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Sample records for analyzing segmental duplications

  1. Association of microsatellite pairs with segmental duplications in insect genomes

    PubMed Central

    2013-01-01

    Background Segmental duplications (SDs), also known as low-copy repeats, are DNA sequences of length greater than 1 kb which are duplicated with a high degree of sequence identity (greater than 90%) causing instability in genomes. SDs are generally found in the genome as mosaic forms of duplicated sequences which are generated by a two-step process: first, multiple duplicated sequences are aggregated at specific genomic regions, and then, these primary duplications undergo multiple secondary duplications. However, the mechanism of how duplicated sequences are aggregated in the first place is not well understood. Results By analyzing the distribution of microsatellite sequences among twenty insect species in a genome-wide manner it was found that pairs of microsatellites along with the intervening sequences were duplicated multiple times in each genome. They were found as low copy repeats or segmental duplications when the duplicated loci were greater than 1 kb in length and had greater than 90% sequence similarity. By performing a sliding-window genomic analysis for number of paired microsatellites and number of segmental duplications, it was observed that regions rich in repetitive paired microsatellites tend to get richer in segmental duplication suggesting a “rich-gets-richer” mode of aggregation of the duplicated loci in specific regions of the genome. Results further show that the relationship between number of paired microsatellites and segmental duplications among the species is independent of the known phylogeny suggesting that association of microsatellites with segmental duplications may be a species-specific evolutionary process. It was also observed that the repetitive microsatellite pairs are associated with gene duplications but those sequences are rarely retained in the orthologous genes between species. Although some of the duplicated sequences with microsatellites as termini were found within transposable elements (TEs) of Drosophila, most of

  2. Duplication of coding segments in genetic programming

    SciTech Connect

    Haynes, T.

    1996-12-31

    Research into the utility of non-coding segments, or introns, in genetic-based encodings has shown that they expedite the evolution of solutions in domains by protecting building blocks against destructive crossover. We consider a genetic programming system where non-coding segments can be removed, and the resultant chromosomes returned into the population. This parsimonious repair leads to premature convergence, since as we remove the naturally occurring non-coding segments, we strip away their protective backup feature. We then duplicate the coding segments in the repaired chromosomes, and place the modified chromosomes into the population. The duplication method significantly improves the learning rate in the domain we have considered. We also show that this method can be applied to other domains.

  3. Chromosomal Translocation and Segmental Duplication in Cryptococcus neoformans†

    PubMed Central

    Fraser, James A.; Huang, Johnny C.; Pukkila-Worley, Read; Alspaugh, J. Andrew; Mitchell, Thomas G.; Heitman, Joseph

    2005-01-01

    Large chromosomal events such as translocations and segmental duplications enable rapid adaptation to new environments. Here we marshal genomic, genetic, meiotic mapping, and physical evidence to demonstrate that a chromosomal translocation and segmental duplication occurred during construction of a congenic strain pair in the fungal human pathogen Cryptococcus neoformans. Two chromosomes underwent telomere-telomere fusion, generating a dicentric chromosome that broke to produce a chromosomal translocation, forming two novel chromosomes sharing a large segmental duplication. The duplication spans 62,872 identical nucleotides and generated a second copy of 22 predicted genes, and we hypothesize that this event may have occurred during meiosis. Gene disruption studies of one embedded gene (SMG1) corroborate that this region is duplicated in an otherwise haploid genome. These findings resolve a genome project assembly anomaly and illustrate an example of rapid genome evolution in a fungal genome rich in repetitive elements. PMID:15701802

  4. Analysis of recent segmental duplications in the bovine genome

    USDA-ARS?s Scientific Manuscript database

    Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We describe the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimat...

  5. Retrotransposon "Qian" mediated segmental duplication in silkworm, Bombyx mori.

    PubMed

    Xu, Yunmin; Jiang, Ning; Zou, Ziliang; Tu, Zhijian; Chen, Anli; Zhao, Qiaoling; Xiang, Zhonghuai; He, Ningjia

    2014-03-01

    Transposable elements constitute a large fraction of the eukaryotic genomes. They have the potential to alter genome structure and play a major role in genome evolution. Here, we report a segmental duplication mediated by a novel long terminal repeat (LTR) retrotransposon as the cause of an egg-shell recessive lethal mutant (l-em mutant) in silkworm (Bombyx mori). The segmental duplication resulted in the duplication of six genes and the disruption of two genes. Disruption of BmEP80 (B. mori egg protein 80), a gene encoding a major egg-shell structure protein, is likely responsible for the lethal water-loss phenotype in the l-em/l-em mutant. Our data revealed that BmEP80 is present in the inner egg-shell layer and plays important roles in resistance to water efflux form eggs. A novel LTR retrotransposon (named as "Qian") was identified and the model for the Qian-mediated chromosomal segmental duplication was proposed. Detail biochemical and genomic analyses on the l-em mutant offer an opportunity to demonstrate that an LTR retrotransposon could trigger duplication of a chromosomal segment (∼96.3 kb) and confer novel phenotype.

  6. The origins and impact of primate segmental duplications

    PubMed Central

    Marques-Bonet, Tomas; Girirajan, Santhosh; Eichler, Evan E.

    2009-01-01

    Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses. PMID:19796838

  7. A segmental genomic duplication generates a functional intron

    PubMed Central

    Hellsten, Uffe; Aspden, Julie L.; Rio, Donald C.; Rokhsar, Daniel S.

    2011-01-01

    An intron is an extended genomic feature whose function requires multiple constrained positions—donor and acceptor splice sites, a branch point, a polypyrimidine tract and suitable splicing enhancers—that may be distributed over hundreds or thousands of nucleotides. New introns are therefore unlikely to emerge by incremental accumulation of functional sub-elements. Here we demonstrate that a functional intron can be created de novo in a single step by a segmental genomic duplication. This experiment recapitulates in vivo the birth of an intron that arose in the ancestral jawed vertebrate lineage nearly half-a-billion years ago. PMID:21878908

  8. Use of FISH for determining duplication of segments of chromosomes: Analysis of a chromosome 9q34 duplication in Tuberous sclerosis

    SciTech Connect

    Bengtsson, U.; Williams, L.; Flodman, K.P.

    1994-09-01

    FISH analysis of interphase nuclei has facilitated identification of segments of DNA duplication. In equating the presence of 3 signals for a particular DNA probe in interphase nuclei to the presence of a duplication, duplication events must be distinguished from replication. Frequency of replication events is reduced by synchronizing cell cultures to obtain a very high percentage of G1 nuclei. We demonstrated that although it is possible to synchronize fibroblast cultures, it is very difficult to totally synchronize lymphoblastoid cells. An appropriate control to distinguish duplication and replication events is the use of a second DNA probe close to the duplication region but outside of the duplication. In analyzing the chromosome 9q34 duplication in a sporadic case of Tuberous sclerosis we examined interphase nuclei using one fluorescein labelled probe from within the duplicated region, and a second rhodamine labelled probe which mapped outside the duplication. Nuclei were scored as having 2 or 3 red signals and 2 or 3 yellow signals. We used as a test statistic McNemar`s chi square for matched observations (one tailed test). Using this form of analysis we were able to demonstrate that lymphoblasts from the patient showed 3 D9S66 signals significantly more often than 3 DBH signals (p<.005). Three signals were demonstrated significantly more frequently using a D9S66 contiguous cosmid than with the CEL locus cosmid in patient`s lymphoblasts (p<.005) and in patient`s fibroblasts.

  9. SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region

    PubMed Central

    HOUSLEY, D. J. E.; NIKOLAS, M.; VENTA, P. J.; JERNIGAN, K. A.; WALDMAN, I. D.; NIGG, J. T.; FRIDERICI, K. H.

    2009-01-01

    SUMMARY The dopamine receptor 5 gene (DRD5) holds much promise as a candidate locus for contributing to neuropsychiatric disorders and other diseases influenced by the dopaminergic system, as well as having potential to affect normal behavioral variation. However, detailed analyses of this gene have been complicated by its location within a segmentally duplicated chromosomal region. Microsatellites and SNPs upstream from the coding region have been used for association studies, but we find, using bioinformatics resources, that these markers all lie within a previously unrecognized second segmental duplication (SD). In order to accurately analyze the DRD5 locus for polymorphisms in the absence of contaminating pseudogene sequences, we developed a fast and reliable method for sequence analysis and genotyping within the DRD5 coding region. We employed restriction enzyme digestion of genomic DNA to eliminate the pseudogenes prior to PCR amplification of the functional gene. This approach allowed us to determine the DRD5 haplotype structure using 31 trios and to reveal additional rare variants in 171 unrelated individuals. We clarify the inconsistencies and errors of the recorded SNPs in dbSNP and HapMap and illustrate the importance of using caution when choosing SNPs in regions of suspected duplications. The simple and relatively inexpensive method presented herein allows for convenient analysis of sequence variation in DRD5 and can be easily adapted to other duplicated genomic regions in order to obtain good quality sequence data. PMID:19397556

  10. SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region.

    PubMed

    Housley, Donna J E; Nikolas, Molly; Venta, Patrick J; Jernigan, Kathrine A; Waldman, Irwin D; Nigg, Joel T; Friderici, Karen H

    2009-05-01

    The dopamine receptor 5 gene (DRD5) holds much promise as a candidate locus for contributing to neuropsychiatric disorders and other diseases influenced by the dopaminergic system, as well as having potential to affect normal behavioral variation. However, detailed analyses of this gene have been complicated by its location within a segmentally duplicated chromosomal region. Microsatellites and SNPs upstream from the coding region have been used for association studies, but we find, using bioinformatics resources, that these markers all lie within a previously unrecognized second segmental duplication (SD). In order to accurately analyze the DRD5 locus for polymorphisms in the absence of contaminating pseudogene sequences, we developed a fast and reliable method for sequence analysis and genotyping within the DRD5 coding region. We employed restriction enzyme digestion of genomic DNA to eliminate the pseudogenes prior to PCR amplification of the functional gene. This approach allowed us to determine the DRD5 haplotype structure using 31 trios and to reveal additional rare variants in 171 unrelated individuals. We clarify the inconsistencies and errors of the recorded SNPs in dbSNP and HapMap and illustrate the importance of using caution when choosing SNPs in regions of suspected duplications. The simple and relatively inexpensive method presented herein allows for convenient analysis of sequence variation in DRD5 and can be easily adapted to other duplicated genomic regions in order to obtain good quality sequence data.

  11. Generating new prions by targeted mutation or segment duplication

    PubMed Central

    Paul, Kacy R.; Hendrich, Connor G.; Waechter, Aubrey; Harman, Madison R.; Ross, Eric D.

    2015-01-01

    Yeasts contain various protein-based genetic elements, termed prions, that result from the structural conversion of proteins into self-propagating amyloid forms. Most yeast prion proteins contain glutamine/asparagine (Q/N)-rich prion domains that drive prion activity. Here, we explore two mechanisms by which new prion domains could evolve. First, it has been proposed that mutation and natural selection will tend to result in proteins with aggregation propensities just low enough to function under physiological conditions and thus that a small number of mutations are often sufficient to cause aggregation. We hypothesized that if the ability to form prion aggregates was a sufficiently generic feature of Q/N-rich domains, many nonprion Q/N-rich domains might similarly have aggregation propensities on the edge of prion formation. Indeed, we tested four yeast Q/N-rich domains that had no detectable aggregation activity; in each case, a small number of rationally designed mutations were sufficient to cause the proteins to aggregate and, for two of the domains, to create prion activity. Second, oligopeptide repeats are found in multiple prion proteins, and expansion of these repeats increases prion activity. However, it is unclear whether the effects of repeat expansion are unique to these specific sequences or are a generic result of adding additional aggregation-prone segments into a protein domain. We found that within nonprion Q/N-rich domains, repeating aggregation-prone segments in tandem was sufficient to create prion activity. Duplication of DNA elements is a common source of genetic variation and may provide a simple mechanism to rapidly evolve prion activity. PMID:26100899

  12. Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR.

    PubMed

    Tai, Derek J C; Ragavendran, Ashok; Manavalan, Poornima; Stortchevoi, Alexei; Seabra, Catarina M; Erdin, Serkan; Collins, Ryan L; Blumenthal, Ian; Chen, Xiaoli; Shen, Yiping; Sahin, Mustafa; Zhang, Chengsheng; Lee, Charles; Gusella, James F; Talkowski, Michael E

    2016-03-01

    Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent a valuable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, single-guide CRISPR/Cas targeting of repetitive elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11.2 and 15q13.3, including alteration of one copy-equivalent of the SDs that mediate NAHR in vivo. The method is reproducible, and RNA sequencing reliably clusters transcriptional signatures from human subjects with in vivo CNVs and their corresponding in vitro models. This new approach will provide broad applicability for the study of genomic disorders and, with further development, may also permit efficient correction of these defects.

  13. Gene structure variation in segmental duplication block C of human chromosome 7q 11.23 during primate evolution.

    PubMed

    Kim, Yun-Ji; Ahn, Kung; Gim, Jeong-An; Oh, Man Hwan; Han, Kyudong; Kim, Heui-Soo

    2015-12-01

    Segmental duplication, or low-copy repeat (LCR) event, occurs during primate evolution and is an important source of genomic diversity, including gain or loss of gene function. The human chromosome 7q 11.23 is related to the William-Beuren syndrome and contains large region-specific LCRs composed of blocks A, B, and C that have different copy numbers in humans and different primates. We analyzed the structure of POM121, NSUN5, FKBP6, and TRIM50 genes in the LCRs of block C. Based on computational analysis, POM121B created by a segmental duplication acquired a new exonic region, whereas NSUN5B (NSUN5C) showed structural variation by integration of HERV-K LTR after duplication from the original NSUN5 gene. The TRIM50 gene originally consists of seven exons, whereas the duplicated TRIM73 and TRIM74 genes present five exons because of homologous recombination-mediated deletion. In addition, independent duplication events of the FKBP6 gene generated two pseudogenes at different genomic locations. In summary, these clustered genes are created by segmental duplication, indicating that they show dynamic evolutionary events, leading to structure variation in the primate genome. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Detection and correction of false segmental duplications caused by genome mis-assembly.

    PubMed

    Kelley, David R; Salzberg, Steven L

    2010-01-01

    Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

  15. Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae.

    PubMed

    Takahashi, Tadashi; Sato, Atsushi; Ogawa, Masahiro; Hanya, Yoshiki; Oguma, Tetsuya

    2014-08-01

    We describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5'-deleted pyrG upstream of the region targeted for tandem chromosomal duplication and a 3'-deleted pyrG downstream of the target region. Consequently,strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks(DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

  16. Segmental duplications and copy-number variation in the human genome.

    PubMed

    Sharp, Andrew J; Locke, Devin P; McGrath, Sean D; Cheng, Ze; Bailey, Jeffrey A; Vallente, Rhea U; Pertz, Lisa M; Clark, Royden A; Schwartz, Stuart; Segraves, Rick; Oseroff, Vanessa V; Albertson, Donna G; Pinkel, Daniel; Eichler, Evan E

    2005-07-01

    The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement associated with genomic disease. However, an assessment of the role of segmental duplications in normal variation has not yet been made. On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. We observed an equal frequency of duplications and deletions, as well as a 4-fold enrichment of CNPs within hotspot regions, compared with control BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-scale variation in the human genome. Importantly, segmental duplications themselves were also significantly enriched >4-fold within regions of CNP. Almost without exception, CNPs were not confined to a single population, suggesting that these either are recurrent events, having occurred independently in multiple founders, or were present in early human populations. Our study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and it suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements. Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic

  17. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications

    PubMed Central

    2012-01-01

    Introduction Segmental duplications (low-copy repeats) are the recently duplicated genomic segments in the human genome that display nearly identical (> 90%) sequences and account for about 5% of euchromatic regions. In germline, duplicated segments mediate nonallelic homologous recombination and thus cause both non-disease-causing copy-number variants and genomic disorders. To what extent duplicated segments play a role in somatic DNA rearrangements in cancer remains elusive. Duplicated segments often cluster and form genomic blocks enriched with both direct and inverted repeats (complex genomic regions). Such complex regions could be fragile and play a mechanistic role in the amplification of the ERBB2 gene in breast tumors, because repeated sequences are known to initiate gene amplification in model systems. Methods We conducted polymerase chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors. We further used molecular, bioinformatics, and population-genetics approaches to define duplication contents, structural variants, and haplotypes within the common breakpoint. Results We found a large (> 300-kb) block of duplicated segments that was colocalized with a common-copy number breakpoint for ERBB2 amplification. The breakpoint that potentially initiated ERBB2 amplification localized in a region 1.5 megabases (Mb) on the telomeric side of ERBB2. The region is very complex, with extensive duplications of KRTAP genes, structural variants, and, as a result, a paucity of single-nucleotide polymorphism (SNP) markers. Duplicated segments are varied in size and degree of sequence homology, indicating that duplications have occurred recurrently during genome evolution. Conclusions Amplification of the ERBB2 gene in breast tumors is potentially initiated by a complex region that has unusual genomic features and

  18. Divergent origins and concerted expansion of two segmental duplications on chromosome 16.

    PubMed

    Eichler, E E; Johnson, M E; Alkan, C; Tuzun, E; Sahinalp, C; Misceo, D; Archidiacono, N; Rocchi, M

    2001-01-01

    An unexpected finding of the human genome was the large fraction of the genome organized as blocks of interspersed duplicated sequence. We provide a comparative and phylogenetic analysis of a highly duplicated region of 16p12.2, which is composed of at least four different segmental duplications spanning in excess of 160 kb. We contrast the dispersal of two different segmental duplications (LCR16a and LCR16u). LCR16a, a 20 kb low-copy repeat sequence A from chromosome 16, was shown previously to contain a rapidly evolving novel hominoid gene family (morpheus) that had expanded within the last 10 million years of great ape/human evolution. We compare the dispersal of this genomic segment with a second adjacent duplication called LCR16u. The duplication contains a second putative gene family (KIAA0220/SMG1) that is represented approximately eight times within the human genome. A high degree of sequence identity (approximately 98%) was observed among the various copies of LCR16u. Comparative analyses with Old World monkey species show that LCR16a and LCR16u originated from two distinct ancestral loci. Within the human genome, at least 70% of the LCR16u copies were duplicated in concert with the LCR16a duplication. In contrast, only 30% of the chimpanzee loci show an association between LCR16a and LCR16u duplications. The data suggest that the two copies of genomic sequence were brought together during the chimpanzee/human divergence and were subsequently duplicated as a larger cassette specifically within the human lineage. The evolutionary history of these two chromosome-specific duplications supports a model of rapid expansion and evolutionary turnover among the genomes of man and the great apes.

  19. Prenatal diagnosis of trisomy 21, 18 and 13 by quantitative pyrosequencing of segmental duplications.

    PubMed

    Tong, H; Jin, Y; Xu, Y; Zou, B; Ye, H; Wu, H; Kumar, S; Pitman, J L; Zhou, G; Song, Q

    2016-11-01

    Chromosomal aberration mostly occurs in chromosomes 21, 18 and 13, with an incidence approximately 1 out of 160 live births in humans, therefore making prenatal diagnosis necessary in clinics. Current methods have drawbacks such as time consuming, high cost, complicated operations and low sensitivity. In this paper, a novel method for rapid and accurate prenatal diagnosis of aneuploidy is proposed based on pyrosequencing, which quantitatively detects the peak height ratio (PHR) of different bases of segmental duplication. A direct polymerase chain reaction (PCR) approach was undertaken, where a small volume of amniotic fluid was used as the starting material without DNA extraction. Single-stranded DNA was prepared from PCR products and subsequently analyzed using pyrosequencing. The PHR between target and reference chromosome of 2.2 for euploid and 3:2 for a trisomy fetus were used as reference. The reference intervals and z scores were calculated for discrimination of aneuploidy. A total of 132 samples were collected, within trisomy 21 (n = 11), trisomy 18 (n = 3), trisomy 13 (n = 2), and unaffected controls (n = 116). A set of six segmental duplications were chosen for analysis. This method had consistent results with karyotyping analysis, a correct diagnosis with 100% sensitivity and 99.9% specificity. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Two complementary recessive genes in duplicated segments control etiolation in rice.

    PubMed

    Mao, Donghai; Yu, Huihui; Liu, Touming; Yang, Gaiyu; Xing, Yongzhong

    2011-02-01

    The main objective of this study was to identify the genes causing etiolation in a rice mutant, the thylakoids of which were scattered. Three populations were employed to map the genes for etiolation using bulked segregant analysis. Genetic analysis confirmed that etiolation was controlled by two recessive genes, et11 and et12, which were fine mapped to an approximately 147-kb region and an approximately 209-kb region on the short arms of chromosomes 11 and 12, respectively. Both regions were within the duplicated segments on chromosomes 11 and 12. They possessed a highly similar sequence of 38 kb at the locations of a pair of duplicated genes with protein sequences very similar to that of HCF152 in Arabidopsis that are required for the processing of chloroplast RNA. These genes are likely the candidates for et11 and et12. Expression profiling was used to compare the expression patterns of paralogs in the duplicated segments. Expression profiling indicated that the duplicated segments had been undergone concerted evolution, and a large number of the paralogs within the duplicated segments were functionally redundant like et11 and et12.

  1. Comparison between Two Scheimpflug Anterior Segment Analyzers

    PubMed Central

    Baradaran-Rafii, Alireza; Motevasseli, Tahmineh; Yazdizadeh, Forouzan; Karimian, Farid; Fekri, Sahba; Baradaran-Rafii, Amir

    2017-01-01

    Purpose: To compare the anterior segment indices measured by two Scheimpflug camera machines; Galilei and Pentacam. Methods: In this observational case series, the anterior segment indices of myopic healthy subjects seeking for refractive surgery were measured by Pentacam and Galilei on the same day. Analyzed parameters were anterior and posterior best fit spheres (BFS), axial curvature, true corneal power, central corneal thickness (CCT), anterior chamber (AC) depth, AC volume, AC angle, and pupil diameter. Results: This study included 176 eyes of 88 participants. Mean radius of the anterior BFS was 7.79 ± 0.34 mm versus 7.75 ± 0.39 mm measured by Pentacam and Galilei, respectively (r = 0.877, P < 0.001). Corresponding values for the mean radius of posterior BFS were 6.42 ± 0.32 and 6.47 ± 0.38 mm, respectively (r = 0.879, P < 0.001). Anterior corneal mean power was 43.8 ± 1.9 diopters (D) with Pentacam and 43.8 ± 2.4 D with Galilei (r = 0.905,P < 0.001). Posterior corneal mean power was measured − 6.3 ± 0.3 and − 6.3 ± 0.4 D using Pentacam and Galilei, respectively (r = 0.873, P < 0.001). True corneal power was 43.9 ± 1.9 D with Pentacam and 43.5 ± 2.3 D with Galilei (r = 0.909, P < 0.001). CCT was 537 ± 44 and 553 ± 51 μm measured by Pentacam and Galilei, respectively (r = 0.796, P < 0.001). AC depth measurements using Pentacam and Galilei were 3.29 ± 0.4 and 3.3 ± 0.38 mm (P < 0.001), respectively; AC volume was 207 ± 50 and 129 ± 39 mm3≥ (P = 0.004), and AC angle was 39.7 ± 9.2 and 54.2 ± 5.2 degrees (P = 0.051), respectively. Average pupil diameter was measured 3.91 ± 1.77 mm by Pentacam and 3.34 ± 0.89 mm by Galilei (P = 0.018). Conclusions: There was a significant correlation between the Pentacam and Galilei in all measured parameters except AC angle, AC volume, and average pupil diameter. PMID:28299003

  2. Individualized cattle copy number and segmental duplication maps using next generation sequencing

    USDA-ARS?s Scientific Manuscript database

    Copy Number Variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one ...

  3. The genomic architecture of segmental duplications and associated copy number variants in dogs.

    PubMed

    Nicholas, Thomas J; Cheng, Ze; Ventura, Mario; Mealey, Katrina; Eichler, Evan E; Akey, Joshua M

    2009-03-01

    Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise approximately 4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, approximately 68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies.

  4. Analysis of segmental duplications reveals a distinct pattern of continuation-of-synteny between human and mouse genomes.

    PubMed

    Mehan, Michael R; Almonte, Maricel; Slaten, Erin; Freimer, Nelson B; Rao, P Nagesh; Ophoff, Roel A

    2007-03-01

    About 5% of the human genome consists of large-scale duplicated segments of almost identical sequences. Segmental duplications (SDs) have been proposed to be involved in non-allelic homologous recombination leading to recurrent genomic variation and disease. It has also been suggested that these SDs are associated with syntenic rearrangements that have shaped the human genome. We have analyzed 14 members of a single family of closely related SDs in the human genome, some of which are associated with common inversion polymorphisms at chromosomes 8p23 and 4p16. Comparative analysis with the mouse genome revealed syntenic inversions for these two human polymorphic loci. In addition, 12 of the 14 SDs, while absent in the mouse genome, occur at the breaks of synteny; suggesting a non-random involvement of these sequences in genome evolution. Furthermore, we observed a syntenic familial relationship between 8 and 12 breakpoint-loci, where broken synteny that ends at one family member resumes at another, even across different chromosomes. Subsequent genome-wide assessment revealed that this relationship, which we named continuation-of-synteny, is not limited to the 8p23 family and occurs 46 times in the human genome with high frequency at specific chromosomes. Our analysis supports a non-random breakage model of genomic evolution with an active involvement of segmental duplications for specific regions of the human genome.

  5. The evolution and population diversity of human-specific segmental duplications.

    PubMed

    Dennis, Megan Y; Harshman, Lana; Nelson, Bradley J; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; Baker, Carl; Mark, Kenneth; Malig, Maika; Janke, Nicolette; Espinoza, Claudia; Stessman, Holly A F; Nuttle, Xander; Hoekzema, Kendra; Lindsay-Graves, Tina A; Wilson, Richard K; Eichler, Evan E

    2017-01-01

    Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed "core duplicons", and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.

  6. The evolution and population diversity of human-specific segmental duplications.

    PubMed

    Dennis, Megan Y; Harshman, Lana; Nelson, Bradley J; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; Baker, Carl; Mark, Kenneth; Malig, Maika; Janke, Nicolette; Espinoza, Claudia; Stessman, Holly A F; Nuttle, Xander; Hoekzema, Kendra; Lindsay-Graves, Tina A; Wilson, Richard K; Eichler, Evan E

    2017-02-17

    Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed 'core duplicons' and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (such as TCAF1/TCAF2), we highlight ten gene families (for example, ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.

  7. The evolution and population diversity of human-specific segmental duplications

    PubMed Central

    Dennis, Megan Y.; Harshman, Lana; Nelson, Bradley J.; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; Baker, Carl; Mark, Kenneth; Malig, Maika; Janke, Nicolette; Espinoza, Claudia; Stessman, Holly A.F.; Nuttle, Xander; Hoekzema, Kendra; Lindsay-Graves, Tina A.; Wilson, Richard K.; Eichler, Evan E.

    2017-01-01

    SUMMARY Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits. PMID:28580430

  8. De novo direct duplication of chromosome segment 22q11.2-q13.1

    SciTech Connect

    Fujimoto, Atsuko; Lin, Ming S.

    1996-03-29

    Lindsay et al. [1995] reported a case of de novo duplication of the segment 22q11-q12. Molecular cytogenetics studies showed that the segment includes the regions responsible for the {open_quotes}cat eye,{close_quotes} DiGeorge, and velo-cardio-facial syndrome, and extends distal to the breakpoint cluster region. The phenotype was milder than that of complete trisomy 22 and der(22)t(11;22) (q23;q11) syndrome and was similar in type and severity to that of {open_quotes}cat eye{close_quotes} syndrome (CES). They suggested that trisomy of gene(s) responsible for the CES might have a predominant phenotypic effect over other genes present in the region duplicated in their patient. 3 refs., 2 figs.

  9. Bleeding peptic ulcer caused by ectopic gastric mucosa in a duplicated segment of jejunum

    SciTech Connect

    Newmark, H.; Ching, G.; Halls, J.; Levy, I.J.

    1981-02-01

    The authors present a case in which a patient suffered a bleeding jejunal ulcer caused by heterotopic gastric mucosa in a congenital duplication of a segment of jejunum. This is the first case diagnosed preoperatively by two different radiographic means. These lesions were shown by both pertechnetate flow and barium small bowel studies. The rarity of these entities and the modalities used for diagnosis are described.

  10. Segmental Duplication, Microinversion, and Gene Loss Associated with a Complex Inversion Breakpoint Region in Drosophila

    PubMed Central

    Calvete, Oriol; González, Josefa; Betrán, Esther; Ruiz, Alfredo

    2012-01-01

    Chromosomal inversions are usually portrayed as simple two-breakpoint rearrangements changing gene order but not gene number or structure. However, increasing evidence suggests that inversion breakpoints may often have a complex structure and entail gene duplications with potential functional consequences. Here, we used a combination of different techniques to investigate the breakpoint structure and the functional consequences of a complex rearrangement fixed in Drosophila buzzatii and comprising two tandemly arranged inversions sharing the middle breakpoint: 2m and 2n. By comparing the sequence in the breakpoint regions between D. buzzatii (inverted chromosome) and D. mojavensis (noninverted chromosome), we corroborate the breakpoint reuse at the molecular level and infer that inversion 2m was associated with a duplication of a ∼13 kb segment and likely generated by staggered breaks plus repair by nonhomologous end joining. The duplicated segment contained the gene CG4673, involved in nuclear transport, and its two nested genes CG5071 and CG5079. Interestingly, we found that other than the inversion and the associated duplication, both breakpoints suffered additional rearrangements, that is, the proximal breakpoint experienced a microinversion event associated at both ends with a 121-bp long duplication that contains a promoter. As a consequence of all these different rearrangements, CG5079 has been lost from the genome, CG5071 is now a single copy nonnested gene, and CG4673 has a transcript ∼9 kb shorter and seems to have acquired a more complex gene regulation. Our results illustrate the complex effects of chromosomal rearrangements and highlight the need of complementing genomic approaches with detailed sequence-level and functional analyses of breakpoint regions if we are to fully understand genome structure, function, and evolutionary dynamics. PMID:22328714

  11. Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

    PubMed Central

    Uddin, Mohammed; Sturge, Mitch; Peddle, Lynette; O'Rielly, Darren D.; Rahman, Proton

    2011-01-01

    The primary objective of this study was to create a genome-wide high resolution map (i.e., >100 bp) of ‘rearrangement hotspots’ which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs) into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a ‘seed and extend’ approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (18× coverage), including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs). These regions are correlated with increased non-allelic homologous recombination (NAHR) event frequency which presumably represents the origin of copy number variations (CNVs) and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of ‘rearrangement hotspots’, which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s) for development of constitutional and acquired diseases. PMID:22194928

  12. Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

    PubMed Central

    Darai-Ramqvist, Eva; Sandlund, Agneta; Müller, Stefan; Klein, George; Imreh, Stefan; Kost-Alimova, Maria

    2008-01-01

    We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 (∼75 Mb position) and 3q21.3-q22.1 (∼130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large (∼250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and “instability elements,” including satellite repeats and retroviral sequences. PMID:18230801

  13. Segmental duplication and copy number variation of the patched domain containing 3 (PTCHD3) locus on pig chromosome 10

    USDA-ARS?s Scientific Manuscript database

    Mammalian genomes contain numerous blocks of highly homologous duplicated regions that can vary in copy number. We identified a segmental duplication encompassing the PTCHD3 gene, which has predicted hedgehog receptor activity, in a QTL region for nipple number on SSC10. A 3-fold coverage BAC screen...

  14. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean.

    PubMed

    Bolon, Yung-Tsi; Stec, Adrian O; Michno, Jean-Michel; Roessler, Jeffrey; Bhaskar, Pudota B; Ries, Landon; Dobbels, Austin A; Campbell, Benjamin W; Young, Nathan P; Anderson, Justin E; Grant, David M; Orf, James H; Naeve, Seth L; Muehlbauer, Gary J; Vance, Carroll P; Stupar, Robert M

    2014-11-01

    Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.

  15. Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus

    PubMed Central

    Wang, Dafang; Yu, Chuanhe; Zuo, Tao; Zhang, Jianbo; Weber, David F.; Peterson, Thomas

    2015-01-01

    The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize. PMID:26434719

  16. Tandem configurations of variably duplicated segments of 22q11.2 confirmed by fiber-FISH analysis.

    PubMed

    Shimojima, Keiko; Okamoto, Nobuhiko; Inazu, Tetsuya; Yamamoto, Toshiyuki

    2011-11-01

    22q11.2 duplication syndrome has recently been established as a new syndrome manifesting broad clinical phenotypes including mental retardation. It is reciprocal to DiGeorge (DGS)/velo-cardio-facial syndrome (VCFS), in which the same portion of the chromosome is hemizygously deleted. Deletions and duplications of the 22q11.2 region are facilitated by the low-copy repeats (LCRs) flanking this region. In this study, we aimed to identify the directions of the duplicated segments of 22q11.2 to better understand the mechanism of chromosomal duplication. To achieve this aim, we accumulated samples from four patients with 22q11.2 duplications. One of the patients had an atypically small (741 kb) duplication of 22q11.2. The centromeric end of the breakpoint was on LCR22A, but the telomeric end was between LCR22A and B. Therefore, the duplicated segment did not include T-box 1 gene (TBX1), the gene primarily responsible for the DGS/VCFS. As this duplication was shared by the patient's healthy mother, this appears to be a benign copy-number variation rather than a disease-causing alteration. The other three patients showed 3.0 or 4.0 Mb duplications flanked by LCRs. The directions of the duplicated segments were investigated by fiber-fluorescence in situ hybridization analysis. All samples showed tandem configurations. These results support the hypothesized mechanism of non-allelic homologous recombination with flanking LCRs and add additional evidence that many interstitial duplications are aligned as tandem configurations.

  17. A non-human primate BAC resource to study interchromosomal segmental duplications.

    PubMed

    Kirsch, S; Hodler, C; Schempp, W

    2009-01-01

    Segmental duplications (SDs) are involved in the reshaping and evolutionary development of primate genome architecture. Their intrinsic property to promote genomic instability facilitates genome rearrangements, thereby contributing to karyotype diversity in primates. However, comparative analyses of SDs based on whole-genome shotgun assemblies of primate genomes may lead to a distorted view of their evolutionary dynamics as this method will incorrectly assemble or simply not represent these regions. Therefore high-quality sequences of chromosomally assigned SDs are indispensable for unraveling the amplification and dispersal pattern of SDs during primate evolution. Here, we use an updated version of the ancestral duplicon state of the non-palindromic SDs of all 4 human Y-chromosome euchromatin/heterochromatin transition regions to perform a survey of duplicons genome-wide across 7 primate species. By adjusting experimental conditions to the mean nucleotide sequence divergence to human we identified 11,075 BAC clones carrying primate orthologs or paralogs of human Y chromosome-derived duplicons. Preliminary results indicate lineage-specific amplification of duplicons in prosimians and gibbons. This BAC-based framework represents the first complete set of a defined number of duplicons over 60 million years of primate evolution. Comparative sequence analysis of this genetic resource can contribute to our deeper understanding of the impact of segmental duplications on primate genome evolution. (c) 2009 S. Karger AG, Basel.

  18. Duplication of small segments within the major breakpoint cluster region in chronic myelogenous leukemia.

    PubMed

    Litz, C E; McClure, J S; Copenhaver, C M; Brunning, R D

    1993-03-15

    The t(9;22) in chronic myelogenous leukemia (CML) may be reciprocal or, in a minority of cases, may result in an extensive deletion of a portion of the major breakpoint cluster region (M-bcr) of the BCR. This report provides evidence of the duplication of small segments within the M-bcr in a small group of patients with CML. Southern blots of Bgl II and Bgl II/BamHI double-digested DNA from the blood or bone marrow of 46 patients with CML were probed with a 5' 1.4-kb Taq I/HindIII M-bcr probe and a 3' 2-kb HindIII/BamHI M-bcr probe. In three patients, rearrangements were noted with both probes in Bgl II-digested DNA, but were not present in Bgl II/BamHI-digested DNA with either probe. Southern analysis of DNA samples double-digested with Bgl II and BspHI from two of these three cases showed no rearrangements with either probe; the M-bcr BspHI site is located 26 bp 3' of the BamHI site in the second intron of the M-bcr. The presence of a rearranged M-bcr with both probes in Bgl II-digested DNA and the lack of rearrangement in Bgl II/BamHI and Bgl II/BspHI double-digested DNA suggest the presence of M-bcr BamHI and BspHI sites on both 9q+ chromosome (9q+) and the Philadelphia chromosome (Ph). This implies a duplication of at least the 26-bp M-bcr BamHI/BspHI fragment in these two samples. Sequence data from one of these two cases confirmed the M-bcr breakpoints to be staggered; the Ph M-bcr breakpoint occurred 258 bp downstream from the 9q+ M-bcr breakpoint. It is concluded that a duplication of small segments within the M-bcr occurs in a small group of patients with CML, which may lead to pseudogermline patterns on Southern blot. Such a duplication may provide insight into the mechanism of some chromosomal translocations in neoplasia.

  19. Hominoid fission of chromosome 14/15 and the role of segmental duplications.

    PubMed

    Giannuzzi, Giuliana; Pazienza, Michele; Huddleston, John; Antonacci, Francesca; Malig, Maika; Vives, Laura; Eichler, Evan E; Ventura, Mario

    2013-11-01

    Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin-heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14-qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in "stitching" together rearrangement breakpoints.

  20. Angiographic Pitfall: Duplicated Tapered A1 Segment of the Anterior Cerebral Artery Mimicking an Anterior Communicating Artery Aneurysm

    PubMed Central

    Weil, A.G.; Bojanowski, M.W.; Scholtes, F.; Darsaut, T.E.; Signorelli, F.; Weill, A.

    2011-01-01

    Summary We describe a misleading case of a partially occluded A1 segment duplication that mimicked an ACoA aneurysm on computed tomography angiography and conventional angiography and led to surgical intervention. The location of such an anomaly at the ACoA on the side of least hemodynamic stress may provide a clue to recognizing this variant. PMID:21696655

  1. Explosive Tandem and Segmental Duplications of Multigenic Families in Eucalyptus grandis

    PubMed Central

    Li, Qiang; Yu, Hong; Cao, Phi Bang; Fawal, Nizar; Mathé, Catherine; Azar, Sahar; Cassan-Wang, Hua; Myburg, Alexander A.; Grima-Pettenati, Jacqueline; Marque, Christiane; Teulières, Chantal; Dunand, Christophe

    2015-01-01

    Plant organisms contain a large number of genes belonging to numerous multigenic families whose evolution size reflects some functional constraints. Sequences from eight multigenic families, involved in biotic and abiotic responses, have been analyzed in Eucalyptus grandis and compared with Arabidopsis thaliana. Two transcription factor families APETALA 2 (AP2)/ethylene responsive factor and GRAS, two auxin transporter families PIN-FORMED and AUX/LAX, two oxidoreductase families (ascorbate peroxidases [APx] and Class III peroxidases [CIII Prx]), and two families of protective molecules late embryogenesis abundant (LEA) and DNAj were annotated in expert and exhaustive manner. Many recent tandem duplications leading to the emergence of species-specific gene clusters and the explosion of the gene numbers have been observed for the AP2, GRAS, LEA, PIN, and CIII Prx in E. grandis, while the APx, the AUX/LAX and DNAj are conserved between species. Although no direct evidence has yet demonstrated the roles of these recent duplicated genes observed in E. grandis, this could indicate their putative implications in the morphological and physiological characteristics of E. grandis, and be the key factor for the survival of this nondormant species. Global analysis of key families would be a good criterion to evaluate the capabilities of some organisms to adapt to environmental variations. PMID:25769696

  2. Resolving genomic disorder–associated breakpoints within segmental DNA duplications using massively parallel sequencing

    PubMed Central

    Nuttle, Xander; Itsara, Andy; Shendure, Jay; Eichler, Evan E.

    2014-01-01

    The most common recurrent copy number variants associated with autism, developmental delay, and epilepsy are flanked by segmental duplications. Complete genetic characterization of these events is challenging because their breakpoints often occur within high-identity, copy number polymorphic paralogous sequences that cannot be specifically assayed using hybridization-based methods. Here, we provide a protocol for breakpoint resolution with sequence-level precision. Massively parallel sequencing is performed on libraries generated from haplotype-resolved chromosomes, genomic DNA, or molecular inversion probe–captured breakpoint-informative regions harboring paralog-distinguishing variants. Quantifying sequencing depth over informative sites enables breakpoint localization, typically within several kilobases to tens of kilobases. Depending on the approach employed, the sequencing platform, and the accuracy and completeness of the reference genome sequence, this protocol takes from a few days to several months to complete. Once established for a specific genomic disorder, it is possible to process thousands of DNA samples within as little as 3–4 weeks. PMID:24874815

  3. Segmental Duplications in Euchromatic Regions of Human Chromosome 5: A Source of Evolutionary Instability and Transcriptional Innovation

    PubMed Central

    Courseaux, Anouk; Richard, Florence; Grosgeorge, Josiane; Ortola, Christine; Viale, Agnes; Turc-Carel, Claude; Dutrillaux, Bernard; Gaudray, Patrick; Nahon, Jean-Louis

    2003-01-01

    Recent analyses of the structure of pericentromeric and subtelomeric regions have revealed that these particular regions of human chromosomes are often composed of blocks of duplicated genomic segments that have been associated with rapid evolutionary turnover among the genomes of closely related primates. In the present study, we show that euchromatic regions of human chromosome 5—5p14, 5p13, 5q13, 5q15–5q21—also display such an accumulation of segmental duplications. The structure, organization and evolution of those primate-specific sequences were studied in detail by combining in silico and comparative FISH analyses on human, chimpanzee, gorilla, orangutang, macaca, and capuchin chromosomes. Our results lend support to a two-step model of transposition duplication in the euchromatic regions, with a founder insertional event at the time of divergence between Platyrrhini and Catarrhini (25–35 million years ago) and an apparent burst of inter- and intrachromosomal duplications in the Hominidae lineage. Furthermore, phylogenetic analysis suggests that the chronology and, likely, molecular mechanisms, differ regarding the region of primary insertion—euchromatic versus pericentromeric regions. Lastly, we show that as their counterparts located near the heterochromatic region, the euchromatic segmental duplications have consistently reshaped their region of insertion during primate evolution, creating putative mosaic genes, and they are obvious candidates for causing ectopic rearrangements that have contributed to evolutionary/genomic instability. [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: D. Le Paslier, A. McKenzie, J. Melki, C. Sargent, J. Scharf and S. Selig.] PMID:12618367

  4. The idic(X)(q13) in myeloid malignancies: breakpoint clustering in segmental duplications and association with TET2 mutations.

    PubMed

    Paulsson, Kajsa; Haferlach, Claudia; Fonatsch, Christa; Hagemeijer, Anne; Andersen, Mette Klarskov; Slovak, Marilyn L; Johansson, Bertil

    2010-04-15

    Myelodysplastic syndromes and acute myeloid leukemia with an isodicentric X chromosome [idic(X)(q13)] occur in elderly women and frequently display ringed sideroblasts. Because of the rarity of idic(X)(q13), little is known about its formation, whether a fusion gene is generated, and patterns of additional aberrations. We here present an SNP array study of 14 idic(X)-positive myeloid malignancies, collected through an international collaborative effort. The breakpoints clustered in two regions of segmental duplications and were not in a gene, making dosage effects from the concurrent gain of Xpter-q13 and loss of Xq13-qter, rather than a fusion gene, the most likely pathogenetic outcome. Methylation analysis revealed involvement of the inactive X chromosomes in five cases and of the active in two. The ABCB7 gene, mutated in X-linked sideroblastic anemia and spinocerebellar ataxia, is in the deleted region, suggesting that loss of this gene underlies the frequent presence of ringed sideroblasts. Additional genetic abnormalities were present in 12/14 (86%), including partial uniparental disomies for 9p (one case) and 4q (two cases) associated with homozygous mutations of JAK2 and TET2, respectively. In total, TET2 mutations were seen in 4/11 (36%) analyzed cases, thus constituting a common secondary event in idic(X)-positive malignancies.

  5. Comparison of the segmental duplication pattern on two cattle genome assemblies using FISH

    USDA-ARS?s Scientific Manuscript database

    We previously estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>= 1kb in length, >= 90% sequence identity) using two distinct computational analyses (WGAC and WSSD). In this study, we further validated selected large duplications and compared their distri...

  6. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements.

    PubMed

    D'Angelo, Carla S; Gajecka, Marzena; Kim, Chong A; Gentles, Andrew J; Glotzbach, Caron D; Shaffer, Lisa G; Koiffmann, Célia P

    2009-06-01

    The mechanisms involved in the formation of subtelomeric rearrangements are now beginning to be elucidated. Breakpoint sequencing analysis of 1p36 rearrangements has made important contributions to this line of inquiry. Despite the unique architecture of segmental duplications inherent to human subtelomeres, no common mechanism has been identified thus far and different nonexclusive recombination-repair mechanisms seem to predominate. In order to gain further insights into the mechanisms of chromosome breakage, repair, and stabilization mediating subtelomeric rearrangements in humans, we investigated the constitutional rearrangements of 1p36. Cloning of the breakpoint junctions in a complex rearrangement and three non-reciprocal translocations revealed similarities at the junctions, such as microhomology of up to three nucleotides, along with no significant sequence identity in close proximity to the breakpoint regions. All the breakpoints appeared to be unique and their occurrence was limited to non-repetitive, unique DNA sequences. Several recombination- or cleavage-associated motifs that may promote non-homologous recombination were observed in close proximity to the junctions. We conclude that NHEJ is likely the mechanism of DNA repair that generates these rearrangements. Additionally, two apparently pure terminal deletions were also investigated, and the refinement of the breakpoint regions identified two distinct genomic intervals ~25-kb apart, each containing a series of 1p36 specific segmental duplications with 90-98% identity. Segmental duplications can serve as substrates for ectopic homologous recombination or stimulate genomic rearrangements.

  7. Human-specific evolution of novel SRGAP2 genes by incomplete segmental duplication

    PubMed Central

    Dennis, Megan Y.; Nuttle, Xander; Sudmant, Peter H.; Antonacci, Francesca; Graves, Tina A.; Nefedov, Mikhail; Rosenfeld, Jill A.; Sajjadian, Saba; Malig, Maika; Kotkiewicz, Holland; Curry, Cynthia J.; Shafer, Susan; Shaffer, Lisa G.; de Jong, Pieter J.; Wilson, Richard K.; Eichler, Evan E.

