinding, the contaminant was detected in product produced from both the parent combo and the combo bin added directly after the parent combo bin; however, for those days on which three combo bins (approximately 2,700 kg) were available for sampling, the contaminant was not detected from product representing the third combo bin. Similarly, at the packaging step, the contaminant was detected in the product produced by both the parent and second combo bins; however, on those days when a third combo bin was available for sampling (repetitions 2 and 3), the contaminant was not detected from product produced from the third combo bin.

Small cell ovarian carcinoma: genomic stability and responsiveness to therapeutics.

PubMed

Gamwell, Lisa F; Gambaro, Karen; Merziotis, Maria; Crane, Colleen; Arcand, Suzanna L; Bourada, Valerie; Davis, Christopher; Squire, Jeremy A; Huntsman, David G; Tonin, Patricia N; Vanderhyden, Barbara C

2013-02-21

The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. The tumourigenic potential of BIN-67 cells was determined and the tumours formed in a xenograft model was compared to human SCCOHT. DNA sequencing, spectral karyotyping and high density SNP array analysis was performed. The sensitivity of the BIN-67 cells to standard chemotherapeutic agents and to vesicular stomatitis virus (VSV) and the JX-594 vaccinia virus was tested. BIN-67 cells were capable of forming spheroids in hanging drop cultures. When xenografted into immunodeficient mice, BIN-67 cells developed into tumours that reflected the hypercalcemia and histology of human SCCOHT, notably intense expression of WT-1 and vimentin, and lack of expression of inhibin. Somatic mutations in TP53 and the most common activating mutations in KRAS and BRAF were not found in BIN-67 cells by DNA sequencing. Spectral karyotyping revealed a largely normal diploid karyotype (in greater than 95% of cells) with a visibly shorter chromosome 20 contig. High density SNP array analysis also revealed few genomic anomalies in BIN-67 cells, which included loss of heterozygosity of an estimated 16.7 Mb interval on chromosome 20. SNP array analyses of four SCCOHT samples also indicated a low frequency of genomic anomalies in the majority of cases. Although resistant to platinum chemotherapeutic drugs, BIN-67 cell viability in vitro was reduced by > 75% after infection with oncolytic viruses. These results show that SCCOHT differs from high-grade serous carcinomas by exhibiting few chromosomal anomalies and lacking TP53 mutations. Although BIN-67 cells are resistant to standard chemotherapeutic agents, their sensitivity to oncolytic viruses suggests that their therapeutic use in SCCOHT should be considered.

Method of multiplexed analysis using ion mobility spectrometer

DOEpatents

Belov, Mikhail E [Richland, WA; Smith, Richard D [Richland, WA

2009-06-02

A method for analyzing analytes from a sample introduced into a Spectrometer by generating a pseudo random sequence of a modulation bins, organizing each modulation bin as a series of submodulation bins, thereby forming an extended pseudo random sequence of submodulation bins, releasing the analytes in a series of analyte packets into a Spectrometer, thereby generating an unknown original ion signal vector, detecting the analytes at a detector, and characterizing the sample using the plurality of analyte signal subvectors. The method is advantageously applied to an Ion Mobility Spectrometer, and an Ion Mobility Spectrometer interfaced with a Time of Flight Mass Spectrometer.

Radiometric age map of Aleutian Islands

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southcentral Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southwest Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southeast Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of northern Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans.

PubMed

Green, J W M; Snoek, L B; Kammenga, J E; Harvey, S C

2013-10-01

In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly investigated. Here, we report extensive natural genetic variation in dauer larvae development within growing populations across multiple wild isolates. Moreover, bin mapping of introgression lines (ILs) derived from the genetically divergent isolates N2 and CB4856 reveals 10 quantitative trait loci (QTLs) affecting dauer formation. Comparison of individual ILs to N2 identifies an additional eight QTLs, and sequential IL analysis reveals six more QTLs. Our results also show that a behavioural, laboratory-derived, mutation controlled by the neuropeptide Y receptor homolog npr-1 can affect dauer larvae development in growing populations. These findings illustrate the complex genetic architecture of variation in dauer larvae formation in C. elegans and may help to understand how the control of variation in dauer larvae development has evolved.

SAMPEX/PET model of the low altitude trapped proton environment

NASA Astrophysics Data System (ADS)

Heynderickx, D.; Looper, M. D.; Blake, J. B.

The low-altitude trapped proton population exhibits strong time variations related to geomagnetic secular variation and neutral atmosphere conditions. The flux measurements of the Proton Electron Telescope (PET) onboard the polar satellite SAMPEX constitute an adequate data set to distinguish different time scales and to characterise the respective variations. As a first step towards building a dynamic model of the low altitude proton environment we binned the 1995-1996 PET data into a model map with functional dependencies of the proton fluxes on the F10.7 solar radio flux and on the time of year to represent variations on the time scale of the solar cycle and seasonal variations. Now, a full solar cycle of SAMPEX/PET data is available, so that the preliminary model could be extended. The secular variation of the geomagnetic field is included in the model, as it is constructed using Kaufmann's K=I √{B} instead of McIlwain's L as a map coordinate.