    2012-01-01

    SUMMARY Gene duplication is an important source of phenotypic change and adaptive evolution. We use a novel genomic approach to identify highly identical sequence missing from the reference genome, confirming the cortical development gene Slit-Robo Rho GTPase activating protein 2 (SRGAP2) duplicated three times in humans. We show that the promoter and first nine exons of SRGAP2 duplicated from 1q32.1 (SRGAP2A) to 1q21.1 (SRGAP2B) ~3.4 million years ago (mya). Two larger duplications later copied SRGAP2B to chromosome 1p12 (SRGAP2C) and to proximal 1q21.1 (SRGAP2D), ~2.4 and ~1 mya, respectively. Sequence and expression analysis shows SRGAP2C is the most likely duplicate to encode a functional protein and among the most fixed human-specific duplicate genes. Our data suggest a mechanism where incomplete duplication created a novel function —at birth, antagonizing parental SRGAP2 function 2–3 mya a time corresponding to the transition from Australopithecus to Homo and the beginning of neocortex expansion. PMID:22559943

  8. A Burst of Segmental Duplications in the African Great Ape Ancestor

    PubMed Central

    Marques-Bonet, Tomas; Kidd, Jeffrey M.; Ventura, Mario; Graves, Tina A.; Cheng, Ze; Hillier, LaDeanna W.; Jiang, Zhaoshi; Baker, Carl; Malfavon-Borja, Ray; Fulton, Lucinda A.; Alkan, Can; Aksay, Gozde; Girirajan, Santhosh; Siswara, Priscillia; Chen, Lin; Cardone, Maria Francesca; Navarro, Arcadi; Mardis, Elaine R.; Wilson, Richard K.; Eichler, Evan E.

    2009-01-01

    Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical1,2; cytogenetically there are few rearrangements that distinguish ape-human chromosomes3; rates of single-basepair change4-7 and retroposon activity8-10 have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution. PMID:19212409

  9. Complex segmental duplications mediate a recurrent dup(X)(p11.22-p11.23) associated with mental retardation, speech delay, and EEG anomalies in males and females.

    PubMed

    Giorda, Roberto; Bonaglia, M Clara; Beri, Silvana; Fichera, Marco; Novara, Francesca; Magini, Pamela; Urquhart, Jill; Sharkey, Freddie H; Zucca, Claudio; Grasso, Rita; Marelli, Susan; Castiglia, Lucia; Di Benedetto, Daniela; Musumeci, Sebastiano A; Vitello, Girolamo A; Failla, Pinella; Reitano, Santina; Avola, Emanuela; Bisulli, Francesca; Tinuper, Paolo; Mastrangelo, Massimo; Fiocchi, Isabella; Spaccini, Luigina; Torniero, Claudia; Fontana, Elena; Lynch, Sally Ann; Clayton-Smith, Jill; Black, Graeme; Jonveaux, Philippe; Leheup, Bruno; Seri, Marco; Romano, Corrado; dalla Bernardina, Bernardo; Zuffardi, Orsetta

    2009-09-01

    Submicroscopic copy-number variations make a considerable contribution to the genetic etiology of human disease. We have analyzed subjects with idiopathic mental retardation (MR) by using whole-genome oligonucleotide-based array comparative genomic hybridization (aCGH) and identified familial and de novo recurrent Xp11.22-p11.23 duplications in males and females with MR, speech delay, and a peculiar electroencephalographic (EEG) pattern in childhood. The size of the duplications ranges from 0.8-9.2 Mb. Most affected females show preferential activation of the duplicated X chromosome. Carriers of the smallest duplication show X-linked recessive inheritance. All other affected individuals present dominant expression and comparable clinical phenotypes irrespective of sex, duplication size, and X-inactivation pattern. The majority of the rearrangements are mediated by recombination between flanking complex segmental duplications. The identification of common clinical features, including the typical EEG pattern, predisposing genomic structure, and peculiar X-inactivation pattern, suggests that duplication of Xp11.22-p11.23 constitutes a previously undescribed syndrome.

  10. Complex Segmental Duplications Mediate a Recurrent dup(X)(p11.22-p11.23) Associated with Mental Retardation, Speech Delay, and EEG Anomalies in Males and Females

    PubMed Central

    Giorda, Roberto; Bonaglia, M. Clara; Beri, Silvana; Fichera, Marco; Novara, Francesca; Magini, Pamela; Urquhart, Jill; Sharkey, Freddie H.; Zucca, Claudio; Grasso, Rita; Marelli, Susan; Castiglia, Lucia; Di Benedetto, Daniela; Musumeci, Sebastiano A.; Vitello, Girolamo A.; Failla, Pinella; Reitano, Santina; Avola, Emanuela; Bisulli, Francesca; Tinuper, Paolo; Mastrangelo, Massimo; Fiocchi, Isabella; Spaccini, Luigina; Torniero, Claudia; Fontana, Elena; Lynch, Sally Ann; Clayton-Smith, Jill; Black, Graeme; Jonveaux, Philippe; Leheup, Bruno; Seri, Marco; Romano, Corrado; Bernardina, Bernardo dalla; Zuffardi, Orsetta

    2009-01-01

    Submicroscopic copy-number variations make a considerable contribution to the genetic etiology of human disease. We have analyzed subjects with idiopathic mental retardation (MR) by using whole-genome oligonucleotide-based array comparative genomic hybridization (aCGH) and identified familial and de novo recurrent Xp11.22-p11.23 duplications in males and females with MR, speech delay, and a peculiar electroencephalographic (EEG) pattern in childhood. The size of the duplications ranges from 0.8–9.2 Mb. Most affected females show preferential activation of the duplicated X chromosome. Carriers of the smallest duplication show X-linked recessive inheritance. All other affected individuals present dominant expression and comparable clinical phenotypes irrespective of sex, duplication size, and X-inactivation pattern. The majority of the rearrangements are mediated by recombination between flanking complex segmental duplications. The identification of common clinical features, including the typical EEG pattern, predisposing genomic structure, and peculiar X-inactivation pattern, suggests that duplication of Xp11.22-p11.23 constitutes a previously undescribed syndrome. PMID:19716111

  11. The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups

    PubMed Central

    2013-01-01

    Background WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species. Results We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean. Conclusions In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have

  12. Analyzing training information from random forests for improved image segmentation.

    PubMed

    Mahapatra, Dwarikanath

    2014-04-01

    Labeled training data are used for challenging medical image segmentation problems to learn different characteristics of the relevant domain. In this paper, we examine random forest (RF) classifiers, their learned knowledge during training and ways to exploit it for improved image segmentation. Apart from learning discriminative features, RFs also quantify their importance in classification. Feature importance is used to design a feature selection strategy critical for high segmentation and classification accuracy, and also to design a smoothness cost in a second-order MRF framework for graph cut segmentation. The cost function combines the contribution of different image features like intensity, texture, and curvature information. Experimental results on medical images show that this strategy leads to better segmentation accuracy than conventional graph cut algorithms that use only intensity information in the smoothness cost.

  13. Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen.

    PubMed

    Rowen, Lee; Williams, Eleanor; Glusman, Gustavo; Linardopoulou, Elena; Friedman, Cynthia; Ahearn, Mary Ellen; Seto, Jason; Boysen, Cecilie; Qin, Shizhen; Wang, Kai; Kaur, Amardeep; Bloom, Scott; Hood, Leroy; Trask, Barbara J

    2005-08-01

    Homo sapiens possess several trypsinogen or trypsinogen-like genes of which three (PRSS1, PRSS2, and PRSS3) produce functional trypsins in the digestive tract. PRSS1 and PRSS2 are located on chromosome 7q35, while PRSS3 is found on chromosome 9p13. Here, we report a variation of the theme of new gene creation by duplication: the PRSS3 gene was formed by segmental duplications originating from chromosomes 7q35 and 11q24. As a result, PRSS3 transcripts display two variants of exon 1. The PRSS3 transcript whose gene organization most resembles PRSS1 and PRSS2 encodes a functional protein originally named mesotrypsinogen. The other variant is a fusion transcript, called trypsinogen IV. We show that the first exon of trypsinogen IV is derived from the noncoding first exon of LOC120224, a chromosome 11 gene. LOC120224 codes for a widely conserved transmembrane protein of unknown function. Comparative analyses suggest that these interchromosomal duplications occurred after the divergence of Old World monkeys and hominids. PRSS3 transcripts consist of a mixed population of mRNAs, some expressed in the pancreas and encoding an apparently functional trypsinogen and others of unknown function expressed in brain and a variety of other tissues. Analysis of the selection pressures acting on the trypsinogen gene family shows that, while the apparently functional genes are under mild to strong purifying selection overall, a few residues appear under positive selection. These residues could be involved in interactions with inhibitors.

  14. Duplication of chromosome segment 12q13-15 in a lipomatous tumor with minimal nuclear atypia: A case report

    PubMed Central

    NISHIO, JUN; IWASAKI, HIROSHI; SHIBATA, TERUFUMI; NABESHIMA, KAZUKI; NAITO, MASATOSHI

    2016-01-01

    Ordinary lipoma is cytogenetically characterized by structural rearrangements, particularly translocations, of 12q13-15. By contrast, atypical lipomatous tumors exhibit supernumerary ring or giant marker chromosomes that are composed mainly of amplified material from the 12q13-15 chromosome segment. The present study describes the cytogenetic and molecular cytogenetic findings from a lipomatous tumor with minimal nuclear atypia that was identified in a 49-year-old female patient. Magnetic resonance imaging of the right shoulder revealed a 13-cm fatty mass in the subcutaneous layer that possessed only pencil-line septa. Contrast-enhanced fat-suppressed T1-weighted images demonstrated faint enhancement. A marginal excision was performed. Histologically, the tumor was composed of lobules that consisted of mature adipocytes separated by thin fibrous septa. There was minimal nuclear atypia in certain cells, and a small number of binucleated cells were also observed within the tumor. Immunohistochemically, the tumor cells did not reveal the expression of murine double-minute 2 (MDM2). Cytogenetic analysis revealed a complex karyotype with several numerical and structural alterations, including 12q rearrangements. Spectral karyotyping demonstrated a duplication of chromosome segment 12q13-15. Interphase fluorescence in situ hybridization analysis revealed no MDM2 gene amplification. The present case indicates that duplication of 12q may be associated with minimal nuclear atypia in a subset of lipomatous tumors. PMID:27073568

  15. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility.

    PubMed

    Gonzalez, Enrique; Kulkarni, Hemant; Bolivar, Hector; Mangano, Andrea; Sanchez, Racquel; Catano, Gabriel; Nibbs, Robert J; Freedman, Barry I; Quinones, Marlon P; Bamshad, Michael J; Murthy, Krishna K; Rovin, Brad H; Bradley, William; Clark, Robert A; Anderson, Stephanie A; O'connell, Robert J; Agan, Brian K; Ahuja, Seema S; Bologna, Rosa; Sen, Luisa; Dolan, Matthew J; Ahuja, Sunil K

    2005-03-04

    Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the phenotypic consequences for host defense are unknown. We show that there are significant interindividual and interpopulation differences in the copy number of a segmental duplication encompassing the gene encoding CCL3L1 (MIP-1alphaP), a potent human immunodeficiency virus-1 (HIV-1)-suppressive chemokine and ligand for the HIV coreceptor CCR5. Possession of a CCL3L1 copy number lower than the population average is associated with markedly enhanced HIV/acquired immunodeficiency syndrome (AIDS) susceptibility. This susceptibility is even greater in individuals who also possess disease-accelerating CCR5 genotypes. This relationship between CCL3L1 dose and altered HIV/AIDS susceptibility points to a central role for CCL3L1 in HIV/AIDS pathogenesis and indicates that differences in the dose of immune response genes may constitute a genetic basis for variable responses to infectious diseases.

  16. Algebraic Distribution of Segmental Duplication Lengths in Whole-Genome Sequence Self-Alignments

    PubMed Central

    Gao, Kun; Miller, Jonathan

    2011-01-01

    Distributions of duplicated sequences from genome self-alignment are characterized, including forward and backward alignments in bacteria and eukaryotes. A Markovian process without auto-correlation should generate an exponential distribution expected from local effects of point mutation and selection on localised function; however, the observed distributions show substantial deviation from exponential form – they are roughly algebraic instead – suggesting a novel kind of long-distance correlation that must be non-local in origin. PMID:21779315

  17. A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid.

    PubMed

    Zhang, Hua; Zhang, Chang-Quan; Sun, Zhi-Zhong; Yu, Wen; Gu, Ming-Hong; Liu, Qiao-Quan; Li, Yang-Sheng

    2011-11-01

    Chromosome segment duplications are integral in genome evolution by providing a source for the origin of new genes. In the rice genome, besides an ancient polyploidy event known in the rice common ancestor, it had been identified that there was a special segmental duplication involving chromosomes 11 and 12, but the biological role of this duplication remains unknown. In this study, by using a set of chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) derived from the indica cultivar 9311 and japonica cultivar Nipponbare, a major QTL (qS12) resulting in hybrid male sterility was mapped within ~400 kb region adjacent to the special duplicated segment on the short arm of chromosome 12. Compared to the japonica cultivar Nipponbare, the two sides of the qS12 candidate region were inverted in the indica cultivar 9311. Among 47 of the 111 rice genotypes evaluated by molecular markers, the inverted sides were detected, and found completely homologous to indica cultivar 9311. These results suggested that the two inverted sides protect the sequence in the qS12 regions from recombination. On the short-arm of chromosome 12, two QTLs S-e and S25, in addition to qS12, were previously detected as a distinct segregation distortion and pollen semi-sterility loci. We propose these three hybrid sterility loci are the same locus, and the duplicated segment on chromosome 12 may play a prominent role in diversification, i.e., sub-speciation of cultivated rice.

  18. Two-dimensional segmentation for analyzing Hi-C data

    PubMed Central

    Lévy-Leduc, Celine; Delattre, M.; Mary-Huard, T.; Robin, S.

    2014-01-01

    Motivation: The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem. Results: We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions. Availability and implementation: The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author. Contact: celine.levy-leduc@agroparistech.fr PMID:25161224

  19. Genomic evolution and polymorphism: segmental duplications and haplotypes at 108 regions on 21 chromosomes.

    PubMed

    McLure, Craig A; Hinchliffe, Peter; Lester, Susan; Williamson, Joseph F; Millman, John A; Keating, Peter J; Stewart, Brent J; Dawkins, Roger L

    2013-07-01

    We describe here extensive, previously unknown, genomic polymorphism in 120 regions, covering 19 autosomes and both sex chromosomes. Each contains duplication within multigene clusters. Of these, 108 are extremely polymorphic with multiple haplotypes. We used the genomic matching technique (GMT), previously used to characterise the major histocompatibility complex (MHC) and regulators of complement activation (RCA). This genome-wide extension of this technique enables the examination of many underlying cis, trans and epistatic interactions responsible for phenotypic differences especially in relation to individuality, evolution and disease susceptibility. The extent of the diversity could not have been predicted and suggests a new model of primate evolution based on conservation of polymorphism rather than de novo mutation. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data.

    PubMed

    Sanzol, Javier

    2010-05-14

    Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species. This study evaluates the gene duplication and polyploidy history of the apple by characterizing duplicated genes in this species using EST data. Overall, 68% of the apple genes were clustered into families with a mean copy-number of 4.6. Analysis of the age distribution of gene duplications supported a continuous mode of small-scale duplications, plus two episodes of large-scale duplicates of vastly different ages. The youngest was consistent with the polyploid origin of the Pyrinae 37-48 MYBP, whereas the older may be related to gamma-triplication; an ancient hexapolyploidization previously characterized in the four sequenced eurosid genomes and basal to the eurosid-asterid divergence. Duplicated genes were studied for functional diversification with an emphasis on young paralogs; those originated during or after the formation of the Pyrinae lineage. Unequal assignment of single-copy genes and gene families to Gene Ontology categories suggested functional bias in the pattern of gene retention of paralogs. Young paralogs related to signal transduction, metabolism, and energy pathways have been preferentially retained. Non-random retention of duplicated genes seems to have mediated the expansion of gene families, some of which may have substantially increased their members after the origin of the Pyrinae. The joint analysis of over-duplicated functional categories and phylogenies, allowed evaluation of the role of both polyploidy and small-scale duplications during this process. Finally, gene expression analysis indicated that 82% of duplicated genes, including 80% of young

  1. Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data

    PubMed Central

    2010-01-01

    Background Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species. Results This study evaluates the gene duplication and polyploidy history of the apple by characterizing duplicated genes in this species using EST data. Overall, 68% of the apple genes were clustered into families with a mean copy-number of 4.6. Analysis of the age distribution of gene duplications supported a continuous mode of small-scale duplications, plus two episodes of large-scale duplicates of vastly different ages. The youngest was consistent with the polyploid origin of the Pyrinae 37-48 MYBP, whereas the older may be related to γ-triplication; an ancient hexapolyploidization previously characterized in the four sequenced eurosid genomes and basal to the eurosid-asterid divergence. Duplicated genes were studied for functional diversification with an emphasis on young paralogs; those originated during or after the formation of the Pyrinae lineage. Unequal assignment of single-copy genes and gene families to Gene Ontology categories suggested functional bias in the pattern of gene retention of paralogs. Young paralogs related to signal transduction, metabolism, and energy pathways have been preferentially retained. Non-random retention of duplicated genes seems to have mediated the expansion of gene families, some of which may have substantially increased their members after the origin of the Pyrinae. The joint analysis of over-duplicated functional categories and phylogenies, allowed evaluation of the role of both polyploidy and small-scale duplications during this process. Finally, gene expression analysis indicated that 82% of duplicated genes

  2. Identification of a Recurrent Microdeletion at 17q23.1q23.2 Flanked by Segmental Duplications Associated with Heart Defects and Limb Abnormalities

    PubMed Central

    Ballif, Blake C.; Theisen, Aaron; Rosenfeld, Jill A.; Traylor, Ryan N.; Gastier-Foster, Julie; Thrush, Devon Lamb; Astbury, Caroline; Bartholomew, Dennis; McBride, Kim L.; Pyatt, Robert E.; Shane, Kate; Smith, Wendy E.; Banks, Valerie; Gallentine, William B.; Brock, Pamela; Rudd, M. Katharine; Adam, Margaret P.; Keene, Julia A.; Phillips, John A.; Pfotenhauer, Jean P.; Gowans, Gordon C.; Stankiewicz, Pawel; Bejjani, Bassem A.; Shaffer, Lisa G.

    2010-01-01

    Segmental duplications, which comprise ∼5%–10% of the human genome, are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination (NAHR) and have been suggested to be hot spots in chromosome evolution and human genomic instability. We report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization (aCGH). Six of the seven deletions are ∼2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in the same orientation. One of the deletions is ∼2.8 Mb in size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint falls between segmental duplications. These characteristics suggest that NAHR mediated six out of seven of these rearrangements. These individuals have common features, including mild to moderate developmental delay (particularly speech delay), microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. Although all individuals had at least mild dysmorphic facial features, there was no characteristic constellation of features that would elicit clinical suspicion of a specific disorder. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome. Furthermore, the inclusion in the minimal deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. PMID:20206336

  3. Identification of a recurrent microdeletion at 17q23.1q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities.

    PubMed

    Ballif, Blake C; Theisen, Aaron; Rosenfeld, Jill A; Traylor, Ryan N; Gastier-Foster, Julie; Thrush, Devon Lamb; Astbury, Caroline; Bartholomew, Dennis; McBride, Kim L; Pyatt, Robert E; Shane, Kate; Smith, Wendy E; Banks, Valerie; Gallentine, William B; Brock, Pamela; Rudd, M Katharine; Adam, Margaret P; Keene, Julia A; Phillips, John A; Pfotenhauer, Jean P; Gowans, Gordon C; Stankiewicz, Pawel; Bejjani, Bassem A; Shaffer, Lisa G

    2010-03-12

    Segmental duplications, which comprise approximately 5%-10% of the human genome, are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination (NAHR) and have been suggested to be hot spots in chromosome evolution and human genomic instability. We report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization (aCGH). Six of the seven deletions are approximately 2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in the same orientation. One of the deletions is approximately 2.8 Mb in size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint falls between segmental duplications. These characteristics suggest that NAHR mediated six out of seven of these rearrangements. These individuals have common features, including mild to moderate developmental delay (particularly speech delay), microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. Although all individuals had at least mild dysmorphic facial features, there was no characteristic constellation of features that would elicit clinical suspicion of a specific disorder. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome. Furthermore, the inclusion in the minimal deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  4. A common 56-kilobase deletion in a primate-specific segmental duplication creates a novel butyrophilin-like protein

    PubMed Central

    2013-01-01

    Background The Butyrophilin-like (BTNL) proteins are likely to play an important role in inflammation and immune response. Like the B7 protein family, many human and murine BTNL members have been shown to control T lymphocytes response, and polymorphisms in human BTNL2 have been linked to several inflammatory diseases, such as pulmonary sarcoidosis, inflammatory bowel disease and neonatal lupus. Results In this study we provide a comprehensive population, genomic and transcriptomic analysis of a 56-kb deletion copy number variant (CNV), located within two segmental duplications of two genes belonging to the BTNL family, namely BTNL8 and BTNL3. We confirm the presence of a novel BTNL8*3 fusion-protein product, and show an influence of the deletion variant on the expression level of several genes involved in immune function, including BTNL9, another member of the same family. Moreover, by genotyping HapMap and human diversity panel (HGDP) samples, we demonstrate a clear difference in the stratification of the BTNL8_BTNL3-del allele frequency between major continental human populations. Conclusion Despite tremendous progress in the field of structural variation, rather few CNVs have been functionally characterized so far. Here, we show clear functional consequences of a new deletion CNV (BTNL8_BTNL3-del) with potentially important implication in the human immune system and in inflammatory and proliferative disorders. In addition, the marked population differences found of BTNL8_BTNL3-del frequencies suggest that this deletion CNV might have evolved under positive selection due to environmental conditions in some populations, with potential phenotypic consequences. PMID:23829304

  5. The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication.

    PubMed

    Park, Eunji; Song, Jun-Im; Won, Yong-Jin

    2011-10-15

    Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12.

    PubMed

    Martin, J W; Yoshimoto, M; Ludkovski, O; Thorner, P S; Zielenska, M; Squire, J A; Nuin, P A S

    2010-06-01

    It has been proposed that regions of microhomology in the human genome could facilitate genomic rearrangements, copy number transitions, and rapid genomic change during tumor progression. To investigate this idea, this study examines the role of repetitive sequence elements, and corresponding syntenic mouse genomic features, in targeting cancer-associated genomic instability of specific regions of the human genome. Automated database-mining algorithms designed to search for frequent copy number transitions and genomic breakpoints were applied to 2 publicly-available online databases and revealed that 6p21-p12 is one of the regions of the human genome most frequently involved in tumor-specific alterations. In these analyses, 6p21-p12 exhibited the highest frequency of genomic amplification in osteosarcomas. Analysis of repetitive elements in regions of homology between human chromosome 6p and the syntenic regions of the mouse genome revealed a strong association between the location of segmental duplications greater than 5 kilobase-pairs and the position of discontinuities at the end of the syntenic region. The presence of clusters of segmental duplications flanking these syntenic regions also correlated with a high frequency of amplification and genomic alteration. Collectively, the experimental findings, in silico analyses, and comparative genomic studies presented here suggest that segmental duplications may facilitate cancer-associated copy number transitions and rearrangements at chromosome 6p21-p12. This process may involve homology-dependent DNA recombination and/or repair, which may also contribute towards the overall plasticity of the human genome.

  7. Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion.

    PubMed

    Cuscó, Ivon; Corominas, Roser; Bayés, Mònica; Flores, Raquel; Rivera-Brugués, Núria; Campuzano, Victoria; Pérez-Jurado, Luis A

    2008-05-01

    Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused by a heterozygous deletion of contiguous genes at 7q11.23 mediated by nonallelic homologous recombination (NAHR) between large flanking LCRs and facilitated by a structural variant of the region, a approximately 2-Mb paracentric inversion present in 20%-25% of WBS-transmitting progenitors. We now report that eight out of 180 (4.44%) WBS-transmitting progenitors are carriers of a CNV, displaying a chromosome with large deletion of LCRs. The prevalence of this CNV among control individuals and non-transmitting progenitors is much lower (1%, n=600), thus indicating that it is a predisposing factor for the WBS deletion (odds ratio 4.6-fold, P= 0.002). LCR duplications were found in 2.22% of WBS-transmitting progenitors but also in 1.16% of controls, which implies a non-statistically significant increase in WBS-transmitting progenitors. We have characterized the organization and breakpoints of these CNVs, encompassing approximately 100-300 kb of genomic DNA and containing several pseudogenes but no functional genes. Additional structural variants of the region have also been defined, all generated by NAHR between different blocks of segmental duplications. Our data further illustrate the highly dynamic structure of regions rich in segmental duplications, such as the WBS locus, and indicate that large CNVs can act as susceptibility alleles for disease-associated genomic rearrangements in the progeny.

  8. Breast tumor segmentation in high resolution x-ray phase contrast analyzer based computed tomography

    SciTech Connect

    Brun, E.; Grandl, S.; Sztrókay-Gaul, A.; Gasilov, S.; Barbone, G.; Mittone, A.; Coan, P.; Bravin, A.

    2014-11-01

    Purpose: Phase contrast computed tomography has emerged as an imaging method, which is able to outperform present day clinical mammography in breast tumor visualization while maintaining an equivalent average dose. To this day, no segmentation technique takes into account the specificity of the phase contrast signal. In this study, the authors propose a new mathematical framework for human-guided breast tumor segmentation. This method has been applied to high-resolution images of excised human organs, each of several gigabytes. Methods: The authors present a segmentation procedure based on the viscous watershed transform and demonstrate the efficacy of this method on analyzer based phase contrast images. The segmentation of tumors inside two full human breasts is then shown as an example of this procedure’s possible applications. Results: A correct and precise identification of the tumor boundaries was obtained and confirmed by manual contouring performed independently by four experienced radiologists. Conclusions: The authors demonstrate that applying the watershed viscous transform allows them to perform the segmentation of tumors in high-resolution x-ray analyzer based phase contrast breast computed tomography images. Combining the additional information provided by the segmentation procedure with the already high definition of morphological details and tissue boundaries offered by phase contrast imaging techniques, will represent a valuable multistep procedure to be used in future medical diagnostic applications.

  9. Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes.

    PubMed

    Pagel, Janice; Walling, Jason G; Young, Nevin D; Shoemaker, Randy C; Jackson, Scott A

    2004-08-01

    Soybean (Glycine max L. Merr.) is presumed to be an ancient polyploid based on chromosome number and multiple RFLP fragments in genetic mapping. Direct cytogenetic observation of duplicated regions within the soybean genome has not heretofore been reported. Employing fluorescence in situ hybridization (FISH) of genetically anchored bacterial artificial chromosomes (BACs) in soybean, we were able to observe that the distal ends of molecular linkage group E had duplicated regions on linkage groups A2 and B2. Further, using fiber-FISH, it was possible to measure the molecular size and organization of one of the duplicated regions. As FISH did not require repetitive DNA for blocking fluorescence signals, we assume that the 200-kb genome region is relatively low in repetitive sequences. This observation, along with the observation that the BACs are located in distal euchromatin regions, has implications for genome structure/evolution and the approach used to sequence the soybean genome.

  10. Analyzing the medical image by using clustering algorithms through segmentation process

    NASA Astrophysics Data System (ADS)

    Kumar, Papendra; Kumar, Suresh

    2011-12-01

    Basic aim of our study is to analyze the medical image. In computer vision, segmentationRefers to the process of partitioning a digital image into multiple regions. The goal ofSegmentation is to simplify and/or change the representation of an image into something thatIs more meaningful and easier to analyze. Image segmentation is typically used to locateObjects and boundaries (lines, curves, etc.) in images.There is a lot of scope of the analysis that we have done in our project; our analysis couldBe used for the purpose of monitoring the medical image. Medical imaging refers to theTechniques and processes used to create images of the human body (or parts thereof) forClinical purposes (medical procedures seeking to reveal, diagnose or examine disease) orMedical science (including the study of normal anatomy and function).As a discipline and in its widest sense, it is part of biological imaging and incorporatesRadiology (in the wider sense), radiological sciences, endoscopy, (medical) thermography, Medical photography and microscopy (e.g. for human pathological investigations).Measurement and recording techniques which are not primarily designed to produce images.

  11. Interlocus gene conversion explains at least 2.7% of single nucleotide variants in human segmental duplications.

    PubMed

    Dumont, Beth L

    2015-06-16

    Interlocus gene conversion (IGC) is a recombination-based mechanism that results in the unidirectional transfer of short stretches of sequence between paralogous loci. Although IGC is a well-established mechanism of human disease, the extent to which this mutagenic process has shaped overall patterns of segregating variation in multi-copy regions of the human genome remains unknown. One expected manifestation of IGC in population genomic data is the presence of one-to-one paralogous SNPs that segregate identical alleles. Here, I use SNP genotype calls from the low-coverage phase 3 release of the 1000 Genomes Project to identify 15,790 parallel, shared SNPs in duplicated regions of the human genome. My approach for identifying these sites accounts for the potential redundancy of short read mapping in multi-copy genomic regions, thereby effectively eliminating false positive SNP calls arising from paralogous sequence variation. I demonstrate that independent mutation events to identical nucleotides at paralogous sites are not a significant source of shared polymorphisms in the human genome, consistent with the interpretation that these sites are the outcome of historical IGC events. These putative signals of IGC are enriched in genomic contexts previously associated with non-allelic homologous recombination, including clear signals in gene families that form tandem intra-chromosomal clusters. Taken together, my analyses implicate IGC, not point mutation, as the mechanism generating at least 2.7% of single nucleotide variants in duplicated regions of the human genome.

  12. Deletions, duplications and transpositions of the COR segment that encompasses the structural gene of yeast iso-1-cytochrome c

    SciTech Connect

    Stiles, J.I.; Friedman, L.R.; Sherman, F.

    1980-01-01

    It has been recently found that a specific chromosomal segment, in certain but not all laboratory strains of Saccharomyces cerevisiae, is deleted and transposed at high frequencies. This segment, denoted COR, encompasses the three closely linked loci CYC1, OSM1 and RAD7 which control iso-1-cytochrome c, osmotic sensitivity and UV-sensitivity, respectively. Two types of apparently normal laboratory strains of yeast designated COR1 and COR2, were uncovered after the examination of the frequencies and types of mutations causing either deficiencies or overproduction of iso-1-cytochrome c; in contrast to COR1 strains which give predominantly point mutations causing deficiencies of iso-1-cytochrome c, COR2 strains give rise to deletions and transpositions of the COR segment. We have undertaken a systematic investigation of the physical structure and genetic properties of the COR region and of the aberrations arising in COR2 strains.

  13. A Bayesian spatial random parameters Tobit model for analyzing crash rates on roadway segments.

    PubMed

    Zeng, Qiang; Wen, Huiying; Huang, Helai; Abdel-Aty, Mohamed

    2017-03-01

    This study develops a Bayesian spatial random parameters Tobit model to analyze crash rates on road segments, in which both spatial correlation between adjacent sites and unobserved heterogeneity across observations are accounted for. The crash-rate data for a three-year period on road segments within a road network in Florida, are collected to compare the performance of the proposed model with that of a (fixed parameters) Tobit model and a spatial (fixed parameters) Tobit model in the Bayesian context. Significant spatial effect is found in both spatial models and the results of Deviance Information Criteria (DIC) show that the inclusion of spatial correlation in the Tobit regression considerably improves model fit, which indicates the reasonableness of considering cross-segment spatial correlation. The spatial random parameters Tobit regression has lower DIC value than does the spatial Tobit regression, suggesting that accommodating the unobserved heterogeneity is able to further improve model fit when the spatial correlation has been considered. Moreover, the random parameters Tobit model provides a more comprehensive understanding of the effect of speed limit on crash rates than does its fixed parameters counterpart, which suggests that it could be considered as a good alternative for crash rate analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping

    PubMed Central

    Zeng, Xin; Li, Bo; Welch, Rene; Rojo, Constanza; Zheng, Ye; Dewey, Colin N.; Keleş, Sündüz

    2015-01-01

    Segmental duplications and other highly repetitive regions of genomes contribute significantly to cells’ regulatory programs. Advancements in next generation sequencing enabled genome-wide profiling of protein-DNA interactions by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). However, interactions in highly repetitive regions of genomes have proven difficult to map since short reads of 50–100 base pairs (bps) from these regions map to multiple locations in reference genomes. Standard analytical methods discard such multi-mapping reads and the few that can accommodate them are prone to large false positive and negative rates. We developed Perm-seq, a prior-enhanced read allocation method for ChIP-seq experiments, that can allocate multi-mapping reads in highly repetitive regions of the genomes with high accuracy. We comprehensively evaluated Perm-seq, and found that our prior-enhanced approach significantly improves multi-read allocation accuracy over approaches that do not utilize additional data types. The statistical formalism underlying our approach facilitates supervising of multi-read allocation with a variety of data sources including histone ChIP-seq. We applied Perm-seq to 64 ENCODE ChIP-seq datasets from GM12878 and K562 cells and identified many novel protein-DNA interactions in segmental duplication regions. Our analysis reveals that although the protein-DNA interactions sites are evolutionarily less conserved in repetitive regions, they share the overall sequence characteristics of the protein-DNA interactions in non-repetitive regions. PMID:26484757

  15. Repeatability and comparability of anterior segment biometry obtained by the Sirius and the Pentacam analyzers.

    PubMed

    De la Parra-Colín, Paola; Garza-León, Manuel; Barrientos-Gutierrez, Tonatiuh

    2014-02-01

    To assess the repeatability and comparability of six anterior segment biometry parameters obtained with a novel Scheimpflug camera with a Placido disc topographer (Sirius) and slit-scanning tomography with a Scheimpflug camera (Pentacam), in a sample of 16 unoperated eyes of healthy subjects. The anterior segment was analyzed by a single examiner using the Sirius and the Pentacam analyzers. Mean simulated keratometry (Sim K), flat and steep axis keratometry (K f and K s ), central and thinnest corneal thicknesses (CCT and TCT), and anterior chamber depth (ACD) measurements were evaluated. Repeatability of three sets of measurements from each device was assessed using the coefficient of variation (CV), within-subject standard deviation, and intraclass correlation coefficient (ICC). Bonferroni-adjusted t-tests, and Bland and Altman plots were used to establish agreement between devices. For both devices the CV of repeated measurements was <0.79 %. The ICC was >0.95 in all measurements except for Sirius K s (ICC = 0.869). For all parameters evaluated, the Pentacam systematically yielded higher values, although differences were statistically significant in only three parameters-0.31 diopters for K s , 10.1 μm for CCT and 12.4 μm for TCT. In the assessment of normal corneas both devices showed overall high repeatability. Although good agreement was found in three parameters (Sim K, K f and ACD) these devices do not seem to be interchangeable for pachymetric determination.

  16. Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression

    PubMed Central

    Giorgio, Elisa; Rolyan, Harshvardhan; Kropp, Laura; Chakka, Anish Baswanth; Yatsenko, Svetlana; Gregorio, Eleonora Di; Lacerenza, Daniela; Vaula, Giovanna; Talarico, Flavia; Mandich, Paola; Toro, Camilo; Pierre, Eleonore Eymard; Labauge, Pierre; Capellari, Sabina; Cortelli, Pietro; Vairo, Filippo Pinto; Miguel, Diego; Stubbolo, Danielle; Marques, Lourenco Charles; Gahl, William; Boespflug-Tanguy, Odile; Melberg, Atle; Hassin-Baer, Sharon; Cohen, Oren S; Pjontek, Rastislav; Grau, Armin; Klopstock, Thomas; Fogel, Brent; Meijer, Inge; Rouleau, Guy; Bouchard, Jean-Pierre L; Ganapathiraju, Madhavi; Vanderver, Adeline; Dahl, Niklas; Hobson, Grace; Brusco, Alfredo; Brussino, Alessandro; Padiath, Quasar Saleem

    2013-01-01

    ABSTRACT Autosomal dominant leukodystrophy (ADLD) is an adult onset demyelinating disorder that is caused by duplications of the lamin B1 (LMNB1) gene. However, as only a few cases have been analyzed in detail, the mechanisms underlying LMNB1 duplications are unclear. We report the detailed molecular analysis of the largest collection of ADLD families studied, to date. We have identified the minimal duplicated region necessary for the disease, defined all the duplication junctions at the nucleotide level and identified the first inverted LMNB1 duplication. We have demonstrated that the duplications are not recurrent; patients with identical duplications share the same haplotype, likely inherited from a common founder and that the duplications originated from intrachromosomal events. The duplication junction sequences indicated that nonhomologous end joining or replication-based mechanisms such fork stalling and template switching or microhomology-mediated break induced repair are likely to be involved. LMNB1 expression was increased in patients’ fibroblasts both at mRNA and protein levels and the three LMNB1 alleles in ADLD patients show equal expression, suggesting that regulatory regions are maintained within the rearranged segment. These results have allowed us to elucidate duplication mechanisms and provide insights into allele-specific LMNB1 expression levels. PMID:23649844

  17. Genome-Wide Investigation of Hsf Genes in Sesame Reveals Their Segmental Duplication Expansion and Their Active Role in Drought Stress Response

    PubMed Central

    Dossa, Komivi; Diouf, Diaga; Cissé, Ndiaga

    2016-01-01

    Sesame is a survivor crop cultivated for ages in arid areas under high temperatures and limited water conditions. Since its entire genome has been sequenced, revealing evolution, and functional characterization of its abiotic stress genes became a hot topic. In this study, we performed a whole-genome identification and analysis of Hsf gene family in sesame. Thirty genes encoding Hsf domain were found and classified into 3 major classes A, B, and C. The class A members were the most representative one and Hsf genes were distributed in 12 of the 16 linkage groups (except the LG 8, 9, 13, and 16). Evolutionary analysis revealed that, segmental duplication events which occurred around 67 MYA, were the primary force underlying Hsf genes expansion in sesame. Comparative analysis also suggested that sesame has retained most of its Hsf genes while its relatives viz. tomato and potato underwent extensive gene losses during evolution. Continuous purifying selection has played a key role in the maintenance of Hsf genes in sesame. Expression analysis of the Hsf genes in sesame revealed their putative involvement in multiple tissue-/developmental stages. Time-course expression profiling of Hsf genes in response to drought stress showed that 90% Hsfs are drought responsive. We infer that classes B-Hsfs might be the primary regulators of drought response in sesame by cooperating with some class A genes. This is the first insight into this gene family and the results provide some gene resources for future gene cloning and functional studies toward the improvement in stress tolerance of sesame. PMID:27790233

  18. Genome-Wide Investigation of Hsf Genes in Sesame Reveals Their Segmental Duplication Expansion and Their Active Role in Drought Stress Response.

    PubMed

    Dossa, Komivi; Diouf, Diaga; Cissé, Ndiaga

    2016-01-01

    Sesame is a survivor crop cultivated for ages in arid areas under high temperatures and limited water conditions. Since its entire genome has been sequenced, revealing evolution, and functional characterization of its abiotic stress genes became a hot topic. In this study, we performed a whole-genome identification and analysis of Hsf gene family in sesame. Thirty genes encoding Hsf domain were found and classified into 3 major classes A, B, and C. The class A members were the most representative one and Hsf genes were distributed in 12 of the 16 linkage groups (except the LG 8, 9, 13, and 16). Evolutionary analysis revealed that, segmental duplication events which occurred around 67 MYA, were the primary force underlying Hsf genes expansion in sesame. Comparative analysis also suggested that sesame has retained most of its Hsf genes while its relatives viz. tomato and potato underwent extensive gene losses during evolution. Continuous purifying selection has played a key role in the maintenance of Hsf genes in sesame. Expression analysis of the Hsf genes in sesame revealed their putative involvement in multiple tissue-/developmental stages. Time-course expression profiling of Hsf genes in response to drought stress showed that 90% Hsfs are drought responsive. We infer that classes B-Hsfs might be the primary regulators of drought response in sesame by cooperating with some class A genes. This is the first insight into this gene family and the results provide some gene resources for future gene cloning and functional studies toward the improvement in stress tolerance of sesame.

  19. Analyzing the impact of vibrations on E-ELT primary segmented mirror

    NASA Astrophysics Data System (ADS)

    Sedghi, B.; Müller, M.; Dimmler, M.

    2016-08-01

    The E-ELT primary mirror is 39m in diameter composed of 798 segments. It is exposed to external large but slow amplitude perturbations, mostly gravity, thermal and wind. These perturbations are efficiently rejected by a combination of edge sensor loop and adaptive optics (AO) in order to leave a small residual wavefront error (WFE). Vibrations induced by various equipment in the observatory are typically smaller amplitude but higher frequency perturbations exceeding the rejection capabilities of these control loops. They generate both, low spatial frequency and high spatial frequency WFE. Especially segment phasing errors, i.e. high spatial frequency errors, cannot be compensated by AO. The effect of vibrations is characterized by excitation sources and transmission of the telescope structure and segment support. They all together define the WFE caused by M1 due to vibrations. It is important to build a proper vibration error budget and specification requirements from an early stage of the project. This paper presents the vibration analysis and budgeting approach developed for E-ELT M1 and addresses the impact of vibrations onto WFE.

  20. Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

    PubMed Central

    2013-01-01

    Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the

  1. Tubular Colonic Duplication Presenting as Rectovestibular Fistula.

    PubMed

    Karkera, Parag J; Bendre, Pradnya; D'souza, Flavia; Ramchandra, Mukunda; Nage, Amol; Palse, Nitin

    2015-09-01

    Complete colonic duplication is a very rare congenital anomaly that may have different presentations according to its location and size. Complete colonic duplication can occur in about 15% of all gastrointestinal duplications. Double termination of tubular colonic duplication in the perineum is even more uncommon. We present a case of a Y-shaped tubular colonic duplication which presented with a rectovestibular fistula and a normal anus. Radiological evaluation and initial exploration for sigmoidostomy revealed duplicated colons with a common vascular supply. Endorectal mucosal resection of theduplicated distal segment till the colostomy site with division of the septum of the proximal segment and colostomy closure proved curative without compromise of the continence mechanism. Tubular colonic duplication should always be ruled out when a diagnosis of perineal canal is considered in cases of vestibular fistula alongwith a normal anus.

  2. Tubular Colonic Duplication Presenting as Rectovestibular Fistula

    PubMed Central

    Bendre, Pradnya; D'souza, Flavia; Ramchandra, Mukunda; Nage, Amol; Palse, Nitin

    2015-01-01

    Complete colonic duplication is a very rare congenital anomaly that may have different presentations according to its location and size. Complete colonic duplication can occur in about 15% of all gastrointestinal duplications. Double termination of tubular colonic duplication in the perineum is even more uncommon. We present a case of a Y-shaped tubular colonic duplication which presented with a rectovestibular fistula and a normal anus. Radiological evaluation and initial exploration for sigmoidostomy revealed duplicated colons with a common vascular supply. Endorectal mucosal resection of theduplicated distal segment till the colostomy site with division of the septum of the proximal segment and colostomy closure proved curative without compromise of the continence mechanism. Tubular colonic duplication should always be ruled out when a diagnosis of perineal canal is considered in cases of vestibular fistula alongwith a normal anus. PMID:26473141

  3. [Evidence of the public-private mix in healthcare systems in countries with duplicated coverage: greater inequities and segmentation in National Health Systems].

    PubMed

    Santos, Isabela Soares

    2011-06-01

    This paper seeks to identify the potential negative effects of private health insurance on the universality of National Health Systems. It systematizes the operational concepts of the public-private mix model and presents the results from international research into duplicated and supplementary coverage that shows that universality is negatively affected by inequities derived from duplicated coverage though not from supplementary coverage. It demystifies the supplementary nature of private health insurance as the villain in the Brazilian healthcare system and recommends that public policies should be fully oriented to improving the public health system instead of private health insurance.

  4. Segments.

    ERIC Educational Resources Information Center

    Zemsky, Robert; Shaman, Susan; Shapiro, Daniel B.

    2001-01-01

    Presents a market taxonomy for higher education, including what it reveals about the structure of the market, the model's technical attributes, and its capacity to explain pricing behavior. Details the identification of the principle seams separating one market segment from another and how student aspirations help to organize the market, making…

  5. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4.

    PubMed

    Terryn, N; Heijnen, L; De Keyser, A; Van Asseldonck, M; De Clercq, R; Verbakel, H; Gielen, J; Zabeau, M; Villarroel, R; Jesse, T; Neyt, P; Hogers, R; Van Den Daele, H; Ardiles, W; Schueller, C; Mayer, K; Déhais, P; Rombauts, S; Van Montagu, M; Rouzé, P; Vos, P

    1999-02-26

    As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis.

  6. Chromosomal duplications in bacteria, fruit flies, and humans

    SciTech Connect

    Lupski, J.R.; Weinstock, G.M.; Roth, J.R.

    1996-01-01

    Tandem duplication of chromosomal segments has been recognized as a frequent mutational mechanism in several genetic model systems. In bacteria, fruit flies, and humans, duplications form by similar molecular mechanisms and appear to be important in genome evolution. 80 refs.

  7. Use of Diagnostic Imaging in the Evaluation of Gastrointestinal Tract Duplications

    PubMed Central

    Laskowska, Katarzyna; Gałązka, Przemysław; Daniluk-Matraś, Irena; Leszczyński, Waldemar; Serafin, Zbigniew

    2014-01-01

    Summary Background Gastrointestinal tract duplication is a rare malformation associated with the presence of additional segment of the fetal gut. The aim of this study was to retrospectively review clinical features and imaging findings in intraoperatively confirmed cases of gastrointestinal tract duplication in children. Material/Methods The analysis included own material from the years 2002–2012. The analyzed group included 14 children, among them 8 boys and 6 girls. The youngest patient was diagnosed at the age of three weeks, and the oldest at 12 years of age. Results The duplication cysts were identified in the esophagus (n=2), stomach (n=5), duodenum (n=1), terminal ileum (n=5), and rectum (n=1). In four cases, the duplication coexisted with other anomalies, such as patent urachus, Meckel’s diverticulum, mesenteric cyst, and accessory pancreas. Clinical manifestation of gastrointestinal duplication cysts was variable, and some of them were detected accidently. Thin- or thick-walled cystic structures adjacent to the wall of neighboring gastrointestinal segment were documented on diagnostic imaging. Conclusions Ultrasound and computed tomography are the methods of choice in the evaluation of gastrointestinal duplication cysts. Apart from the diagnosis of the duplication cyst, an important issue is the detection of concomitant developmental pathologies, including pancreatic heterotopy. PMID:25114725

  8. Detecting long tandem duplications in genomic sequences

    PubMed Central

    2012-01-01

    Background Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. Results In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,a we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. Conclusions ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations. PMID:22568762

  9. Spinal Cord Segmentation by One Dimensional Normalized Template Matching: A Novel, Quantitative Technique to Analyze Advanced Magnetic Resonance Imaging Data.

    PubMed

    Cadotte, Adam; Cadotte, David W; Livne, Micha; Cohen-Adad, Julien; Fleet, David; Mikulis, David; Fehlings, Michael G

    2015-01-01

    Spinal cord segmentation is a developing area of research intended to aid the processing and interpretation of advanced magnetic resonance imaging (MRI). For example, high resolution three-dimensional volumes can be segmented to provide a measurement of spinal cord atrophy. Spinal cord segmentation is difficult due to the variety of MRI contrasts and the variation in human anatomy. In this study we propose a new method of spinal cord segmentation based on one-dimensional template matching and provide several metrics that can be used to compare with other segmentation methods. A set of ground-truth data from 10 subjects was manually-segmented by two different raters. These ground truth data formed the basis of the segmentation algorithm. A user was required to manually initialize the spinal cord center-line on new images, taking less than one minute. Template matching was used to segment the new cord and a refined center line was calculated based on multiple centroids within the segmentation. Arc distances down the spinal cord and cross-sectional areas were calculated. Inter-rater validation was performed by comparing two manual raters (n = 10). Semi-automatic validation was performed by comparing the two manual raters to the semi-automatic method (n = 10). Comparing the semi-automatic method to one of the raters yielded a Dice coefficient of 0.91 +/- 0.02 for ten subjects, a mean distance between spinal cord center lines of 0.32 +/- 0.08 mm, and a Hausdorff distance of 1.82 +/- 0.33 mm. The absolute variation in cross-sectional area was comparable for the semi-automatic method versus manual segmentation when compared to inter-rater manual segmentation. The results demonstrate that this novel segmentation method performs as well as a manual rater for most segmentation metrics. It offers a new approach to study spinal cord disease and to quantitatively track changes within the spinal cord in an individual case and across cohorts of subjects.

  10. DNA segment in chromosome 9q34 which is duplicated in a sporadic case of Tuberous sclerosis encodes a new gene with homology to oncogenes in the Ras signaling pathway

    SciTech Connect

    Smith, M.; Handa, K.; Bengstsson, U.

    1994-09-01

    The TSC1 gene has been mapped to a 1 megabase region on chromosome 9q34. This region is flanked by markers D9S125 and D9S114. D9S10 and D9S66 loci map within this region. In a sporadic case of Tuberous sclerosis we demonstrated the presence of a DNA duplication using probes for the D9S10, and D9S66 loci and cosmids which overlap the telomeric end of the D9S66 cosmid. The duplication was demonstrated by analysis of the D9S66 polymorphism which revealed the presence of two maternal alleles in the patient. It was also demonstrated using FISH to analyze metaphase and interphase chromosomes, and by pulsed field gel electrophoresis which revealed novel M1u1 fragments in patient cellular DNA examined using as probes unique sequence regions of D9S10, or unique sequence regions of cosmids flanking the telomeric end of D9S66. There was no evidence for duplication of DBH or ABL. We carried out DNA sequence analysis of regions of D9S10 and cosmids which overlap D9S10 at its telomeric end, and determined that these cosmids contain exons with regions of high homology to portions of the Vav oncogene. We used a unique sequence region of D9S10 to examine mRNA and demonstrated a transcript of 4 kb. These studies are important since they have refined the map position of the TSC1 locus and secondly because they have led to the identification of a new oncogene with high homology to oncogenes in the RAS signalling pathway.

  11. Genome Duplication in Soybean (Glycine Subgenus Soja)

    PubMed Central

    Shoemaker, R. C.; Polzin, K.; Labate, J.; Specht, J.; Brummer, E. C.; Olson, T.; Young, N.; Concibido, V.; Wilcox, J.; Tamulonis, J. P.; Kochert, G.; Boerma, H. R.

    1996-01-01

    Restriction fragment length polymorphism mapping data from nine populations (Glycine max X G. soja and G. max X G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes. PMID:8878696

  12. Plant Genome Duplication Database.

    PubMed

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  13. Clinical characterization and identification of duplication breakpoints in a Japanese family with Xq28 duplication syndrome including MECP2.

    PubMed

    Fukushi, Daisuke; Yamada, Kenichiro; Nomura, Noriko; Naiki, Misako; Kimura, Reiko; Yamada, Yasukazu; Kumagai, Toshiyuki; Yamaguchi, Kumiko; Miyake, Yoshishige; Wakamatsu, Nobuaki

    2014-04-01

    Xq28 duplication syndrome including MECP2 is a neurodevelopmental disorder characterized by axial hypotonia at infancy, severe intellectual disability, developmental delay, mild characteristic facial appearance, epilepsy, regression, and recurrent infections in males. We identified a Japanese family of Xq28 duplications, in which the patients presented with cerebellar ataxia, severe constipation, and small feet, in addition to the common clinical features. The 488-kb duplication spanned from L1CAM to EMD and contained 17 genes, two pseudo genes, and three microRNA-coding genes. FISH and nucleotide sequence analyses demonstrated that the duplication was tandem and in a forward orientation, and the duplication breakpoints were located in AluSc at the EMD side, with a 32-bp deletion, and LTR50 at the L1CAM side, with "tc" and "gc" microhomologies at the duplication breakpoints, respectively. The duplicated segment was completely segregated from the grandmother to the patients. These results suggest that the duplication was generated by fork-stalling and template-switching at the AluSc and LTR50 sites. This is the first report to determine the size and nucleotide sequences of the duplicated segments at Xq28 of three generations of a family and provides the genotype-phenotype correlation of the patients harboring the specific duplicated segment.

  14. Pathology Report: Presacral Noncommunicating Enteric Duplication Cyst.

    PubMed

    Seydafkan, Shabnam; Shibata, David; Sanchez, Julian; Tran, Nam D; Leon, Marino; Coppola, Domenico

    2016-04-01

    Gastrointestinal (GI) tract duplication cysts or enteric duplication cysts are rare congenital malformations sometimes found on the mesenteric aspect of segments of the alimentary tract. Enteric duplication cysts are lined by normal GI epithelium and may be classified as foregut, mid-gut, and hindgut cysts. Except in very rare cases of retroperitoneal enteric duplication cysts, these cysts communicate with the GI tract and share a common blood supply. Concurrent congenital malformations are not uncommon and malignant transformation within enteric duplication cysts has also been reported. We describe a case of a noncommunicating enteric duplication cyst in a 52-year-old woman. The patient presented with a presacral cystic mass requiring frequent drainage procedures that was primarily believed to be of neural origin. Upon resection, the lesion contained heterotopic tissue, including ciliated bronchial epithelium, squamous and transitional epithelia, and pancreatic and gastric tissue. Focal, low-grade intestinal adenoma was present, but malignancy was not detected in this case. To our knowledge, this is the sixth reported case of a noncommunicating enteric duplication cyst in the English medical literature.

  15. Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids

    PubMed Central

    Barbier, Michaël; Jaensch, Steffen; Cornelissen, Frans; Vidic, Suzana; Gjerde, Kjersti; de Hoogt, Ronald; Graeser, Ralph; Gustin, Emmanuel; Chong, Yolanda T.

    2016-01-01

    In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation. PMID:27303813

  16. Application of mid-infrared spectroscopy in analyzing different segmented production of Angelica by AB-8 macroporous resin

    NASA Astrophysics Data System (ADS)

    Guo, Yizhen; Wang, Jingjuan; Lu, Lina; Sun, Suqin; Liu, Yang; Xiao, Yao; Qin, Youwen; Xiao, Lijuan; Wen, Haoran; Qu, Lei

    2016-01-01

    As complicated mixture systems, chemical components of Angelica are very difficult to identify and discriminate, so as not to control its quality effectively. In recent years, Mid-infrared spectroscopy has been innovatively employed to identify and assess the quality of Traditional Chinese medicine (TCM) products. In this paper, the macroscopic IR fingerprint method including Fourier transform infrared spectroscopy (FT-IR), the second derivative infrared spectroscopy (SD-IR) and two-dimensional correlation infrared spectroscopy (2D-IR), are applied to study and identify Angelica raw material, the decoction and different segmented production of AB-8 macroporous resin. FT-IR spectrum indicates that Angelica raw material is rich in sucrose and the correlation coefficient is 0.8465. The decoction of Angelica contains varieties of polysaccharides components and the content is gradually decreased with increasing concentration of ethanol. In addition, the decoction of Angelica contains a certain amount of protein components and 50% ethanol eluate has more protein than other eluates. Their second derivative spectra amplify the differences and reveal the potentially characteristic IR absorption bands, then we conclude that the decoction of Angelica contains a certain amount of ferulic acid and ligustilide. And 30% ethanol eluate, 50% ethanol eluate and 70% ethanol eluate are similar to ligustilide. Further, 2D-IR spectra enhance the spectral resolution and obtain much new information for discriminating the similar complicated samples. It is demonstrated that the above three-step infrared spectroscopy could be applicable for effective, visual and accurate analysis and identification of very complicated and similar mixture systems of traditional Chinese medicines.

  17. Genome changes after gene duplication: haploidy vs. diploidy.

    PubMed

    Xue, Cheng; Huang, Ren; Maxwell, Taylor J; Fu, Yun-Xin

    2010-09-01

    Since genome size and the number of duplicate genes observed in genomes increase from haploid to diploid organisms, diploidy might provide more evolutionary probabilities through gene duplication. It is still unclear how diploidy promotes genomic evolution in detail. In this study, we explored the evolution of segmental gene duplication in haploid and diploid populations by analytical and simulation approaches. Results show that (1) under the double null recessive (DNR) selective model, given the same recombination rate, the evolutionary trajectories and consequences are very similar between the same-size gene-pool haploid vs. diploid populations; (2) recombination enlarges the probability of preservation of duplicate genes in either haploid or diploid large populations, and haplo-insufficiency reinforces this effect; and (3) the loss of duplicate genes at the ancestor locus is limited under recombination while under complete linkage the loss of duplicate genes is always random at the ancestor and newly duplicated loci. Therefore, we propose a model to explain the advantage of diploidy: diploidy might facilitate the increase of recombination rate, especially under sexual reproduction; more duplicate genes are preserved under more recombination by originalization (by which duplicate genes are preserved intact at a special quasi-mutation-selection balance under the DNR or haplo-insufficient selective model), so genome sizes and the number of duplicate genes in diploid organisms become larger. Additionally, it is suggested that small genomic rearrangements due to the random loss of duplicate genes might be limited under recombination.

  18. Duplication in DNA Sequences

    NASA Astrophysics Data System (ADS)

    Ito, Masami; Kari, Lila; Kincaid, Zachary; Seki, Shinnosuke

    The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

  19. Discovery of Disposal of Low-Level Waste in Slit Trench Segments Shallower than Analyzed in Performance Assessment

    SciTech Connect

    Cook, J.R.

    2002-10-15

    The effect of disposing of low-level waste in slit trenches that are shallower than those analyzed in the revised performance assessment for the E-Area low-level waste facility is evaluated. The conclusion of the evaluation is that such disposal is bounded by the performance assessment if all of the disposed waste packages meet the slit trench Waste Acceptance Criteria and if at least four feet of soil is placed over the disposed waste packages.

  20. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

    PubMed Central

    Casneuf, Tineke; De Bodt, Stefanie; Raes, Jeroen; Maere, Steven; Van de Peer, Yves

    2006-01-01

    Background Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. Results Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. Conclusion By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication. PMID:16507168

  1. Multiple Isolated Enteric Duplication Cysts in an Infant - A Diagnostic Dilemma.

    PubMed

    Udiya, Alok Kumar; Shetty, Gurucharan S; Chauhan, Udit; Singhal, Shweta; Prabhu, Shailesh M

    2016-01-01

    Completely isolated enteric duplication cysts are a rare variety of enteric duplication cysts having an independent blood supply with no communication with any part of the adjacent bowel segment. We report a case showing two completely isolated enteric duplication cysts originating in the greater omentum and transverse mesocolon in an infant. Multiple isolated enteric duplication cysts involving non-contiguous bowel segments have not been previously reported in the literature. In addition the transverse mesocolon duplication cyst was infected showing septations and loss of double wall sign resulting in difficulty in imaging diagnosis. Both the cysts were excised and confirmed on histopathology.

  2. Interstitial duplication 19p

    SciTech Connect

    Stratton, R.F.; DuPont, B.R.; Moore, C.M.

    1995-07-17

    We report on a 9-month-old girl with an interstitial duplication of 19p, developmental delay, and multiple anomalies including bifrontal prominence, obtuse frontonasal angle, short columella, additional midline philtral pillar, midline ridge on the tongue, vertical midline ridge at the mental symphysis, and a complex congenital heart defect including severe branch pulmonary artery stenosis, secundum atrial septal defect (ASD), and several ventricular septal defects (VSDs). Use of fluorescent in situ hybridization (FISH) with chromosome 19- specific probes showed a direct duplication of bands 19p13.13 and 19p13.2. 6 refs., 1 fig.

  3. Adenocarcinoma arising in an elderly patient's large ileal duplication.

    PubMed

    de Tullio, Damiano; Rinaldi, Rosa; Pellegrini, Davide; Stano, Rocco; Messina, Federico; Cavazzini, Luigi; Azzena, Gianfranco; Occhionorelli, Savino

    2011-10-01

    Bowel duplications are rare congenital anomalies commonly found in pediatric patients; few cases may remain undetected until adulthood. Malignant carcinomatous changes are rare complications in intestinal duplications. An 88-year-old female patient was referred to our surgical unit with the diagnosis of a large abdominal mass. An explorative laparotomy was performed, revealing a large (22 × 11 cm) neoplasm strictly connected to the lowest ileal segment and completely filling the pelvis. Definitive histology revealed a moderately differentiated adenocarcinoma developing in a duplication of the terminal ileum. The hypothesis of a gastrointestinal duplication should be evaluated in the differential diagnosis of large, complex, indeterminate masses located in or near the bowel; the possibility of neoplasm within the duplication should be considered.

  4. Duplication of 10q confirmed by DNA in situ hybridization

    SciTech Connect

    Johnson, V.P.; Sutliff, W.C.

    1994-08-15

    Partial duplication of 10q is a recognizable clinical entity. In most of the reported cases, the trisomic segment is identified by a balanced translocation state in a parent. Verification remains a problem in de novo cases. However, the recent availability of whole chromosome probes allows for confirmatory diagnosis of suspected cases. We describe a case of de novo duplication (10q) with verification using DNA is situ hybridization. 9 refs., 5 figs.

  5. Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar

    PubMed Central

    2010-01-01

    Background The Atlantic salmon (Salmo salar) immunoglobulin heavy chain (IgH) locus possesses two parallel IgH isoloci (IGH-A and IGH-B), that are related to the genomic duplication event in the family Salmonidae. These duplicated IgH loci in Atlantic salmon provide a unique opportunity to examine the mechanisms of genome diversity and genome evolution of the IgH loci in vertebrates. In this study, we defined the structure of these loci in Atlantic salmon, and sequenced 24 bacterial artificial chromosome (BAC) clones that were assembled into the IGH-A (1.1 Mb) and IGH-B (0.9 Mb) loci. In addition, over 7,000 cDNA clones from the IgH variable (VH) region have been sequenced and analyzed. Results The present study shows that the genomic organization of the duplicated IgH loci in Atlantic salmon differs from that in other teleosts and other vertebrates. The loci possess multiple Cτ genes upstream of the Cμ region, with three of the Cτ genes being functional. Moreover, the duplicated loci possess over 300 VH segments which could be classified into 18 families. This is the largest number of VH families currently defined in any vertebrate. There were significant structural differences between the two loci, indicating that both IGH-A and -B loci have evolved independently in the short time after the recent genome duplication approximately 60 mya. Conclusions Our results indicate that the duplication of the IgH loci in Atlantic salmon significantly contributes to the increased diversity of the antibody repertoire, as compared with the single IgH locus in other vertebrates. PMID:20813058

  6. Current Duplicating Processes

    ERIC Educational Resources Information Center

    Groneman, Nancy

    1978-01-01

    While business instructors are still teaching spirit and stencil duplicating processes, most businesses now use copiers or offset printing processes. The article discusses offset and copier skills needed by office workers, pointing out that the processes being taught should be compatible with those used in business. (MF)

  7. Duplication Is Ubiquitous

    ERIC Educational Resources Information Center

    Tenopir, Carol

    2005-01-01

    This article discusses how Phil Davis, Life Sciences Bibliographer at Cornell University, found duplicate articles in Emerald/MCB University Press journals. According to Davis, he has found hundreds of examples of the same article published in more than one journal in at least 73 Emerald/MCB journals over 30 years. This article gives the details…

  8. Perspectives on Program Duplication

    ERIC Educational Resources Information Center

    Morrison, Gail M.

    2010-01-01

    Concerns about program duplication in higher education are often reminiscent of Supreme Court Justice Potter Stewart's now famous remark about pornography: "I know it when I see it." The problem with that reaction is that, at least on its surface, this response seems intuitive and emotional, to say nothing of subjective and personal. The…

  9. Duplication Is Ubiquitous

    ERIC Educational Resources Information Center

    Tenopir, Carol

    2005-01-01

    This article discusses how Phil Davis, Life Sciences Bibliographer at Cornell University, found duplicate articles in Emerald/MCB University Press journals. According to Davis, he has found hundreds of examples of the same article published in more than one journal in at least 73 Emerald/MCB journals over 30 years. This article gives the details…

  10. A Duplicate Construction Experiment.

    ERIC Educational Resources Information Center

    Bridgeman, Brent

    This experiment was designed to assess the ability of item writers to construct truly parallel tests based on a "duplicate-construction experiment" in which Cronbach argues that if the universe description and sampling are ideally refined, the two independently constructed tests will be entirely equivalent, and that within the limits of item…

  11. Detection of tandem duplications and implications for linkage analysis.

    PubMed Central

    Matise, T. C.; Chakravarti, A.; Patel, P. I.; Lupski, J. R.; Nelis, E.; Timmerman, V.; Van Broeckhoven, C.; Weeks, D. E.

    1994-01-01

    The first demonstration of an autosomal dominant human disease caused by segmental trisomy came in 1991 for Charcot-Marie-Tooth disease type 1A (CMT1A). For this disorder, the segmental trisomy is due to a large tandem duplication of 1.5 Mb of DNA located on chromosome 17p11.2-p12. The search for the CMT1A disease gene was misdirected and impeded because some chromosome 17 genetic markers that are linked to CMT1A lie within this duplication. To better understand how such a duplication might affect genetic analyses in the context of disease gene mapping, we studied the effects of marker duplication on transmission probabilities of marker alleles, on linkage analysis of an autosomal dominant disease, and on tests of linkage homogeneity. We demonstrate that the undetected presence of a duplication distorts transmission ratios, hampers fine localization of the disease gene, and increases false evidence of linkage heterogeneity. In addition, we devised a likelihood-based method for detecting the presence of a tandemly duplicated marker when one is suspected. We tested our methods through computer simulations and on CMT1A pedigrees genotyped at several chromosome 17 markers. On the simulated data, our method detected 96% of duplicated markers (with a false-positive rate of 5%). On the CMT1A data our method successfully identified two of three loci that are duplicated (with no false positives). This method could be used to identify duplicated markers in other regions of the genome and could be used to delineate the extent of duplications similar to that involved in CMT1A. PMID:8198134

  12. Detection of tandam duplications and implications for linkage analysis

    SciTech Connect

    Matise, T.C.; Weeks, D.E. ); Chakravarti, A. ); Patel, P.I.; Lupski, J.R. ); Nelis, E.; Timmerman, V.; Van Broeckhoven, C. )

    1994-06-01

    The first demonstration of an autosomal dominant human disease caused by segmental trisomy came in 1991 for Charcot-Marie-Tooth disease type 1A (CMT1A). For this disorder, the segmental trisomy is due to a large tandem duplication of 1.5 Mb of DNA located on chromosome 17p11.2-p12. The search for the CMT1A disease gene was misdirected and impeded because some chromosome 17 genetic markers that are linked to CMT1A lie within this duplication. To better understand how such a duplication might affect genetic analyses in the context of disease gene mapping, the authors studied the effects of marker duplication on transmission probabilities of marker alleles, on linkage analysis of an autosomal dominant disease, and on tests of linkage homogeneity. They demonstrate that the undetected presence of a duplication distorts transmission ratios, hampers fine localization of the disease gene, and increases false evidence of linkage heterogeneity. In addition, they devised a likelihood-based method for detecting the presence of a tandemly duplicated marker when one is suspected. They tested their methods through computer simulations and on CMT1A pedigrees genotyped at several chromosome 17 markers. On the simulated data, the method detected 96% of duplicated markers (with a false-positive rate of 5%). On the CMT1A data the method successfully identified two of three loci that are duplicated (with no false positives). This method could be used to identify duplicated markers in other regions of the genome and could be used to delineate the extent of duplications similar to that involved in CMT1A. 18 refs., 5 figs., 6 tabs.

  13. Evaluation of anterior and posterior surfaces of the cornea using a dual Scheimpflug analyzer in keratoconus patients implanted with intrastromal corneal ring segments

    PubMed Central

    Torquetti, Leonardo; Arce, Carlos; Merayo-Lloves, Jesús; Ferrara, Guilherme; Ferrara, Paulo; Signorelli, Brenno; Signorelli, Armando

    2016-01-01

    AIM To evaluate corneal parameters measured with a dual Scheimpflug analyzer in keratoconus patients implanted with intrastromal corneal ring segments (ICRS). METHODS Fifty eyes of 40 keratoconus patients had Ferrara ICRS implantation from November 2010 to April 2014. Uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA), refraction, keratometry, asphericity, elevation, pachymetry, root mean square (RMS), spherical aberration and coma were studied. All patients were evaluated using a dual Scheimpflug system. RESULTS The mean follow-up time after the procedure was 12.7mo. The mean UCVA improved from 0.82 to 0.31 (P<0.001); the mean BCVA improved from 0.42 to 0.05 (P<0.0001), the mean spherical refraction changed from -3.06±3.80 D to -0.80±2.5 D (P<0.0001) and the mean refraction astigmatism reduced from -4.51±2.08 D to -2.26±1.18 D (P<0.0001). The changes from preoperative to postoperative, in parameters of the anterior and posterior surface of the cornea, were statistically significant except the elevation posterior at the apex of the cornea and posterior asphericity. CONCLUSION The implantation of Ferrara ICRS induces changes in both anterior and posterior surfaces of the cornea. PMID:27672592

  14. Tandem duplication of the terminal band of the long arm of chromosome 7 (dir dup (7)(q36----qter)).

    PubMed Central

    Verma, R S; Conte, R A; Pitter, J H

    1992-01-01

    We report on a new case of a single band duplication of the long arm of chromosome 7, dir dup (7)(q36----qter). The major manifestations are developmental delay (particularly speech), frontal bossing, macrocrania, and constant drooling. When compared with other cases involving a 7q duplication of various segments, our patient has a few minor anomalies. This case illustrates the genotype/phenotype correlation in a child with a single band duplication which has resulted in duplication of 7q36----qter. A tabulation of reported cases with duplication of various segments of 7q is provided, which may serve as an aid for clinicians. Images PMID:1583663

  15. Optimal delineation of ambulatory holter ECG events via false-alarm bounded segmentation of a wavelet-based principal components analyzed decision statistic.

    PubMed

    Homaeinezhad, M R; Ghaffari, A; Toosi, H Najjaran; Tahmasebi, M; Daevaeiha, M M

    2010-09-01

    The aim of this study is to develop and describe a new ambulatory holter electrocardiogram (ECG) events detection-delineation algorithm with the major focus on the bounded false-alarm probability (FAP) segmentation of an information-optimized decision statistic. After implementation of appropriate preprocessing methods to the discrete wavelet transform (DWT) of the original ECG data, a uniform length sliding window is applied to the obtained signal and in each slid, six feature vectors namely as summation of the nonlinearly amplified Hilbert transform, summation of absolute first order differentiation, summation of absolute second order differentiation, curve length, area and variance of the excerpted segment are calculated to construct a newly proposed principal components analyzed geometric index (PCAGI) by application of a linear orthonormal projection. In the next step, the α-level Neyman-Pearson classifier (which is a FAP controlled tester) is implemented to detect and delineate QRS complexes. The presented method was applied to MIT-BIH Arrhythmia Database, QT Database, and T-Wave Alternans Database and as a result, the average values of sensitivity and positive predictivity Se = 99.96% and P+ = 99.96% are obtained for the detection of QRS complexes, with the average maximum delineation error of 5.7, 3.8 and 6.1 m for P-wave, QRS complex and T-wave, respectively. Also, the proposed method was applied to DAY general hospital high resolution holter data (more than 1,500,000 beats including Bundle Branch Blocks-BBB, Premature Ventricular Complex-PVC and Premature Atrial Complex-PAC) and average values of Se = 99.98% and P+ = 99.97% are obtained for QRS detection. In summary, marginal performance improvement of ECG events detection-delineation process in a widespread values of signal to noise ratio (SNR), reliable robustness against strong noise, artifacts and probable severe arrhythmia(s) of high resolution holter data and the processing speed 155

  16. Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22.

    PubMed

    Bailey, Jeffrey A; Yavor, Amy M; Viggiano, Luigi; Misceo, Doriana; Horvath, Juliann E; Archidiacono, Nicoletta; Schwartz, Stuart; Rocchi, Mariano; Eichler, Evan E

    2002-01-01

    In recent decades, comparative chromosomal banding, chromosome painting, and gene-order studies have shown strong conservation of gross chromosome structure and gene order in mammals. However, findings from the human genome sequence suggest an unprecedented degree of recent (<35 million years ago) segmental duplication. This dynamism of segmental duplications has important implications in disease and evolution. Here we present a chromosome-wide view of the structure and evolution of the most highly homologous duplications (> or = 1 kb and > or = 90%) on chromosome 22. Overall, 10.8% (3.7/33.8 Mb) of chromosome 22 is duplicated, with an average sequence identity of 95.4%. To organize the duplications into tractable units, intron-exon structure and well-defined duplication boundaries were used to define 78 duplicated modules (minimally shared evolutionary segments) with 157 copies on chromosome 22. Analysis of these modules provides evidence for the creation or modification of 11 novel transcripts. Comparative FISH analyses of human, chimpanzee, gorilla, orangutan, and macaque reveal qualitative and quantitative differences in the distribution of these duplications--consistent with their recent origin. Several duplications appear to be human specific, including a approximately 400-kb duplication (99.4%-99.8% sequence identity) that transposed from chromosome 14 to the most proximal pericentromeric region of chromosome 22. Experimental and in silico data further support a pericentromeric gradient of duplications where the most recent duplications transpose adjacent to the centromere. Taken together, these data suggest that segmental duplications have been an ongoing process of primate genome evolution, contributing to recent gene innovation and the dynamic transformation of genome architecture within and among closely related species.

  17. Systematic Imaging Module in Complete Hindgut Duplication

    PubMed Central

    Verma, Ashish; Gupta, Prashant Nath; Pandey, Vaibhav; Jain, Shivi; Upadhyay, Ashish; Sharma, Jitendra; Shukla, Ram C.

    2015-01-01

    Complete hind gut and anal canal duplication is a rare entity, usually remaining asymptomatic till the disease comes to light due to associated anomalies or due to cosmetic reasons. Classical imaging consisting of barium enema examination served a limited role, in terms of depicting the length of gut segment involved. Technical advances in magnetic resonance imaging (MRI) with three-dimensional (3D) reformations cannot only solve the above purpose but further evaluate key points needed for surgical planning. The present technical report lays out a systematic module for evaluation of various aspects of complete hindgut duplication, critical for management. The role of 3D MRI is emphasized upon, for evaluation of pelvic floor and anorectum, even in infants with a distorted anatomy. PMID:26171317

  18. Aligning Two Genomic Sequences That Contain Duplications

    NASA Astrophysics Data System (ADS)

    Hou, Minmei; Riemer, Cathy; Berman, Piotr; Hardison, Ross C.; Miller, Webb

    It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.

  19. Gastrointestinal tract duplications: clinical, pathologic, etiologic, and radiologic considerations.

    PubMed

    Macpherson, R I

    1993-09-01

    Gastrointestinal tract duplications are uncommon congenital abnormalities. By definition, they are located in or adjacent to the wall of part of the gastrointestinal tract, have smooth muscle in their walls, and are lined by alimentary tract mucosa. The lining mucosa is not necessarily that of the adjacent segment of the gastrointestinal tract. The only clinically important ectopic tissues are gastric mucosa and pancreatic tissue. Although ectopic gastric mucosa is found in duplications at all levels of the gastrointestinal tract, it is most prevalent (43%) in esophageal duplications. Peptic ulcer within this ectopic tissue can account for unusual, often misleading symptoms. Ectopic pancreatic tissue is most common (37%) in gastric duplications and is associated with pancreatitis and elevated amylase levels. Detection of associated vertebral anomalies is a helpful clue in the radiographic diagnosis of duplications. Barium studies usually reveal an intraluminal, intramural, or extrinsic mass, and ultrasonography (US) demonstrates its cystic nature. When US findings are inconclusive, computed tomography can be used to show the true nature, location, and extent of the lesion, as well as associated vertebral anomalies and possible other duplications. Technetium-99m pertechnetate scintigraphy provides definitive evidence of a duplication when it contains ectopic gastric mucosa and is particularly useful for suspected esophageal, duodenal, and small bowel lesions.

  20. Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes.

    PubMed

    Lin, Yongxiang; Cheng, Ying; Jin, Jing; Jin, Xiaolei; Jiang, Haiyang; Yan, Hanwei; Cheng, Beijiu

    2014-01-01

    Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species.

  1. Genome Duplication and Gene Loss Affect the Evolution of Heat Shock Transcription Factor Genes in Legumes

    PubMed Central

    Jin, Jing; Jin, Xiaolei; Jiang, Haiyang; Yan, Hanwei; Cheng, Beijiu

    2014-01-01

    Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species. PMID:25047803

  2. The Sequence and Analysis of Duplication Rich Human Chromosome 16

    DOE R&D Accomplishments Database

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-01-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  3. The sequence and analysis of duplication rich human chromosome 16

    SciTech Connect

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-08-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  4. The sequence and analysis of duplication rich human chromosome 16

    SciTech Connect

    Martin, J; Han, C; Gordon, L A; Terry, A; Prabhakar, S; She, X; Xie, G; Hellsten, U; Chan, Y M; Altherr, M; Couronne, O; Aerts, A; Bajorek, E; Black, S; Blumer, H; Branscomb, E; Brown, N; Bruno, W J; Buckingham, J; Callen, D F; Campbell, C S; Campbell, M L; Campbell, E W; Caoile, C; Challacombe, J F; Chasteen, L A; Chertkov, O; Chi, H C; Christensen, M; Clark, L M; Cohn, J D; Denys, M; Detter, J C; Dickson, M; Dimitrijevic-Bussod, M; Escobar, J; Fawcett, J J; Flowers, D; Fotopulos, D; Glavina, T; Gomez, M; Gonzales, E; Goodstein, D; Goodwin, L A; Grady, D L; Grigoriev, I; Groza, M; Hammon, N; Hawkins, T; Haydu, L; Hildebrand, C E; Huang, W; Israni, S; Jett, J; Jewett, P B; Kadner, K; Kimball, H; Kobayashi, A; Krawczyk, M; Leyba, T; Longmire, J L; Lopez, F; Lou, Y; Lowry, S; Ludeman, T; Manohar, C F; Mark, G A; McMurray, K L; Meincke, L J; Morgan, J; Moyzis, R K; Mundt, M O; Munk, A C; Nandkeshwar, R D; Pitluck, S; Pollard, M; Predki, P; Parson-Quintana, B; Ramirez, L; Rash, S; Retterer, J; Ricke, D O; Robinson, D; Rodriguez, A; Salamov, A; Saunders, E H; Scott, D; Shough, T; Stallings, R L; Stalvey, M; Sutherland, R D; Tapia, R; Tesmer, J G; Thayer, N; Thompson, L S; Tice, H; Torney, D C; Tran-Gyamfi, M; Tsai, M; Ulanovsky, L E; Ustaszewska, A; Vo, N; White, P S; Williams, A L; Wills, P L; Wu, J; Wu, K; Yang, J; DeJong, P; Bruce, D; Doggett, N A; Deaven, L; Schmutz, J; Grimwood, J; Richardson, P; Rokhsar, D S; Eichler, E E; Gilna, P; Lucas, S M; Myers, R M; Rubin, E M; Pennacchio, L A

    2005-04-06

    Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes, and 3 RNA pseudogenes. These genes include metallothionein, cadherin, and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. While the segmental duplications of chromosome 16 are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events likely to have had an impact on the evolution of primates and human disease susceptibility.

  5. Exploring duplicated regions in natural images.

    PubMed

    Bashar, M; Noda, K; Ohnishi, N; Mori, K

    2010-01-01

    Duplication of image regions is a common method for manipulating original images, using typical software like Adobe Photoshop, 3DS MAX, etc. In this study, we propose a duplication detection approach that can adopt two robust features based on discrete wavelet transform (DWT) and kernel principal component analysis (KPCA). Both schemes provide excellent representations of the image data for robust block matching. Multiresolution wavelet coefficients and KPCA-based projected vectors corresponding to image-blocks are arranged into a matrix for lexicographic sorting. Sorted blocks are used for making a list of similar point-pairs and for computing their offset frequencies. Duplicated regions are then segmented by an automatic technique that refines the list of corresponding point-pairs and eliminates the minimum offset-frequency threshold parameter in the usual detection method. A new technique that extends the basic algorithm for detecting Flip and Rotation types of forgeries is also proposed. This method uses global geometric transformation and the labeling technique to indentify the mentioned forgeries. Experiments with a good number of natural images show very promising results, when compared with the conventional PCA-based approach. A quantitative analysis indicate that the wavelet-based feature outperforms PCA- or KPCA-based features in terms of average precision and recall in the noiseless, or uncompressed domain, while KPCA-based feature obtains excellent performance in the additive noise and lossy JPEG compression environments.

  6. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time.

    PubMed

    Conant, Gavin C; Birchler, James A; Pires, J Chris

    2014-06-01

    Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications, gene copy number variations (CNV), and epigenetic marks. Like neofunctionalization and subfunctionalization, the impact of absolute and relative dosage varies over time. These variations are of particular importance in understanding the role of dosage in the evolution of polyploid organisms. Numerous investigations have found the consequences of polyploidy remain distinct from small-scale duplications (SSD). This observation is significant as all flowering plants have experienced at least two ancient polyploid events, and many angiosperm lineages have undergone additional rounds of polyploidy. Intriguingly, recent studies indicate a link between how epigenetic marks in recent allopolyploids may induce immediate changes in gene expression and the longer-term patterns of biased fractionation and chromosomal evolution. We argue that dosage effects represent one aspect of an emerging pluralistic framework, a framework that will use biophysics, genomic technologies, and systems-level models of cells to broaden our view of how genomes evolve. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Duplicated middle cerebral artery.

    PubMed

    Perez, Jesus; Machado, Calixto; Scherle, Claudio; Hierro, Daniel

    2009-01-01

    Duplicated middle cerebral artery (DMCA) is an anomalous vessel arising from the internal carotid artery. The incidence DMCA is relatively law, and an association between this anomaly and cerebral aneurysms has been documented. There is a controversy whether DMCA may have perforating arteries. This is an important fact to consider in aneurysm surgery. We report the case of a 34-year-old black woman who suffered a subarachnoid hemorrhage and the angiography a left DMCA, and an aneurysm in an inferior branch of the main MCA. The DMCA and the MCA had perforating arteries. The aneurysm was clipped without complications. The observation of perforating arteries in our patient confirms that the DMCA may have perforating arteries. This is very important to be considered in cerebral aneurysms surgery. Moreover, the DMCA may potentially serve as a collateral blood supply to the MCA territory in cases of MCA occlusion.

  8. Gene duplication and the properties of biological networks.

    PubMed

    Hughes, Austin L; Friedman, Robert

    2005-12-01

    Patterns of network connection of members of multigene families were examined for two biological networks: a genetic network from the yeast Saccharomyces cerevisiae and a protein-protein interaction network from Caenorhabditis elegans. In both networks, genes belonging to gene families represented by a single member in the genome ("singletons") were disproportionately represented among the nodes having large numbers of connections. Of 68 single-member yeast families with 25 or more network connections, 28 (44.4%) were located in duplicated genomic segments believed to have originated from an ancient polyploidization event; thus, each of these 28 loci was thus presumably duplicated along with the genomic segment to which it belongs, but one of the two duplicates has subsequently been deleted. Nodes connected to major "hubs" with a large number of connections, tended to be relatively sparsely interconnected among themselves. Furthermore, duplicated genes, even those arising from recent duplication, rarely shared many network connections, suggesting that network connections are remarkably labile over evolutionary time. These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature.

  9. Evolution after whole-genome duplication: a network perspective.

    PubMed

    Zhu, Yun; Lin, Zhenguo; Nakhleh, Luay

    2013-11-06

    Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this work, we analyze a data set of gene pairs that arose through whole-genome duplication (WGD) in yeast. All these pairs have the same duplication time, making them ideal for evolutionary investigation. We investigated the interplay between evolution after WGD at the sequence and network levels and correlated these two levels of divergence with gene expression and fitness data. We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences. Furthermore, we find that divergence of WGD pairs correlates strongly with gene expression and fitness data. Because of the role of gene duplication in determining redundancy in biological systems and particularly at the network level, we investigated the role of interaction networks in elucidating the evolutionary fate of duplicated genes. We find that gene neighborhoods in interaction networks provide a mechanism for inferring these fates, and we developed an algorithm for achieving this task. Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques. Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

  10. [Intestinal cystic duplication. Case report].

    PubMed

    Herranz Barbero, Ana; Prat Ortells, Jordi; Muñoz Fernández, M Elena; Castañón García-Alix, Montserrat; Figueras Aloy, Josep

    2017-08-01

    Intestinal cystic duplications are rare congenital anomalies, with an estimated incidence of approximately 1:4500 autopsies. The etiopathogenesis is uncertain. These duplications are cystic, tubular or diverticular structures lined with gastrointestinal mucosa. They share a common smooth muscle wall with the gastrointestinal tract but usually their lumens do not communicate with each other. Gastric duplication cysts represent 7-9% of the gastrointestinal tract duplication. They can be diagnosed prenatally by fetal ultrasound; magnetic resonance imaging characterizes the cyst and excludes other malformations. Postnatal ultrasound shows a characteristic double walled cyst. Newborns are usually asymptomatic, although nonspecific gastrointestinal symptoms, intestinal obstruction due to mass effect, volvulus or infection are described. In asymptomatic patients, clinical follow-up and periodic image controls are recommended. Elective surgical resection is the treatment of choice, using minimally invasive technique whenever possible. A case of prenatally suspected intestinal cystic duplication is presented. Sociedad Argentina de Pediatría.

  11. Mucinous cystadenoma arising in a completely isolated infected ileal duplication cyst.

    PubMed

    Collaud, Stéphane; Bayerl, Christian; Wille, Georg; Zehnder, Adrian; Grieder, Felix; Meili, Severin; Decurtins, Marco

    2012-03-29

    Gastrointestinal duplications are uncommon congenital lesions that can occur anywhere along the alimentary tract, and the symptoms of which generally develop during infancy or childhood. Completely isolated duplication cysts are an extremely rare variant of duplication, where no communication between the cyst and the adjacent bowel segment is present. We report the unique case of an adult who presented with right lower abdominal pain and systemic signs of inflammation caused by infection of a completely isolated ileal duplication cyst. Histological examination of the cyst additionally revealed a low-grade mucinous cystadenoma. We discuss the clinical presentations, diagnosis and treatment of this rare entity.

  12. Accurate quantitation of Ki67-positive proliferating hepatocytes in rabbit liver by a multicolor immunohistochemical (IHC) approach analyzed with automated tissue and cell segmentation software.

    PubMed

    van der Loos, Chris M; de Boer, Onno J; Mackaaij, Claire; Hoekstra, Lisette T; van Gulik, Thomas M; Verheij, Joanne

    2013-01-01

    Determination of hepatocyte proliferation activity is hampered by the presence of Ki67-positive non-parenchymal cells. We validated a multicolor immunohistochemical (IHC) approach using multispectral tissue and cell segmentation software. Portal vein branches to the cranial liver lobes of 10 rabbits were embolized, leading to atrophy of the cranial lobes and hyperplasia of the caudal lobes. Slides from cranial and caudal lobes (n=20) were double-stained (CK8+18 and Ki67) and triple-stained (CK8+18, Ki67, and CD31). The Ki67 proliferation index was calculated using automated tissue and cell segmentation software and compared with manual counting by two independent observers. A substantial variation was seen in the number of Ki67-positive hepatocytes in the different specimens in both double and triple staining (range, 0-50). Correlation coefficients between manual counting and the digital analysis were 0.76 for observer 1 (p<0.001) and 0.78 for observer 2 (p<0.001) with double staining and R(2) = 0.91 for observer 1 and R(2) = 0.89 for observer 2, p<0.001 with triple staining. In conclusion, in rabbit, the hepatocellular proliferation index can be reliably determined using automated tissue and cell segmentation software in combination with IHC multiple staining. Our findings may be useful in clinical practice when Ki67 proliferation index yields prognostic significance.

  13. A multi-directional and multi-scale roughness filter to detect lineament segments on digital elevation models - analyzing spatial objects in R

    NASA Astrophysics Data System (ADS)

    Baumann, Sebastian; Robl, Jörg; Wendt, Lorenz; Willingshofer, Ernst; Hilberg, Sylke

    2016-04-01

    Automated lineament analysis on remotely sensed data requires two general process steps: The identification of neighboring pixels showing high contrast and the conversion of these domains into lines. The target output is the lineaments' position, extent and orientation. We developed a lineament extraction tool programmed in R using digital elevation models as input data to generate morphological lineaments defined as follows: A morphological lineament represents a zone of high relief roughness, whose length significantly exceeds the width. As relief roughness any deviation from a flat plane, defined by a roughness threshold, is considered. In our novel approach a multi-directional and multi-scale roughness filter uses moving windows of different neighborhood sizes to identify threshold limited rough domains on digital elevation models. Surface roughness is calculated as the vertical elevation difference between the center cell and the different orientated straight lines connecting two edge cells of a neighborhood, divided by the horizontal distance of the edge cells. Thus multiple roughness values depending on the neighborhood sizes and orientations of the edge connecting lines are generated for each cell and their maximum and minimum values are extracted. Thereby negative signs of the roughness parameter represent concave relief structures as valleys, positive signs convex relief structures as ridges. A threshold defines domains of high relief roughness. These domains are thinned to a representative point pattern by a 3x3 neighborhood filter, highlighting maximum and minimum roughness peaks, and representing the center points of lineament segments. The orientation and extent of the lineament segments are calculated within the roughness domains, generating a straight line segment in the direction of least roughness differences. We tested our algorithm on digital elevation models of multiple sources and scales and compared the results visually with shaded relief map

  14. Evolution of Gene Duplication in Plants.

    PubMed

    Panchy, Nicholas; Lehti-Shiu, Melissa; Shiu, Shin-Han

    2016-08-01

    Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

  15. Classification of the stages of hyperplasia in breast ducts by analyzing different depths and segmentation of ultrasound breast scans into ductal areas.

    PubMed

    Taslidere, Ezgi; Cohen, Fernand S; Georgiou, Georgia

    2006-01-01

    In this paper, we study in depth the potential of detection of epithelium hyperplastic growth in the breast ducts leading to early breast cancer detection. Towards that end, we use a stochastic decomposition algorithm of the RF echo into its coherent and diffuse components that yields image parameters related to the structural parameters of the hyperplastic stages of the breast tissue. Previously, we proved that the two parameters, in particular the number of coherent scatterers and the Rayleigh scattering degree show very high ability to discriminate between various stages of hyperplasia even in cases of low resolution and low SNR values. In this paper, the discrimination power of the other parameters is studied further considering different depths using a point scatterer model simulator that mimics epithelium hyperplastic growth in the breast ducts. Significant improvement is obtained in the performance with the newly adopted method considering depth. Values of Az up to 0.974 are obtained when discriminating between pairs of stages using the parameter residual error variance. In addition, this paper presents a fast nonparametric segmentation procedure to locate the ducts illustrated using phantom data. The performance of the segmentation procedure is obtained as Az>0.948 for various regions of breast scans.

  16. Ideal photon number amplifier and duplicator

    NASA Technical Reports Server (NTRS)

    Dariano, G. M.

    1992-01-01

    The photon number-amplification and number-duplication mechanism are analyzed in the ideal case. The search for unitary evolutions leads to consider also a number-deamplification mechanism, the symmetry between amplification and deamplification being broken by the integer-value nature of the number operator. Both transformations, amplification and duplication, need an auxiliary field which, in the case of amplification, turns out to be amplified in the inverse way. Input-output energy conservation is accounted for using a classical pump or through frequency-conversion of the fields. Ignoring one of the fields is equivalent to considering the amplifier as an open system involving entropy production. The Hamiltonians of the ideal devices are given and compared with those of realistic systems.

  17. Advances on Genome Duplication Distances

    NASA Astrophysics Data System (ADS)

    Gagnon, Yves; Savard, Olivier Tremblay; Bertrand, Denis; El-Mabrouk, Nadia

    Given a phylogenetic tree involving Whole Genome Duplication events, we contribute to the problem of computing the rearrangement distance on a branch of a tree linking a duplication node d to a speciation node or a leaf s. In the case of a genome G at s containing exactly two copies of each gene, the genome halving problem is to find a perfectly duplicated genome D at d minimizing the rearrangement distance with G. We generalize the existing exact linear-time algorithm for genome halving to the case of a genome G with missing gene copies. In the case of a known ancestral duplicated genome D, we develop a greedy approach for computing the distance between G and D that is shown time-efficient and very accurate for both the rearrangement and DCJ distances.

  18. Fast Anomaly Discovery Given Duplicates

    DTIC Science & Technology

    2012-12-01

    skipping the computations for duplicate points in SN(ui) that have ci larger than k, the runtime complexity is enhanced significantly. That is, in...Fast anomaly discovery given duplicates Jay-Yoon Lee, U Kang, Danai Koutra, Christos Faloutsos Dec 2012 CMU-CS-12-146 School of Computer Science...ES) Carnegie Mellon University,School of Computer Science,Pittsburgh,PA,15213 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING

  19. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome.

    PubMed

    Katju, Vaishali; Lynch, Michael

    2003-12-01

    The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with < or =10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.