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

PubMed Central

Zhang, Kai; Fan, Guangyu; Zhang, Xinxin; Zhao, Fang; Wei, Wei; Du, Guohua; Feng, Xiaolei; Wang, Xiaoming; Wang, Feng; Song, Guoliang; Zou, Hongfeng; Zhang, Xiaolei; Li, Shuangdong; Ni, Xuemei; Zhang, Gengyun; Zhao, Zhihai

2017-01-01

Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding. PMID:28364039

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing.

PubMed

Zhang, Kai; Fan, Guangyu; Zhang, Xinxin; Zhao, Fang; Wei, Wei; Du, Guohua; Feng, Xiaolei; Wang, Xiaoming; Wang, Feng; Song, Guoliang; Zou, Hongfeng; Zhang, Xiaolei; Li, Shuangdong; Ni, Xuemei; Zhang, Gengyun; Zhao, Zhihai

2017-05-05

Foxtail millet ( Setaria italica ) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding. Copyright © 2017 Zhang et al.

40 CFR 1037.520 - Modeling CO2 emissions to show compliance.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Test and Modeling..., expressed in m2 and rounded to two decimal places. Where we allow you to group multiple configurations... bin based on the drag area bin of an equivalent high-roof tractor. If the high-roof tractor is in Bin...

40 CFR 1037.520 - Modeling CO2 emissions to show compliance.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Test and Modeling... to two decimal places. Where we allow you to group multiple configurations together, measure the drag... the drag area bin of an equivalent high-roof tractor. If the high-roof tractor is in Bin I or Bin II...

40 CFR 1037.520 - Modeling CO2 emissions to show compliance.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW HEAVY-DUTY MOTOR VEHICLES Test and Modeling... to two decimal places. Where we allow you to group multiple configurations together, measure the drag... the drag area bin of an equivalent high-roof tractor. If the high-roof tractor is in Bin I or Bin II...

A compost bin for handling privy wastes: its fabrication and use

Treesearch

R.E. Leonard; S.C. Fay

1978-01-01

A 24-ft3 (6.8-m3) fiberglass bin was constructed and tested for its effectiveness in composting privy wastes. A mixture of ground hardwood bark and raw sewage was used for composting. Temperatures in excess of 60°C for 36 hours were produced in the bin by aerobic, thermophilic composting. This temperature is...

Development of a Novel Therapeutic Paradigm Utilizing a Mammary Gland-Targeted, Bin-1 Knockout Mouse Model

DTIC Science & Technology

2007-03-01

Cell. Biol. 23, 4295 (Jun, 2003). Bin1 Ablation in Mammary Gland Delays Tissue Remodeling and Drives Cancer Progression Mee Young Chang, 1...Basu A, et al. Bin1 functionally interacts with Myc in cells and inhibits cell proliferation by multiple mechanisms. Oncogene 1999;18:3564–73. 5. Pineda

Causes of Students' Violence at Al-Hussein Bin Talal University

ERIC Educational Resources Information Center

Alrawwad, Theeb M.; Alrfooh, Atif Eid

2014-01-01

This study aimed at identifying the causes of students' violence from the student's point of view, and also aimed at investigating the proper solutions to reduce the spread of violence at Al-Hussein Bin Talal University. The study sample consisted of (906) male and female students from Al-Hussein Bin Talal University, who have enrolled the summer…

Conservative Bin-to-Bin Fractional Collisions

DTIC Science & Technology

2016-06-28

BIN FRACTIONAL COLLISIONS Robert Martin ERC INC., SPACECRAFT PROPULSION BRANCH AIR FORCE RESEARCH LABORATORY EDWARDS AIR FORCE BASE, CA USA 30th...IMPORTANCE OF COLLISION PHYSICS Important Collisions in Spacecraft Propulsion : Discharge and Breakdown in FRC Collisional Radiative Cooling/Ionization...UNLIMITED; PA #16326 3 / 18 IMPORTANCE OF COLLISION PHYSICS Important Collisions in Spacecraft Propulsion : Discharge and Breakdown in FRC Collisional

Development and preliminary evaluation of a new bin filler for apple harvesting and and infield sorting

USDA-ARS?s Scientific Manuscript database

The bin filler, which is used for filling the fruit container or bin with apples coming from the sorting system, plays a critical role for the self-propelled apple harvest and infield sorting (HIS) machine that is being developed in our laboratory. Two major technical challenges in developing the bi...

Development of a new bin filler for apple harvesting and infield sorting with a review of existing technologies

USDA-ARS?s Scientific Manuscript database

The bin filler, which receives apples from the sorting system and then places them in the bin evenly without causing bruise damage, plays a critical role for the self-propelled apple harvest and infield sorting (HIS) machine that is being developed in our laboratory. Two major technical challenges ...

A Software Assurance Framework for Mitigating the Risks of Malicious Software in Embedded Systems Used in Aircraft

DTIC Science & Technology

2011-09-01

to show cryptographic signature # generation on a UNIX system # SHA=/bin/ sha256 CSDB=/tmp/csdb CODEBASE=. touch "$CSDB" find "$CODEBASE" -type f...artifacts generated earlier. 81 #! /bin/sh # # Demo program to show cryptographic signature # verification on a UNIX system # SHA=/bin/ sha256 CSDB=/tmp