  20. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome.

    PubMed Central

    Katju, Vaishali; Lynch, Michael

    2003-01-01

    The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with < or =10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms. PMID:14704166

  1. Identifying duplicate content using statistically improbable phrases

    PubMed Central

    Errami, Mounir; Sun, Zhaohui; George, Angela C.; Long, Tara C.; Skinner, Michael A.; Wren, Jonathan D.; Garner, Harold R.

    2010-01-01

    Motivation: Document similarity metrics such as PubMed's ‘Find related articles’ feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. Results: When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Availability: Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/ Contact: merrami@collin.edu PMID:20472545

  2. Disparity, diversity, and duplications in the Caryophyllales.

    PubMed

    Smith, Stephen A; Brown, Joseph W; Yang, Ya; Bruenn, Riva; Drummond, Chloe P; Brockington, Samuel F; Walker, Joseph F; Last, Noah; Douglas, Norman A; Moore, Michael J

    2017-09-11

    The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution. © 2017 The Authors New Phytologist © 2017 New Phytologist Trust.

  3. Identifying duplicate content using statistically improbable phrases.

    PubMed

    Errami, Mounir; Sun, Zhaohui; George, Angela C; Long, Tara C; Skinner, Michael A; Wren, Jonathan D; Garner, Harold R

    2010-06-01

    Document similarity metrics such as PubMed's 'Find related articles' feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/.

  4. Congenital duplication of the larynx.

    PubMed

    Simpson, A I; Khanna, A; Stanton, A

    2014-06-01

    The larynx is an intricate structure serving three important functions in humans: it protects the lower respiratory airway, facilitates respiration and helps produce sound through a key role in phonation. We report the first published finding of congenital duplication of the larynx in a patient with previously cleared squamous cell carcinoma of the neck and a new diagnosis of squamous cell carcinoma of the lung. We describe the incidental finding of duplication of the larynx in a 62-year-old man with previously completely cleared squamous cell carcinoma of the neck, who presented with worsening dyspnoea. We also provide a brief overview of other published cases in which duplication of the vocal folds and epiglottis has been reported. Our patient experienced no symptoms related to this incidental finding of congenital duplication of the larynx. The first case of congenital duplication of the larynx is currently of academic interest only; however, the possible association with squamous cell carcinoma is postulated to raise awareness in clinicians who may observe further cases in the future.

  5. De Novo duplication in Charcot-Marie-Tooth Type 1A

    SciTech Connect

    Mandich, P.; Bellone, E.; Ajmar, F.

    1996-09-01

    We read with interest the paper on {open_quotes}Prevalence and Origin of De Novo Duplications in Charcot-Marie-Tooth Disease Type 1A: First Report of a De Novo Duplication with a Maternal Origin,{close_quotes}. They reported their experience with 10 sporadic cases of Charcot-Marie-Tooth type 1A (CMT1A) in which it was demonstrated that the disease had arisen as the result of a de novo duplication. They analyzed the de novo-duplication families by using microsatellite markers and identified the parental origin of the duplication in eight cases. In one family the duplication was of maternal origin, whereas in the remaining seven cases it was of paternal origin. The authors concluded that their report was the first evidence of a de novo duplication of maternal origin, suggesting that this is not a phenomenon associated solely with male meiosis. 7 refs.

  6. Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference.

    PubMed

    Robinson-Rechavi, Marc; Boussau, Bastien; Laudet, Vincent

    2004-03-01

    Vertebrates originated in the lower Cambrian. Their diversification and morphological innovations have been attributed to large-scale gene or genome duplications at the origin of the group. These duplications are predicted to have occurred in two rounds, the "2R" hypothesis, or they may have occurred in one genome duplication plus many segmental duplications, although these hypotheses are disputed. Under such models, most genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and the closest invertebrate, amphioxus, but have not set a clear ending. Consideration of chordate phylogeny immediately shows the key position of cartilaginous vertebrates (Chondrichthyes) to answer this question. Did gene duplications occur as frequently during the 45 Myr between the cartilaginous/bony vertebrate split and the fish/tetrapode split as in the previous approximately 100 Myr? Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates. By a systematic appraisal of gene phylogenies, we show that significantly more duplications occurred before than after the cartilaginous/bony vertebrate split. Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events.

  7. Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations.

    PubMed

    Tanaka, Kentaro M; Takahasi, K Ryo; Takano-Shimizu, Toshiyuki

    2009-08-01

    Segmental duplications are enriched within many eukaryote genomes, and their potential consequence is gene duplication. While previous theoretical studies of gene duplication have mainly focused on the gene silencing process after fixation, the process leading to fixation is even more important for segmental duplications, because the majority of duplications would be lost before reaching a significant frequency in a population. Here, by a series of computer simulations, we show that purifying selection against loss-of-function mutations increases the fixation probability of a new duplicate gene, especially when the gene is haplo-insufficient. Theoretically, the probability of simultaneous preservation of both duplicate genes becomes twice the loss-of-function mutation rate (u(c)) when the population size (N), the degree of dominance of mutations (h) and the recombination rate between the duplicate genes (c) are all sufficiently large (Nu(c)>1, h>0.1 and c>u(c)). The preservation probability declines rapidly with h and becomes 0 when h=0 (haplo-sufficiency). We infer that masking deleterious loss-of-function mutations give duplicate genes an immediate selective advantage and, together with effects of increased gene dosage, would predominantly determine the fates of the duplicate genes in the early phase of their evolution.

  8. Duplication. Units of Instruction. Office Duplication Practices. Teacher's Guide.

    ERIC Educational Resources Information Center

    Powell, Theressa

    This teacher's guide is designed for use in helping secondary and postsecondary students in office occupations education programs to become familiar with duplication procedures and machines. Addressed in the individual units of the guide are the following topics: measurement, paper characteristics and classifications, copy preparation for pasteup…

  9. Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants

    PubMed Central

    2010-01-01

    Background Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear. Results Here, we have studied gene duplications in early eukaryotes by phylogenetic relative dating. We have reconstructed gene families (with one or more orthogroups) with members from both animals/fungi and plants by using two different clustering strategies. Extensive phylogenetic analyses of the gene families show that, among nearly 2,600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms. We further found evidence that such duplications were also detected in some highly divergent protists, suggesting that these duplication events occurred in the ancestors of most major extant eukaryotic groups. Conclusions Our phylogenetic analyses show that numerous gene duplications happened at the early stage of eukaryotic evolution, probably before the separation of known major eukaryotic lineages. We discuss the implication of our results in the contexts of different models of eukaryotic phylogeny. One possible explanation for the large number of gene duplication events is one or more large-scale duplications, possibly whole genome or segmental duplication(s), which provides a genomic basis for the successful radiation of early eukaryotes. PMID:20370904

  10. Neuroblastoma in a boy with MCA/MR syndrome, deletion 11q, and duplication 12q

    SciTech Connect

    Koiffmann, C.P.; Vianna-Morgante, A.M.; Wajntal, A.

    1995-07-31

    Deletion 11q23{r_arrow}qter and duplication 12q23{r_arrow}qter are described in a boy with neuroblastoma, multiple congenital anomalies, and mental retardation. The patient has clinical manifestations of 11q deletion and 12q duplication syndromes. The possible involvement of the segment 11q23{r_arrow}24 in the cause of the neuroblastoma is discussed. 18 refs., 2 figs., 1 tab.

  11. De novo interstitial tandem duplication of chromosome 4(q21-q28)

    SciTech Connect

    Navarro, E.G.; Ramon, F.J.H.; Jimenez, R.D.

    1996-03-29

    We describe a girl with a previously unreported de novo duplication of chromosome 4q involving segment q21-q28. Clinical manifestations included growth and psychomotor retardation, facial asymmetry, hypotelorism, epicanthic folds, mongoloid slant of palpebral fissures, apparently low-set auricles, high nasal bridge, long philtrum, small mouth, short neck, low-set thumbs, and bilateral club foot. This phenotype is compared with that of previously reported cases of duplication 4q. 12 refs., 3 figs., 1 tab.

  12. ALTERNATIVES TO DUPLICATE DIET METHODOLOGY

    EPA Science Inventory

    Duplicate Diet (DD) methodology has been used to collect information about the dietary exposure component in the context of total exposure studies. DD methods have been used to characterize the dietary exposure component in the NHEXAS pilot studies. NERL desired to evaluate it...

  13. Office Duplication Practices Curriculum Guide.

    ERIC Educational Resources Information Center

    East Texas State Univ., Commerce. Occupational Curriculum Lab.

    As one of a series of curriculum guides for office education programs in Texas, this guide contains 24 units of instruction in office duplication practices. Each of the units contains a unit outline that lists unit objective, specific objectives, teacher and student activities, estimated completion time, re-teach activities, and resources; and a…

  14. Duplicated Information Acquired by Libraries.

    ERIC Educational Resources Information Center

    White, Carl M.

    The object of this study is to make a start toward determining the extent of duplicated information that is being acquired in spite of customary precautions to avoid it. Referring to a specific case, the percentages in Table II show the frequency of appearance in five other works of 19 items in Mitchell's "Encyclopedia of American Politics." While…

  15. ALTERNATIVES TO DUPLICATE DIET METHODOLOGY

    EPA Science Inventory

    Duplicate Diet (DD) methodology has been used to collect information about the dietary exposure component in the context of total exposure studies. DD methods have been used to characterize the dietary exposure component in the NHEXAS pilot studies. NERL desired to evaluate it...

  16. beta. amyloid gene duplication in Alzheimer's disease and karyotypically normal Down syndrome

    SciTech Connect

    Delabar, J.; Goldgaber, D.; Lamour, Y.; Nicole, A.; Huret, J.; De Groucy, J.; Brown, P.; Gajdusek, D.C.; Sinet, P.

    1987-03-13

    With the recently cloned complementary DNA probe, lambdaAm4 for the chromosome 21 gene encoding brain amyloid polypeptide (..beta.. amyloid protein) of Alzheimer's disease, leukocyte DNA from three patients with sporadic Alzheimer's disease and two patients with karyotypically normal Down syndrome was found to contain three copies of this bene. Because a small region of chromosome 21 containing the ets-2 gene is duplicated in patients with Alzheimer's disease, as well as in karyotypically normal Down syndrome, duplication of a subsection of the critical segment of chromosome 21 that is duplicated in Down syndrome may be the genetic defect in Alzeimer's disease.

  17. A Large Palindrome With Interchromosomal Gene Duplications in the Pericentromeric Region of the D. melanogaster Y Chromosome

    PubMed Central

    Méndez-Lago, María; Bergman, Casey M.; de Pablos, Beatriz; Tracey, Alan; Whitehead, Siobhan L.; Villasante, Alfredo

    2011-01-01

    The non-recombining Y chromosome is expected to degenerate over evolutionary time, however, gene gain is a common feature of Y chromosomes of mammals and Drosophila. Here, we report that a large palindrome containing interchromosomal segmental duplications is located in the vicinity of the first amplicon detected in the Y chromosome of D. melanogaster. The recent appearance of such amplicons suggests that duplications to the Y chromosome, followed by the amplification of the segmental duplications, are a mechanism for the continuing evolution of Drosophila Y chromosomes. PMID:21297157

  18. Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar)

    PubMed Central

    Davidson, William S.

    2017-01-01

    Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates--often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well. PMID:28241055

  19. Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar).

    PubMed

    Christensen, Kris A; Davidson, William S

    2017-01-01

    Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates--often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well.

  20. Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins.

    PubMed

    Brandon, Christopher S; Greenwold, Matthew J; Dudycha, Jeffry L

    2017-01-01

    Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss. We further analyzed sequence variation to assess possible functional diversification among Daphnia opsins. Much of the opsin expansion occurred before the D. pulex-D. magna split more than 145 Mya, and both Daphnia lineages preserved most ancient opsins. More recent expansion occurred in pteropsins and long-wavelength visual opsins in both species, particularly D. pulex. Recent duplications were not random: the same ancestral genes duplicated independently in each modern species. Most ancient and some recent duplications involved differentiation at residues known to influence spectral tuning of visual opsins. Arthropsins show evidence of gene conversion between tandemly arrayed paralogs in functionally important domains. Intron-exon gene structure was generally conserved within clades inferred from sequences, although pteropsins showed substantial intron size variation. Overall, our analyses support the hypotheses that diverse opsins are maintained due to diverse functional roles in photoreception and vision, that functional diversification is both ancient and recent, and that multiple evolutionary processes have influenced different types of opsins.

  1. Defects arising from whole-genome duplications in Saccharomyces cerevisiae.

    PubMed Central

    Andalis, Alex A; Storchova, Zuzana; Styles, Cora; Galitski, Timothy; Pellman, David; Fink, Gerald R

    2004-01-01

    Comparisons among closely related species have led to the proposal that the duplications found in many extant genomes are the remnants of an ancient polyploidization event, rather than a result of successive duplications of individual chromosomal segments. If this interpretation is correct, it would support Ohno's proposal that polyploidization drives evolution by generating the genetic material necessary for the creation of new genes. Paradoxically, analysis of contemporary polyploids suggests that increased ploidy is an inherently unstable state. To shed light on this apparent contradiction and to determine the effects of nascent duplications of the entire genome, we generated isogenic polyploid strains of the budding yeast Saccharomyces cerevisiae. Our data show that an increase in ploidy results in a marked decrease in a cell's ability to survive during stationary phase in growth medium. Tetraploid cells die rapidly, whereas isogenic haploids remain viable for weeks. Unlike haploid cells, which arrest growth as unbudded cells, tetraploid cells continue to bud and form mitotic spindles in stationary phase. The stationary-phase death of tetraploids can be prevented by mutations or conditions that result in growth arrest. These data show that whole-genome duplications are accompanied by defects that affect viability and subsequent survival of the new organism. PMID:15280227

  2. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

    PubMed Central

    Clarke, Thomas H.; Garb, Jessica E.; Hayashi, Cheryl Y.; Arensburger, Peter; Ayoub, Nadia A.

    2015-01-01

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

  3. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

    PubMed

    Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

    2015-06-08

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Novel duplication pattern of the mitochondrial control region in Cantor's Giant softshell turtle Pelochelys cantorii.

    PubMed

    Zhang, Xin-Cheng; Li, Wei; Zhao, Jian; Chen, Hai-Gang; Zhu, Xin-Ping

    2016-11-15

    Cantor's Giant Softshell Turtle, Pelochelys cantorii has become one of the most critically endangered species in the world. When comparative analyses of the P. cantorii complete mitochondrial genome sequences were conducted, we discovered a duplication of a segment of the control region in the mitochondrial genome of P. cantorii. The duplication is characterized by two copies of conserved sequence box 2 (CSB2) and CSB3 in a single control region. In contrast to previous reports of duplications involving the control regions of other animals, this particular pattern of duplications appears to be unique to P. cantorii. Copies of the CSB2 and CSB3 show many of the conserved sequence features typically found in mitochondrial control regions, and rare differences were found between the paralogous copies. Using the primer design principle of simple sequence repeats (SSR) and the reference sequence of the duplicated CSBs, specific primers were designed to amplify the duplicated CSBs. These primers were validated among different individuals and populations of P. cantorii. This unique duplication structure suggests the two copies of the CSB2 and CSB3 may have arisen through occasional tandem duplication and subsequent concerted evolution.

  5. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  6. Enzyme evolution beyond gene duplication

    PubMed Central

    Noda-García, Lianet; Barona-Gómez, Francisco

    2013-01-01

    Understanding the evolution of enzyme function after gene duplication has been a major goal of molecular biologists, biochemists and evolutionary biologists alike, for almost half a century. In contrast, the impact that horizontal gene transfer (HGT) has had on the evolution of enzyme specialization and the assembly of metabolic networks has just started to being investigated. Traditionally, evolutionary studies of enzymes have been limited to either the function of enzymes in vitro, or to sequence variability at the population level, where in almost all cases the starting conceptual framework embraces gene duplication as the mechanism responsible for the appearance of genetic redundancy. Very recently, we merged comparative phylogenomics, detection of selection signals, enzyme kinetics, X-ray crystallography and computational molecular dynamics, to characterize the sub-functionalization process of an amino acid biosynthetic enzyme prompted by an episode of HGT in bacteria. Some of the evolutionary implications of these functional studies, including a proposed model of enzyme specialization independent of gene duplication, are developed in this commentary. PMID:24251070

  7. Thumb Duplication: Concepts and Techniques

    PubMed Central

    2012-01-01

    Within the Oberg, Manske, Tonkin (OMT) classification, thumb duplications are a failure of formation and/or differentiation affecting the radial-ulnar axis of the hand plate. The Wassel description of seven types of thumb duplication provides a good structure from which an approach to management is based. The aim of surgical reconstruction is to obtain a stable, mobile thumb of adequate size and appropriate shape. The most common form of reconstruction is removal of the lesser digit and reconstruction of the dominant digit. Surgical techniques address the problems of deviation, instability and lack of size. The disadvantages of the Bilhaut-Cloquet procedure, these being joint stiffness and a nail ridge, may be lesser concerns when reconstruction of one digit will not create a satisfactory thumb of adequate mobility, stability, alignment and size. Complicated problems of triphalangism, triplication, ulnar dimelia and the rare circumstance in which neither of the duplicated thumbs may be adequately reconstructed present specific challenges which demand alternative techniques. PMID:22379552

  8. Duplication and maintenance of the Myb genes of vertebrate animals.

    PubMed

    Davidson, Colin J; Guthrie, Erin E; Lipsick, Joseph S

    2013-02-15

    Gene duplication is an important means of generating new genes. The major mechanisms by which duplicated genes are preserved in the face of purifying selection are thought to be neofunctionalization, subfunctionalization, and increased gene dosage. However, very few duplicated gene families in vertebrate species have been analyzed by functional tests in vivo. We have therefore examined the three vertebrate Myb genes (c-Myb, A-Myb, and B-Myb) by cytogenetic map analysis, by sequence analysis, and by ectopic expression in Drosophila. We provide evidence that the vertebrate Myb genes arose by two rounds of regional genomic duplication. We found that ubiquitous expression of c-Myb and A-Myb, but not of B-Myb or Drosophila Myb, was lethal in Drosophila. Expression of any of these genes during early larval eye development was well tolerated. However, expression of c-Myb and A-Myb, but not of B-Myb or Drosophila Myb, during late larval eye development caused drastic alterations in adult eye morphology. Mosaic analysis implied that this eye phenotype was cell-autonomous. Interestingly, some of the eye phenotypes caused by the retroviral v-Myb oncogene and the normal c-Myb proto-oncogene from which v-Myb arose were quite distinct. Finally, we found that post-translational modifications of c-Myb by the GSK-3 protein kinase and by the Ubc9 SUMO-conjugating enzyme that normally occur in vertebrate cells can modify the eye phenotype caused by c-Myb in Drosophila. These results support a model in which the three Myb genes of vertebrates arose by two sequential duplications. The first duplication was followed by a subfunctionalization of gene expression, then neofunctionalization of protein function to yield a c/A-Myb progenitor. The duplication of this progenitor was followed by subfunctionalization of gene expression to give rise to tissue-specific c-Myb and A-Myb genes.

  9. Early evolutionary history and genomic features of gene duplicates in the human genome.

    PubMed

    Bu, Lijing; Katju, Vaishali

    2015-08-20

    Human gene duplicates have been the focus of intense research since the development of array-based and targeted next-generation sequencing approaches in the last decade. These studies have primarily concentrated on determining the extant copy-number variation from a population-genomic perspective but lack a robust evolutionary framework to elucidate the early structural and genomic characteristics of gene duplicates at emergence and their subsequent evolution with increasing age. We analyzed 184 gene duplicate pairs comprising small gene families in the draft human genome with 10% or less synonymous sequence divergence. Human gene duplicates primarily originate from DNA-mediated events, taking up genomic residence as intrachromosomal copies in direct or inverse orientation. The distribution of paralogs on autosomes follows random expectations in contrast to their significant enrichment on the sex chromosomes. Furthermore, human gene duplicates exhibit a skewed gradient of distribution along the chromosomal length with significant clustering in pericentromeric regions. Surprisingly, despite the large average length of human genes, the majority of extant duplicates (83%) are complete duplicates, wherein the entire ORF of the ancestral copy was duplicated. The preponderance of complete duplicates is in accord with an extremely large median duplication span of 36 kb, which enhances the probability of capturing ancestral ORFs in their entirety. With increasing evolutionary age, human paralogs exhibit declines in (i) the frequency of intrachromosomal paralogs, and (ii) the proportion of complete duplicates. These changes may reflect lower survival rates of certain classes of duplicates and/or the role of purifying selection. Duplications arising from RNA-mediated events comprise a small fraction (11.4%) of all human paralogs and are more numerous in older evolutionary cohorts of duplicates. The degree of structural resemblance, genomic location and duplication span

  10. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

    USDA-ARS?s Scientific Manuscript database

    We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 11 unrelated subjects. Notably, only two brea...

  11. On the retention of gene duplicates prone to dominant deleterious mutations.

    PubMed

    Malaguti, Giulia; Singh, Param Priya; Isambert, Hervé

    2014-05-01

    Recent studies have shown that gene families from different functional categories have been preferentially expanded either by small scale duplication (SSD) or by whole-genome duplication (WGD). In particular, gene families prone to dominant deleterious mutations and implicated in cancers and other genetic diseases in human have been greatly expanded through two rounds of WGD dating back from early vertebrates. Here, we strengthen this intriguing observation, showing that human oncogenes involved in different primary tumors have retained many WGD duplicates compared to other human genes. In order to rationalize this evolutionary outcome, we propose a consistent population genetics model to analyze the retention of SSD and WGD duplicates taking into account their propensity to acquire dominant deleterious mutations. We solve a deterministic haploid model including initial duplicated loci, their retention through sub-functionalization or their neutral loss-of-function or deleterious gain-of-function at one locus. Extensions to diploid genotypes are presented and population size effects are analyzed using stochastic simulations. The only difference between the SSD and WGD scenarios is the initial number of individuals with duplicated loci. While SSD duplicates need to spread through the entire population from a single individual to reach fixation, WGD duplicates are de facto fixed in the small initial post-WGD population arising through the ploidy incompatibility between post-WGD individuals and the rest of the pre-WGD population. WGD duplicates prone to dominant deleterious mutations are then shown to be indirectly selected through purifying selection in post-WGD species, whereas SSD duplicates typically require positive selection. These results highlight the long-term evolution mechanisms behind the surprising accumulation of WGD duplicates prone to dominant deleterious mutations and are shown to be consistent with cancer genome data on the prevalence of human

  12. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution.

    PubMed

    Gu, Xun; Wang, Yufeng; Gu, Jianying

    2002-06-01

    The classical (two-round) hypothesis of vertebrate genome duplication proposes two successive whole-genome duplication(s) (polyploidizations) predating the origin of fishes, a view now being seriously challenged. As the debate largely concerns the relative merits of the 'big-bang mode' theory (large-scale duplication) and the 'continuous mode' theory (constant creation by small-scale duplications), we tested whether a significant proportion of paralogous genes in the contemporary human genome was indeed generated in the early stage of vertebrate evolution. After an extensive search of major databases, we dated 1,739 gene duplication events from the phylogenetic analysis of 749 vertebrate gene families. We found a pattern characterized by two waves (I, II) and an ancient component. Wave I represents a recent gene family expansion by tandem or segmental duplications, whereas wave II, a rapid paralogous gene increase in the early stage of vertebrate evolution, supports the idea of genome duplication(s) (the big-bang mode). Further analysis indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome.

  13. Formation of Regulatory Modules by Local Sequence Duplication

    PubMed Central

    Nourmohammad, Armita; Lässig, Michael

    2011-01-01

    Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms. PMID:21998564

  14. Chromosome I Duplications in Caenorhabditis Elegans

    PubMed Central

    McKim, K. S.; Rose, A. M.

    1990-01-01

    We have isolated and characterized 76 duplications of chromosome I in the genome of Caenorhabditis elegans. The region studied is the 20 map unit left half of the chromosome. Sixty-two duplications were induced with gamma radiation and 14 arose spontaneously. The latter class was apparently the result of spontaneous breaks within the parental duplication. The majority of duplications behave as if they are free. Three duplications are attached to identifiable sequences from other chromosomes. The duplication breakpoints have been mapped by complementation analysis relative to genes on chromosome I. Nineteen duplication breakpoints and seven deficiency breakpoints divide the left half of the chromosome into 24 regions. We have studied the relationship between duplication size and segregational stability. While size is an important determinant of mitotic stability, it is not the only one. We observed clear exceptions to a size-stability correlation. In addition to size, duplication stability may be influenced by specific sequences or chromosome structure. The majority of the duplications were stable enough to be powerful tools for gene mapping. Therefore the duplications described here will be useful in the genetic characterization of chromosome I and the techniques we have developed can be adapted to other regions of the genome. PMID:2307351

  15. Genomic evidence for adaptation by gene duplication.

    PubMed

    Qian, Wenfeng; Zhang, Jianzhi

    2014-08-01

    Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for this hypothesis has been found in only a small number of cases. Although gene duplication may increase the fitness of the involved organisms by doubling gene dosage or neofunctionalization, it may also result in a simple division of ancestral functions into daughter genes, which need not promote adaptation. Hence, the general validity of the adaptation by gene duplication hypothesis remains uncertain. Indeed, a genome-scale experiment found similar fitness effects of deleting pairs of duplicate genes and deleting individual singleton genes from the yeast genome, leading to the conclusion that duplication rarely results in adaptation. Here we contend that the above comparison is unfair because of a known duplication bias among genes with different fitness contributions. To rectify this problem, we compare homologous genes from the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. We discover that simultaneously deleting a duplicate gene pair in S. cerevisiae reduces fitness significantly more than deleting their singleton counterpart in S. pombe, revealing post-duplication adaptation. The duplicates-singleton difference in fitness effect is not attributable to a potential increase in gene dose after duplication, suggesting that the adaptation is owing to neofunctionalization, which we find to be explicable by acquisitions of binary protein-protein interactions rather than gene expression changes. These results provide genomic evidence for the role of gene duplication in organismal adaptation and are important for understanding the genetic mechanisms of evolutionary innovation.

  16. Hox gene duplications correlate with posterior heteronomy in scorpions.

    PubMed

    Sharma, Prashant P; Schwager, Evelyn E; Extavour, Cassandra G; Wheeler, Ward C

    2014-10-07

    The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the ancestor of arthropods. With six different posterior segmental identities divided into two tagmata, the bauplan of scorpions is the most heteronomous within Chelicerata. Expression domains of the anterior eight Hox genes are conserved in previously surveyed chelicerates, but it is unknown how Hox genes regionalize the three tagmata of scorpions. Here, we show that the scorpion Centruroides sculpturatus has two paralogues of all Hox genes except Hox3, suggesting cluster and/or whole genome duplication in this arachnid order. Embryonic anterior expression domain boundaries of each of the last four pairs of Hox genes (two paralogues each of Antp, Ubx, abd-A and Abd-B) are unique and distinguish segmental groups, such as pectines, book lungs and the characteristic tail, while maintaining spatial collinearity. These distinct expression domains suggest neofunctionalization of Hox gene paralogues subsequent to duplication. Our data reconcile previous understanding of Hox gene function across arthropods with the extreme heteronomy of scorpions.

  17. Hox gene duplications correlate with posterior heteronomy in scorpions

    PubMed Central

    Sharma, Prashant P.; Schwager, Evelyn E.; Extavour, Cassandra G.; Wheeler, Ward C.

    2014-01-01

    The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the ancestor of arthropods. With six different posterior segmental identities divided into two tagmata, the bauplan of scorpions is the most heteronomous within Chelicerata. Expression domains of the anterior eight Hox genes are conserved in previously surveyed chelicerates, but it is unknown how Hox genes regionalize the three tagmata of scorpions. Here, we show that the scorpion Centruroides sculpturatus has two paralogues of all Hox genes except Hox3, suggesting cluster and/or whole genome duplication in this arachnid order. Embryonic anterior expression domain boundaries of each of the last four pairs of Hox genes (two paralogues each of Antp, Ubx, abd-A and Abd-B) are unique and distinguish segmental groups, such as pectines, book lungs and the characteristic tail, while maintaining spatial collinearity. These distinct expression domains suggest neofunctionalization of Hox gene paralogues subsequent to duplication. Our data reconcile previous understanding of Hox gene function across arthropods with the extreme heteronomy of scorpions. PMID:25122224

  18. Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche.

    PubMed

    Miller, Scott R; Wood, A Michelle; Blankenship, Robert E; Kim, Maria; Ferriera, Steven

    2011-01-01

    Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.

  19. Comparative genomic hybridization: Detection of segmental aneusomies

    SciTech Connect

    Cronin, J.E.; Magrane, G.G.; Gray, J.W.

    1994-09-01

    Comparative genomic hybridization (CGH) has been used successfully to detect whole chromosome and segmental aneusomies. However, its sensitivity for detection of segmental aneusomies is still not well known. We present here an analysis of CGH sensitivity with emphasis on detection of abnormalities commonly found during pre-and neo-natal diagnosis. CGH is performed by hybridizing green and red fluorescing test and normal DNA samples, respectively, to normal metaphase spreads and measuring green:red fluorescence ratios along all chromosomes. The ratios are normalized such that 2 copies of a normal chromosome region in the test sample gives a ratio of 1.0. Alterations in test vs. control gene copy number range from 1.5 [trisomy] to 0.5 [monosomy]. Clinical samples analyzed included Wolf Hirschhorn (4p-), Cri du Chat (5p-) and DiGeorge (22q-). In addition, 7 cell lines with chromosome 21 segmental aneusomies were analyzed. These included 3 with terminal duplications, 1 with a terminal deletion, 1 with an interstitial deletion and 2 with interstitial amplifications. The DiGeorge deletion was the only deletion not deleted by CGH. This is not surprising as standard G banding does not routinely detect this 1-2 megabase deletion. The 4p- and 5p- monosomies were detected and breakpoints correctly assigned prospectively. Proximal alterations involving 21q22.11 are unambiguously defined. Specifically, two interstitial aneusomies involving this region are detected. Studies involving late prophase chromosome normal spreads gave identical breakpoints. Thus, analysis of extended chromosomes did not improve the sensitivity of the technique. Taken together, these data suggest that CGH can detect segmental aneusomies greater than 8 megabases in extent. Smaller aneusomies can, at times, be detected. Work is now underway to modify the analysis software to increase sensitivity and to decrease the amount of material needed for analysis.

  20. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome.

    PubMed

    Meisel, Richard P; Hilldorfer, Benedict B; Koch, Jessica L; Lockton, Steven; Schaeffer, Stephen W

    2010-08-01

    Drosophila X chromosomes are disproportionate sources of duplicated genes, and these duplications are usually the result of retrotransposition of X-linked genes to the autosomes. The excess duplication is thought to be driven by natural selection for two reasons: X chromosomes are inactivated during spermatogenesis, and the derived copies of retroposed duplications tend to be testis expressed. Therefore, autosomal derived copies of retroposed genes provide a mechanism for their X-linked paralogs to "escape" X inactivation. Once these duplications have fixed, they may then be selected for male-specific functions. Throughout the evolution of the Drosophila genus, autosomes have fused with X chromosomes along multiple lineages giving rise to neo-X chromosomes. There has also been excess duplication from the two independent neo-X chromosomes that have been examined--one that occurred prior to the common ancestor of the willistoni species group and another that occurred along the lineage leading to Drosophila pseudoobscura. To determine what role natural selection plays in the evolution of genes duplicated from the D. pseudoobscura neo-X chromosome, we analyzed DNA sequence divergence between paralogs, polymorphism within each copy, and the expression profiles of these duplicated genes. We found that the derived copies of all duplicated genes have elevated nonsynonymous polymorphism, suggesting that they are under relaxed selective constraints. The derived copies also tend to have testis- or male-biased expression profiles regardless of their chromosome of origin. Genes duplicated from the neo-X chromosome appear to be under less constraints than those duplicated from other chromosome arms. We also find more evidence for historical adaptive evolution in genes duplicated from the neo-X chromosome, suggesting that they are under a unique selection regime in which elevated nonsynonymous polymorphism provides a large reservoir of functional variants, some of which are fixed

  1. Chromosomal Duplication Involving the Forkhead Transcription Factor Gene FOXC1 Causes Iris Hypoplasia and Glaucoma

    PubMed Central

    Lehmann, Ordan J.; Ebenezer, Neil D.; Jordan, Tim; Fox, Margaret; Ocaka, Louise; Payne, Annette; Leroy, Bart P.; Clark, Brian J.; Hitchings, Roger A.; Povey, Sue; Khaw, Peng T.; Bhattacharya, Shomi S.

    2000-01-01

    The forkhead transcription factor gene FOXC1 (formerly FKHL7) is responsible for a number of glaucoma phenotypes in families in which the disease maps to 6p25, although mutations have not been found in all families in which the disease maps to this region. In a large pedigree with iris hypoplasia and glaucoma mapping to 6p25 (peak LOD score 6.20 [recombination fraction 0] at D6S967), no FOXC1 mutations were detected by direct sequencing. However, genotyping with microsatellite repeat markers suggested the presence of a chromosomal duplication that segregated with the disease phenotype. The duplication was confirmed in affected individuals by FISH with markers encompassing FOXC1. These results provide evidence of gene duplication causing developmental disease in humans, with increased gene dosage of either FOXC1 or other, as yet unknown genes within the duplicated segment being the probable mechanism responsible for the phenotype. PMID:11007653

  2. The sequence and analysis of duplication-rich human chromosome 16.

    PubMed

    Martin, Joel; Han, Cliff; Gordon, Laurie A; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Chan, Yee Man; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C; Bruno, William J; Buckingham, Judith M; Callen, David F; Campbell, Connie S; Campbell, Mary L; Campbell, Evelyn W; Caoile, Chenier; Challacombe, Jean F; Chasteen, Leslie A; Chertkov, Olga; Chi, Han C; Christensen, Mari; Clark, Lynn M; Cohn, Judith D; Denys, Mirian; Detter, John C; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A; Grady, Deborah L; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip B; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Manohar, Chitra F; Mark, Graham A; McMurray, Kimberly L; Meincke, Linda J; Morgan, Jenna; Moyzis, Robert K; Mundt, Mark O; Munk, A Christine; Nandkeshwar, Richard D; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O; Robinson, Donna L; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H; Scott, Duncan; Shough, Timothy; Stallings, Raymond L; Stalvey, Malinda; Sutherland, Robert D; Tapia, Roxanne; Tesmer, Judith G; Thayer, Nina; Thompson, Linda S; Tice, Hope; Torney, David C; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E; Ustaszewska, Anna; Vo, Nu; White, P Scott; Williams, Albert L; Wills, Patricia L; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; Dejong, Pieter; Bruce, David; Doggett, Norman A; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; Rokhsar, Daniel S; Eichler, Evan E; Gilna, Paul; Lucas, Susan M; Myers, Richard M; Rubin, Edward M; Pennacchio, Len A

    2004-12-23

    Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

  3. The MECP2 Duplication Syndrome

    PubMed Central

    Ramocki, Melissa B.; Tavyev, Y. Jane; Peters, Sarika U.

    2009-01-01

    In this review, we detail the history, molecular diagnosis, epidemiology, and clinical features of the MECP2 duplication syndrome, including considerations for the care of patients with this X-linked neurodevelopmental disorder. MECP2 duplication syndrome is 100% penetrant in affected males and is associated with infantile hypotonia, severe to profound mental retardation, autism or autistic features, poor speech development, recurrent infections, epilepsy, progressive spasticity, and, in some cases, developmental regression. Most of the reported cases are inherited, however, de novo cases have been documented. While carrier females have been reported to be unaffected, more recent research demonstrates that despite normal intelligence, female carriers display a range of neuropsychiatric phenotypes that pre-date the birth of an affected son. Given what we know of the syndrome to date, we propose that genetic testing is warranted in cases of males with infantile hypotonia and in cases of boys with mental retardation and autistic features with or without recurrent infections, progressive spasticity, epilepsy, or developmental regression. We discuss recommendations for clinical management and surveillance as well as the need for further clinical, genotype-phenotype, and molecular studies to assist the patients and their families who are affected by this syndrome. PMID:20425814

  4. Mechanisms of Gene Duplication and Amplification

    PubMed Central

    Reams, Andrew B.; Roth, John R.

    2015-01-01

    Changes in gene copy number are among the most frequent mutational events in all genomes and were among the mutations for which a physical basis was first known. Yet mechanisms of gene duplication remain uncertain because formation rates are difficult to measure and mechanisms may vary with position in a genome. Duplications are compared here to deletions, which seem formally similar but can arise at very different rates by distinct mechanisms. Methods of assessing duplication rates and dependencies are described with several proposed formation mechanisms. Emphasis is placed on duplications formed in extensively studied experimental situations. Duplications studied in microbes are compared with those observed in metazoan cells, specifically those in genomes of cancer cells. Duplications, and especially their derived amplifications, are suggested to form by multistep processes often under positive selection for increased copy number. PMID:25646380

  5. Gene duplication, silencing and expression alteration govern the molecular evolution of PRC2 genes in plants.

    PubMed

    Furihata, Hazuka Y; Suenaga, Kazuya; Kawanabe, Takahiro; Yoshida, Takanori; Kawabe, Akira

    2016-10-13

    PRC2 genes were analyzed for their number of gene duplications, dN/dS ratios and expression patterns among Brassicaceae and Gramineae species. Although both amino acid sequences and copy number of the PRC2 genes were generally well conserved in both Brassicaceae and Gramineae species, we observed that some rapidly evolving genes experienced duplications and expression pattern changes. After multiple duplication events, all but one or two of the duplicated copies tend to be silenced. Silenced copies were reactivated in the endosperm and showed ectopic expression in developing seeds. The results indicated that rapid evolution of some PRC2 genes is initially caused by a relaxation of selective constraint following the gene duplication events. Several loci could become maternally expressed imprinted genes and acquired functional roles in the endosperm.

  6. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

    PubMed Central

    Carvalho, Claudia M. B.; Ramocki, Melissa B.; Pehlivan, Davut; Franco, Luis M.; Gonzaga-Jauregui, Claudia; Fang, Ping; McCall, Alanna; Pivnick, Eniko Karman; Hines-Dowell, Stacy; Seaver, Laurie; Friehling, Linda; Lee, Sansan; Smith, Rosemarie; del Gaudio, Daniela; Withers, Marjorie; Liu, Pengfei; Cheung, Sau Wai; Belmont, John W.; Zoghbi, Huda Y.; Hastings, P. J.; Lupski, James R.

    2011-01-01

    We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at both the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 12 unrelated subjects. Interestingly, only two novel breakpoint junctions were generated during each rearrangement formation. Remarkably, all the complex rearrangement products share the common genomic organization duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) wherein the triplicated segment is inverted and located between directly oriented duplicated genomic segments. We provide evidence that the DUP-TRP/INV-DUP structures are mediated by inverted repeats that can be separated by over 300 kb; a genomic architecture that apparently leads to susceptibility to such complex rearrangements. A similar inverted repeat mediated mechanism may underlie structural variation in many other regions of the human genome. We propose a mechanism that involves both homology driven, via inverted repeats, and microhomologous/nonhomologous events. PMID:21964572

  7. Duplication and diversifying selection among termite antifungal peptides.

    PubMed

    Bulmer, Mark S; Crozier, Ross H

    2004-12-01

    We have identified and analyzed the mRNA sequence of 20 new defensin-like peptides from 11 Australian termite species of Nasutitermes and from an outgroup, Drepanotermes rubriceps. The sequence was amplified by reverse transcriptase PCR with a degenerate primer designed from termicin, an antifungal peptide previously characterized from the termite Pseudocanthotermes spiniger. All 20 genes show high sequence identity with P. spiniger termicin and have duplicated repeatedly during the radiation of Nasutitermes. Comparison of the relative fixation rates of synonymous (silent) and nonsynonymous (amino acid altering) mutations indicates that the Nasutitermes termicins are positively selected. This positive selection appears to drive a decrease in termicin charge. In termites with two genes, the decrease in charge is predominantly restricted to one termicin. Furthermore, the spread of charge is significantly greater within species than across species among amino acid sites that appear to be under strong positive selection and this spread is attributable to only three sites. Our results suggest that after termicin duplication, certain critical sites have maintained a positive charge in one duplicate and evolved towards neutrality in the other and that positive selection has directed these changes repeatedly and independently. This diversification among duplicated genes may be a counter-response to the evolution of fungal resistance in social insects that are particularly vulnerable to fungal epidemics.

  8. Exon duplications in the ATP7A gene: Frequency and Transcriptional Behaviour

    PubMed Central

    2011-01-01

    Background Menkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene. Methods The ATP7A gene was screened for exon duplications using multiplex ligation-dependent probe amplification (MLPA). The expression level of ATP7A was investigated by real-time PCR and detailed analysis of the ATP7A mRNA was performed by RT-PCR followed by sequencing. In order to investigate whether the identified duplicated fragments originated from a single or from two different X-chromosomes, polymorphic markers located in the duplicated fragments were analyzed. Results Partial ATP7A gene duplication was identified in 20 unrelated patients including one patient with Occipital Horn Syndrome (OHS). Duplications in the ATP7A gene are estimated from our material to be the disease causing mutation in 4% of the Menkes disease patients. The duplicated regions consist of between 2 and 15 exons. In at least one of the cases, the duplication was due to an intra-chromosomal event. Characterization of the ATP7A mRNA transcripts in 11 patients revealed that the duplications were organized in tandem, in a head to tail direction. The reading frame was disrupted in all 11 cases. Small amounts of wild-type transcript were found in all patients as a result of exon-skipping events occurring in the duplicated regions. In the OHS patient with a duplication of exon 3 and 4, the duplicated out-of-frame transcript coexists with an almost equally represented wild-type transcript, presumably leading to the milder phenotype. Conclusions In general, patients with duplication of only 2 exons exhibit a milder phenotype as compared to patients with duplication of more than 2 exons. This study provides insight into exon duplications in the ATP7A gene. PMID:22074552

  9. 10 CFR 9.35 - Duplication fees.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Duplication fees. 9.35 Section 9.35 Energy NUCLEAR REGULATORY COMMISSION PUBLIC RECORDS Freedom of Information Act Regulations § 9.35 Duplication fees. (a)(1...″ reduced). Pages 11″ × 17″ are $0.30 per page. Pages larger than 11″ × 17″, including engineering...

  10. Some asymptotic properties of duplication graphs

    NASA Astrophysics Data System (ADS)

    Raval, Alpan

    2003-12-01

    Duplication graphs are graphs that grow by duplication of existing vertices, and are important models of biological networks, including protein-protein interaction networks and gene regulatory networks. Three models of graph growth are studied: pure duplication growth, and two two-parameter models in which duplication forms one element of the growth dynamics. A power-law degree distribution is found to emerge in all three models. However, the parameter space of the latter two models is characterized by a range of parameter values for which duplication is the predominant mechanism of graph growth. For parameter values that lie in this “duplication-dominated” regime, it is shown that the degree distribution either approaches zero asymptotically, or approaches a nonzero power-law degree distribution very slowly. In either case, the approach to the true asymptotic degree distribution is characterized by a dependence of the scaling exponent on properties of the initial degree distribution. It is therefore conjectured that duplication-dominated, scale-free networks may contain identifiable remnants of their early structure. This feature is inherited from the idealized model of pure duplication growth, for which the exact finite-size degree distribution is found and its asymptotic properties studied.

  11. 40 CFR 710.35 - Duplicative reporting.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Duplicative reporting. 710.35 Section 710.35 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS 2002 Inventory Update Reporting § 710.35 Duplicative...

  12. 40 CFR 710.35 - Duplicative reporting.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Duplicative reporting. 710.35 Section 710.35 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS 2002 Inventory Update Reporting § 710.35 Duplicative...

  13. 40 CFR 711.22 - Duplicative reporting.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Duplicative reporting. 711.22 Section 711.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.22 Duplicative reporting. (a) With regard to TSCA...

  14. 40 CFR 711.22 - Duplicative reporting.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Duplicative reporting. 711.22 Section 711.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.22 Duplicative reporting. (a) With regard to TSCA...

  15. Duplicated genes evolve independently in allopolyploid cotton.

    Treesearch

    Richard C. Cronn; Randall L. Small; Jonathan F. Wendel

    1999-01-01

    Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci...

  16. 15 CFR 750.9 - Duplicate licenses.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Duplicate licenses. 750.9 Section 750.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU... PROCESSING, ISSUANCE, AND DENIAL § 750.9 Duplicate licenses. (a) Lost, stolen or destroyed. If a license...

  17. 15 CFR 750.9 - Duplicate licenses.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 2 2011-01-01 2011-01-01 false Duplicate licenses. 750.9 Section 750.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU... PROCESSING, ISSUANCE, AND DENIAL § 750.9 Duplicate licenses. (a) Lost, stolen or destroyed. If a license...

  18. 15 CFR 750.9 - Duplicate licenses.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 2 2014-01-01 2014-01-01 false Duplicate licenses. 750.9 Section 750.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU... PROCESSING, ISSUANCE, AND DENIAL § 750.9 Duplicate licenses. (a) Lost, stolen or destroyed. If a license...

  19. 15 CFR 750.9 - Duplicate licenses.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 2 2013-01-01 2013-01-01 false Duplicate licenses. 750.9 Section 750.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU... PROCESSING, ISSUANCE, AND DENIAL § 750.9 Duplicate licenses. (a) Lost, stolen or destroyed. If a license...

  20. 15 CFR 750.9 - Duplicate licenses.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 2 2012-01-01 2012-01-01 false Duplicate licenses. 750.9 Section 750.9 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU... PROCESSING, ISSUANCE, AND DENIAL § 750.9 Duplicate licenses. (a) Lost, stolen or destroyed. If a license...

  1. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates.

    PubMed

    Cañestro, Cristian; Albalat, Ricard; Irimia, Manuel; Garcia-Fernàndez, Jordi

    2013-02-01

    The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster.

    PubMed

    Kaneko, Ryosuke; Abe, Manabu; Hirabayashi, Takahiro; Uchimura, Arikuni; Sakimura, Kenji; Yanagawa, Yuchio; Yagi, Takeshi

    2014-09-02

    Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.

  3. Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster

    PubMed Central

    Kaneko, Ryosuke; Abe, Manabu; Hirabayashi, Takahiro; Uchimura, Arikuni; Sakimura, Kenji; Yanagawa, Yuchio; Yagi, Takeshi

    2014-01-01

    Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5′-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence. PMID:25179445

  4. Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications.

    PubMed

    Coate, Jeremy E; Doyle, Jeff J

    2011-04-01

    Gene and genome duplication are recurring processes in flowering plants, and elucidating the mechanisms by which duplicated genes are lost or deployed is a key component of understanding plant evolution. Using gene ontologies (GO) or protein family (PFAM) domains, distinct patterns of duplicate retention and loss have been identified depending on gene functional properties and duplication mechanism, but little is known about how gene networks encoding interacting proteins (protein complexes or signaling cascades) evolve in response to duplication. We examined patterns of duplicate retention within four major gene networks involved in photosynthesis (the Calvin cycle, photosystem I, photosystem II, and the light harvesting complex) across three species and four whole genome duplications, as well as small-scale duplications, and showed that photosystem gene family evolution is governed largely by dosage sensitivity. ( 1) In contrast, Calvin cycle gene families are not dosage sensitive, but exhibit a greater capacity for functional differentiation. Here we review these findings, highlight how this study, by analyzing defined gene networks, is complementary to global studies using functional annotations such as GO and PFAM, and elaborate on one example of functional differentiation in the Calvin cycle gene family, transketolase.

  5. Social network analysis of duplicative prescriptions: One-month analysis of medical facilities in Japan.

    PubMed

    Takahashi, Yoshimitsu; Ishizaki, Tatsuro; Nakayama, Takeo; Kawachi, Ichiro

    2016-03-01

    Duplicative prescriptions refer to situations in which patients receive medications for the same condition from two or more sources. Health officials in Japan have expressed concern about medical "waste" resulting from this practices. We sought to conduct descriptive analysis of duplicative prescriptions using social network analysis and to report their prevalence across ages. We analyzed a health insurance claims database including 1.24 million people from December 2012. Through social network analysis, we examined the duplicative prescription networks, representing each medical facility as nodes, and individual prescriptions for patients as edges. The prevalence of duplicative prescription for any drug class was strongly correlated with its frequency of prescription (r=0.90). Among patients aged 0-19, cough and colds drugs showed the highest prevalence of duplicative prescriptions (10.8%). Among people aged 65 and over, antihypertensive drugs had the highest frequency of prescriptions, but the prevalence of duplicative prescriptions was low (0.2-0.3%). Social network analysis revealed clusters of facilities connected via duplicative prescriptions, e.g., psychotropic drugs showed clustering due to a few patients receiving drugs from 10 or more facilities. Overall, the prevalence of duplicative prescriptions was quite low - less than 10% - although the extent of the problem varied by drug class and age group. Our approach illustrates the potential utility of using a social network approach to understand these practices. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Gene duplication and concerted evolution of mitochondrial DNA in crane species.

    PubMed

    Akiyama, Takuya; Nishida, Chizuko; Momose, Kunikazu; Onuma, Manabu; Takami, Kazutoshi; Masuda, Ryuichi

    2017-01-01

    The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication in cranes and investigate the molecular evolutionary features of crane mtDNA, we analyzed the gene organization and the molecular phylogeny of mtDNA from 13 crane species. We found that the mtDNA in 13 crane species shared a tandem duplicated region, which consists of duplicated sequence sets including cytochrome b (Cytb), NADH6, control region (CR) and three genes of tRNA. The gene order in the duplicated region was identical among all the 13 crane species, and the nucleotide sequences found within each individual showed high similarities. In addition, phylogenetic trees based on homologous sequences of CR and Cytb indicated the possibility of concerted evolution among the duplicated genes. The results suggested that the duplication event occurred in the common ancestor of crane species or some older ancestors. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. A pure familial 6q15q21 split duplication associated with obesity and transmitted with partial reduction.

    PubMed

    Landais, Emilie; Leroy, Camille; Kleinfinger, Pascale; Brunet, Stéphanie; Koubi, Valérie; Pietrement, Christine; Poli-Mérol, Marie-Laurence; Fiquet, Caroline; Souchon, Pierre-François; Beri, Mylène; Jonveaux, Philippe; Garnotel, Roselyne; Gaillard, Dominique; Doco-Fenzy, Martine

    2015-06-01

    Familial transmission of chromosome 6 duplications is rare. We report on the first observation of a maternally-inherited pure segmental 6q duplication split into two segments, 6q15q16.3 and 6q16.3q21, and associated with obesity. Obesity has previously been correlated to chromosome 6 q-arm deletion but has not yet been assessed in duplications. The aim of this study was to characterize the structure of these intrachromosomal insertional translocations by classic cytogenetic banding, array-CGH, FISH, M-banding and genotyping using microsatellites and SNP array analysis, in a mother and four offspring. The duplicated 6q segments, 9.75 Mb (dup 1) and 7.05 Mb (dup 2) in size in the mother, were inserted distally into two distinct chromosome 6q regions. They were transmitted to four offspring. A son and a daughter inherited the two unbalanced insertions and displayed, like the mother, an abnormal phenotype with facial dysmorphism, intellectual disability, and morbid obesity. Curiously, two daughters with a normal phenotype inherited only the smaller segment, 6q16.3q21. The abnormal phenotype was associated with the larger proximal 6q15q16.3 duplication. We hypothesize a mechanism for this exceptional phenomenon of recurrent reduction and transmission of the duplication during meiosis in a family. We expect the interpretation of our findings to be useful for genetic counseling and for understanding the mechanisms underlying these large segmental 6q duplications and their evolution.

  8. The birth of a human-specific neural gene by incomplete duplication and gene fusion.

    PubMed

    Dougherty, Max L; Nuttle, Xander; Penn, Osnat; Nelson, Bradley J; Huddleston, John; Baker, Carl; Harshman, Lana; Duyzend, Michael H; Ventura, Mario; Antonacci, Francesca; Sandstrom, Richard; Dennis, Megan Y; Eichler, Evan E

    2017-03-09

    Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.

  9. Current incidence of duplicate publication in otolaryngology.

    PubMed

    Cheung, Veronique Wan Fook; Lam, Gilbert O A; Wang, Yun Fan; Chadha, Neil K

    2014-03-01

    Duplicate publication--deemed highly unethical--is the reproduction of substantial content in another article by the same authors. In 1999, Rosenthal et al. identified an 8.5% incidence of duplicate articles in two otolaryngology journals. We explored the current incidence in three otolaryngology journals in North America and Europe. Retrospective literature review. Index articles in 2008 in Archives of Otolaryngology-Head and Neck Surgery, Laryngoscope, and Clinical Otolaryngology were searched using MEDLINE. Potential duplicate publications in 2006 through 2010 were identified using the first, second, and last authors' names. Three authors independently investigated suspected duplicate publications--classifying them by degree of duplication. Of 358 index articles screened, 75 (20.9%) had 119 potential duplicates from 2006 to 2010. Full review of these 119 potential duplicates revealed a total of 40 articles with some form of redundancy (33.6% of the potential duplicates) involving 27 index articles (7.5% of 358 index articles); one (0.8%) "dual" publication (identical or nearly identical data and conclusions to the index article); three (2.5%) "suspected" dual publications (less than 50% new data and same conclusions); and 36 (30.3%) publications with "salami-slicing" (portion of the index article data repeated) were obtained. Further analysis compared the likelihood of duplicate publication by study source and subspecialty within otolaryngology. The incidence of duplicate publication has not significantly changed over 10 years. "Salami-slicing" was a concerning practice, with no cross-referencing in 61% of these cases. Detecting and eliminating redundant publications is a laborious task, but it is essential in upholding the journal quality and research integrity. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  10. Duplication of OsHAP family genes and their association with heading date in rice.

    PubMed

    Li, Qiuping; Yan, Wenhao; Chen, Huaxia; Tan, Cong; Han, Zhongmin; Yao, Wen; Li, Guangwei; Yuan, Mengqi; Xing, Yongzhong

    2016-03-01

    Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering in plants. It is not clear how many HAP genes regulate heading date in rice. In this study, we identified 35 HAP genes, including seven newly identified genes, and performed gene duplication and candidate gene-based association analyses. Analyses showed that segmental duplication and tandem duplication are the main mechanisms of HAP gene duplication. Expression profiling and functional identification indicated that duplication probably diversifies the functions of HAP genes. A nucleotide diversity analysis revealed that 13 HAP genes underwent selection. A candidate gene-based association analysis detected four HAP genes related to heading date. An investigation of transgenic plants or mutants of 23 HAP genes confirmed that overexpression of at least four genes delayed heading date under long-day conditions, including the previously cloned Ghd8/OsHAP3H. Our results indicate that the large number of HAP genes in rice was mainly produced by gene duplication, and a few HAP genes function to regulate heading date. Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading.

  11. A partial MECP2 duplication in a mildly affected adult male: a putative role for the 3' untranslated region in the MECP2 duplication phenotype

    PubMed Central

    2012-01-01

    Background Duplications of the X-linked MECP2 gene are associated with moderate to severe intellectual disability, epilepsy, and neuropsychiatric illness in males, while triplications are associated with a more severe phenotype. Most carrier females show complete skewing of X-inactivation in peripheral blood and an apparent susceptibility to specific personality traits or neuropsychiatric symptoms. Methods We describe the clinical phenotype of a pedigree segregating a duplication of MECP2 found on clinical array comparative genomic hybridization. The position, size, and extent of the duplication were delineated in peripheral blood samples from affected individuals using multiplex ligation-dependent probe amplification and fluorescence in situ hybridization, as well as targeted high-resolution oligonucleotide microarray analysis and long-range PCR. The molecular consequences of the rearrangement were studied in lymphoblast cell lines using quantitative real-time PCR, reverse transcriptase PCR, and western blot analysis. Results We observed a partial MECP2 duplication in an adult male with epilepsy and mild neurocognitive impairment who was able to function independently; this phenotype has not previously been reported among males harboring gains in MECP2 copy number. The same duplication was inherited by this individual’s daughter who was also affected with neurocognitive impairment and epilepsy and carried an additional copy-number variant. The duplicated segment involved all four exons of MECP2, but excluded almost the entire 3' untranslated region (UTR), and the genomic rearrangement resulted in a MECP2-TEX28 fusion gene mRNA transcript. Increased expression of MECP2 and the resulting fusion gene were both confirmed; however, western blot analysis of lysates from lymphoblast cells demonstrated increased MeCP2 protein without evidence of a stable fusion gene protein product. Conclusion The observations of a mildly affected adult male with a MECP2 duplication and

  12. A partial MECP2 duplication in a mildly affected adult male: a putative role for the 3' untranslated region in the MECP2 duplication phenotype.

    PubMed

    Hanchard, Neil A; Carvalho, Claudia M B; Bader, Patricia; Thome, Aaron; Omo-Griffith, Lisa; del Gaudio, Daniela; Pehlivan, Davut; Fang, Ping; Schaaf, Christian P; Ramocki, Melissa B; Lupski, James R; Cheung, Sau Wai

    2012-08-10

    Duplications of the X-linked MECP2 gene are associated with moderate to severe intellectual disability, epilepsy, and neuropsychiatric illness in males, while triplications are associated with a more severe phenotype. Most carrier females show complete skewing of X-inactivation in peripheral blood and an apparent susceptibility to specific personality traits or neuropsychiatric symptoms. We describe the clinical phenotype of a pedigree segregating a duplication of MECP2 found on clinical array comparative genomic hybridization. The position, size, and extent of the duplication were delineated in peripheral blood samples from affected individuals using multiplex ligation-dependent probe amplification and fluorescence in situ hybridization, as well as targeted high-resolution oligonucleotide microarray analysis and long-range PCR. The molecular consequences of the rearrangement were studied in lymphoblast cell lines using quantitative real-time PCR, reverse transcriptase PCR, and western blot analysis. We observed a partial MECP2 duplication in an adult male with epilepsy and mild neurocognitive impairment who was able to function independently; this phenotype has not previously been reported among males harboring gains in MECP2 copy number. The same duplication was inherited by this individual's daughter who was also affected with neurocognitive impairment and epilepsy and carried an additional copy-number variant. The duplicated segment involved all four exons of MECP2, but excluded almost the entire 3' untranslated region (UTR), and the genomic rearrangement resulted in a MECP2-TEX28 fusion gene mRNA transcript. Increased expression of MECP2 and the resulting fusion gene were both confirmed; however, western blot analysis of lysates from lymphoblast cells demonstrated increased MeCP2 protein without evidence of a stable fusion gene protein product. The observations of a mildly affected adult male with a MECP2 duplication and paternal transmission of this

  13. Evolution of Gene Duplication in Plants1[OPEN

    PubMed Central

    2016-01-01

    Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication. PMID:27288366

  14. Duplicate Gene Divergence by Changes in MicroRNA Binding Sites in Arabidopsis and Brassica

    PubMed Central

    Wang, Sishuo; Adams, Keith L.

    2015-01-01

    Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes. PMID:25644246

  15. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.

    PubMed

    Wang, Sishuo; Adams, Keith L

    2015-02-02

    Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes.

  16. ANSYS duplicate finite-element checker routine

    NASA Technical Reports Server (NTRS)

    Ortega, R.

    1995-01-01

    An ANSYS finite-element code routine to check for duplicated elements within the volume of a three-dimensional (3D) finite-element mesh was developed. The routine developed is used for checking floating elements within a mesh, identically duplicated elements, and intersecting elements with a common face. A space shuttle main engine alternate turbopump development high pressure oxidizer turbopump finite-element model check using the developed subroutine is discussed. Finally, recommendations are provided for duplicate element checking of 3D finite-element models.

  17. Duplicate pancreas meets gastric duplication cyst: A tale of two anomalies

    PubMed Central

    Christians, Kathleen K.; Pappas, Sam; Pilgrim, Charles; Tsai, Susan; Quebbeman, Edward

    2013-01-01

    INTRODUCTION Congenital anomalies are a rare cause of pancreatitis in adults. Gastric duplications are the least common duplication of the gastrointestinal tract and are even more uncommon in the setting of a duplicate pancreas. PRESENTATION OF CASE This manuscript contains a case report and review of the literature of an adult who presented with recurrent pancreatitis and was found to have a gastric duplication cyst that communicated with a duplicate pancreas. The study aim is to alert practitioners to the duplicate anomaly and recommend appropriate therapy. DISCUSSION Combined gastric and pancreatic duplications usually occur in young females with nonspecific, recurrent abdominal pain. This combined duplication can result in pancreatitis when the gastric duplication is contiguous with the stomach. Heightened awareness of the condition, appropriate diagnostics with accurate interpretation and a minimalist approach to resection are warranted. CONCLUSION Recurrent abdominal pain and pancreatitis in young adults devoid of risk factors should lead to consideration of congenital anomalies. Not all cysts near the pancreas and stomach are pseudocysts. ECRP and abdominal CT/MRI provide critical diagnostic information. This dual anomaly is best treated by simple excision of the gastric duplication and heterotopic pancreas. PMID:23827696

  18. All duplicates are not equal: the difference between small-scale and genome duplication

    PubMed Central

    Hakes, Luke; Pinney, John W; Lovell, Simon C; Oliver, Stephen G; Robertson, David L

    2007-01-01

    Background Genes in populations are in constant flux, being gained through duplication and occasionally retained or, more frequently, lost from the genome. In this study we compare pairs of identifiable gene duplicates generated by small-scale (predominantly single-gene) duplications with those created by a large-scale gene duplication event (whole-genome duplication) in the yeast Saccharomyces cerevisiae. Results We find a number of quantifiable differences between these data sets. Whole-genome duplicates tend to exhibit less profound phenotypic effects when deleted, are functionally less divergent, and are associated with a different set of functions than their small-scale duplicate counterparts. At first sight, either of these latter two features could provide a plausible mechanism by which the difference in dispensability might arise. However, we uncover no evidence suggesting that this is the case. We find that the difference in dispensability observed between the two duplicate types is limited to gene products found within protein complexes, and probably results from differences in the relative strength of the evolutionary pressures present following each type of duplication event. Conclusion Genes, and the proteins they specify, originating from small-scale and whole-genome duplication events differ in quantifiable ways. We infer that this is not due to their association with different functional categories; rather, it is a direct result of biases in gene retention. PMID:17916239

  19. The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications

    PubMed Central

    Djogbénou, Luc S.; Berthomieu, Arnaud; Makoundou, Patrick; Baba-Moussa, Lamine S.; Fiston-Lavier, Anna-Sophie; Belkhir, Khalid; Labbé, Pierrick; Weill, Mylène

    2016-01-01

    Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype level, to investigate the influence of duplication architecture and gene-dosage on mosquito fitness. We found that both heterogeneous (i.e., one susceptible and one resistant ace-1 copy) and homogeneous (i.e., identical resistant copies) duplications segregated in field populations. The number of copies in homogeneous duplications was variable and positively correlated with acetylcholinesterase activity and resistance level. Determining the genomic structure of the duplicated region revealed that, in both types of duplication, ace-1 and 11 other genes formed tandem 203kb amplicons. We developed a diagnostic test for duplications, which showed that ace-1 was amplified in all 173 resistant mosquitoes analyzed (field-collected in several African countries), in heterogeneous or homogeneous duplications. Each type was associated with different fitness trade-offs: heterogeneous duplications conferred an intermediate phenotype (lower resistance and fitness costs), whereas homogeneous duplications tended to increase both resistance and fitness cost, in a complex manner. The type of duplication selected seemed thus to depend on the intensity and distribution of selection pressures. This versatility of trade-offs available through gene duplication highlights the importance of large mutation events in adaptation to environmental variation. This impressive adaptability could have a major impact on vector

  20. Pelizaeus-Merzbacher disease: identification of Xq22 proteolipid-protein duplications and characterization of breakpoints by interphase FISH.

    PubMed Central

    Woodward, K; Kendall, E; Vetrie, D; Malcolm, S

    1998-01-01

    Pelizaeus-Merzbacher disease (PMD) is an X-linked, dysmyelinating disorder of the CNS. Duplications of the proteolipid protein (PLP) gene have been found in a proportion of patients, suggesting that, in addition to coding-region or splice-site mutations, overdosage of the gene can cause PMD. We show that the duplication can be detected by interphase FISH, using a PLP probe in five patients and their four asymptomatic carrier mothers. The extent of the duplication was analyzed in each family by interphase FISH, with probes from a 1. 7-Mb region surrounding the PLP gene between markers DXS83 and DXS94. A large duplication >=500 kb was detected, with breakpoints that differed, between families, at the proximal end. Distinct separation of the duplicated PLP signals could be seen only on metaphase chromosomes in one family, providing further evidence that different duplication events are involved. Quantitative fluorescent multiplex PCR was used to confirm the duplication in patients, by the detection of increased copy number of the PLP gene. Multiallelic markers from the duplicated region were analyzed, since the identification of two alleles in an affected boy would indicate a duplication. The majority of boys were homozygous for all four markers, compared with their mothers, who were heterozygous for one to three of the markers. These results suggest that intrachromosomal rearrangements may be a common mechanism by which duplications arise in PMD. One boy was heterozygous for the PLP marker, indicating a duplication and suggesting that interchromosomal rearrangements of maternal origin also can be involved. Since duplications are a major cause of PMD, we propose that interphase FISH is a reliable method for diagnosis and identification of female carriers. PMID:9634530

  1. Pelizaeus-Merzbacher disease: identification of Xq22 proteolipid-protein duplications and characterization of breakpoints by interphase FISH.

    PubMed

    Woodward, K; Kendall, E; Vetrie, D; Malcolm, S

    1998-07-01

    Pelizaeus-Merzbacher disease (PMD) is an X-linked, dysmyelinating disorder of the CNS. Duplications of the proteolipid protein (PLP) gene have been found in a proportion of patients, suggesting that, in addition to coding-region or splice-site mutations, overdosage of the gene can cause PMD. We show that the duplication can be detected by interphase FISH, using a PLP probe in five patients and their four asymptomatic carrier mothers. The extent of the duplication was analyzed in each family by interphase FISH, with probes from a 1. 7-Mb region surrounding the PLP gene between markers DXS83 and DXS94. A large duplication >=500 kb was detected, with breakpoints that differed, between families, at the proximal end. Distinct separation of the duplicated PLP signals could be seen only on metaphase chromosomes in one family, providing further evidence that different duplication events are involved. Quantitative fluorescent multiplex PCR was used to confirm the duplication in patients, by the detection of increased copy number of the PLP gene. Multiallelic markers from the duplicated region were analyzed, since the identification of two alleles in an affected boy would indicate a duplication. The majority of boys were homozygous for all four markers, compared with their mothers, who were heterozygous for one to three of the markers. These results suggest that intrachromosomal rearrangements may be a common mechanism by which duplications arise in PMD. One boy was heterozygous for the PLP marker, indicating a duplication and suggesting that interchromosomal rearrangements of maternal origin also can be involved. Since duplications are a major cause of PMD, we propose that interphase FISH is a reliable method for diagnosis and identification of female carriers.

  2. Duplication/deletion of chromosome 8p

    SciTech Connect

    Priest, J.H.

    1995-09-11

    The article by Guo et al. provides evidence for deletion of D8S596 loci (assigned to 8p23) in at least some patients with inverted duplications of 8p. Cytogenetic break points forming the inverted duplication are remarkably similar among most of their patients and those reported previously, suggesting a common mechanism for this interesting rearrangement. Why should similar breaks occur in 8p and why is a FISH signal absent in the distal short arm when the ONCOR digoxigenin-labeled probe for loci D8S596 is used? Other studies also indicate that duplication for the region 8p12-p22 is associated with a deletion distal to the duplication itself. 4 refs.

  3. NASA wide electronic publishing system: Electronic printing and duplicating. Stage 3 evaluation report

    NASA Technical Reports Server (NTRS)

    Tuey, Richard C.; Moore, Fred W.; Ryan, Christine A.

    1995-01-01

    The report is presented in four sections: The Introduction describes the duplicating configuration under evaluation and the Background contains a chronological description of the evaluation segmented by phases 1 and 2. This section includes the evaluation schedule, printing and duplicating requirements, storage and communication requirements, electronic publishing system configuration, existing processes and proposed processes, billing rates, costs and productivity analysis, and the return on investment based upon the data gathered to date. The third section contains the phase 1 comparative cost and productivity analysis. This analysis demonstrated that LaRC should proceed with a 90-day evaluation of the DocuTech and follow with a phase 2 cycle to actually demonstrate that the proposed system would meet the needs of LaRC's printing and duplicating requirements, benchmark results, cost comparisons, benchmark observations, and recommendations. These are documented after the recommendations.

  4. Active Segmentation

    PubMed Central

    Mishra, Ajay; Aloimonos, Yiannis

    2009-01-01

    The human visual system observes and understands a scene/image by making a series of fixations. Every fixation point lies inside a particular region of arbitrary shape and size in the scene which can either be an object or just a part of it. We define as a basic segmentation problem the task of segmenting that region containing the fixation point. Segmenting the region containing the fixation is equivalent to finding the enclosing contour- a connected set of boundary edge fragments in the edge map of the scene - around the fixation. This enclosing contour should be a depth boundary. We present here a novel algorithm that finds this bounding contour and achieves the segmentation of one object, given the fixation. The proposed segmentation framework combines monocular cues (color/intensity/texture) with stereo and/or motion, in a cue independent manner. The semantic robots of the immediate future will be able to use this algorithm to automatically find objects in any environment. The capability of automatically segmenting objects in their visual field can bring the visual processing to the next level. Our approach is different from current approaches. While existing work attempts to segment the whole scene at once into many areas, we segment only one image region, specifically the one containing the fixation point. Experiments with real imagery collected by our active robot and from the known databases 1 demonstrate the promise of the approach. PMID:20686671

  5. NASA printing, duplicating, and copying management handbook

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This handbook provides information and procedures for the implementation of NASA policy and applicable laws and regulations relating to printing, duplicating, and copying. The topics addressed include a description of relevant laws and regulations, authorizations required, and responsible entities for NASA printing, duplicating, and copying. The policy of NASA is to ensure understanding and application of authority and responsibility on printing matters. Where necessary, the handbook clarifies the intent of basic laws and regulations applicable to NASA.

  6. EVENT SEGMENTATION

    PubMed Central

    Zacks, Jeffrey M.; Swallow, Khena M.

    2012-01-01

    One way to understand something is to break it up into parts. New research indicates that segmenting ongoing activity into meaningful events is a core component of ongoing perception, with consequences for memory and learning. Behavioral and neuroimaging data suggest that event segmentation is automatic and that people spontaneously segment activity into hierarchically organized parts and sub-parts. This segmentation depends on the bottom-up processing of sensory features such as movement, and on the top-down processing of conceptual features such as actors’ goals. How people segment activity affects what they remember later; as a result, those who identify appropriate event boundaries during perception tend to remember more and learn more proficiently. PMID:22468032

  7. Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

    PubMed Central

    Treangen, Todd J.; Rocha, Eduardo P. C.

    2011-01-01

    Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes—xenologs—persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes—paralogs—are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein–protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families. PMID:21298028

  8. Gastrointestinal Duplication Presenting as Neonatal Intestinal Obstruction: An Experience of 15 Years at Tertiary Care Centre

    PubMed Central

    Rattan, Kamal Nain; Bansal, Shruti; Dhamija, Aastha

    2017-01-01

    Background: Gastrointestinal tract (GIT) duplications are one of the rare congenital anomalies and can occur in any portion of the gastrointestinal tract but are more commonly encountered in small intestine. The duplication cysts cause symptoms like abdominal mass and intestinal obstruction requiring surgery or may remain asymptomatic. We are reporting our 15 years’ experience duplication cysts presenting in neonates. Methods: It is a retrospective study undertaken in the department of pediatric surgery between 2001 and 2015 for GIT duplications in neonates. Patients were analyzed for their antenatal diagnosis, age, sex, clinical diagnosis, investigatory approach, operative management and surgical outcomes. Results: Total number of neonates, diagnosed with gastrointestinal duplication in the last 15 years, was 17. Male to female ratio was 3.3:1. The most common location was found to be the ileum occurring in 71% of cases. Apart from ileum, 2 cases of duodenal and 1 case each of gastric, colonic and cecal duplication cyst were encountered. Majority cases presented with sub-acute intestinal obstruction and were managed successfully by resection and end to end anastomosis. Associated gut atresia was found in 4 cases while 1 case was found to be associated with perforation of gut. Conclusion: Gastrointestinal tract duplications often present with typical symptoms of gastrointestinal tract obstruction. Early diagnosis and management is required to prevent postoperative morbidity and mortality. PMID:28083491

  9. Pattern of Duplicate Presentations at National Hematology-Oncology Meetings: Influence of the Pharmaceutical Industry.

    PubMed

    Ramchandren, Radhakrishnan; Schiffer, Charles A

    2016-03-01

    The major large US hematology-oncology meetings sponsored by the American Society of Hematology (ASH) and American Society of Clinical Oncology (ASCO) have specific guidelines in place discouraging submission of scientific information presented previously at other meetings. Nonetheless, duplicate submissions are frequent. The incidence and motivations for duplicate hematologic presentations and the influence of the pharmaceutical industry on this process have not been thoroughly analyzed. Therefore, were viewed four consecutive ASH and ASCO meetings to assess the frequency of duplicate abstract presentations. All abstracts presented at ASCO2010 in the area of malignant hematology were compared with abstracts from ASCO and ASH 2009 and ASH 2010, and funding sources were reviewed. More than half (54%) of all abstracts submitted to ASCO 2010 acknowledged pharmaceutical company support. Almost one third (31%) of ASCO 2010 abstracts were resubmitted in the 2-year time period, and it was notable that a high fraction (75%) of these duplicate abstracts had pharmaceutical industry sponsorship, compared with 42% of the abstracts that were submitted only once. Despite current guidelines prohibiting duplicate abstract presentation, a substantial proportion (31%) of abstracts at large international hematology-oncology meetings are duplicative, with potential negative consequences. In addition, a disproportionate percentage of the duplicate abstracts rely on pharmaceutical industry support (75%), suggesting that marketing strategies may be a motivation for some of these repetitive submissions.

  10. Consensus properties and their large-scale applications for the gene duplication problem.

    PubMed

    Moon, Jucheol; Lin, Harris T; Eulenstein, Oliver

    2016-06-01

    Solving the gene duplication problem is a classical approach for species tree inference from gene trees that are confounded by gene duplications. This problem takes a collection of gene trees and seeks a species tree that implies the minimum number of gene duplications. Wilkinson et al. posed the conjecture that the gene duplication problem satisfies the desirable Pareto property for clusters. That is, for every instance of the problem, all clusters that are commonly present in the input gene trees of this instance, called strict consensus, will also be found in every solution to this instance. We prove that this conjecture does not generally hold. Despite this negative result we show that the gene duplication problem satisfies a weaker version of the Pareto property where the strict consensus is found in at least one solution (rather than all solutions). This weaker property contributes to our design of an efficient scalable algorithm for the gene duplication problem. We demonstrate the performance of our algorithm in analyzing large-scale empirical datasets. Finally, we utilize the algorithm to evaluate the accuracy of standard heuristics for the gene duplication problem using simulated datasets.

  11. Brain evolution by brain pathway duplication

    PubMed Central

    Chakraborty, Mukta; Jarvis, Erich D.

    2015-01-01

    Understanding the mechanisms of evolution of brain pathways for complex behaviours is still in its infancy. Making further advances requires a deeper understanding of brain homologies, novelties and analogies. It also requires an understanding of how adaptive genetic modifications lead to restructuring of the brain. Recent advances in genomic and molecular biology techniques applied to brain research have provided exciting insights into how complex behaviours are shaped by selection of novel brain pathways and functions of the nervous system. Here, we review and further develop some insights to a new hypothesis on one mechanism that may contribute to nervous system evolution, in particular by brain pathway duplication. Like gene duplication, we propose that whole brain pathways can duplicate and the duplicated pathway diverge to take on new functions. We suggest that one mechanism of brain pathway duplication could be through gene duplication, although other mechanisms are possible. We focus on brain pathways for vocal learning and spoken language in song-learning birds and humans as example systems. This view presents a new framework for future research in our understanding of brain evolution and novel behavioural traits. PMID:26554045

  12. Drosophila melanogaster metallothionein genes: Selection for duplications

    SciTech Connect

    Lange, B.W.

    1989-01-01

    The metallothionein genes of Drosophila melanogaster, Mtn and Mto, may play an important role in heavy-metal detoxification. In order to investigate the possibility of increased selection for duplications of these genes in natural populations exposed to high levels of heavy metals, I compared the frequencies of such duplications among flies collected from metal-contaminated and non-contaminated orchards in Pennsylvania, Tennessee, and Georgia. Contaminated of collection sites and of local flies was confirmed by atomic absorption spectrosphotometry. Six-nucleotide-recognizing restriction enzyme analysis was used to screen 1666 wild third chromosomes for Mtn duplications. A subset (327) of these lines was screened for Mto duplications: none were found. Cadmium tolerance test performed on F{sub 2} progeny of wild females failed to detect a difference in tolerance levels between flies from contaminated orchards and flies from control orchards. Estimates of sequence diversity among a subsample (92) of the chromosomes used in the duplication survey, including all 27 Mtn duplication chromosomes, were obtained using four-nucleotide-recognizing restriction enzyme analysis.

  13. Brain evolution by brain pathway duplication.

    PubMed

    Chakraborty, Mukta; Jarvis, Erich D

    2015-12-19

    Understanding the mechanisms of evolution of brain pathways for complex behaviours is still in its infancy. Making further advances requires a deeper understanding of brain homologies, novelties and analogies. It also requires an understanding of how adaptive genetic modifications lead to restructuring of the brain. Recent advances in genomic and molecular biology techniques applied to brain research have provided exciting insights into how complex behaviours are shaped by selection of novel brain pathways and functions of the nervous system. Here, we review and further develop some insights to a new hypothesis on one mechanism that may contribute to nervous system evolution, in particular by brain pathway duplication. Like gene duplication, we propose that whole brain pathways can duplicate and the duplicated pathway diverge to take on new functions. We suggest that one mechanism of brain pathway duplication could be through gene duplication, although other mechanisms are possible. We focus on brain pathways for vocal learning and spoken language in song-learning birds and humans as example systems. This view presents a new framework for future research in our understanding of brain evolution and novel behavioural traits. © 2015 The Authors.

  14. The Instability of Neurospora Duplication Dp(IL→IR)H4250 , and Its Genetic Control

    PubMed Central

    Newmeyer, Dorothy; Galeazzi, Donna R.

    1977-01-01

    Previous work (Newmeyer and Taylor 1967) showed that a nontandem duplication, Dp(IL→IR)H4250, is regularly produced by recombination in crosses heterozygous for the effectively terminal pericentric inversion In(IL→IR)H4250. The duplications initially have strongly inhibited growth because they are heterozygous for mating type, which behaves like a vegetative-incompatibility (het) locus. Such cultures "escape" from the inhibition as a result of events that eliminate the mating-type heterozygosity. The product of a given escape event may be barren or fertile. (Neurospora duplications are characteristically barren; that is, when crossed, they make many perithecia but few ascospores.)—The present paper reports on a genetic analysis of the instability of Dp(IL→IR)H4250 . Most of the barren escape products behave as if due either to mitotic crossovers, which make mating type and distal markers homozygous, or to very long deletions which uncover mating type and all distal markers; presumably the latter would retain enough duplicated material to render them barren. It is difficult to distinguish between these two possibilities, but homozygosis seems more probable and has been clearly demonstrated in one case. Only a few barren escapes could be due to short deletions or to changes at the mating-type locus.—The fertile escape products appear to be euploid. Most of these behave as if they arose by precise deletion of one or the other duplicated segment, thus restoring one of the parental sequences. A large majority of the precise deletions restore normal sequence; only a few restore inversion sequence. Preferential restoration of the normal sequence has also been found by other workers for Neurospora duplications from several other rearrangements. A hypothesis is presented to explain these findings; it is posulated that the precise deletions result from mitotic crossing over in homologous material located at chromosome tips and tip-break-points.—There is a smaller

  15. Evidence of duplicated Hox genes in the most recent common ancestor of extant scorpions.

    PubMed

    Sharma, Prashant P; Santiago, Marc A; González-Santillán, Edmundo; Monod, Lionel; Wheeler, Ward C

    2015-01-01

    Scorpions (order Scorpiones) are unusual among arthropods, both for the extreme heteronomy of their bauplan and for the high gene family turnover exhibited in their genomes. These phenomena appear to be correlated, as two scorpion species have been shown to possess nearly twice the number of Hox genes present in most arthropods. Segmentally offset anterior expression boundaries of a subset of Hox paralogs have been shown to correspond to transitions in segmental identities in the scorpion posterior tagmata, suggesting that posterior heteronomy in scorpions may have been achieved by neofunctionalization of Hox paralogs. However, both the first scorpion genome sequenced and the developmental genetic data are based on exemplars of Buthidae, one of 19 families of scorpions. It is therefore not known whether Hox paralogy is limited to Buthidae or widespread among scorpions. We surveyed 24 high throughput transcriptomes and the single whole genome available for scorpions, in order to test the prediction that Hox gene duplications are common to the order. We used gene tree parsimony to infer whether the paralogy was consistent with a duplication event in the scorpion common ancestor. Here we show that duplicated Hox genes in non-buthid scorpions occur in six of the ten Hox classes. Gene tree topologies and parsimony-based reconciliation of the gene trees are consistent with a duplication event in the most recent common ancestor of scorpions. These results suggest that a Hox paralogy, and by extension the model of posterior patterning established in a buthid, can be extended to non-Buthidae scorpions.

  16. Natural History of Human Respiratory Syncytial Virus Inferred from Phylogenetic Analysis of the Attachment (G) Glycoprotein with a 60-Nucleotide Duplication

    PubMed Central

    Trento, Alfonsina; Viegas, Mariana; Galiano, Mónica; Videla, Cristina; Carballal, Guadalupe; Mistchenko, Alicia S.; Melero, José A.

    2006-01-01

    A total of 47 clinical samples were identified during an active surveillance program of respiratory infections in Buenos Aires (BA) (1999 to 2004) that contained sequences of human respiratory syncytial virus (HRSV) with a 60-nucleotide duplication in the attachment (G) protein gene. This duplication was analogous to that previously described for other three viruses also isolated in Buenos Aires in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003). Phylogenetic analysis indicated that BA sequences with that duplication shared a common ancestor (dated about 1998) with other HRSV G sequences reported worldwide after 1999. The duplicated nucleotide sequence was an exact copy of the preceding 60 nucleotides in early viruses, but both copies of the duplicated segment accumulated nucleotide substitutions in more recent viruses at a rate apparently higher than in other regions of the G protein gene. The evolution of the viruses with the duplicated G segment apparently followed the overall evolutionary pattern previously described for HRSV, and this genotype has replaced other prevailing antigenic group B genotypes in Buenos Aires and other places. Thus, the duplicated segment represents a natural tag that can be used to track the dissemination and evolution of HRSV in an unprecedented setting. We have taken advantage of this situation to reexamine the molecular epidemiology of HRSV and to explore the natural history of this important human pathogen. PMID:16378999

  17. Natural history of human respiratory syncytial virus inferred from phylogenetic analysis of the attachment (G) glycoprotein with a 60-nucleotide duplication.

    PubMed

    Trento, Alfonsina; Viegas, Mariana; Galiano, Mónica; Videla, Cristina; Carballal, Guadalupe; Mistchenko, Alicia S; Melero, José A

    2006-01-01

    A total of 47 clinical samples were identified during an active surveillance program of respiratory infections in Buenos Aires (BA) (1999 to 2004) that contained sequences of human respiratory syncytial virus (HRSV) with a 60-nucleotide duplication in the attachment (G) protein gene. This duplication was analogous to that previously described for other three viruses also isolated in Buenos Aires in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003). Phylogenetic analysis indicated that BA sequences with that duplication shared a common ancestor (dated about 1998) with other HRSV G sequences reported worldwide after 1999. The duplicated nucleotide sequence was an exact copy of the preceding 60 nucleotides in early viruses, but both copies of the duplicated segment accumulated nucleotide substitutions in more recent viruses at a rate apparently higher than in other regions of the G protein gene. The evolution of the viruses with the duplicated G segment apparently followed the overall evolutionary pattern previously described for HRSV, and this genotype has replaced other prevailing antigenic group B genotypes in Buenos Aires and other places. Thus, the duplicated segment represents a natural tag that can be used to track the dissemination and evolution of HRSV in an unprecedented setting. We have taken advantage of this situation to reexamine the molecular epidemiology of HRSV and to explore the natural history of this important human pathogen.

  18. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

    PubMed Central

    2009-01-01

    Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64%) consisted of both mitochondrial and cytosolic (non-mitochondrial) proteins (mt-cy families) while the remaining 33 (36%) were composed of mitochondrial proteins (mt-mt families). Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1) relocalization from mitochondria to cytosol, 2) from cytosol to mitochondria and 3) multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on the genomic scale was

  19. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications.

    PubMed

    Smith, Jeramiah J; Keinath, Melissa C

    2015-08-01

    It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution. © 2015 Smith and Keinath; Published by Cold Spring Harbor Laboratory Press.

  20. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

    PubMed Central

    Smith, Jeramiah J.; Keinath, Melissa C.

    2015-01-01

    It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution. PMID:26048246

  1. Analyses of nuclearly encoded mitochondrial genes suggest gene duplication as a mechanism for resolving intralocus sexually antagonistic conflict in Drosophila.

    PubMed

    Gallach, Miguel; Chandrasekaran, Chitra; Betrán, Esther

    2010-01-01

    Gene duplication is probably the most important mechanism for generating new gene functions. However, gene duplication has been overlooked as a potentially effective way to resolve genetic conflicts. Here, we analyze the entire set of Drosophila melanogaster nuclearly encoded mitochondrial duplicate genes and show that both RNA- and DNA-mediated mitochondrial gene duplications exhibit an unexpectedly high rate of relocation (change in location between parental and duplicated gene) as well as an extreme tendency to avoid the X chromosome. These trends are likely related to our observation that relocated genes tend to have testis-specific expression. We also infer that these trends hold across the entire Drosophila genus. Importantly, analyses of gene ontology and functional interaction networks show that there is an overrepresentation of energy production-related functions in these mitochondrial duplicates. We discuss different hypotheses to explain our results and conclude that our findings substantiate the hypothesis that gene duplication for male germline function is likely a mechanism to resolve intralocus sexually antagonistic conflicts that we propose are common in testis. In the case of nuclearly encoded mitochondrial duplicates, our hypothesis is that past sexually antagonistic conflict related to mitochondrial energy function in Drosophila was resolved by gene duplication.

  2. An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.

    PubMed

    Shao, Mingfu; Lin, Yu; Moret, Bernard M E

    2015-05-01

    Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be computed in linear time for genomes without duplicate genes, while the problem becomes NP-hard in the presence of duplicate genes. In this article, we propose an integer linear programming (ILP) formulation to compute the DCJ distance between two genomes with duplicate genes. We also provide an efficient preprocessing approach to simplify the ILP formulation while preserving optimality. Comparison on simulated genomes demonstrates that our method outperforms MSOAR in computing the edit distance, especially when the genomes contain long duplicated segments. We also apply our method to assign orthologous gene pairs among human, mouse, and rat genomes, where once again our method outperforms MSOAR.

  3. 48 CFR 1331.205-70 - Duplication of effort.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Duplication of effort....205-70 Duplication of effort. The Department will not pay any costs for work that is duplicative of..., Duplication of Effort, in all cost-reimbursement, time and materials, and labor hour solicitations...

  4. Welder analyzer

    NASA Technical Reports Server (NTRS)

    Miller, L. L.

    1968-01-01

    Welder analyzer circuit evaluates and certifies resistance welding machines. The analyzer measures peak current, peak voltage, peak power, total energy, and first-pulse energy. It is used as an energy monitor while welding is being performed, or a precision shunt load for a pure electrical evaluation of the weld machine.

  5. De novo tandem duplication of chromosome segement 22q11-q12: Clinical, cytogenetic, and molecular characterization

    SciTech Connect

    Lindsay, E.A.; Shaffer, L.G.; Carrozzo, R.

    1995-04-10

    We report on a case of duplication of the segment 22q11-q12 due to a de novo duplication. Molecular cytogenetics studies demonstrated this to be a tandem duplication, flanked proximally by the marker D22Z4, a centromeric alpha satellite DNA repeat, and distally by D22S260, an anonymous DNA marker proximal to the Ewing sarcoma breakpoint. The segment includes the regions responsible for the {open_quotes}cat-eye{close_quotes}, Di George, and velo-cardio-facial syndromes and extends distal to the breakpoint cluster region (BCR). The clinical picture is dominated by the cardiac defects and includes findings reminiscent of {open_quotes}cat-eye{close_quotes} syndrome. These findings reinforce the hypothesis that the proximal 22q region contains dosage-sensitive genes involved in development. 20 refs., 3 figs.

  6. Pervasive and Persistent Redundancy among Duplicated Genes in Yeast

    PubMed Central

    Dean, E. Jedediah; Davis, Jerel C.; Davis, Ronald W.; Petrov, Dmitri A.

    2008-01-01

    The loss of functional redundancy is the key process in the evolution of duplicated genes. Here we systematically assess the extent of functional redundancy among a large set of duplicated genes in Saccharomyces cerevisiae. We quantify growth rate in rich medium for a large number of S. cerevisiae strains that carry single and double deletions of duplicated and singleton genes. We demonstrate that duplicated genes can maintain substantial redundancy for extensive periods of time following duplication (∼100 million years). We find high levels of redundancy among genes duplicated both via the whole genome duplication and via smaller scale duplications. Further, we see no evidence that two duplicated genes together contribute to fitness in rich medium substantially beyond that of their ancestral progenitor gene. We argue that duplicate genes do not often evolve to behave like singleton genes even after very long periods of time. PMID:18604285

  7. Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci

    PubMed Central

    Vaccarelli, Giovanna; Miccoli, Maria C; Antonacci, Rachele; Pesole, Graziano; Ciccarese, Salvatrice

    2008-01-01

    Background In humans and mice ("γδ low species") less than 5% of the peripheral blood T lymphocytes are gamma/delta T cells, whereas in chicken and artiodactyls ("γδ high species") gamma/delta T cells represent about half of the T cells in peripheral blood. In cattle and sheep (Bovidae) two paralogous T cell receptor gamma loci (TRG1 and TRG2) have been found. TRG1 is located on 4q3.1, within a region of homology with the human TRG locus on chromosome 7, while TRG2 localizes on 4q2.2 and appears to be unique to ruminants. The purpose of this study was the sequencing of the genomic regions encompassing both loci in a "γδ high" organism and the analysis of their evolutionary history. Results We obtained the contiguous genomic sequences of the complete sheep TRG1 and TRG2 loci gene repertoire and we performed cattle/sheep sequence analysis comparison using data available through public databases. Dot plot similarity matrix comparing the two sheep loci with each other has shown that variable (V), joining (J) and constant (C) genes have evolved through a series of duplication events involving either entire cassettes, each containing the basic V-J-J-C recombinational unit, or single V genes. The phylogenetic behaviour of the eight enhancer-like elements found in the sheep, compared with the single copy present in the human TRG locus, and evidence from concordant insertions of repetitive elements in all analyzed TRGJ blocks allowed us to infer an evolutionary scenario which highlights the genetic "flexibility" of this region and the duplication-driven evolution of gene cassettes. The strong similarity of the human and Bovidae intergenic J-J-C regions, which display an enhancer-like element at their 3' ends, further supports their key role in duplications. Conclusion We propose that only duplications of entire J-J-C regions that possessed an enhancer-like element at their 3' end, and acquired at least one V segment at their 5' end, were selected and fixed as

  8. Do Children Think that Duplicating the Body also Duplicates the Mind?

    ERIC Educational Resources Information Center

    Hood, Bruce; Gjersoe, Nathalia L.; Bloom, Paul

    2012-01-01

    Philosophers use hypothetical duplication scenarios to explore intuitions about personal identity. Here we examined 5- to 6-year-olds' intuitions about the physical properties and memories of a live hamster that is apparently duplicated by a machine. In Study 1, children thought that more of the original's physical properties than episodic…

  9. Do Children Think that Duplicating the Body also Duplicates the Mind?

    ERIC Educational Resources Information Center

    Hood, Bruce; Gjersoe, Nathalia L.; Bloom, Paul

    2012-01-01

    Philosophers use hypothetical duplication scenarios to explore intuitions about personal identity. Here we examined 5- to 6-year-olds' intuitions about the physical properties and memories of a live hamster that is apparently duplicated by a machine. In Study 1, children thought that more of the original's physical properties than episodic…

  10. DIFFERENTIAL ANALYZER

    DOEpatents

    Sorensen, E.G.; Gordon, C.M.

    1959-02-10

    Improvements in analog eomputing machines of the class capable of evaluating differential equations, commonly termed differential analyzers, are described. In general form, the analyzer embodies a plurality of basic computer mechanisms for performing integration, multiplication, and addition, and means for directing the result of any one operation to another computer mechanism performing a further operation. In the device, numerical quantities are represented by the rotation of shafts, or the electrical equivalent of shafts.

  11. Genome Duplication: The Heartbeat of Developing Organisms

    PubMed Central

    DePamphilis, Melvin L.

    2016-01-01

    The mechanism that duplicates the nuclear genome during the trillions of cell divisions required to develop from zygote to adult is the same throughout the eukarya, but the mechanisms that determine where, when and how much nuclear genome duplication occur regulate development and differ among the eukarya. They allow organisms to change the rate of cell proliferation during development, to activate zygotic gene expression independently of DNA replication, and to restrict nuclear DNA replication to once per cell division. They allow specialized cells to exit their mitotic cell cycle and differentiate into polyploid cells, and in some cases, to amplify the number of copies of specific genes. It is genome duplication that drives evolution, by virtue of the errors that inevitably occur when the same process is repeated trillions of times. It is, unfortunately, the same errors that produce age-related genetic disorders such as cancer. PMID:26970621

  12. Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation

    PubMed Central

    López-Leal, Gamaliel; Cevallos, Miguel A.; Castillo-Ramírez, Santiago

    2016-01-01

    Sigma factors are an essential part of bacterial gene regulation and have been extensively studied as far as their molecular mechanisms and protein structure are concerned. However, their molecular evolution, especially for the alternative sigma factors, is poorly understood. Here, we analyze the evolutionary forces that have shaped the rpoH sigma factors within the alphaproteobacteria. We found that an ancient duplication gave rise to two major groups of rpoH sigma factors and that after this event horizontal gene transfer (HGT) occurred in rpoH1 group. We also noted that purifying selection has differentially affected distinct parts of the gene; singularly, the gene segment that encodes the region 4.2, which interacts with the −35 motif of the RpoH-dependent genes, has been under relaxed purifying selection. Furthermore, these two major groups are clearly differentiated from one another regarding their promoter selectivity, as rpoH1 is under the transcriptional control of σ70 and σ32, whereas rpoH2 is under the transcriptional control of σ24. Our results suggest a scenario in which HGT, gene loss, variable purifying selection and clear promoter specialization occurred after the ancestral duplication event. More generally, our study offers insights into the molecular evolution of alternative sigma factors and highlights the importance of analyzing not only the coding regions but also the promoter regions. PMID:27199915

  13. Medical image segmentation by MDP model

    NASA Astrophysics Data System (ADS)

    Lu, Yisu; Chen, Wufan

    2011-11-01

    MDP (Dirichlet Process Mixtures) model is applied to segment medical images in this paper. Segmentation can been automatically done without initializing segmentation class numbers. The MDP model segmentation algorithm is used to segment natural images and MR (Magnetic Resonance) images in the paper. To demonstrate the accuracy of the MDP model segmentation algorithm, many compared experiments, such as EM (Expectation Maximization) image segmentation algorithm, K-means image segmentation algorithm and MRF (Markov Field) image segmentation algorithm, have been done to segment medical MR images. All the methods are also analyzed quantitatively by using DSC (Dice Similarity Coefficients). The experiments results show that DSC of MDP model segmentation algorithm of all slices exceed 90%, which show that the proposed method is robust and accurate.

  14. Single Incision Laparoscopic Cholecystectomy for Gallbladder Duplication

    PubMed Central

    Kabul Gürbulak, Esin; Özşahin, Hamdi; Düzköylü, Yiğit; Akgün, Ismail Ethem; Battal, Muharrem; Gürbulak, Bünyamin

    2015-01-01

    Duplication of the gallbladder is a rare congenital anomaly of the gallbladder, with an estimated prevalence of 1–3 per 3800 individuals. Unless properly diagnosed preoperatively, it can lead to biliary tract injuries and postoperative complications which may require reoperative surgeries. While previously reported cases have been treated with conventional laparoscopic cholecystectomy (LC), treatment with single incision laparoscopic surgery (SILS) has not been reported yet. We herein present the case of a 58-year-old female with gallbladder duplication who was successfully treated with SILS cholecystectomy. PMID:26266074

  15. Gall-bladder duplication - case report.

    PubMed

    Koszman, Bogusław

    2014-12-18

    Gall-bladder duplication is a rare anatomical variation, which can affect safe performance of cholecystectomy and be a cause of persistent symptoms and a need for reoperation in case of accessory gall-bladder omission. A case of successfully performed elective laparoscopic cholecystectomy in a patient with duplicated gall-bladder accidentally intraoperatively disclosed is presented. The identified anomaly was classified according to the Harlaftis Classification of Multiple Gall-bladders. Attention was drawn to the uneffectivenes of ultrasound scanning in multiple gall-bladders preoperative detecting, and presence of other non-biliary anatomical variation in the same individual as well.

  16. The human chromosomal fragile sites more often involved in constitutional deletions and duplications - A genetic and statistical assessment

    NASA Astrophysics Data System (ADS)

    Gomes, Dora Prata; Sequeira, Inês J.; Figueiredo, Carlos; Rueff, José; Brás, Aldina

    2016-12-01

    Human chromosomal fragile sites (CFSs) are heritable loci or regions of the human chromosomes prone to exhibit gaps, breaks and rearrangements. Determining the frequency of deletions and duplications in CFSs may contribute to explain the occurrence of human disease due to those rearrangements. In this study we analyzed the frequency of deletions and duplications in each human CFS. Statistical methods, namely data display, descriptive statistics and linear regression analysis were applied to analyze this dataset. We found that FRA15C, FRA16A and FRAXB are the most frequently involved CFSs in deletions and duplications occurring in the human genome.

  17. Photon number amplification/duplication through parametric conversion

    NASA Technical Reports Server (NTRS)

    Dariano, G. M.; Macchiavello, C.; Paris, M.

    1993-01-01

    The performance of parametric conversion in achieving number amplification and duplication is analyzed. It is shown that the effective maximum gains G(sub *) remain well below their integer ideal values, even for large signals. Correspondingly, one has output Fano factors F(sub *) which are increasing functions of the input photon number. On the other hand, in the inverse (deamplifier/recombiner) operating mode quasi-ideal gains G(sub *) and small factors F(sub *) approximately equal to 10 percent are obtained. Output noise and non-ideal gains are ascribed to spontaneous parametric emission.

  18. Process Analyzer

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The ChemScan UV-6100 is a spectrometry system originally developed by Biotronics Technologies, Inc. under a Small Business Innovation Research (SBIR) contract. It is marketed to the water and wastewater treatment industries, replacing "grab sampling" with on-line data collection. It analyzes the light absorbance characteristics of a water sample, simultaneously detects hundreds of individual wavelengths absorbed by chemical substances in a process solution, and quantifies the information. Spectral data is then processed by ChemScan analyzer and compared with calibration files in the system's memory in order to calculate concentrations of chemical substances that cause UV light absorbance in specific patterns. Monitored substances can be analyzed for quality and quantity. Applications include detection of a variety of substances, and the information provided enables an operator to control a process more efficiently.

  19. Blood Analyzer

    NASA Technical Reports Server (NTRS)

    1992-01-01

    In the 1970's, NASA provided funding for development of an automatic blood analyzer for Skylab at the Oak Ridge National Laboratory (ORNL). ORNL devised "dynamic loading," which employed a spinning rotor to load, transfer, and analyze blood samples by centrifugal processing. A refined, commercial version of the system was produced by ABAXIS and is marketed as portable ABAXIS MiniLab MCA. Used in a doctor's office, the equipment can perform 80 to 100 chemical blood tests on a single drop of blood and report results in five minutes. Further development is anticipated.

  20. Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome

    PubMed Central

    Zimin, Aleksey V.; Kelley, David R.; Roberts, Michael; Marçais, Guillaume; Salzberg, Steven L.; Yorke, James A.

    2012-01-01

    We analyzed the whole genome sequence coverage in two versions of the Bos taurus genome and identified all regions longer than five kilobases (Kbp) that are duplicated within chromosomes with >99% sequence fidelity in both copies. We call these regions High Fidelity Duplications (HFDs). The two assemblies were Btau 4.2, produced by the Human Genome Sequencing Center at Baylor College of Medicine, and UMD Bos taurus 3.1 (UMD 3.1), produced by our group at the University of Maryland. We found that Btau 4.2 has a far greater number of HFDs, 3111 versus only 69 in UMD 3.1. Read coverage analysis shows that 39 million base pairs (Mbp) of sequence in HFDs in Btau 4.2 appear to be a result of a mis-assembly and therefore cannot be qualified as segmental duplications. UMD 3.1 has only 0.41 Mbp of sequence in HFDs that are due to a mis-assembly. PMID:22880081

  1. Insertion of the IL1RAPL1 gene into the duplication junction of the dystrophin gene.

    PubMed

    Zhang, Zhujun; Yagi, Mariko; Okizuka, Yo; Awano, Hiroyuki; Takeshima, Yasuhiro; Matsuo, Masafumi

    2009-08-01

    Duplications of one or more exons of the dystrophin gene are the second most common mutation in dystrophinopathies. Even though duplications are suggested to occur with greater complexity than thought earlier, they have been considered an intragenic event. Here, we report the insertion of a part of the IL1RAPL1 (interleukin-1 receptor accessory protein-like 1) gene into the duplication junction site. When the actual exon junction was examined in 15 duplication mutations in the dystrophin gene by analyzing dystrophin mRNA, one patient was found to have an unknown 621 bp insertion at the junction of duplication of exons from 56 to 62. Unexpectedly, the inserted sequence was found completely identical to sequences of exons 3-5 of the IL1RAPL1 gene that is nearly 100 kb distal from the dystrophin gene. Accordingly, the insertion of IL1RAPL1 exons 3-5 between dystrophin exons 62 and 56 was confirmed at the genomic sequence level. One junction between the IL1RAPL1 intron 5 and dystrophin intron 55 was localized within an Alu sequence. These results showed that a fragment of the IL1RAPL1 gene was inserted into the duplication junction of the dystrophin gene in the same direction as the dystrophin gene. This suggests the novel possibility of co-occurrence of complex genomic rearrangements in dystrophinopathy.

  2. Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution.

    PubMed

    Ajmal, Wajya; Khan, Hiba; Abbasi, Amir Ali

    2014-12-01

    Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history. Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently. Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Analysis of filtering techniques and image quality in pixel duplicated images

    NASA Astrophysics Data System (ADS)

    Mehrubeoglu, Mehrube; McLauchlan, Lifford

    2009-08-01

    When images undergo filtering operations, valuable information can be lost besides the intended noise or frequencies due to averaging of neighboring pixels. When the image is enlarged by duplicating pixels, such filtering effects can be reduced and more information retained, which could be critical when analyzing image content automatically. Analysis of retinal images could reveal many diseases at early stage as long as minor changes that depart from a normal retinal scan can be identified and enhanced. In this paper, typical filtering techniques are applied to an early stage diabetic retinopathy image which has undergone digital pixel duplication. The same techniques are applied to the original images for comparison. The effects of filtering are then demonstrated for both pixel duplicated and original images to show the information retention capability of pixel duplication. Image quality is computed based on published metrics. Our analysis shows that pixel duplication is effective in retaining information on smoothing operations such as mean filtering in the spatial domain, as well as lowpass and highpass filtering in the frequency domain, based on the filter window size. Blocking effects due to image compression and pixel duplication become apparent in frequency analysis.

  4. The evolutionary fate of alternatively spliced homologous exons after gene duplication.

    PubMed

    Abascal, Federico; Tress, Michael L; Valencia, Alfonso

    2015-04-29

    Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

  5. Defibrillator analyzers.

    PubMed

    1999-12-01

    Defibrillator analyzers automate the inspection and preventive maintenance (IPM) testing of defibrillators. They need to be able to test at least four basic defibrillator performance characteristics: discharge energy, synchronized-mode operation, automated external defibrillation, and ECG monitoring. We prefer that they also be able to test a defibrillator's external noninvasive pacing function--but this is not essential if a facility already has a pacemaker analyzer that can perform this testing. In this Evaluation, we tested seven defibrillator analyzers from six suppliers. All seven units accurately measure the energies of a variety of discharge wave-forms over a wide range of energy levels--from 1 J for use in a neonatal intensive care unit to 360 J for use on adult patients requiring maximum discharge energy. Most of the analyzers are easy to use. However, only three of the evaluated units could perform the full range of defibrillator tests that we prefer. We rated these units Acceptable--Preferred. Three more units could perform four of the five tests, they could not test the pacing feature of a defibrillator. These units were rated Acceptable. The seventh unit could perform only discharge energy testing and synchronized-mode testing and was difficult to use. We rate that unit Acceptable--Not Recommended.

  6. Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.

    PubMed

    Willemsen, Anouk; Zwart, Mark P; Higueras, Pablo; Sardanyés, Josep; Elena, Santiago F

    2016-10-12

    One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Assessment and Reconstruction of Novel HSP90 Genes: Duplications, Gains and Losses in Fungal and Animal Lineages

    PubMed Central

    Pantzartzi, Chrysoula N.; Drosopoulou, Elena; Scouras, Zacharias G.

    2013-01-01

    Hsp90s, members of the Heat Shock Protein class, protect the structure and function of proteins and play a significant task in cellular homeostasis and signal transduction. In order to determine the number of hsp90 gene copies and encoded proteins in fungal and animal lineages and through that key duplication events that this family has undergone, we collected and evaluated Hsp90 protein sequences and corresponding Expressed Sequence Tags and analyzed available genomes from various taxa. We provide evidence for duplication events affecting either single species or wider taxonomic groups. With regard to Fungi, duplicated genes have been detected in several lineages. In invertebrates, we demonstrate key duplication events in certain clades of Arthropoda and Mollusca, and a possible gene loss event in a hymenopteran family. Finally, we infer that the duplication event responsible for the two (a and b) isoforms in vertebrates occurred probably shortly after the split of Hyperoartia and Gnathostomata. PMID:24066039

  8. A new resource for characterizing X-linked genes in Drosophila melanogaster: systematic coverage and subdivision of the X chromosome with nested, Y-linked duplications.

    PubMed

    Cook, R Kimberley; Deal, Megan E; Deal, Jennifer A; Garton, Russell D; Brown, C Adam; Ward, Megan E; Andrade, Rachel S; Spana, Eric P; Kaufman, Thomas C; Cook, Kevin R

    2010-12-01

    Interchromosomal duplications are especially important for the study of X-linked genes. Males inheriting a mutation in a vital X-linked gene cannot survive unless there is a wild-type copy of the gene duplicated elsewhere in the genome. Rescuing the lethality of an X-linked mutation with a duplication allows the mutation to be used experimentally in complementation tests and other genetic crosses and it maps the mutated gene to a defined chromosomal region. Duplications can also be used to screen for dosage-dependent enhancers and suppressors of mutant phenotypes as a way to identify genes involved in the same biological process. We describe an ongoing project in Drosophila melanogaster to generate comprehensive coverage and extensive breakpoint subdivision of the X chromosome with megabase-scale X segments borne on Y chromosomes. The in vivo method involves the creation of X inversions on attached-XY chromosomes by FLP-FRT site-specific recombination technology followed by irradiation to induce large internal X deletions. The resulting chromosomes consist of the X tip, a medial X segment placed near the tip by an inversion, and a full Y. A nested set of medial duplicated segments is derived from each inversion precursor. We have constructed a set of inversions on attached-XY chromosomes that enable us to isolate nested duplicated segments from all X regions. To date, our screens have provided a minimum of 78% X coverage with duplication breakpoints spaced a median of nine genes apart. These duplication chromosomes will be valuable resources for rescuing and mapping X-linked mutations and identifying dosage-dependent modifiers of mutant phenotypes.

  9. Process Analyzer

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Under a NASA Small Business Innovation Research (SBIR) contract, Axiomatics Corporation developed a shunting Dielectric Sensor to determine the nutrient level and analyze plant nutrient solutions in the CELSS, NASA's space life support program. (CELSS is an experimental facility investigating closed-cycle plant growth and food processing for long duration manned missions.) The DiComp system incorporates a shunt electrode and is especially sensitive to changes in dielectric property changes in materials at measurements much lower than conventional sensors. The analyzer has exceptional capabilities for predicting composition of liquid streams or reactions. It measures concentrations and solids content up to 100 percent in applications like agricultural products, petrochemicals, food and beverages. The sensor is easily installed; maintenance is low, and it can be calibrated on line. The software automates data collection and analysis.

  10. Oxygen analyzer

    DOEpatents

    Benner, William H.

    1986-01-01

    An oxygen analyzer which identifies and classifies microgram quantities of oxygen in ambient particulate matter and for quantitating organic oxygen in solvent extracts of ambient particulate matter. A sample is pyrolyzed in oxygen-free nitrogen gas (N.sub.2), and the resulting oxygen quantitatively converted to carbon monoxide (CO) by contact with hot granular carbon (C). Two analysis modes are made possible: (1) rapid determination of total pyrolyzable oxygen obtained by decomposing the sample at 1135.degree. C., or (2) temperature-programmed oxygen thermal analysis obtained by heating the sample from room temperature to 1135.degree. C. as a function of time. The analyzer basically comprises a pyrolysis tube containing a bed of granular carbon under N.sub.2, ovens used to heat the carbon and/or decompose the sample, and a non-dispersive infrared CO detector coupled to a mini-computer to quantitate oxygen in the decomposition products and control oven heating.

  11. Oxygen analyzer

    DOEpatents

    Benner, W.H.

    1984-05-08

    An oxygen analyzer which identifies and classifies microgram quantities of oxygen in ambient particulate matter and for quantitating organic oxygen in solvent extracts of ambient particulate matter. A sample is pyrolyzed in oxygen-free nitrogen gas (N/sub 2/), and the resulting oxygen quantitatively converted to carbon monoxide (CO) by contact with hot granular carbon (C). Two analysis modes are made possible: (1) rapid determination of total pyrolyzable obtained by decomposing the sample at 1135/sup 0/C, or (2) temperature-programmed oxygen thermal analysis obtained by heating the sample from room temperature to 1135/sup 0/C as a function of time. The analyzer basically comprises a pyrolysis tube containing a bed of granular carbon under N/sub 2/, ovens used to heat the carbon and/or decompose the sample, and a non-dispersive infrared CO detector coupled to a mini-computer to quantitate oxygen in the decomposition products and control oven heating.

  12. Atmosphere Analyzer

    NASA Technical Reports Server (NTRS)

    1982-01-01

    California Measurements, Inc.'s model PC-2 Aerosol Particle Analyzer is produced in both airborne and ground-use versions. Originating from NASA technology, it is a quick and accurate method of detecting minute amounts of mass loadings on a quartz crystal -- offers utility as highly sensitive detector of fine particles suspended in air. When combined with suitable air delivery system, it provides immediate information on the size distribution and mass concentrations of aerosols. William Chiang, obtained a NASA license for multiple crystal oscillator technology, and initially developed a particle analyzer for NASA use with Langley Research Center assistance. Later his company produced the modified PC-2 for commercial applications Brunswick Corporation uses the device for atmospheric research and in studies of smoke particles in Fires. PC-2 is used by pharmaceutical and chemical companies in research on inhalation toxicology and environmental health. Also useful in testing various filters for safety masks and nuclear installations.

  13. 47 CFR 54.672 - Duplicate support.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Healthcare Connect Fund may not also request support from any other universal service program for the same... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) UNIVERSAL SERVICE Universal Service Support for Health Care Providers General Provisions § 54.672 Duplicate support...

  14. 47 CFR 54.672 - Duplicate support.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Healthcare Connect Fund may not also request support from any other universal service program for the same... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES (CONTINUED) UNIVERSAL SERVICE Universal Service Support for Health Care Providers General Provisions § 54.672 Duplicate support...

  15. 40 CFR 710.55 - Duplicative reporting.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Duplicative reporting. 710.55 Section 710.55 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS Inventory Update Reporting for 2006 and Beyond §...

  16. 40 CFR 710.55 - Duplicative reporting.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Duplicative reporting. 710.55 Section 710.55 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS Inventory Update Reporting for 2006 and Beyond §...

  17. Duplication of the nipples and areolae.

    PubMed

    Hundleby, Christopher J B; Beighton, Peter

    2007-04-01

    A young South African woman has bilateral duplication of the nipples and areolae in an apparently horizontal plane on each breast. She is otherwise normal in every respect, and her family history is negative. This configuration of breast tissue is very unusual and, to the best of our knowledge, it has not previously been reported.

  18. Filtering duplicate reads from 454 pyrosequencing data

    PubMed Central

    Balzer, Susanne; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge

    2013-01-01

    Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the estimation of diversity and composition of a sample. To date, there are several tools that aim to remove both sequencing noise and duplicates. Nevertheless, duplicate removal is often based on nucleotide sequences rather than on the underlying flow values, which contain additional information. Results: With the novel tool JATAC, we present an approach towards a more accurate duplicate removal by analysing flow values directly. Making use of previous findings on 454 flow data characteristics, we combine read clustering with Bayesian distance measures. Finally, we provide a benchmark with an existing algorithm. Availability: JATAC is freely available under the General Public License from http://malde.org/ketil/jatac/. Contact: Ketil.Malde@imr.no Supplementary information: Supplementary data are available at Bioinformatics online PMID:23376350

  19. Fetal Cyst Reveling Retroperitoneal Enteric Duplication

    PubMed Central

    Ayadi, Imene Dahmane; Bezzine, Ahlem; Hamida, Emira Ben; Marrakchi, Zahra

    2017-01-01

    Retroperitoneum is a very uncommon site of enteric duplication (ED). We report a new case of retroperitoneal ED cyst suspected in utero. Prenatal ultrasound showed an abdominal cystic mass. Noncommunicating retroperitoneal ED cyst measuring 70 mm × 30 mm was resected. Histopathologic examination confirmed the diagnosis. PMID:28082784

  20. 20 CFR 410.705 - Duplicate claims.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Duplicate claims. 410.705 Section 410.705 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Rules for the Review of Denied and Pending Claims Under the Black...

  1. 20 CFR 410.705 - Duplicate claims.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Duplicate claims. 410.705 Section 410.705 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Rules for the Review of Denied and Pending Claims Under the Black...

  2. Esophageal duplication and congenital esophageal stenosis.

    PubMed

    Trappey, A Francois; Hirose, Shinjiro

    2017-04-01

    Esophageal duplication and congenital esophageal stenosis (CES) may represent diseases with common embryologic etiologies, namely, faulty tracheoesophageal separation and differentiation. Here, we will re-enforce definitions for these diseases as well as review their embryology, diagnosis, and treatment. Copyright © 2017. Published by Elsevier Inc.

  3. Organising European technical documentation to avoid duplication.

    PubMed

    Donawa, Maria

    2006-04-01

    The development of comprehensive accurate and well-organised technical documentation that demonstrates compliance with regulatory requirements is a resource-intensive, but critically important activity for medical device manufacturers. This article discusses guidance documents and method of organising technical documentation that may help avoid costly and time-consuming duplication.

  4. Duplicated Publication Fundamentals for Student Periodicals.

    ERIC Educational Resources Information Center

    Columbia Scholastic Press Association, New York, NY.

    This handbook provides the 1973 basic principles of the Columbia Scholastic Press Association for determining the quality of high school and college student periodicals which are intended for duplication. The handbook begins with an explanation of rating procedures used in this evaluation and then provides sample scorebooks for student newspapers,…

  5. MULTICHANNEL ANALYZER

    DOEpatents

    Kelley, G.G.

    1959-11-10

    A multichannel pulse analyzer having several window amplifiers, each amplifier serving one group of channels, with a single fast pulse-lengthener and a single novel interrogation circuit serving all channels is described. A pulse followed too closely timewise by another pulse is disregarded by the interrogation circuit to prevent errors due to pulse pileup. The window amplifiers are connected to the pulse lengthener output, rather than the linear amplifier output, so need not have the fast response characteristic formerly required.

  6. Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene.

    PubMed

    Trento, Alfonsina; Casas, Inmaculada; Calderón, Ana; Garcia-Garcia, Maria L; Calvo, Cristina; Perez-Breña, Pilar; Melero, José A

    2010-08-01

    The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host.

  7. Ten Years of Global Evolution of the Human Respiratory Syncytial Virus BA Genotype with a 60-Nucleotide Duplication in the G Protein Gene▿ †

    PubMed Central

    Trento, Alfonsina; Casas, Inmaculada; Calderón, Ana; Garcia-Garcia, Maria L.; Calvo, Cristina; Perez-Breña, Pilar; Melero, José A.

    2010-01-01

    The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host. PMID:20504933

  8. Contamination Analyzer

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Measurement of the total organic carbon content in water is important in assessing contamination levels in high purity water for power generation, pharmaceutical production and electronics manufacture. Even trace levels of organic compounds can cause defects in manufactured products. The Sievers Model 800 Total Organic Carbon (TOC) Analyzer, based on technology developed for the Space Station, uses a strong chemical oxidizing agent and ultraviolet light to convert organic compounds in water to carbon dioxide. After ionizing the carbon dioxide, the amount of ions is determined by measuring the conductivity of the deionized water. The new technique is highly sensitive, does not require compressed gas, and maintenance is minimal.

  9. CCFP Analyzer

    NASA Image and Video Library

    2016-05-06

    ISS047e106715 (05/06/2016) --- ESA (European Space Agency astronaut Tim Peake unpacks a cerebral and cochlear fluid pressure (CCFP) analyzer. The device is being tested to measure the pressure of the fluid in the skull, also known as intracranial pressure, which may increase due to fluid shifts in the body while in microgravity. It is hypothesized that the headward fluid shift that occurs during space flight leads to increased pressure in the brain, which may push on the back of the eye, causing it to change shape.

  10. Gas Analyzer

    NASA Technical Reports Server (NTRS)

    1983-01-01

    A miniature gas chromatograph, a system which separates a gaseous mixture into its components and measures the concentration of the individual gases, was designed for the Viking Lander. The technology was further developed under National Institute for Occupational Safety and Health (NIOSH) and funded by Ames Research Center/Stanford as a toxic gas leak detection device. Three researchers on the project later formed Microsensor Technology, Inc. to commercialize the product. It is a battery-powered system consisting of a sensing wand connected to a computerized analyzer. Marketed as the Michromonitor 500, it has a wide range of applications.

  11. An Analysis of Duplicate Presentations at the 2014 Through 2016 AOSSM and AANA Annual Meetings.

    PubMed

    Kraeutler, Matthew J; Carver, Trevor J; McCarty, Eric C

    2017-07-01

    Previous studies have shown a high incidence of duplicate presentations at research conferences within different medical disciplines. To determine the rate and analyze characteristics of duplicate presentations at the American Orthopaedic Society for Sports Medicine (AOSSM) and Arthroscopy Association of North America (AANA) Annual Meetings. Cross-sectional study. Meeting programs for the 2014 to 2016 AOSSM and AANA Annual Meetings were searched. All podium presentation abstracts from each AOSSM meeting were cross-referenced with podium presentation abstracts from AANA meetings from all 3 years of the study period to locate all duplicate presentations. Duplicate presentations were then analyzed for changes in abstract title, author order, and addition or removal of authors. A total of 192 and 213 abstracts were accepted for podium presentations at the AOSSM and AANA Annual Meetings, respectively, during the study period. This included 65 presentations at the 2014 AOSSM Annual Meeting, 72 in 2015, and 55 in 2016. Overall, 28 AOSSM presentations (15%) were also presented at an AANA Annual Meeting, including 9 (14%) from the 2014 AOSSM meeting, 15 (21%) from the 2015 meeting, and 4 (7%) from the 2016 meeting. Of the 28 duplicate presentations, authors often altered their abstracts in several ways, including changing the abstract title (14; 50%), changing the author order (17; 61%), and adding or removing authors (10; 36%). Duplication rates were not significantly different between the years (P = .10). A moderate proportion of abstracts presented at the AOSSM and AANA Annual Meetings are duplicates. Meeting committees may want to consider stricter guidelines to ensure only original work is presented at these meetings.

  12. Internal duplication in human alpha 1 and beta 1 interferons.

    PubMed Central

    Erickson, B W; May, L T; Sehgal, P B

    1984-01-01

    Metric analysis of the nucleotide sequence of the intron-free human interferon beta 1 (IFN-beta 1) gene by using the Sellers TT algorithm revealed that this gene contains two major repeated segments, which span the entire coding region. These repeats are each approximately 300 nucleotides in length and have 45% identical aligned nucleotides (common bases). When these metrically aligned DNA repeats were translated into amino acids, 9 (19%) of the 47 in-phase amino acid residues were identical (common acids). This internal duplication was also apparent on visual inspection of the amino acid sequence of IFN-beta 1. In addition, metric analysis of the nucleotide sequence of the intron-free IFN-alpha 1 gene showed that this gene also contains two repeats, each approximately 300 nucleotides long, having 47% common bases and 19% common acids. Since the IFN-alpha 1 and -beta 1 genes are known to be related (by the present metric analysis they contain 53% common bases and 45% common acids), a consensus DNA sequence was derived from all four of these repeats. Manual alignment of the separate metric alignments corresponding to the two halves of the IFN-alpha 1 and -beta 1 genes provided a composite alignment with 58% of the alignment positions having the same nucleotide in at least three of the four repeats. When this composite nucleotide alignment was translated to define a composite alignment of the four protein segments, 10 (31%) of the 32 in-phase amino acid residues contained the same amino acid in at least three of the four segments. These sequences relationships provide insight into the origin of the IFN-alpha 1 and -beta 1 genes and furnish an additional basis for comparing them with other related genes. PMID:6594689

  13. A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep

    PubMed Central

    Norris, Belinda J.; Whan, Vicki A.

    2008-01-01

    Agouti signaling protein (ASIP) functions to regulate pigmentation in mice, while its role in many other animals and in humans has not been fully determined. In this study, we identify a 190-kb tandem duplication encompassing the ovine ASIP and AHCY coding regions and the ITCH promoter region as the genetic cause of white coat color of dominant white/tan (AWt) agouti sheep. The duplication 5′ breakpoint is located upstream of the ASIP coding sequence. Ubiquitous expression of a second copy of the ASIP coding sequence regulated by a duplicated copy of the nearby ITCH promoter causes the white sheep phenotype. A single copy ASIP gene with a silenced ASIP promoter occurs in recessive black sheep. In contrast, a single copy functional wild-type (A+) ASIP is responsible for the ancient Barbary sheep coat color phenotype. The gene duplication was facilitated by homologous recombination between two non-LTR SINE sequences flanking the duplicated segment. This is the first sheep trait attributable to gene duplication and shows nonallelic homologous recombination and gene conversion events at the ovine ASIP locus could have an important role in the evolution of sheep pigmentation. PMID:18493018

  14. Analyzing Orientations

    NASA Astrophysics Data System (ADS)

    Ruggles, Clive L. N.

    Archaeoastronomical field survey typically involves the measurement of structural orientations (i.e., orientations along and between built structures) in relation to the visible landscape and particularly the surrounding horizon. This chapter focuses on the process of analyzing the astronomical potential of oriented structures, whether in the field or as a desktop appraisal, with the aim of establishing the archaeoastronomical "facts". It does not address questions of data selection (see instead Chap. 25, "Best Practice for Evaluating the Astronomical Significance of Archaeological Sites", 10.1007/978-1-4614-6141-8_25) or interpretation (see Chap. 24, "Nature and Analysis of Material Evidence Relevant to Archaeoastronomy", 10.1007/978-1-4614-6141-8_22). The main necessity is to determine the azimuth, horizon altitude, and declination in the direction "indicated" by any structural orientation. Normally, there are a range of possibilities, reflecting the various errors and uncertainties in estimating the intended (or, at least, the constructed) orientation, and in more formal approaches an attempt is made to assign a probability distribution extending over a spread of declinations. These probability distributions can then be cumulated in order to visualize and analyze the combined data from several orientations, so as to identify any consistent astronomical associations that can then be correlated with the declinations of particular astronomical objects or phenomena at any era in the past. The whole process raises various procedural and methodological issues and does not proceed in isolation from the consideration of corroborative data, which is essential in order to develop viable cultural interpretations.

  15. Characterization of duplicated Dunaliella viridis SPT1 genes provides insights into early gene divergence after duplication.

    PubMed

    Guan, Zhenwei; Meng, Xiangzong; Sun, Zhenhua; Xu, Zhengkai; Song, Rentao

    2008-10-15

    The sodium-dependent phosphate transporter gene from unicellular green algae Dunaliella viridis, DvSPT1, shares similarity with members of Pi transporter family. Sequencing analysis of D. viridis BAC clone containing the DvSPT1 gene revealed two inverted duplicated copies of this gene (DvSPT1 and DvSPT1-2 respectively). The duplication covered most of both genes except for their 3' downstream region. The duplicated genomic sequences exhibited 97.9% identity with a synonymous divergence of Ks=0.0126 in the coding region. This data indicated very recent gene duplication in D. viridis genome, providing an excellent opportunity to investigate sequence and expression divergence of duplicated genes at an early stage. Scattered point mutations and length polymorphism of simple sequence repeats (SSRs) were predominant among the sequence divergence soon after gene duplication. Due to sequence divergence in the 5' regulatory regions and a swap of the entire 3' downstream regions (3'-UTR), DvSPT1 and DvSPT1-2 showed expression divergence in response to extra-cellular NaCl concentration changes. According to their expression patterns, the two diverged gene copies would provide better adaptation to a broader range of extra-cellular NaCl concentration. Furthermore, Southern blot analysis indicated that there might be a large phosphate transporter gene family in D. viridis.

  16. Differential retention and divergent resolution of duplicate genes following whole-genome duplication

    PubMed Central

    McGrath, Casey L.; Gout, Jean-Francois; Johri, Parul; Doak, Thomas G.

    2014-01-01

    The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are presented and compared to the published sequence of P. tetraurelia. Levels of duplicate-gene retention from the recent WGD differ by >10% across species, with P. sexaurelia losing significantly more genes than P. biaurelia or P. tetraurelia. In addition, historically high rates of gene conversion have homogenized WGD paralogs, probably extending the paralogs’ lifetimes. The probability of duplicate retention is positively correlated with GC content and expression level; ribosomal proteins, transcription factors, and intracellular signaling proteins are overrepresented among maintained duplicates. Finally, multiple sources of evidence indicate that P. sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species. Additionally, though P. biaurelia and P. tetraurelia diverged from each other much later, there are still more than 100 cases of divergent resolution between these two species. Taken together, these results indicate that divergent resolution of duplicate genes between lineages acts to reinforce reproductive isolation between species in the Paramecium aurelia complex. PMID:25085612

  17. Use of a Trellis Device for Endovascular Treatment of Venous Thrombosis Involving a Duplicated Inferior Vena Cava

    SciTech Connect

    Saettele, Megan R.; Morelli, John N.; Chesis, Paul; Wible, Brandt C.

    2013-12-15

    Congenital anomalies of the inferior vena cava (IVC) are increasingly recognized with CT and venography techniques. Although many patients with IVC anomalies are asymptomatic, recent studies have suggested an association with venous thromboembolism. We report the case of a 62-year-old woman with extensive venous clot involving the infrarenal segment of a duplicated left IVC who underwent pharmacomechanical thrombectomy and tissue plasminogen activator catheter-directed thrombolysis with complete deep venous thrombosis resolution. To our knowledge this is the first reported case in the English literature of the use of a Trellis thrombectomy catheter in the setting of duplicated IVC.

  18. Speech analyzer

    NASA Technical Reports Server (NTRS)

    Lokerson, D. C. (Inventor)

    1977-01-01

    A speech signal is analyzed by applying the signal to formant filters which derive first, second and third signals respectively representing the frequency of the speech waveform in the first, second and third formants. A first pulse train having approximately a pulse rate representing the average frequency of the first formant is derived; second and third pulse trains having pulse rates respectively representing zero crossings of the second and third formants are derived. The first formant pulse train is derived by establishing N signal level bands, where N is an integer at least equal to two. Adjacent ones of the signal bands have common boundaries, each of which is a predetermined percentage of the peak level of a complete cycle of the speech waveform.

  19. Optical analyzer

    DOEpatents

    Hansen, A.D.

    1987-09-28

    An optical analyzer wherein a sample of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter is placed in a combustion tube, and light from a light source is passed through the sample. The temperature of the sample is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample is detected as the temperature is raised. A data processor, differentiator and a two pen recorder provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample. These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample. Additional information is obtained by repeating the run in different atmospheres and/or different rates or heating with other samples of the same particulate material collected on other filters. 7 figs.

  20. Gene Duplication and Multiplicity of Collagenases in Clostridium histolyticum

    PubMed Central

    Matsushita, Osamu; Jung, Chang-Min; Katayama, Seiichi; Minami, Junzaburo; Takahashi, Yukie; Okabe, Akinobu

    1999-01-01

    Clostridium histolyticum collagenase contains a number of different active components. Previously we have shown that colH encodes a 116-kDa collagenase (ColH) and a 98-kDa gelatinase. We purified a different 116-kDa collagenase (ColG) from the culture supernatant and sequenced its gene (colG). We also identified four other gelatinases (105, 82, 78, and 67 kDa) and determined their N-terminal amino acid sequences, all of which coincided with that of either ColG or ColH. Hybridization experiments showed that each gene is present in a single copy and each gene is transcribed into a single mRNA. These results suggest that all the gelatinases are produced from the respective full-length collagenase by the proteolytic removal of C-terminal fragments. The substrate specificities of the enzymes suggest that colG and colH encode class I and class II enzymes, respectively. Analysis of their DNA locations by pulsed-field gel electrophoresis and nucleotide sequencing of their surrounding regions revealed that the two genes are located in different sites on the chromosome. C. histolyticum colG is more similar to C. perfringens colA than to colH in terms of domain structure. Both colG and colA have a homologous gene, mscL, at their 3′ ends. These results suggest that gene duplication and segment duplication have occurred in an ancestor cell common to C. histolyticum and C. perfringens and that further divergence of the parent gene produced colG and colA. PMID:9922257

  1. Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

    PubMed

    Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

  2. Dissecting the structure and mechanism of a complex duplication-triplication rearrangement in the DMD gene.

    PubMed

    Ishmukhametova, Aliya; Chen, Jian-Min; Bernard, Rafaëlle; de Massy, Bernard; Baudat, Frédéric; Boyer, Amandine; Méchin, Déborah; Thorel, Delphine; Chabrol, Brigitte; Vincent, Marie-Claire; Khau Van Kien, Philippe; Claustres, Mireille; Tuffery-Giraud, Sylvie

    2013-08-01

    Pathogenic complex genomic rearrangements are being increasingly characterized at the nucleotide level, providing unprecedented opportunities to evaluate the complexities of mutational mechanisms. Here, we report the molecular characterization of a complex duplication-triplication rearrangement involving exons 45-60 of the DMD gene. Inverted repeats facilitated this complex rearrangement, which shares common genomic organization with the recently described duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) events; specifically, a 690-kb region comprising DMD exons from 45 to 60 was duplicated in tandem, and another 46-kb segment containing exon 51 was inserted inversely in between them. Taking into consideration (1) the presence of a predicted PRDM9 binding site in the near vicinity of the junction involving two inverted L1 elements and (2) the inherent properties of X-Y chromosome recombination during male meiosis, we proposed an alternative two-step model for the generation of this X-linked DMD DUP-TRP/INV-DUP event.

  3. Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling

    PubMed Central

    Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development. PMID:25745864

  4. A Meiotic Uv-Sensitive Mutant That Causes Deletion of Duplications in Neurospora

    PubMed Central

    Newmeyer, Dorothy; Galeazzi, Donna R.

    1978-01-01

    The meiotic-3 (mei-3) mutant of Neurospora crassa has several effects: (1) When homozygous, it almost completely blocks meiosis and ascospore formation, (2) it is sensitive to UV, (3) its growth is inhibited by histidine and, (4) it increases the instability of nontandem duplications. This was shown for duplications produced by five different rearrangements and was demonstrated by two different criteria. The effects on meiosis and duplication instability are expressed strongly at 25°; the effects on sensitivity to UV and to histidine are expressed strongly at 38.5° but only slightly at 25°. Nevertheless, all four effects were shown to be due to a single gene. mei-3 is not allelic with previously reported UV-sensitive mutants.—Two other results were obtained that are not necessarily due to mei-3: (1) A cross involving mei-3 produced a new unlinked meiotic mutant, mei-4, which is not sensitive to UV or histidine, and (2) a burst of several new mutants occurred in a different mei-3 stock, including a partial revertant of mei-3.—mei-3 has previously been shown to cause frequent complete loss of a terminal duplicate segment, beginning exactly at the original rearrangement breakpoint. Possible mechanisms are discussed by which a UV-sensitive mutant could cause such precise deletions. PMID:17248837

  5. DUPLICATE OF THE HISTORIC VIEW SHOWING HOW THE SOUTHEAST (FRONT) ...

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

    DUPLICATE OF THE HISTORIC VIEW SHOWING HOW THE SOUTHEAST (FRONT) WALL AFTER THE 1862 BATTLE LOOKS IN 1998 (DUPLICATE OF HABS No. GA-2158-54) - Fort Pulaski, Cockspur Island, Savannah, Chatham County, GA

  6. Duplication cysts: Diagnosis, management, and the role of endoscopic ultrasound.

    PubMed

    Liu, Roy; Adler, Douglas G

    2014-07-01

    Gastrointestinal tract duplication cysts are rare congenital gastrointestinal malformation in young patients and adults. They consist of foregut duplication cysts, small bowel duplication cysts, and large bowel duplication cysts. Endoscopic ultrasound (EUS) has been widely used as a modality for the evaluation and diagnosis of duplication cysts. EUS is the diagnostic tool of choice to investigate duplication cysts since it can distinguish between solid and cystic lesions. The question of whether or not to perform EUS-fine needle aspiration (EUS-FNA) on a lesion suspected of being a duplication cyst is controversial as these lesions can become infected with significant consequences, although EUS-FNA is often required to obtain a definitive diagnosis and to rule out more ominous lesions. This manuscript will review the literature on duplication cysts throughout the body and will also focus on the role of EUS and FNA with regards to these lesions.

  7. Robust vessel segmentation

    NASA Astrophysics Data System (ADS)

    Bock, Susanne; Kühnel, Caroline; Boskamp, Tobias; Peitgen, Heinz-Otto

    2008-03-01

    In the context of cardiac applications, the primary goal of coronary vessel analysis often consists in supporting the diagnosis of vessel wall anomalies, such as coronary plaque and stenosis. Therefore, a fast and robust segmentation of the coronary tree is a very important but challenging task. We propose a new approach for coronary artery segmentation. Our method is based on an earlier proposed progressive region growing. A new growth front monitoring technique controls the segmentation and corrects local leakage by retrospective detection and removal of leakage artifacts. While progressively reducing the region growing threshold for the whole image, the growing process is locally analyzed using criteria based on the assumption of tubular, gradually narrowing vessels. If a voxel volume limit or a certain shape constraint is exceeded, the growing process is interrupted. Voxels affected by a failed segmentation are detected and deleted from the result. To avoid further processing at these positions, a large neighborhood is blocked for growing. Compared to a global region growing without local correction, our new local growth control and the adapted correction can deal with contrast decrease even in very small coronary arteries. Furthermore, our algorithm can efficiently handle noise artifacts and partial volume effects near the myocardium. The enhanced segmentation of more distal vessel parts was tested on 150 CT datasets. Furthermore, a comparison between the pure progressive region growing and our new approach was conducted.

  8. The human VK locus. Characterization of a duplicated region encoding 28 different immunoglobulin genes.

    PubMed

    Straubinger, B; Huber, E; Lorenz, W; Osterholzer, E; Pargent, W; Pech, M; Pohlenz, H D; Zimmer, F J; Zachau, H G

    1988-01-05

    Two large regions of the human multigene family coding for the variable parts of the immunoglobulin light chains of the K type (VK) have been characterized on cosmid clones. The two germline regions, called Aa and Ab, span together 250,000 base-pairs and comprise 28 different VK gene segments, nine of which have been sequenced. There is a preponderance of VKII genes but genes belonging to subgroups I and III, and genes that cannot be easily assigned to one of the known subgroups, are interspersed within the VKII gene clusters. A number of pseudogenes have been identified. Within the Aa and Ab regions, all gene segments are organized in the same transcriptional orientation. The regions Aa and Ab, whose restriction maps are highly homologous, were shown not to be allelic structures; they must have arisen by a duplication event. Taken together with previous results, one can conclude that the major part of the VK locus exists in duplicated form. One individual has been found who has only one copy of some of the duplicated regions. By chromosomal walking, the A regions could be linked to the O regions, an analysis of which has been reported. The A regions contribute about one-third of the VK genes so far identified.

  9. The role of human-specific gene duplications during brain development and evolution.

    PubMed

    Sassa, Takayuki

    2013-09-01

    One of the most fascinating questions in evolutionary biology is how traits unique to humans, such as their high cognitive abilities, erect bipedalism, and hairless skin, are encoded in the genome. Recent advances in genomics have begun to reveal differences between the genomes of the great apes. It has become evident that one of the many mutation types, segmental duplication, has drastically increased in the primate genomes, and most remarkably in the human genome. Genes contained in these segmental duplications have a tremendous potential to cause genetic innovation, probably accounting for the acquisition of human-specific traits. In this review, I begin with an overview of the genes, which have increased their copy number specifically in the human lineage, following its separation from the common ancestor with our closest living relative, the chimpanzee. Then, I introduce the recent experimental approaches, focusing on SRGAP2, which has been partially duplicated, to elucidate the role of SRGAP2 protein and its human-specific paralogs in human brain development and evolution.

  10. Dietary intakes of pesticides based on community duplicate diet samples.

    PubMed

    Melnyk, Lisa Jo; Xue, Jianping; Brown, G Gordon; McCombs, Michelle; Nishioka, Marcia; Michael, Larry C

    2014-01-15

    The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from which intake assessments of organophosphate (OP) and pyrethroid pesticides were made. From these nine participants, sixty-seven individual samples were collected and subsequently analyzed by gas chromatography/mass spectrometry. Measured concentrations were used to estimate dietary intakes for individuals and for the community. Individual intakes of total OP and pyrethroid pesticides ranged from 6.7 to 996 ng and 1.2 to 16,000 ng, respectively. The community intake was 256 ng for OPs and 3430 ng for pyrethroid pesticides. The most commonly detected pesticide was permethrin, but the highest overall intake was of bifenthrin followed by esfenvalerate. These data indicate that the community in Apopka, FL, as represented by the nine individuals, was potentially exposed to both OP and pyrethroid pesticides at levels consistent with a dietary model and other field studies in which standard duplicate diet samples were collected. Higher levels of pyrethroid pesticides were measured than OPs, which is consistent with decreased usage of OPs. The diversity of pyrethroid pesticides detected in food samples was greater than expected. Continually changing pesticide usage patterns need to be considered when determining analytes of interest for large scale epidemiology studies. The Community Duplicate Diet Methodology is a tool for researchers to meet emerging exposure measurement needs that will lead to more accurate assessments of intake which may enhance decisions for chemical regulation. Successfully determining the intake of pesticides through the dietary route will allow for accurate assessments of pesticide exposures to a community of individuals, thereby significantly enhancing the research benefit

  11. Inherited partial direct duplication of 11q: First report and possible association with a midline developmental field defect

    SciTech Connect

    Witt, D.R.; Jenkins, L.; Pinheiro, S.

    1994-09-01

    A 36-year-old woman underwent amniocentesis for advanced maternal age. The fetal karyotype had an extra dark staining G band on the long arm of chromosome 11 with no other identifiable abnormalities. FISH studies using a chromosome 11 paint probe confirmed the origin of the extra band. The abnormality was identified as a partial duplication of 11q: 46,XX dir dup (11)(q13.5q21) or (q21q23.1). The specific duplicated band could not be identified with certainty. Detailed fetal sonograms were normal. Family studies revealed the identical duplication in the mother but normal karyotypes in both maternal grandparents. The mother had strabismus and a short tongue frenulum which required surgical correction. Menses occurred late in adolescence and complete development of secondary sexual characteristics was delayed until adulthood. An infertility evaluation revealed duplication of the uterus, cervix, and vagina. An evaluation for metorrhagia identified a pituitary adenoma which was resected. Her intelligence was normal. To our knowledge this is the first report of a heritable direct duplication of 11q. It is possible that one or more gene in the duplicated segment played a causal role in the pathophysiology of the patient`s anomalies through a disturbance of the so-called {open_quotes}midline developmental field{close_quotes}. Alternatively, the cytogenetic findings could be unrelated to the malformations. Rare instances of partial gain or loss of specific late-replicating heterochromatic regions without phenotypic effect have been reported. This region of 11q is also relatively late-replicating. This is consistent with previous reports suggesting a paucity of expressed genes in this 11q region. Molecular studies of the duplication are underway to determine the specific location and extent of duplication. Phenotypic evaluation of the patient`s baby will also be reported.

  12. Optical analyzer

    DOEpatents

    Hansen, Anthony D.

    1989-01-01

    An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

  13. Optical analyzer

    DOEpatents

    Hansen, Anthony D.

    1989-02-07

    An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

  14. 48 CFR 1352.231-71 - Duplication of effort.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Duplication of effort. 1352.231-71 Section 1352.231-71 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE CLAUSES... Duplication of effort. As prescribed in 48 CFR 1331.205-70, insert the following clause: Duplication of...

  15. 47 CFR 76.1508 - Network non-duplication.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Network non-duplication. 76.1508 Section 76... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Open Video Systems § 76.1508 Network non-duplication. (a... regarding the exercise of network non-duplication rights immediately available to all appropriate video...

  16. 47 CFR 76.122 - Satellite network non-duplication.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Satellite network non-duplication. 76.122... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.122 Satellite network non-duplication. (a) Upon receiving notification pursuant to...

  17. 47 CFR 76.1508 - Network non-duplication.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Network non-duplication. 76.1508 Section 76... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Open Video Systems § 76.1508 Network non-duplication. (a... regarding the exercise of network non-duplication rights immediately available to all appropriate video...

  18. 47 CFR 76.122 - Satellite network non-duplication.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Satellite network non-duplication. 76.122... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.122 Satellite network non-duplication. (a) Upon receiving notification pursuant to...

  19. 47 CFR 76.122 - Satellite network non-duplication.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Satellite network non-duplication. 76.122... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.122 Satellite network non-duplication. (a) Upon receiving notification pursuant to...

  20. 47 CFR 76.1508 - Network non-duplication.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Network non-duplication. 76.1508 Section 76... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Open Video Systems § 76.1508 Network non-duplication. (a... regarding the exercise of network non-duplication rights immediately available to all appropriate video...

  1. 47 CFR 76.122 - Satellite network non-duplication.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Satellite network non-duplication. 76.122... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.122 Satellite network non-duplication. (a) Upon receiving notification pursuant to...

  2. 47 CFR 76.1508 - Network non-duplication.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Network non-duplication. 76.1508 Section 76... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Open Video Systems § 76.1508 Network non-duplication. (a... regarding the exercise of network non-duplication rights immediately available to all appropriate video...

  3. 47 CFR 76.1508 - Network non-duplication.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Network non-duplication. 76.1508 Section 76... MULTICHANNEL VIDEO AND CABLE TELEVISION SERVICE Open Video Systems § 76.1508 Network non-duplication. (a... regarding the exercise of network non-duplication rights immediately available to all appropriate video...

  4. 44 CFR 204.62 - Duplication and recovery of assistance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Duplication and recovery of assistance. 204.62 Section 204.62 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY... Administration § 204.62 Duplication and recovery of assistance. (a) Duplication of benefits. We...

  5. Case report: Antenatal MRI diagnosis of esophageal duplication cyst.

    PubMed

    Rangasami, Rajeswaran; Chandrasekharan, Anupama; Archana, Lal; Santhosh, Joseph

    2009-02-01

    Esophageal duplication cysts are classified as a subgroup of foregut duplication cysts. They are very rare and are predominantly detected in children. Antenatal detection is very rare. We report a case of an esophageal duplication cyst that was accurately identified antenatally by USG and MRI.

  6. Complete tracheal duplication with unilateral atelectasis in an adult.

    PubMed

    Chihaya, Keisuke; Yamashiro, Tsuneo; Matsuoka, Shin; Nobuyama, Seiichi; Handa, Hiroshi; Inoue, Takeo; Kida, Hirotaka; Kurimoto, Noriaki; Matsushita, Shoichiro; Fujikawa, Atsuko; Kurihara, Yasuyuki; Mineshita, Masamichi; Miyazawa, Teruomi; Nakajima, Yasuo

    2014-01-01

    Duplication of the trachea is an extremely rare condition that has been infrequently reported in the medical literature. We report an adult case with complete tracheal duplication associated with unilateral atelectasis, which was incidentally detected by computed tomography. Tracheal duplication should be considered as a possible cause of severe atelectasis in adults.

  7. 38 CFR 10.52 - Duplication of payments prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Duplication of payments prohibited. 10.52 Section 10.52 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS ADJUSTED COMPENSATION Payments § 10.52 Duplication of payments prohibited. Duplication of payments...

  8. 47 CFR 80.467 - Duplication of VHF service.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Duplication of VHF service. 80.467 Section 80... STATIONS IN THE MARITIME SERVICES Public Coast Stations Use of Telephony § 80.467 Duplication of VHF service. No duplication of service areas as determined by subpart P of this part will be permitted...

  9. 14. Interior of Original Grandstand. East segment of 'Main Line' ...

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

    14. Interior of Original Grandstand. East segment of 'Main Line' betting room. Camera pointed S. (HABS negative is a duplicate negative made from original in the collection of John Stamets, Seattle, WA.) (Sept. 1992) - Longacres, Original Grandstand, 1621 Southwest Sixteenth Street, Renton, King County, WA

  10. 17. Interior of Original Grandstand. West segment and betting windows ...

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

    17. Interior of Original Grandstand. West segment and betting windows on the 'Main Line.' (HABS negative is a duplicate negative made from original in the collection of John Stamets, Seattle, WA.) (Sept. 1992) - Longacres, Original Grandstand, 1621 Southwest Sixteenth Street, Renton, King County, WA

  11. 16. Interior of Original Grandstand. Middle segment of 'Main Line' ...

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

    16. Interior of Original Grandstand. Middle segment of 'Main Line' betting room. Camera pointed S. (HABS negative is a duplicate negative made from original in the collection of John Stamets, Seattle, WA.) (Sept. 1992) - Longacres, Original Grandstand, 1621 Southwest Sixteenth Street, Renton, King County, WA

  12. ABSORPTION ANALYZER

    DOEpatents

    Brooksbank, W.A. Jr.; Leddicotte, G.W.; Strain, J.E.; Hendon, H.H. Jr.

    1961-11-14

    A means was developed for continuously computing and indicating the isotopic assay of a process solution and for automatically controlling the process output of isotope separation equipment to provide a continuous output of the desired isotopic ratio. A counter tube is surrounded with a sample to be analyzed so that the tube is exactly in the center of the sample. A source of fast neutrons is provided and is spaced from the sample. The neutrons from the source are thermalized by causing them to pass through a neutron moderator, and the neutrons are allowed to diffuse radially through the sample to actuate the counter. A reference counter in a known sample of pure solvent is also actuated by the thermal neutrons from the neutron source. The number of neutrons which actuate the detectors is a function of a concentration of the elements in solution and their neutron absorption cross sections. The pulses produced by the detectors responsive to each neu tron passing therethrough are amplified and counted. The respective times required to accumulate a selected number of counts are measured by associated timing devices. The concentration of a particular element in solution may be determined by utilizing the following relation: T2/Ti = BCR, where B is a constant proportional to the absorption cross sections, T2 is the time of count collection for the unknown solution, Ti is the time of count collection for the pure solvent, R is the isotopic ratlo, and C is the molar concentration of the element to be determined. Knowing the slope constant B for any element and when the chemical concentration is known, the isotopic concentration may be readily determined, and conversely when the isotopic ratio is known, the chemical concentrations may be determined. (AEC)

  13. Evolution by leaps: gene duplication in bacteria

    PubMed Central

    2009-01-01

    Background Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Results Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes. Conclusions Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria. Reviewers This article was reviewed by Drs. Iyer Aravind, Ardcady Mushegian, and Pierre Pontarotti. PMID:19930658

  14. Pseudomyxoma peritonei originating from an intestinal duplication.

    PubMed

    Lemahieu, Julie; D'Hoore, André; Deloose, Stijn; Sciot, Raf; Moerman, Philippe

    2013-01-01

    Alimentary tract duplications are rare congenital anomalies. They most often become symptomatic in childhood and rarely undergo malignant transformation. Pseudomyxoma peritonei (PMP) is an equally uncommon condition, most frequently originating from a primary appendiceal mucinous neoplasm. We report an extremely unusual case of PMP arising from an intestinal duplication. A 67-year-old woman presented with vague upper abdominal pain, and, unexpectedly, explorative laparoscopy revealed diffuse jelly-like peritoneal implants. The histopathological diagnosis of a low-grade PMP or "disseminated peritoneal adenomucinosis" was made. At that moment, no primary tumor was found. During later surgery, a cystic lesion located in the mesentery of the small bowel could be resected. Histologically, the cyst wall clearly showed the concentric layering of a normal bowel wall. The mucosa, however, displayed a diffuse low-grade villous adenoma. We concluded that this histological picture was most consistent with a small intestinal duplication, containing a low-grade villous adenoma. The adenoma caused a mucocele, which subsequently leaked or ruptured, giving rise to noninvasive mucinous peritoneal implants or low-grade PMP, also known as "disseminated peritoneal adenomucinosis" (DPAM).

  15. Pseudomyxoma Peritonei Originating from an Intestinal Duplication

    PubMed Central

    Lemahieu, Julie; D'Hoore, André; Deloose, Stijn; Sciot, Raf; Moerman, Philippe

    2013-01-01

    Alimentary tract duplications are rare congenital anomalies. They most often become symptomatic in childhood and rarely undergo malignant transformation. Pseudomyxoma peritonei (PMP) is an equally uncommon condition, most frequently originating from a primary appendiceal mucinous neoplasm. We report an extremely unusual case of PMP arising from an intestinal duplication. A 67-year-old woman presented with vague upper abdominal pain, and, unexpectedly, explorative laparoscopy revealed diffuse jelly-like peritoneal implants. The histopathological diagnosis of a low-grade PMP or “disseminated peritoneal adenomucinosis” was made. At that moment, no primary tumor was found. During later surgery, a cystic lesion located in the mesentery of the small bowel could be resected. Histologically, the cyst wall clearly showed the concentric layering of a normal bowel wall. The mucosa, however, displayed a diffuse low-grade villous adenoma. We concluded that this histological picture was most consistent with a small intestinal duplication, containing a low-grade villous adenoma. The adenoma caused a mucocele, which subsequently leaked or ruptured, giving rise to noninvasive mucinous peritoneal implants or low-grade PMP, also known as “disseminated peritoneal adenomucinosis” (DPAM). PMID:24024058

  16. Tubular duplication of the oesophagus presenting with dysphagia.

    PubMed

    Saha, A K; Kundu, A K

    2014-06-01

    Duplications of the alimentary tract are rare congenital malformations, with the ileum being the most commonly affected site, followed by the oesophagus. Among oesophageal duplications, cystic duplication is the most common and the tubular variety, the rarest. Herein, we report a rare case of tubular oesophageal duplication, complicated by adenosquamous carcinoma at the lower end of the oesophagus, in a 32-year-old man who presented with progressive dysphagia. Although proton pump inhibitors may relieve dysphagia, oesophagectomy and gastric interpositioning should be the first-line treatment for patients with tubular oesophageal duplication, in order to reduce the risk of malignant transformation at the lower end of the oesophagus.

  17. Surgical management of complete penile duplication accompanied by multiple anomalies

    PubMed Central

    Karaca, Irfan; Turk, Erdal; Ucan, A. Basak; Yayla, Derya; Itirli, Gulcin; Ercal, Derya

    2014-01-01

    Diphallus (penile duplication) is very rare and seen once every 5.5 million births. It can be isolated, but is usually accompanied by other congenital anomalies. Previous studies have reported many concurrent anomalies, such as bladder extrophy, cloacal extrophy, duplicated bladder, scrotal abnormalities, hypospadias, separated symphysis pubis, intestinal anomalies and imperforate anus; no penile duplication case accompanied by omphalocele has been reported. We present the surgical management of a patient with multiple anomalies, including complete penile duplication, hypo-gastric omphalocele and extrophic rectal duplication. PMID:25408817

  18. Gastric Duplication Cyst Presenting as Acute Abdomen: A Case Report

    PubMed Central

    Sheikh, Afzal

    2010-01-01

    Gastric duplication cysts are rare variety of gastrointestinal duplications. Sometimes they may present with complications like hemorrhage, infection, perforation, volvulus, intussusception and rarely neoplastic changes in the gastric duplication cyst. We present one and half year old male child who developed sudden abdominal distension with pain and fever for two days. Ultrasound revealed a cystic mass in the hypochondrium and epigastric regions. On exploration an infected and perforated gastric duplication cyst was found. Surgical excision of most part of cyst wall with mucosal stripping of the rest was performed. Histopathology confirmed the diagnosis of gastric duplication cyst. Early surgical intervention can result in good outcome. PMID:22953249

  19. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

    PubMed

    Schwager, Evelyn E; Sharma, Prashant P; Clarke, Thomas; Leite, Daniel J; Wierschin, Torsten; Pechmann, Matthias; Akiyama-Oda, Yasuko; Esposito, Lauren; Bechsgaard, Jesper; Bilde, Trine; Buffry, Alexandra D; Chao, Hsu; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dugan, Shannon; Eibner, Cornelius; Extavour, Cassandra G; Funch, Peter; Garb, Jessica; Gonzalez, Luis B; Gonzalez, Vanessa L; Griffiths-Jones, Sam; Han, Yi; Hayashi, Cheryl; Hilbrant, Maarten; Hughes, Daniel S T; Janssen, Ralf; Lee, Sandra L; Maeso, Ignacio; Murali, Shwetha C; Muzny, Donna M; Nunes da Fonseca, Rodrigo; Paese, Christian L B; Qu, Jiaxin; Ronshaugen, Matthew; Schomburg, Christoph; Schönauer, Anna; Stollewerk, Angelika; Torres-Oliva, Montserrat; Turetzek, Natascha; Vanthournout, Bram; Werren, John H; Wolff, Carsten; Worley, Kim C; Bucher, Gregor; Gibbs, Richard A; Coddington, Jonathan; Oda, Hiroki; Stanke, Mario; Ayoub, Nadia A; Prpic, Nikola-Michael; Flot, Jean-François; Posnien, Nico; Richards, Stephen; McGregor, Alistair P

    2017-07-31

    The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

  20. Opposing Brain Differences in 16p11.2 Deletion and Duplication Carriers

    PubMed Central

    Qureshi, Abid Y.; Mueller, Sophia; Snyder, Abraham Z.; Mukherjee, Pratik; Berman, Jeffrey I.; Roberts, Timothy P.L.; Nagarajan, Srikantan S.; Spiro, John E.; Chung, Wendy K.; Sherr, Elliott H.

    2014-01-01

    Deletions and duplications of the recurrent ∼600 kb chromosomal BP4–BP5 region of 16p11.2 are associated with a broad variety of neurodevelopmental outcomes including autism spectrum disorder. A clue to the pathogenesis of the copy number variant (CNV)'s effect on the brain is that the deletion is associated with a head size increase, whereas the duplication is associated with a decrease. Here we analyzed brain structure in a clinically ascertained group of human deletion (N = 25) and duplication (N = 17) carriers from the Simons Variation in Individuals Project compared with age-matched controls (N = 29 and 33, respectively). Multiple brain measures showed increased size in deletion carriers and reduced size in duplication carriers. The effects spanned global measures of intracranial volume, brain size, compartmental measures of gray matter and white matter, subcortical structures, and the cerebellum. Quantitatively, the largest effect was on the thalamus, but the collective results suggest a pervasive rather than a selective effect on the brain. Detailed analysis of cortical gray matter revealed that cortical surface area displays a strong dose-dependent effect of CNV (deletion > control > duplication), whereas average cortical thickness is less affected. These results suggest that the CNV may exert its opposing influences through mechanisms that influence early stages of embryonic brain development. PMID:25143601

  1. Clinical and molecular evaluation of four patients with partial duplications of the long arm of chromosome 18.

    PubMed Central

    Mewar, R; Kline, A D; Harrison, W; Rojas, K; Greenberg, F; Overhauser, J

    1993-01-01

    Four individuals with partial duplications of the long arm of chromosome 18 were analyzed at the clinical, cytogenetic, and molecular levels. Two of the individuals had duplications of the long arm from 18q21.1-qter because of inheritance of an unbalanced translocation. Both of these individuals displayed the clinical phenotype characteristic of Edwards syndrome. Two other patients had de novo interstitial duplications of 18q but did not have a clinical diagnosis of Edwards syndrome. The extent of the duplicated material in each patient was determined initially by using cytogenetic analysis and subsequently with more detailed comparisons of the duplicated regions by using molecular probes derived from a chromosome 18-specific lambda phage library. The results demonstrated that one of the de novo interstitial duplications that did not result in the Edwards syndrome phenotype had a more proximal breakpoint than that of the partial duplications of the two patients with features of Edwards syndrome. These results suggest that a single critical region for Edwards syndrome in the proximal portion of 18q is unlikely. Images Figure 1 Figure 3 Figure 4 PMID:8250043

  2. Clinical and molecular evaluation of four patients with partial duplications of the long arm of chromosome 18

    SciTech Connect

    Mewar, R.; Kline, A.D.; Harrison, W.; Rojas, K.; Overhauser, J. ); Greenberg, F. )

    1993-12-01

    Four individuals with partial duplications of the long arm of chromosome 18 were analyzed at the clinical, cytogenetic, and molecular levels. Two of the individuals had duplications of the long arm from 18q21.1-qter because of inheritance of an unbalanced translocation. Both of these individuals displayed the clinical phenotype characteristic of Edwards syndrome. Two other patients had de novo interstitial duplications of 18q but did not have a clinical diagnosis of Edwards syndrome. The extent of the duplicated material in each patient was determined initially by using cytogenetic analysis and subsequently with more detailed comparisons of the duplicated regions by using molecular probes derived from a chromosome 18-specific lambda phage library. The results demonstrated that one of the de novo interstitial duplications that did not result in the Edwards syndrome phenotype had a more proximal breakpoint than that of the partial duplications of the two patients with features of Edwards syndrome. These results suggest that a single critical region for Edwards syndrome in the proximal portion of 18q is unlikely. 24 refs., 5 figs., 2 tabs.

  3. Tandem inversion duplication within F8 Intron 1 associated with mild haemophilia A.

    PubMed

    Lannoy, N; Bandelier, C; Grisart, B; Reginster, M; Ronge-Collard, E; Vikkula, M; Hermans, C

    2015-07-01

    In approximately 90% of mild haemophilia A (HA) patients, a missense mutation can be identified using complete gene sequencing. In this study, multiplex ligation-dependent probe amplification analysis was performed as a second step in 10 French-speaking Belgian with mild HA presenting no detectable causal mutation by complete sequencing of the factor VIII (FVIII) (F8) gene's 26 exons and its 1.2 kb of contiguous promoter sequence. This gene dosage technique enabled the detection of exon 1 duplications of F8 in three apparently unrelated subjects. Using array-comparative genomic hybridization, breakpoint analysis delimited the duplication extent to 210 kb in the F8 intron 1 and VBP1 gene intragenic position. We postulated that the rearrangement responsible for this duplication, never before reported, could be attributed to a symmetrical tandem inversion duplication, resulting in a large 233 kb rearrangement of F8 intron 1. This rearranged intron should lead to the production of a small number of normal mRNA transcripts in relation to the mild HA phenotype. Our analysis of the entire F8 mRNA from index case 1, particularly the segment containing exons 1-9, revealed normal amplification and sequencing. Reduced plasma FVIII antigen levels caused by cross-reacting material is associated with a quantitative deficiency of plasma FVIII. Male patients were unresponsive to desmopressin (1-deamino-8-D-arginine vasopressin). All patients displayed identical F8 haplotypes, despite not being related, which suggests a possible founder effect caused by a 210 kb duplication involving F8 exon 1.

  4. Divergent evolution of part of the involucrin gene in the hominoids: Unique intragenic duplications in the gorilla and human

    SciTech Connect

    Teumer, J.; Green, H. )

    1989-02-01

    The gene for involucrin, an epidermal protein, has been remodeled in the higher primates. Most of the coding region of the human gene consists of a modern segment of repeats derived from a 10-codon sequence present in the ancestral segment of the gene. The modern segment can be divided into early, middle, and late regions. The authors report here the nucleotide sequence of three alleles of the gorilla involucrin gene. Each possesses a modern segment homologous to that of the human and consisting of 10-codon repeats. The early and middle regions are similar to the corresponding regions of the human allele and are nearly identical among the different gorilla alleles. The late region consists of recent duplications whose pattern is unique in each of the gorilla alleles and in the human allele. The early region is located in what is now the 3{prime} third of the modern segment, and the late, polymorphic region is located in what is now the 5{prime} third. Therefore, as the modern segment expanded during evolution, its 3{prime} end became stabilized, and continuing duplications became confined to its 5{prime} end. The expansion of the involucrin coding region, which began long before the separation of the gorilla and human, has continued in both species after their separation.

  5. An atypical 0.8 Mb inherited duplication of 22q11.2 associated with psychomotor impairment.

    PubMed

    Pebrel-Richard, Céline; Kemeny, Stéphan; Gouas, Laetitia; Eymard-Pierre, Eléonore; Blanc, Nathalie; Francannet, Christine; Tchirkov, Andreï; Goumy, Carole; Vago, Philippe

    2012-11-01

    Microduplications 22q11.2 have been recently characterized as a new genomic duplication syndrome showing an extremely variable phenotype ranging from normal or mild learning disability to multiple congenital defects and sharing some overlapping features with DiGeorge/velocardiofacial syndrome (DGS/VCFS), including heart defects, urogenital abnormalities and velopharyngeal insufficiency. We present an atypical and inherited 0.8-Mb duplication at 22q11.2, in the distal segment of the DGS/VCFS syndrome typically deleted region (TDR), in a 3-year-old boy with motor delay, language disorders and mild facial phenotype. This 22q11.2 microduplication was identified by MLPA, designed to detect recurrent microdeletions and microduplications of chromosomal regions frequently involved in mental retardation syndromes and was further characterized by aCGH. The duplicated region encompasses 14 genes, excluding TBX1 but including CRKL, ZNF74, PIK4CA, SNAP29 and PCQAP known to contribute to several aspects of the DGS/VCFS phenotype. To the best of our knowledge, only one case of an isolated duplication in the distal segment of the TDR between chromosome 22-specific low-copy repeats B (LCR22-B) and D (LCR22-D) has been published, but the present report is the first one with a detailed description of physical and developmental features in a patient carrying this kind of atypical 22q11.2 duplication. This case illustrates the importance of reporting unusual 22q11.2 duplications to further evaluate the incidence of these rearrangements in the general population and to improve genotype-phenotype correlations and genetic counseling.

  6. Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies.

    PubMed

    Shen, Yue; Liu, Mingzhe; Wang, Lili; Li, Zhuowei; Taylor, David C; Li, Zhixi; Zhang, Meng

    2016-04-01

    Caleosins are a class of Ca(2+) binding proteins that appear to be ubiquitous in plants. Some of the main proteins embedded in the lipid monolayer of lipid droplets, caleosins, play critical roles in the degradation of storage lipids during germination and in lipid trafficking. Some of them have been shown to have histidine-dependent peroxygenase activity, which is believed to participate in stress responses in Arabidopsis. In the model plant Arabidopsis thaliana, caleosins have been examined extensively. However, little is known on a genome-wide scale about these proteins in other members of the Brassicaceae. In this study, 51 caleosins in Brassica plants and Arabidopsis lyrata were investigated and analyzed in silico. Among them, 31 caleosins, including 7 in A. lyrata, 11 in Brassica oleracea and 13 in Brassica napus, are herein identified for the first time. Segmental duplication was the main form of gene expansion. Alignment, motif and phylogenetic analyses showed that Brassica caleosins belong to either the H-family or the L-family with different motif structures and physicochemical properties. Our findings strongly suggest that L-caleosins are evolved from H-caleosins. Predicted phosphorylation sites were differentially conserved in H-caleosin and L-caleosins, respectively. 'RY-repeat' elements and phytohormone-related cis-elements were identified in different caleosins, which suggest diverse physiological functions. Gene structure analysis indicated that most caleosins (38 out of 44) contained six exons and five introns and their intron phases were highly conserved. Structurally integrated caleosins, such as BrCLO3-3 and BrCLO4-2, showed high expression levels and may have important roles. Some caleosins, such as BrCLO2 and BoCLO8-2, lost motifs of the calcium binding domain, proline knot, potential phosphorylation sites and haem-binding sites. Combined with their low expression, it is suggested that these caleosins may have lost function.

  7. Molecular mechanisms for CMT1A duplication and HNPP deletion.

    PubMed

    Boerkoel, C F; Inoue, K; Reiter, L T; Warner, L E; Lupski, J R

    1999-09-14

    As the best characterized human genomic disorders, CMT1A and HNPP illustrate several common mechanistic features of genomic rearrangements. These features include the following: (1) Recombination occurs between homologous sequences flanking the duplicated/deleted genomic segment. (2) The evolution of the mammalian genome may result in an architecture consisting of region-specific low-copy repeats that predispose to rearrangement secondary to providing homologous regions as substrate for recombination. (3) Strand exchange occurs preferentially in a region of perfect sequence identity within the flanking repeat sequences. (4) Double-strand breaks likely initiate recombination between the flanking repeats. (5) The mechanism and rate of homologous recombination resulting in DNA rearrangement may differ for male and female gametogenesis. (6) Homologous recombination resulting in DNA rearrangement occurs with high frequency in the human genome. (7) Genomic disorders result from structural features of the human genome and not population specific alleles or founder effects; therefore, genomic disorders appear to occur with equal frequencies in different world populations.

  8. Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae.

    PubMed

    Natesuntorn, Waranya; Iwami, Kotaro; Matsubara, Yuki; Sasano, Yu; Sugiyama, Minetaka; Kaneko, Yoshinobu; Harashima, Satoshi

    2015-07-30

    Segmental aneuploidy can play an important role in environmental adaptation. However, study of segmental aneuploids is severely hampered by the difficulty of creating them in a designed fashion. Here, we describe a PCR-mediated chromosome duplication (PCDup) technology that enables the generation of segmental aneuploidy at any desired chromosomal region in Saccharomyces cerevisiae. We constructed multiple strains harboring 100 kb to 200 kb segmental duplications covering the whole of the S. cerevisiae genome. Interestingly, some segmental aneuploidies confer stress tolerance, such as to high temperature, ethanol and strong acids, while others induce cell lethality and stress sensitivity, presumably as result of the simultaneous increases in dosages of multiple genes. We suggest that our PCDup technology will accelerate studies into the phenotypic changes resulting from alteration of gene dosage balance of multiple genes and will provide new insights into the adaptive molecular mechanisms in the genome in segmental aneuploidy-derived human diseases.

  9. Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins

    PubMed Central

    Opazo, Juan C.; Butts, G. Tyler; Nery, Mariana F.; Storz, Jay F.; Hoffmann, Federico G.

    2013-01-01

    Subsequent to the two rounds of whole-genome duplication that occurred in the common ancestor of vertebrates, a third genome duplication occurred in the stem lineage of teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided genetic raw materials for the physiological, morphological, and behavioral diversification of this highly speciose group. The extreme physiological versatility of teleost fish is manifest in their diversity of blood–gas transport traits, which reflects the myriad solutions that have evolved to maintain tissue O2 delivery in the face of changing metabolic demands and environmental O2 availability during different ontogenetic stages. During the course of development, regulatory changes in blood–O2 transport are mediated by the expression of multiple, functionally distinct hemoglobin (Hb) isoforms that meet the particular O2-transport challenges encountered by the developing embryo or fetus (in viviparous or oviparous species) and in free-swimming larvae and adults. The main objective of the present study was to assess the relative contributions of whole-genome duplication, large-scale segmental duplication, and small-scale gene duplication in producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we integrated phylogenetic reconstructions with analyses of conserved synteny to characterize the genomic organization and evolutionary history of the globin gene clusters of teleosts. These results were then integrated with available experimental data on functional properties and developmental patterns of stage-specific gene expression. Our results indicate that multiple α- and β-globin genes were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived globin gene clusters, each of which has undergone lineage-specific changes in gene content via repeated duplication and

  10. Foregut duplication cyst of the stomach.

    PubMed

    Kim, D H; Kim, J S; Nam, E S; Shin, H S

    2000-02-01

    Foregut duplication cyst of the stomach is an extremely rare disease entity. A 35-year-old Korean man presented with epigastric pain. An abdominal cystic mass, measuring 7 x 6 x 5 cm, was found in the lesser curvature of the stomach. The cyst was unilocular with a grey-white, rubbery wall. Microscopically, the cyst wall was lined by pseudostratified ciliated, columnar epithelium and gastric mucosa with a complete lining of smooth muscle bundles. Although the origin of this lesion remains uncertain, this case suggests that the gastric cyst arose from the embryonic foregut and showed differentiation toward respiratory and gastric structures.

  11. Duplication of the pituitary gland - plus syndrome

    PubMed Central

    Sen, Debraj; Arora, Vijinder

    2016-01-01

    Duplication of the pituitary gland (DPG) is a very rare developmental anomaly that is often associated with other anomalies – the DPG-plus syndrome and occurs due to splitting of the rostral notochord and prechordal plate during blastogenesis. DPG with the constellation of associated anomalies as in our patient has not been reported previously. This article illustrates the importance of imaging the brain in all patients with obvious midline facial anomalies and the complementary role of MRI and CT in such cases. PMID:27081236

  12. Genome duplication and the origin of angiosperms.

    PubMed

    De Bodt, Stefanie; Maere, Steven; Van de Peer, Yves

    2005-11-01

    Despite intensive research, little is known about the origin of the angiosperms and their rise to ecological dominance during the Early Cretaceous. Based on whole-genome analyses of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for the creation of many important developmental and regulatory genes found in extant angiosperm genomes. Here, we argue that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.

  13. Enteric Duplication Cysts in Children: A Single-Institution Series with Forty Patients in Twenty-Six Years.

    PubMed

    Erginel, Basak; Soysal, Feryal Gun; Ozbey, Huseyin; Keskin, Erbug; Celik, Alaattin; Karadag, Aslıhan; Salman, Tansu

    2017-02-01

    The purpose of the study was to evaluate our experience with enteric duplication cysts in 40 children during the past 26 years, while assessing the variability of their presentations and to propose an algorithm for surgical management. We retrospectively analysed sex, age, clinical presentations, duplication site, surgical treatment, presence of ectopic tissue, complications, associated anomalies, and prognosis of 40 patients with gastrointestinal tract duplications who were surgically treated in our clinic. Overall, there was a predominance of boys (28 males, 70 %; 12 females, 30 %). The presenting symptom was vomiting in 23 patients, rectal bleeding in 11 patients, abdominal mass in 10 patients, abdominal pain in 9 patients, constipation in 6 patients, cough in 2 patients, and respiratory distress in 2 patients. In 30 patients, a complete excision of the cyst with additional segmental intestinal resection and anastomosis was performed. Cystectomy was performed in seven patients, while complete excision of the cyst with additional wedge resection was performed in two. A Wrenn procedure (mucosectomy) was performed in one patient. Due to the variability in the site of enteric duplications, a wide range of presenting symptoms can exist, which is challenging for diagnosis. In children with a diagnosis of acute abdomen, enteric duplication cysts should be considered, and these children should be further investigated for additional skeletal, urogenital, and gastrointestinal system pathologies. Surgical treatment depends on the site and type of the cyst.

  14. Multiatlas Segmentation as Nonparametric Regression

    PubMed Central

    Awate, Suyash P.; Whitaker, Ross T.

    2015-01-01

    This paper proposes a novel theoretical framework to model and analyze the statistical characteristics of a wide range of segmentation methods that incorporate a database of label maps or atlases; such methods are termed as label fusion or multiatlas segmentation. We model these multiatlas segmentation problems as nonparametric regression problems in the high-dimensional space of image patches. We analyze the nonparametric estimator’s convergence behavior that characterizes expected segmentation error as a function of the size of the multiatlas database. We show that this error has an analytic form involving several parameters that are fundamental to the specific segmentation problem (determined by the chosen anatomical structure, imaging modality, registration algorithm, and label-fusion algorithm). We describe how to estimate these parameters and show that several human anatomical structures exhibit the trends modeled analytically. We use these parameter estimates to optimize the regression estimator. We show that the expected error for large database sizes is well predicted by models learned on small databases. Thus, a few expert segmentations can help predict the database sizes required to keep the expected error below a specified tolerance level. Such cost-benefit analysis is crucial for deploying clinical multiatlas segmentation systems. PMID:24802528

  15. Multiatlas segmentation as nonparametric regression.

    PubMed

    Awate, Suyash P; Whitaker, Ross T

    2014-09-01

    This paper proposes a novel theoretical framework to model and analyze the statistical characteristics of a wide range of segmentation methods that incorporate a database of label maps or atlases; such methods are termed as label fusion or multiatlas segmentation. We model these multiatlas segmentation problems as nonparametric regression problems in the high-dimensional space of image patches. We analyze the nonparametric estimator's convergence behavior that characterizes expected segmentation error as a function of the size of the multiatlas database. We show that this error has an analytic form involving several parameters that are fundamental to the specific segmentation problem (determined by the chosen anatomical structure, imaging modality, registration algorithm, and label-fusion algorithm). We describe how to estimate these parameters and show that several human anatomical structures exhibit the trends modeled analytically. We use these parameter estimates to optimize the regression estimator. We show that the expected error for large database sizes is well predicted by models learned on small databases. Thus, a few expert segmentations can help predict the database sizes required to keep the expected error below a specified tolerance level. Such cost-benefit analysis is crucial for deploying clinical multiatlas segmentation systems.

  16. Investigating Occurrence of Duplicate Updates in BGP Announcements

    NASA Astrophysics Data System (ADS)

    Park, Jong Han; Jen, Dan; Lad, Mohit; Amante, Shane; McPherson, Danny; Zhang, Lixia

    BGP is a hard-state protocol that uses TCP connections to reliably exchange routing state updates between neighbor BGP routers. According to the protocol, only routing changes should trigger a BGP router to generate updates; updates that do not express any routing changes are superfluous and should not occur. Nonetheless, such 'duplicate' BGP updates have been observed in reports as early as 1998 and as recently as 2007. To date, no quantitative measurement has been conducted on how many of these duplicates get sent, who is sending them, when they are observed, what impact they have on the global health of the Internet, or why these 'duplicate' updates are even being generated. In this paper, we address all of the above through a systematic assessment on the BGP duplicate updates. We first show that duplicates can have a negative impact on router processing loads; routers can receive upto 86.42% duplicates during their busiest times. We then reveal that there is a significant number of duplicates on the Internet - about 13% of all BGP routing updates are duplicates. Finally, through a detailed investigation of duplicate properties, we manage to discover the major cause behind the generation of pathological duplicate BGP updates.

  17. Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae).

    PubMed

    Bellieny-Rabelo, Daniel; Oliveira, Antônia Elenir Amâncio; Venancio, Thiago Motta

    2013-01-01

    F-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. F-box proteins are the substrate recognition modules of SCF E3 ubiquitin ligases. Here we report very distinct trends in family size, duplication, synteny and transcription of F-box genes in two nitrogen-fixing legumes, Glycine max (soybean) and Medicago truncatula (alfafa). While the soybean FBX genes emerged mainly through segmental duplications (including whole-genome duplications), M. truncatula genome is dominated by locally-duplicated (tandem) F-box genes. Many of these young FBX genes evolved complex transcriptional patterns, including preferential transcription in different tissues, suggesting that they have probably been recruited to important biochemical pathways (e.g. nodulation and seed development).

  18. Duplication of 7p: Further delineation of the phenotype and restriction of the critical region to the distal part of the short arm

    SciTech Connect

    Reish, O.; Berry, S.A.; King, R.A.; Dewald, G.

    1996-01-02

    We report on a patient with duplication of 7p15{r_arrow}pter and review of the literature. Patients with partial duplication of the distal 7p, including only the distal segment 7p15{r_arrow}pter, have a syndrome comparable to that of patients with a larger or complete duplication of 7p. This suggests that the critical region for the dup(7p) phenotype is restricted to 7p15{r_arrow}pter. The complete clinical phenotype of dup (7)(p15{r_arrow}pter) includes mental retardation, skull anomalies, large anterior fontanel, cardiovascular defects, joint dislocation and contraction, and gastrointestinal and genital defects. Recognition of the clinical spectrum in patients with a smaller duplication 7p, and the assignment of this critical region, should prove valuable for accurate counseling, prediction of outcome, and further gene mapping. 33 refs., 3 figs., 2 tabs.

  19. Gene duplication as a major force in evolution.

    PubMed

    Magadum, Santoshkumar; Banerjee, Urbi; Murugan, Priyadharshini; Gangapur, Doddabhimappa; Ravikesavan, Rajasekar

    2013-04-01

    Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication and it has contributed tremendously to the evolution of developmental programmes in various organisms. Gene duplication can result from unequal crossing over, retroposition or chromosomal (or genome) duplication. Understanding the mechanisms that generate duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on localized and genomewide aspects of evolutionary forces shaping intra-specific and inter-specific genome contents, evolutionary relationships, and interactions. Based on whole-genome analysis of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for creation of many important developmental and regulatory genes found in extant angiosperm genomes. Recent studies also provide strong indications that even yeast (Saccharomyces cerevisiae), with its compact genome, is in fact an ancient tetraploid. Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited. Whether a duplicate is retained depends upon its function, its mode of duplication, (i.e. whether it was duplicated during a whole-genome duplication event), the species in which it occurs, and its expression rate. The exaptation of preexisting secondary functions is an important feature in gene evolution, just as it is in morphological evolution.

  20. Cytological characterization of an Aspergillus Nidulans mutant from a strain with chromosomic duplication

    PubMed Central

    Giancoli, Ágata Cristiane Huppert; de Azevedo, João Lúcio; Pizzirani-Kleiner, Aline Aparecida

    2010-01-01

    A development mutant, named V103, was obtained spontaneously from the A strain of A. nidulans. The A strain contains a duplicated segment of chromosome I that has undergone translocation to chromosome II (I II). It is mitotically unstable and generates phenotypically deteriorated types, some with enhanced stability. The deteriorated variants of A. nidulans show abnormal development, exhibiting slower colony growth, variations in colony pigmentation and changes in conidiophore structure. The alterations observed in the conidiophore include fewer metulae and phialides, further elongation and ramification of these structures, delayed nuclear migration and the presence of secondary conidiophores. PMID:24031489

  1. Further contribution to the description of phenotypes associated with partial 4q duplication

    SciTech Connect

    Zollino, M.; Zampino, G.; Torrioli, G.

    1995-05-22

    We report on a 15-year-old girl with previously undescribed de novo duplication of segment 4q13.1{r_arrow}q22.2. The origin of the extrachromosomal material on 4q was unequivocally established by fluorescent in situ hybridization with a chromosome 4 painting probe. Clinical manifestations included moderate mental retardation, destructive behavior, and minor physical anomalies. An analysis of the literature on partial 4q trisomy led us to identify a region comprising bands 4q22-q23, which may be involved in the development of the acrorenal field. 17 refs., 5 figs., 21 tabs.

  2. The Duplicate-Replacement System: An Alternative Method of Handling Book Duplicates.

    ERIC Educational Resources Information Center

    Clement, Russell T.

    This report studied the alternative method of using book duplicates as replacement copies for worn or missing stack items. The simple operational procedure which is proposed and evaluated could be adapted to virtually any library setting. When tested in Brigham Young University's Lee Library, it was found that such a procedure cost an estimated…

  3. FT Duplication Coordinates Reproductive and Vegetative Growth

    SciTech Connect

    Hsu, Chuan-Yu; Adams, Joshua P.; Kim, Hyejin; No, Kyoungok; Ma, Caiping; Strauss, Steven; Drnevich, Jenny; Wickett, Norman; Vandervelde, Lindsay; Ellis, Jeffrey D.; Rice, Brandon; Gunter, Lee E; Tuskan, Gerald A; Brunner, Amy M.; Page, Grier P.; Carlson, John E.; DePamphilis, Claude; Luthe, Dawn S.; Yuceer, Cetin

    2011-01-01

    Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.

  4. Preservation of duplicate genes by complementary, degenerative mutations.

    PubMed Central

    Force, A; Lynch, M; Pickett, F B; Amores, A; Yan, Y L; Postlethwait, J

    1999-01-01

    The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between

  5. Moving particle composition analyzer

    NASA Technical Reports Server (NTRS)

    Auer, S. O. (Inventor)

    1976-01-01

    A mass spectrometry apparatus for analyzing the composition of moving microscopic particles is introduced. The apparatus includes a capacitor with a front electrode upon which the particles impinge, a back electrode, and a solid dielectric sandwiched between the front and back electrodes. In one embodiment, the electrodes and dielectric are arcuately shaped as concentric peripheral segments of different spheres having a common center and different radii. The front electrode and dielectric together have a thickness such that an impinging particle can penetrate them. In a second embodiment, the capacitor has planar, parallel electrodes, in which case the ejected positive ions are deflected downstream of a planar grid by a pair of spaced, arcuate capacitor plates having a region between them through which the ejected ions travel.

  6. Multiple bursts of pancreatic ribonuclease gene duplication in insect-eating bats.

    PubMed

    Xu, Huihui; Liu, Yang; Meng, Fanxing; He, Beibei; Han, Naijian; Li, Gang; Rossiter, Stephen J; Zhang, Shuyi

    2013-09-10

    Pancreatic ribonuclease gene (RNASE1) was previously shown to have undergone duplication and adaptive evolution related to digestive efficiency in several mammalian groups that have evolved foregut fermentation, including ruminants and some primates. RNASE1 gene duplications thought to be linked to diet have also been recorded in some carnivores. Of all mammals, bats have evolved the most diverse dietary specializations, mainly including frugivory and insectivory. Here we cloned, sequenced and analyzed RNASE1 gene sequences from a range of bat species to determine whether their dietary adaptation is mirrored by molecular adaptation. We found that seven insect-eating members of the families Vespertilionidae and Molossidae possessed two or more duplicates, and we also detected three pseudogenes. Reconstructed RNASE1 gene trees based on both Bayesian and maximum likelihood methods supported independent duplication events in these two families. Selection tests revealed that RNASE1 gene duplicates have undergone episodes of positive selection indicative of functional modification, and lineage-specific tests revealed strong adaptive evolution in the Tadarida β clade. However, unlike the RNASE1 duplicates that function in digestion in some mammals, the bat RNASE1 sequences were found to be characterized by relatively high isoelectric points, a feature previously suggested to promote defense against viruses via the breakdown of double-stranded RNA. Taken together, our findings point to an adaptive diversification of RNASE1 in these two bat families, although we find no clear evidence that this was driven by diet. Future experimental assays are needed to resolve the functions of these enzymes in bats.

  7. Gene duplication, genome duplication, and the functional diversification of vertebrate globins

    PubMed Central

    Storz, Jay F.; Opazo, Juan C.; Hoffmann, Federico G.

    2015-01-01

    The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α2β2). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages. PMID:22846683

  8. Gene duplication, genome duplication, and the functional diversification of vertebrate globins.

    PubMed

    Storz, Jay F; Opazo, Juan C; Hoffmann, Federico G

    2013-02-01

    The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α(2)β(2)). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.

  9. Duplicate filum terminale noted in an adult: a rare finding.

    PubMed

    Davanzo, Justin R; Christopher Zacko, J; Specht, Charles S; Rizk, Elias B

    2016-09-01

    This is the first reported case of an adult presenting with tethering symptoms, limb discrepancy on physical examination, a low-lying spinal cord, and duplicate filum terminale discovered intraoperatively. Intraoperative imaging and pathological analysis of a specimen confirmed the diagnosis of duplicate filum. This is the first reported adult case with duplication of the filum terminale. Release of both fila was necessary in this case to relieve the tethering symptoms.

  10. Gene duplication and transfer events in plant mitochondria genome

    SciTech Connect

    Xiong Aisheng Peng Rihe; Zhuang Jing; Gao Feng; Zhu Bo; Fu Xiaoyan; Xue Yong; Jin Xiaofen; Tian Yongsheng; Zhao Wei; Yao Quanhong

    2008-11-07

    Gene or genome duplication events increase the amount of genetic material available to increase the genomic, and thereby phenotypic, complexity of organisms during evolution. Gene duplication and transfer events have been important to molecular evolution in all three domains of life, and may be the first step in the emergence of new gene functions. Gene transfer events have been proposed as another accelerator of evolution. The duplicated gene or genome, mainly nuclear, has been the subject of several recent reviews. In addition to the nuclear genome, organisms have organelle genomes, including mitochondrial genome. In this review, we briefly summarize gene duplication and transfer events in the plant mitochondrial genome.

  11. MR Imaging Findings in Xp21.2 Duplication Syndrome

    PubMed Central

    Whitehead, Matthew T; Helman, Guy; Gropman, Andrea L

    2016-01-01

    Xp21.2 duplication syndrome is a rare genetic disorder of undetermined prevalence and clinical relevance. As the use of chromosomal microarray has become first line for the work-up of childhood developmental delay, more gene deletions and duplications have been recognized. To the best of our knowledge, the imaging findings of Xp21.2 duplication syndrome have not been reported. We report a case of a 33 month-old male referred for developmental delay that was found to have an Xp21.2 duplication containing IL1RAPL1 and multiple midline brain malformations. PMID:27761175

  12. MR Imaging Findings in Xp21.2 Duplication Syndrome.

    PubMed

    Whitehead, Matthew T; Helman, Guy; Gropman, Andrea L

    2016-05-01

    Xp21.2 duplication syndrome is a rare genetic disorder of undetermined prevalence and clinical relevance. As the use of chromosomal microarray has become first line for the work-up of childhood developmental delay, more gene deletions and duplications have been recognized. To the best of our knowledge, the imaging findings of Xp21.2 duplication syndrome have not been reported. We report a case of a 33 month-old male referred for developmental delay that was found to have an Xp21.2 duplication containing IL1RAPL1 and multiple midline brain malformations.

  13. Method of making an apertured casting. [using duplicate mold

    NASA Technical Reports Server (NTRS)

    Terray, A. (Inventor)

    1976-01-01

    An apertured casting is made by first forming a duplicate in the shape of the finished casting, positioning refractory metal bodies such as wires in the duplicate at points corresponding to apertures or passageways in finished products, forming a ceramic coating on the duplicate, removing the duplicate material, firing the ceramic in a vacuum or inert atmosphere, vacuum casting the metal in the ceramic form, removing the ceramic form, heating the cast object in an atmospheric furnace to oxidize the refractory metal bodies and then leaching the oxidized refractory bodies from the casting with a molten caustic agent or acid solution.

  14. Functional requirements driving the gene duplication in 12 Drosophila species

    PubMed Central

    2013-01-01

    Background Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue. Results In our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses. Conclusions This study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila. PMID:23945147

  15. Duplicate inferior vena cava filters: more is not always better.

    PubMed

    Katyal, Anup; Javed, Muhammad Ali

    2016-01-01

    Duplication of the inferior vena cava (IVC) has been reported in literature. This achieves clinical significance in the setting of lower extremity venous thromboembolism with a contraindication for anticoagulation. We describe a case of lower extremity deep vein thrombosis with duplicate IVC. Anticoagulation was contraindicated in this case leading to successful treatment with double IVC filters. We conducted a PubMed search for all current English language published literature, where filters were placed in the presence of duplicate IVC. We suggest that patients with deep vein thrombosis should have an accurate assessment of venous anatomy before IVC filter placement. Duplication of IVC, although rare, should be considered as this has management implications.

  16. The Centrosome and Its Duplication Cycle

    PubMed Central

    Fu, Jingyan; Hagan, Iain M.; Glover, David M.

    2015-01-01

    The centrosome was discovered in the late 19th century when mitosis was first described. Long recognized as a key organelle of the spindle pole, its core component, the centriole, was realized more than 50 or so years later also to comprise the basal body of the cilium. Here, we chart the more recent acquisition of a molecular understanding of centrosome structure and function. The strategies for gaining such knowledge were quickly developed in the yeasts to decipher the structure and function of their distinctive spindle pole bodies. Only within the past decade have studies with model eukaryotes and cultured cells brought a similar degree of sophistication to our understanding of the centrosome duplication cycle and the multiple roles of this organelle and its component parts in cell division and signaling. Now as we begin to understand these functions in the context of development, the way is being opened up for studies of the roles of centrosomes in human disease. PMID:25646378

  17. Inherited partial duplication of chromosome No. 15

    PubMed Central

    Fujimoto, Atsuko; Towner, Joseph W.; Ebbin, Allan J.; Kahlstrom, Emily J.; Wilson, Miriam G.

    1974-01-01

    A boy with unusual facial appearance and mental retardation was found to have duplication for the distal half of the long arm of chromosome No. 15 and possibly deficiency for the distal end of the long arm of No. 21. The chromosome abnormality was inherited from his mother, who had a translocation involving chromosomes Nos. 15 and 21. Giemsa-banding localized the break point in chromosome No. 15 just distal to the intense band at the midportion of the long arm. The break point in chromosome No. 21 appeared to be at the distal end of the long arm. The difficulty encountered in cytogenetic analysis of the propositus with conventional staining, the importance of chromosome analysis of the parents, and the application of differential staining techniques are also presented. Images PMID:4139262

  18. Nearby Dwarf Stars: Duplicity, Binarity, and Masses

    NASA Astrophysics Data System (ADS)

    Mason, Brian D.; Hartkopf, William I.; Henry, Todd J.; Jao, Wei-Chun; Subasavage, John; Riedel, Adric; Winters, Jennifer

    2010-02-01

    Double stars have proven to be both a blessing and a curse for astronomers since their discovery over two centuries ago. They remain the only reliable source of masses, the most fundamental parameter defining stars. On the other hand, their sobriquet ``vermin of the sky'' is well-earned, due to the complications they present to both observers and theoreticians. These range from non-linear proper motions to stray light in detectors, to confusion in pointing of instruments due to non-symmetric point spread functions, to angular momentum conservation in multiple stars which results in binaries closer than allowed by evolution of two single stars. This proposal is primarily focused on targets where precise astrophysical information is sorely lacking: white dwarfs, red dwarfs, and subdwarfs. The proposed work will refine current statistics regarding duplicity (chance alignments of nearby point sources) and binarity (actual physical relationships), and improve the precisions and accuracies of stellar masses. Several targets support Riedel's and Winters' theses.

  19. Nearby Dwarf Stars: Duplicity, Binarity, and Masses

    NASA Astrophysics Data System (ADS)

    Mason, Brian D.; Hartkopf, William I.; Henry, Todd J.; Jao, Wei-Chun; Subasavage, John; Riedel, Adric; Winters, Jennifer

    2009-08-01

    Double stars have proven to be both a blessing and a curse for astronomers since their discovery over two centuries ago. They remain the only reliable source of masses, the most fundamental parameter defining stars. On the other hand, their sobriquet ``vermin of the sky'' is well-earned, due to the complications they present to both observers and theoreticians. These range from non-linear proper motions to stray light in detectors, to confusion in pointing of instruments due to non-symmetric point spread functions, to angular momentum conservation in multiple stars which results in binaries closer than allowed by evolution of two single stars. This proposal is primarily focused on targets where precise astrophysical information is sorely lacking: white dwarfs, red dwarfs, and subdwarfs. The proposed work will refine current statistics regarding duplicity (chance alignments of nearby point sources) and binarity (actual physical relationships), and improve the precisions and accuracies of stellar masses. Several targets support Riedel's and Winters' theses.

  20. The centrosome and its duplication cycle.

    PubMed

    Fu, Jingyan; Hagan, Iain M; Glover, David M

    2015-02-02

    The centrosome was discovered in the late 19th century when mitosis was first described. Long recognized as a key organelle of the spindle pole, its core component, the centriole, was realized more than 50 or so years later also to comprise the basal body of the cilium. Here, we chart the more recent acquisition of a molecular understanding of centrosome structure and function. The strategies for gaining such knowledge were quickly developed in the yeasts to decipher the structure and function of their distinctive spindle pole bodies. Only within the past decade have studies with model eukaryotes and cultured cells brought a similar degree of sophistication to our understanding of the centrosome duplication cycle and the multiple roles of this organelle and its component parts in cell division and signaling. Now as we begin to understand these functions in the context of development, the way is being opened up for studies of the roles of centrosomes in human disease.

  1. A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli

    PubMed Central

    2013-01-01

    Background DNA duplications constitute important precursors for genome variation. Here we analyzed an unequal duplication harboring a beneficial mutation that may provide alternative evolutionary outcomes. Results We characterized this evolutionary event during experimental evolution for only 100 generations of an Escherichia coli strain under glucose limitation within chemostats. By combining Insertion Sequence based Restriction Length Polymorphism experiments, pulsed field gel electrophoresis and two independent genome re-sequencing experiments, we identified an evolved lineage carrying a 180 kb duplication of the 46’ region of the E. coli chromosome. This evolved duplication revealed a heterozygous state, with one copy harboring a 2668 bp deletion that included part of the ogrK gene and both the yegR and yegS genes. By genetically manipulating ancestral and evolved strains, we showed that the single yegS inactivation was sufficient to confer a frequency dependent fitness increase under the chemostat selective conditions in both the ancestor and evolved genetic contexts, implying that the duplication itself was not a direct fitness contributor. Nonetheless, the heterozygous duplicated state was relatively stable in the conditions prevailing during evolution in chemostats, in striking contrast to non selective conditions in which the duplication resolved at high frequency into either its ancestral or deleted copy. Conclusions Our results suggest that the duplication state may constitute a second order selection process providing higher evolutionary potential. Moreover, its heterozygous nature may provide differential evolutionary opportunities in alternating environments. Our results also highlighted how careful analyses of whole genome data are needed to identify such complex rearrangements. PMID:23822838

  2. Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes

    PubMed Central

    2013-01-01

    Background Mitochondrial genomic (mitogenomic) reorganizations are rarely found in closely-related animals, yet drastic reorganizations have been found in the Ranoides frogs. The phylogenetic relationships of the three major ranoid taxa (Natatanura, Microhylidae, and Afrobatrachia) have been problematic, and mitogenomic information for afrobatrachians has not been available. Several molecular models for mitochondrial (mt) gene rearrangements have been proposed, but observational evidence has been insufficient to evaluate them. Furthermore, evolutionary trends in rearranged mt genes have not been well understood. To gain molecular and phylogenetic insights into these issues, we analyzed the mt genomes of four afrobatrachian species (Breviceps adspersus, Hemisus marmoratus, Hyperolius marmoratus, and Trichobatrachus robustus) and performed molecular phylogenetic analyses. Furthermore we searched for two evolutionary patterns expected in the rearranged mt genes of ranoids. Results Extensively reorganized mt genomes having many duplicated and rearranged genes were found in three of the four afrobatrachians analyzed. In fact, Breviceps has the largest known mt genome among vertebrates. Although the kinds of duplicated and rearranged genes differed among these species, a remarkable gene rearrangement pattern of non-tandemly copied genes situated within tandemly-copied regions was commonly found. Furthermore, the existence of concerted evolution was observed between non-neighboring copies of triplicated 12S and 16S ribosomal RNA regions. Conclusions Phylogenetic analyses based on mitogenomic data support a close relationship between Afrobatrachia and Microhylidae, with their estimated divergence 100 million years ago consistent with present-day endemism of afrobatrachians on the African continent. The afrobatrachian mt data supported the first tandem and second non-tandem duplication model for mt gene rearrangements and the recombination-based model for concerted

  3. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication.

    PubMed

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-06-27

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the "salicoid" duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants.

  4. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral “Salicoid” Genome Duplication

    PubMed Central

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-01-01

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the “salicoid” duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants. PMID:27352946

  5. Plutonium solution analyzer

    SciTech Connect

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded).

  6. Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities.

    PubMed

    D'Angelo, Debra; Lebon, Sébastien; Chen, Qixuan; Martin-Brevet, Sandra; Snyder, LeeAnne Green; Hippolyte, Loyse; Hanson, Ellen; Maillard, Anne M; Faucett, W Andrew; Macé, Aurélien; Pain, Aurélie; Bernier, Raphael; Chawner, Samuel J R A; David, Albert; Andrieux, Joris; Aylward, Elizabeth; Baujat, Genevieve; Caldeira, Ines; Conus, Philippe; Ferrari, Carrina; Forzano, Francesca; Gérard, Marion; Goin-Kochel, Robin P; Grant, Ellen; Hunter, Jill V; Isidor, Bertrand; Jacquette, Aurélia; Jønch, Aia E; Keren, Boris; Lacombe, Didier; Le Caignec, Cédric; Martin, Christa Lese; Männik, Katrin; Metspalu, Andres; Mignot, Cyril; Mukherjee, Pratik; Owen, Michael J; Passeggeri, Marzia; Rooryck-Thambo, Caroline; Rosenfeld, Jill A; Spence, Sarah J; Steinman, Kyle J; Tjernagel, Jennifer; Van Haelst, Mieke; Shen, Yiping; Draganski, Bogdan; Sherr, Elliott H; Ledbetter, David H; van den Bree, Marianne B M; Beckmann, Jacques S; Spiro, John E; Reymond, Alexandre; Jacquemont, Sébastien; Chung, Wendy K

    2016-01-01

    The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P < .001). However, broad variation in FSIQ was found, with a 19.4- and 2.0-fold increase in the proportion of FSIQ scores that were very low (≤40) and higher than the mean (>100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were

  7. An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome.

    PubMed

    Jehee, Fernanda Sarquis; Rosenberg, Carla; Krepischi-Santos, Ana Cristina; Kok, Fernando; Knijnenburg, Jeroen; Froyen, Guy; Vianna-Morgante, Angela M; Opitz, John M; Passos-Bueno, Maria Rita

    2005-12-15

    FG syndrome is an X-linked multiple congenital anomalies (MCA) syndrome. It has been mapped to four distinct loci FGS1-4, through linkage analysis (Xq13, Xp22.3, and Xp11.4-p11.3) and based on the breakpoints of an X chromosome inversion (Xq11:Xq28), but so far no gene has been identified. We describe a boy with FG syndrome who has an inherited duplication at band Xq22.3 detected by comparative genomic hybridization microarray (Array-CGH). These duplication maps outside all four loci described so far for FG syndrome, representing therefore a new locus, which we propose to be called FGS5. MID2, a gene closely related to MID1, which is known to be mutated in Opitz G/BBB syndrome, maps within the duplicated segment of our patient. Since FG and Opitz G/BBB syndromes share many manifestations we considered MID2 a candidate gene for FG syndrome. We also discuss the involvement of other potential genes within the duplicated segment and its relationship with clinical symptoms of our patient, as well as the laboratory abnormalities found in his mother, a carrier of the duplication.

  8. Characterization of the past and current duplication activities in the human 22q11.2 region

    PubMed Central

    2011-01-01

    Background Segmental duplications (SDs) on 22q11.2 (LCR22), serve as substrates for meiotic non-allelic homologous recombination (NAHR) events resulting in several clinically significant genomic disorders. Results To understand the duplication activity leading to the complicated SD structure of this region, we have applied the A-Bruijn graph algorithm to decompose the 22q11.2 SDs to 523 fundamental duplication sequences, termed subunits. Cross-species syntenic analysis of primate genomes demonstrates that many of these LCR22 subunits emerged very recently, especially those implicated in human genomic disorders. Some subunits have expanded more actively than others, and young Alu SINEs, are associated much more frequently with duplicated sequences that have undergone active expansion, confirming their role in mediating recombination events. Many copy number variations (CNVs) exist on 22q11.2, some flanked by SDs. Interestingly, two chromosome breakpoints for 13 CNVs (mean length 65 kb) are located in paralogous subunits, providing direct evidence that SD subunits could contribute to CNV formation. Sequence analysis of PACs or BACs identified extra CNVs, specifically, 10 insertions and 18 deletions within 22q11.2; four were more than 10 kb in size and most contained young AluYs at their breakpoints. Conclusions Our study indicates that AluYs are implicated in the past and current duplication events, and moreover suggests that DNA rearrangements in 22q11.2 genomic disorders perhaps do not occur randomly but involve both actively expanded duplication subunits and Alu elements. PMID:21269513

  9. 42 CFR 457.626 - Prevention of duplicate payments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Prevention of duplicate payments. 457.626 Section 457.626 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Payments to States § 457.626 Prevention of duplicate payments. (a) General rule. No payment shall be made...

  10. Gene duplication models for directed networks with limits on growth

    NASA Astrophysics Data System (ADS)

    Enemark, Jakob; Sneppen, Kim

    2007-11-01

    Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted that growth via duplication would act as an implicit means of preferential attachment, and thereby provide the observed broad degree distributions of molecular networks. Results: We extend current models of gene duplication and rewiring by including directions and the fact that molecular networks are not a result of unidirectional growth. We introduce upstream sites and downstream shapes to quantify potential links during duplication and rewiring. We find that this in itself generates the observed scaling of transcription factors for genome sites in prokaryotes. The dynamical model can generate a scale-free degree distribution, p(k)\\propto 1/k^{\\gamma } , with exponent γ = 1 in the non-growing case, and with γ>1 when the network is growing. Conclusions: We find that duplication of genes followed by substantial recombination of upstream regions could generate features of genetic regulatory networks. Our steady state degree distribution is however too broad to be consistent with data, thereby suggesting that selective pruning acts as a main additional constraint on duplicated genes. Our analysis shows that gene duplication can only be a main cause for the observed broad degree distributions if there are also substantial recombinations between upstream regions of genes.

  11. 47 CFR 76.122 - Satellite network non-duplication.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Satellite network non-duplication. 76.122... Sports Blackout § 76.122 Satellite network non-duplication. (a) Upon receiving notification pursuant to paragraph (c) of this section, a satellite carrier shall not deliver, to subscribers within zip code...

  12. 10 CFR 7.21 - Cost of duplication of documents.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Cost of duplication of documents. 7.21 Section 7.21 Energy NUCLEAR REGULATORY COMMISSION ADVISORY COMMITTEES § 7.21 Cost of duplication of documents. Copies of the records, reports, transcripts, minutes, appendices, working papers, drafts, studies, agenda, or...

  13. 10 CFR 7.21 - Cost of duplication of documents.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Cost of duplication of documents. 7.21 Section 7.21 Energy NUCLEAR REGULATORY COMMISSION ADVISORY COMMITTEES § 7.21 Cost of duplication of documents. Copies of the records, reports, transcripts, minutes, appendices, working papers, drafts, studies, agenda, or...

  14. 10 CFR 7.21 - Cost of duplication of documents.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Cost of duplication of documents. 7.21 Section 7.21 Energy NUCLEAR REGULATORY COMMISSION ADVISORY COMMITTEES § 7.21 Cost of duplication of documents. Copies of the records, reports, transcripts, minutes, appendices, working papers, drafts, studies, agenda, or...

  15. 10 CFR 7.21 - Cost of duplication of documents.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Cost of duplication of documents. 7.21 Section 7.21 Energy NUCLEAR REGULATORY COMMISSION ADVISORY COMMITTEES § 7.21 Cost of duplication of documents. Copies of the records, reports, transcripts, minutes, appendices, working papers, drafts, studies, agenda, or...

  16. 10 CFR 7.21 - Cost of duplication of documents.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Cost of duplication of documents. 7.21 Section 7.21 Energy NUCLEAR REGULATORY COMMISSION ADVISORY COMMITTEES § 7.21 Cost of duplication of documents. Copies of the records, reports, transcripts, minutes, appendices, working papers, drafts, studies, agenda, or...

  17. Widespread genome duplications throughout the history of flowering plants

    PubMed Central

    Cui, Liying; Wall, P. Kerr; Leebens-Mack, James H.; Lindsay, Bruce G.; Soltis, Douglas E.; Doyle, Jeff J.; Soltis, Pamela S.; Carlson, John E.; Arumuganathan, Kathiravetpilla; Barakat, Abdelali; Albert, Victor A.; Ma, Hong; dePamphilis, Claude W.

    2006-01-01

    Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth–death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella. PMID:16702410

  18. 29 CFR 1912.4 - Avoidance of duplication.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Avoidance of duplication. 1912.4 Section 1912.4 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED) ADVISORY COMMITTEES ON STANDARDS Organizational Matters § 1912.4 Avoidance of duplication....

  19. 47 CFR 80.467 - Duplication of VHF service.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Duplication of VHF service. 80.467 Section 80... STATIONS IN THE MARITIME SERVICES Public Coast Stations Use of Telephony § 80.467 Duplication of VHF... public coast stations operating on the same VHF public correspondence channel. Within the service area...

  20. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

    PubMed

    Chen, Qingyu; Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

    2016-01-01

    First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

  1. Widespread genome duplications throughout the history of flowering plants.

    PubMed

    Cui, Liying; Wall, P Kerr; Leebens-Mack, James H; Lindsay, Bruce G; Soltis, Douglas E; Doyle, Jeff J; Soltis, Pamela S; Carlson, John E; Arumuganathan, Kathiravetpilla; Barakat, Abdelali; Albert, Victor A; Ma, Hong; dePamphilis, Claude W

    2006-06-01

    Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.

  2. 42 CFR 457.626 - Prevention of duplicate payments.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Prevention of duplicate payments. 457.626 Section 457.626 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Payments to States § 457.626 Prevention of duplicate payments. (a) General rule. No payment shall be made...

  3. 12 CFR 1073.205 - No requirement for duplicate notice.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 9 2014-01-01 2014-01-01 false No requirement for duplicate notice. 1073.205 Section 1073.205 Banks and Banking BUREAU OF CONSUMER FINANCIAL PROTECTION PROCEDURES FOR BUREAU DEBT COLLECTION Administrative Offset § 1073.205 No requirement for duplicate notice. Where the...

  4. Duplicated laboratory tests: evaluation of a computerized alert intervention abstract.

    PubMed

    Bridges, Sharon A; Papa, Linda; Norris, Anne E; Chase, Susan K

    2014-01-01

    Redundant testing contributes to reductions in healthcare system efficiency. The purpose of this study was to: (1) determine if the use of a computerized alert would reduce the number and cost of duplicated Acute Hepatitis Profile (AHP) laboratory tests and (2) assess what patient, test, and system factors were associated with duplication. This study used a quasi-experimental pre- and post-test design to determine the proportion of duplication of the AHP test before and after implementation of a computerized alert intervention. The AHP test was duplicated if the test was requested again within 15 days of the initial test being performed and the result present in the medical record. The intervention consisted of a computerized alert (pop-up window) that indicated to the clinician that the test had recently been ordered. A total of 674 AHP tests were performed in the pre-intervention period and 692 in the postintervention group. In the pre-intervention period, 53 (7.9%) were duplicated and in postintervention, 18 (2.6%) were duplicated (p<.001). The implementation of the alert was shown to significantly reduce associated costs of duplicated AHP tests (p≤.001). Implementation of computerized alerts may be useful in reducing duplicate laboratory tests and improving healthcare system efficiency. © 2012 National Association for Healthcare Quality.

  5. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases

    PubMed Central

    Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

    2016-01-01

    Motivation First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. Results We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material. PMID:27489953

  6. 33 CFR 173.73 - Duplicate certificate of number.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Duplicate certificate of number. 173.73 Section 173.73 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... Number § 173.73 Duplicate certificate of number. If a certificate of number is lost or destroyed, the...

  7. Automatic Identification of Duplicates after Multidatabase Online Searching.

    ERIC Educational Resources Information Center

    Onorato, Eveline; Bianchi, Gianfranco

    1981-01-01

    Discusses the problem of duplicate citations resulting from file overlaps in multidatabase searching and shows that such duplicates could be identified automatically and eliminated by a host computer as a complementary service to online retrieval. Steps involved in the realization of this service are described, and 11 references are listed. (RBF)

  8. Gallbladder Duplication Associated with Gastro-Intestinal Atresia

    PubMed Central

    Gupta, Rahul; Gupta, Shilpi; Sharma, Pramila; Bhandari, Anu; Gupta, Arun Kumar; Mathur, Praveen

    2016-01-01

    Gallbladder duplication in association with other GIT anomalies is a rare entity. We report two neonates; one with duodenal atresia and the other newborn with pyloric atresia, ileal atresia and colonic atresia, both were associated with gallbladder duplication which has not been reported earlier. PMID:27123398

  9. 49 CFR 24.3 - No duplication of payments.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false No duplication of payments. 24.3 Section 24.3 Transportation Office of the Secretary of Transportation UNIFORM RELOCATION ASSISTANCE AND REAL PROPERTY ACQUISITION FOR FEDERAL AND FEDERALLY-ASSISTED PROGRAMS General § 24.3 No duplication of payments. No...

  10. 47 CFR 61.73 - Duplication of rates or regulations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Duplication of rates or regulations. 61.73 Section 61.73 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Duplication of rates or regulations. A carrier concurring in schedules of another carrier must not...

  11. MECP2 duplication: possible cause of severe phenotype in females.

    PubMed

    Scott Schwoerer, Jessica; Laffin, Jennifer; Haun, Joanne; Raca, Gordana; Friez, Michael J; Giampietro, Philip F

    2014-04-01

    MECP2 duplication syndrome, originally described in 2005, is an X-linked neurodevelopmental disorder comprising infantile hypotonia, severe to profound intellectual disability, autism or autistic-like features, spasticity, along with a variety of additional features that are not always clinically apparent. The syndrome is due to a duplication (or triplication) of the gene methyl CpG binding protein 2 (MECP2). To date, the disorder has been described almost exclusively in males. Female carriers of the duplication are thought to have no or mild phenotypic features. Recently, a phenotype for females began emerging. We describe a family with ∼290 kb duplication of Xq28 region that includes the MECP2 gene where the proposita and affected family members are female. Twin sisters, presumed identical, presented early with developmental delay, and seizures. Evaluation of the proposita at 25 years of age included microarray comparative genomic hybridization (aCGH) which revealed the MECP2 gene duplication. The same duplication was found in the proposita's sister, who is more severely affected, and the proband's mother who has mild intellectual disability and depression. X-chromosome inactivation studies showed significant skewing in the mother, but was uninformative in the twin sisters. We propose that the MECP2 duplication caused for the phenotype of the proband and her sister. These findings support evidence for varied severity in some females with MECP2 duplications.

  12. Segmentation and segment connection of obstructed colon

    NASA Astrophysics Data System (ADS)

    Medved, Mario; Truyen, Roel; Likar, Bostjan; Pernus, Franjo

    2004-05-01

    Segmentation of colon CT images is the main factor that inhibits automation of virtual colonoscopy. There are two main reasons that make efficient colon segmentation difficult. First, besides the colon, the small bowel, lungs, and stomach are also gas-filled organs in the abdomen. Second, peristalsis or residual feces often obstruct the colon, so that it consists of multiple gas-filled segments. In virtual colonoscopy, it is very useful to automatically connect the centerlines of these segments into a single colon centerline. Unfortunately, in some cases this is a difficult task. In this study a novel method for automated colon segmentation and connection of colon segments' centerlines is proposed. The method successfully combines features of segments, such as centerline and thickness, with information on main colon segments. The results on twenty colon cases show that the method performs well in cases of small obstructions of the colon. Larger obstructions are mostly also resolved properly, especially if they do not appear in the sigmoid part of the colon. Obstructions in the sigmoid part of the colon sometimes cause improper classification of the small bowel segments. If a segment is too small, it is classified as the small bowel segment. However, such misclassifications have little impact on colon analysis.

  13. A case of a duodenal duplication cyst presenting as melena

    PubMed Central

    Ko, Seung Yeon; Ko, Sun Hye; Ha, Sungeun; Kim, Mi Sung; Shin, Hyang Mi; Baeg, Myong Ki

    2013-01-01

    Duodenal duplication cysts are benign rare congenital anomalies reported mainly in the pediatric population, but seldom in adults. Symptoms depend on the type and location and can present as abdominal pain, distension, dysphagia or dyspepsia. They have been reported to be responsible for duodenal obstruction, pancreatitis and, in rare cases, gastrointestinal bleeding. We present a case of a duodenal duplication cyst in a 43-year-old man presenting as melena. Initial gastroduodenoscopy and colonoscopy did not reveal any bleeding focus. However, the patient began passing melena after 3 d, with an acute decrease in hemoglobin levels. Subsequent studies revealed a duplication cyst in the second portion of the duodenum which was surgically resected. Histology revealed a duodenal duplication cyst consisting of intestinal mucosa. There was no further bleeding and the patient recovered completely. In rare cases, duodenal duplication cysts might cause gastrointestinal bleeding and should be included in the differential diagnosis. PMID:24151370

  14. Laparoscopic resection of adult colon duplication causing intussusception.

    PubMed

    Kyo, Kennoki; Azuma, Masaki; Okamoto, Kazuya; Nishiyama, Motohiro; Shimamura, Takahiro; Maema, Atsushi; Shirakawa, Motoaki; Nakamura, Toshio; Koda, Kenji; Yokoyama, Hidetaro

    2016-02-21

    Gastrointestinal duplications are uncommon congenital malformations that can occur anywhere along the gastrointestinal tract. Most cases are recognized before the age of 2 years, and those encountered in adults are rare. We describe here a case of ascending colon duplication in a 20-year-old male that caused intussusception and was treated laparoscopically. Although computed tomography revealed a cystic mass filled with stool-like material, the preoperative diagnosis was a submucosal tumor of the ascending colon. We performed a laparoscopic right colectomy, and the postoperative pathological diagnosis was duplication of the ascending colon, both cystic and tubular components. We conclude that gastrointestinal duplications, although rare, should be considered in the differential diagnosis of all abdominal and submucosal cystic lesions and that laparoscopy is a preferred approach for the surgical treatment of gastrointestinal duplications.

  15. Duplication of the mandible in Klippel-Feil syndrome.

    PubMed

    Durmus Kocaaslan, Nihal; Satır, Tevfik; Celebiler, Ozhan; Numanoğlu, Ayhan

    2013-04-01

    The duplication of the mandible is an extremely rare case, which was first described by McLaughlin in 1948 as a case report of duplication of the mouth, the tongue and the mandible. Betty in 1956 and Davies in 1973 reported similar cases. The duplication of the mandible may be associated with the Klippel-Feil syndrome (KFS). A low hairline, short neck with cervical vertebral fusion and painless limitation of the head movement are the characteristic findings of this syndrome. The incidence of the syndrome varies from 1/30,000 to 1/40,000. Although autosomal recessive inheritance was suggested, no familial inheritance was found in some cases. A very rare case of mandibular duplication in association with KFS, whose duplicated mass was removed following distraction, has been reported. Copyright © 2012 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

  16. Screening for MLL tandem duplication in 387 unselected patients with AML identify a prognostically unfavorable subset of AML.

    PubMed

    Schnittger, S; Kinkelin, U; Schoch, C; Heinecke, A; Haase, D; Haferlach, T; Büchner, T; Wörmann, B; Hiddemann, W; Griesinger, F

    2000-05-01

    Partial tandem duplications of the MLL gene have been associated with trisomy 11 in acute myeloid leukemia (AML) and recently, have also been reported for karyotypically normal AML. In order to test the incidence and prognostic importance of this molecular marker, we have analyzed eight cases of AML with trisomy 11 and 387 unselected consecutive cases with AML for partial duplications of the MLL gene. Patients with normal karyotypes and those with various chromosome aberrations were included. De novo as well as secondary leukemias including all FAB subtypes were analyzed. Performing a one-step RT-PCR with 35 cycles using an exon 9 forward primer and an exon 3 reverse primer partial tandem duplications of the MLL gene were demonstrated in 3/8 (37.5%) patients with trisomy 11. In addition, 13/387 (3.4%) of unselected cases revealed a tandem duplication. Ten of these 13 cases were cytogenetically normal, the other three cases had < or =2 additional chromosomal alterations. Sequencing of the RT-PCR products of all 16 positive cases revealed fusions of MLL exon 9/exon 3 (e9/e3) (six cases), e10/e3 (three cases), e11/e3 (four cases) or combinations of differentially spliced e10/e3 and e11/e3 (three cases) transcripts. The duplications were confirmed by genomic long range PCR and Southern blot hybridization. Twelve cases with the MLL duplication were de novo myeloid leukemia, one was a secondary AML after MDS, three were therapy-related AML (t-AML). Of the 16 MLL-duplication positive cases, seven were classified as FAB M2, two as M1, five as M4, one as M0, one as M5b. The mean age was 62.3 years for patients with MLL duplication vs 50.3 years for the control group. Of 15 adult patients, 12 received treatment. Of these, three were nonresponders, five had early relapse (< or =6 months), four relapsed between 7 and 12 months. Median survival and relapse-free interval of the MLL duplication positive group was significantly worse than those of an age-matched karyotypically

  17. Gene duplication in the evolution of sexual dimorphism.

    PubMed

    Wyman, Minyoung J; Cutter, Asher D; Rowe, Locke

    2012-05-01

    Males and females share most of the same genes, so selection in one sex will typically produce a correlated response in the other sex. Yet, the sexes have evolved to differ in a multitude of behavioral, morphological, and physiological traits. How did this sexual dimorphism evolve despite the presence of a common underlying genome? We investigated the potential role of gene duplication in the evolution of sexual dimorphism. Because duplication events provide extra genetic material, the sexes each might use this redundancy to facilitate sex-specific gene expression, permitting the evolution of dimorphism. We investigated this hypothesis at the genome-wide level in Drosophila melanogaster, using the presence of sex-biased expression as a proxy for the sex-specific specialization of gene function. We expected that if sexually antagonistic selection is a potent force acting upon individual genes, duplication will result in paralog families whose members differ in sex-biased expression. Gene members of the same duplicate family can have different expression patterns in males versus females. In particular, duplicate pairs containing a male-biased gene are found more frequently than expected, in agreement with previous studies. Furthermore, when the singleton ortholog is unbiased, duplication appears to allow one of the paralog copies to acquire male-biased expression. Conversely, female-biased expression is not common among duplicates; fewer duplicate genes are expressed in the female-soma and ovaries than in the male-soma and testes. Expression divergence exists more in older than in younger duplicates pairs, but expression divergence does not correlate with protein sequence divergence. Finally, genomic proximity may have an effect on whether paralogs differ in sex-biased expression. We conclude that the data are consistent with a role of gene duplication in fostering male-biased, but not female-biased, gene expression, thereby aiding the evolution of sexual dimorphism.

  18. The probability of duplicate gene preservation by subfunctionalization.

    PubMed Central

    Lynch, M; Force, A

    2000-01-01

    It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 10(5) or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene. PMID:10629003

  19. Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

    PubMed Central

    Barker, Michael S.; Kane, Nolan C.; Matvienko, Marta; Kozik, Alexander; Michelmore, Richard W.; Knapp, Steven J.; Rieseberg, Loren H.

    2008-01-01

    Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae—a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33–38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest

  20. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years.

    PubMed

    Barker, Michael S; Kane, Nolan C; Matvienko, Marta; Kozik, Alexander; Michelmore, Richard W; Knapp, Steven J; Rieseberg, Loren H

    2008-11-01

    Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae-a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33-38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest that

  1. A new case of de novo 11q duplication in a patient with normal development and intelligence and review of the literature.

    PubMed

    Zarate, Yuri A; Kogan, Jillene M; Schorry, Elizabeth K; Smolarek, Teresa A; Hopkin, Robert J

    2007-02-01

    A new case of 11q interstitial duplication is reported in a patient with mild dysmorphic features but normal development. Chromosome analysis revealed a de novo 11q dup(11)(q14.1q21) on G banding and FISH studies. Additional molecular genetic studies revealed a similar but more distal duplication at the level of 11q21q23.1. Previous cases of isolated 11q duplication that overlapped with this case were associated with a wide variety of clinical findings and variable developmental disability. These cases all included additional material not duplicated in this patient. The current case represents the first de novo case of 11q duplication with normal development suggesting that the segment between 11q14.1 and 11q21 contains few genes that are dose sensitive. Review of other cases that have used conventional cytogenetic resolution studies suggests that the band 11q13.5 may contain genes contributing to the developmental disabilities in the cases previously reported with proximal 11q duplication. Differences between conventional cytogenetic techniques and newer molecular genetic studies are expected. These newer techniques will help refine prognosis and counseling for families in the future. (c) 2007 Wiley-Liss, Inc.

  2. An unusual variant of the abducens nerve duplication with two nerve trunks merging within the orbit: a case report with comments on developmental background.

    PubMed

    Wysiadecki, Grzegorz; Polguj, Michał; Topol, Mirosław

    2016-07-01

    This study reports the first case of abducens nerve duplication along its entire intracranial course, ending within the orbit. A distinct abducens nerve duplication reaching the common tendinous ring (annulus of Zinn), as well as another split within the intraconal segment of the nerve have been revealed. Additionally, two groups (superior and inferior) of abducens nerve sub-branches to the lateral rectus muscle were visualised using Sihler's stain. The analysed anatomical variation has never been reported before and it seems to be in the middle of the spectrum between the cases of duplication occurring only within the intracranial segments of the abducens nerve found in the literature and those continuing throughout the whole course of the nerve. Abducens nerve duplication may be treated as a relic of early stages of ontogenesis. Such a variant might result from alternative developmental pathways in which axons of the abducens nerve, specific for a given segment of the lateral rectus muscle, run separately at some stage, instead of forming a single stem.

  3. Successful management of lower-pole moiety ureteropelvic junction obstruction in a partially duplicated collecting system using minimally invasive retrograde endoscopic techniques.

    PubMed

    Bruno, D; Delvecchio, F C; Preminger, G M

    2000-11-01

    Although the true incidence of ureteropelvic junction (UPJ) obstruction in the lower-pole moiety of an incompletely duplicated renal collecting system remains elusive, the description of this entity in the published literature is exceedingly rare. To our knowledge, we report the first case of this entity managed successfully by ureteroscopic holmium laser incision of the stenotic UPJ segment. This case underscores the utility of minimally invasive techniques in the management of selected cases of UPJ obstruction associated with a partially duplicated collecting system.

  4. Accumulated quiescent neural stem cells in adult hippocampus of the mouse model for the MECP2 duplication syndrome

    PubMed Central

    Chen, Zhifang; Li, Xiao; Zhou, Jingjing; Yuan, Bo; Yu, Bin; Tong, Dali; Cheng, Cheng; Shao, Yinqi; Xia, Shengnan; Zhang, Ran; Lyu, Jingwen; Yu, Xiuya; Dong, Chen; Zhou, Wen-Hao; Qiu, Zilong

    2017-01-01

    Duplications of Methyl CpG binding protein 2 (MECP2) -containing segments lead to the MECP2 duplication syndrome, in which severe autistic symptoms were identified. Whether adult neurogenesis may play a role in pathogenesis of autism and the role of MECP2 on state determination of adult neural stem cells (NSCs) remain largely unclear. Using a MECP2 transgenic (TG) mouse model for the MECP2 duplication syndrome, we found that adult hippocampal quiescent NSCs were significantly accumulated in TG mice comparing to wild type (WT) mice, the neural progenitor cells (NPCs) were reduced and the neuroblasts were increased in adult hippocampi of MECP2 TG mice. Interestingly, we found that parvalbumin (PV) positive interneurons were significantly decreased in MECP2 TG mice, which were critical for determining fates of adult hippocampal NSCs between the quiescence and activation. In summary, we found that MeCP2 plays a critical role in regulating fate determination of adult NSCs. These evidences further suggest that abnormal development of NSCs may play a role in the pathogenesis of the MECP2 duplication syndrome. PMID:28139724

  5. Autism and other Neuropsychiatric Symptoms are Prevalent in Individuals with MECP2 Duplication Syndrome

    PubMed Central

    Ramocki, Melissa B.; Peters, Sarika U.; Tavyev, Y. Jane; Zhang, Feng; Carvalho, Claudia M. B.; Schaaf, Christian P.; Fang, Ronald Richman, Ping; Glaze, Daniel G.; Lupski, James R.; Zoghbi, Huda Y.

    2009-01-01

    Objective There have been no objective assessments to determine whether boys with MECP2 duplication have autism or whether female carriers manifest phenotypes. This study characterizes the clinical and neuropsychiatric phenotypes of affected boys and carrier females. Methods Eight families (9 males and 9 females) with MECP2 duplication participated. A detailed history, physical examination, electroencephalogram, developmental evaluation, Autism Diagnostic Observation Schedule, and Autism Diagnostic Interview – Revised was performed for each boy. Carrier females completed the Symptom Checklist-90-R, Wechsler Abbreviated Scale of Intelligence, Broad Autism Phenotype Questionnaire, and detailed medical and mental health histories. Size and gene content of each duplication were determined by array-CGH. X-chromosome inactivation patterns were analyzed using leukocyte DNA. MECP2 and IRAK1 RNA levels were quantified from lymphoblast cell lines, and Western blots were performed to assess MeCP2 protein levels. Results All of the boys demonstrate mental retardation and autism. Poor expressive language, gaze avoidance, repetitive behaviors, anxiety, and atypical socialization were prevalent. Female carriers have psychiatric symptoms including generalized anxiety, depression, and compulsions that preceded the birth of their children. The majority exhibited features of the broad autism phenotype and had higher nonverbal compared to verbal reasoning skills. Interpretation Autism is a defining feature of the MECP2 duplication syndrome in boys. Females manifest phenotypes despite 100% skewing of X-inactivation and normal MECP2 RNA levels in peripheral blood. Analysis of the duplication size, MECP2 and IRAK1 RNA levels, and MeCP2 protein levels revealed that most of the traits in affected boys are likely due to the genomic region spanning MECP2 and IRAK1. The phenotypes observed in carrier females may be secondary to tissue-specific dosage alterations and require further study

  6. Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors

    PubMed Central

    Radó-Trilla, Núria; Arató, Krisztina; Pegueroles, Cinta; Raya, Alicia; de la Luna, Susana; Albà, M. Mar

    2015-01-01

    The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes. PMID:25931513

  7. Increasing Enrollment through Benefit Segmentation.

    ERIC Educational Resources Information Center

    Goodnow, Betty

    1982-01-01

    The applicability of benefit segmentation, a market research technique which groups people according to benefits expected from a program offering, was tested at the College of DuPage. Preferences and demographic characteristics were analyzed and program improvements adopted, increasing enrollment by 20 percent. (Author/SK)

  8. Increasing Enrollment through Benefit Segmentation.

    ERIC Educational Resources Information Center

    Goodnow, Betty

    1982-01-01

    The applicability of benefit segmentation, a market research technique which groups people according to benefits expected from a program offering, was tested at the College of DuPage. Preferences and demographic characteristics were analyzed and program improvements adopted, increasing enrollment by 20 percent. (Author/SK)

  9. Novel Duplicate Address Detection with Hash Function

    PubMed Central

    Song, GuangJia; Ji, ZhenZhou

    2016-01-01

    Duplicate address detection (DAD) is an important component of the address resolution protocol (ARP) and the neighbor discovery protocol (NDP). DAD determines whether an IP address is in conflict with other nodes. In traditional DAD, the target address to be detected is broadcast through the network, which provides convenience for malicious nodes to attack. A malicious node can send a spoofing reply to prevent the address configuration of a normal node, and thus, a denial-of-service attack is launched. This study proposes a hash method to hide the target address in DAD, which prevents an attack node from launching destination attacks. If the address of a normal node is identical to the detection address, then its hash value should be the same as the “Hash_64” field in the neighboring solicitation message. Consequently, DAD can be successfully completed. This process is called DAD-h. Simulation results indicate that address configuration using DAD-h has a considerably higher success rate when under attack compared with traditional DAD. Comparative analysis shows that DAD-h does not require third-party devices and considerable computing resources; it also provides a lightweight security resolution. PMID:26991901

  10. Robust Duplication with Comparison Methods in Microcontrollers

    SciTech Connect

    Quinn, Heather Marie; Baker, Zachary Kent; Fairbanks, Thomas D.; Tripp, Justin Leonard; Duran Il, Melvin George

    2016-01-01

    Commercial microprocessors could be useful computational platforms in space systems, as long as the risk is bound. Many spacecraft are computationally constrained because all of the computation is done on a single radiation-hardened microprocessor. It is possible that a commercial microprocessor could be used for configuration, monitoring and background tasks that are not mission critical. Most commercial microprocessors are affected by radiation, including single-event effects (SEEs) that could be destructive to the component or corrupt the data. Part screening can help designers avoid components with destructive failure modes, and mitigation can suppress data corruption. We have been experimenting with a method for masking radiation-induced faults through the software executing on the microprocessor. While triple-modular redundancy (TMR) techniques are very effective at masking faults in software, the increased amount of execution time to complete the computation is not desirable. Here in this article we present a technique for combining duplication with compare (DWC) with TMR that decreases observable errors by as much as 145 times with only a 2.35 time decrease in performance.

  11. Robust Duplication with Comparison Methods in Microcontrollers

    DOE PAGES

    Quinn, Heather Marie; Baker, Zachary Kent; Fairbanks, Thomas D.; ...

    2016-01-01

    Commercial microprocessors could be useful computational platforms in space systems, as long as the risk is bound. Many spacecraft are computationally constrained because all of the computation is done on a single radiation-hardened microprocessor. It is possible that a commercial microprocessor could be used for configuration, monitoring and background tasks that are not mission critical. Most commercial microprocessors are affected by radiation, including single-event effects (SEEs) that could be destructive to the component or corrupt the data. Part screening can help designers avoid components with destructive failure modes, and mitigation can suppress data corruption. We have been experimenting with amore » method for masking radiation-induced faults through the software executing on the microprocessor. While triple-modular redundancy (TMR) techniques are very effective at masking faults in software, the increased amount of execution time to complete the computation is not desirable. Here in this article we present a technique for combining duplication with compare (DWC) with TMR that decreases observable errors by as much as 145 times with only a 2.35 time decrease in performance.« less

  12. Nearby Dwarf Stars: Duplicity, Binarity, and Masses

    NASA Astrophysics Data System (ADS)

    Mason, Brian D.; Hatkopf, William I.; Raghavan, Deepak

    2008-02-01

    Double stars have proven to be both a blessing and a curse for astronomers since their discovery over two centuries ago. They remain the only reliable source of masses, the most fundamental parameter defining stars. On the other hand, their sobriquet ``vermin of the sky'' is well-earned, due to the complications they present to both observers and theoreticians. These range from non-linear proper motions to stray light in detectors, to confusion in pointing of instruments due to non-symmetric point spread functions, to angular momentum conservation in multiple stars which results in binaries closer than allowed by evolution of two single stars. This proposal is an effort to address both their positive and negative aspects, through speckle interferometric observations, targeting ~1200 systems where useful information can be obtained with only a single additional observation. The proposed work will refine current statistics regarding duplicity (chance alignments of nearby point sources) and binarity (actual physical relationships), and improve the precisions and accuracies of stellar masses. Several targets support Raghavan's Ph.D. thesis, which is a comprehensive survey aimed at determining the multiplicity fraction among solar-type stars.

  13. Nearby Dwarf Stars: Duplicity, Binarity, and Masses

    NASA Astrophysics Data System (ADS)

    Mason, Brian D.; Hartkopf, William I.; Raghavan, Deepak

    2007-08-01

    Double stars have proven to be both a blessing and a curse for astronomers since their discovery over two centuries ago. They remain the only reliable source of masses, the most fundamental parameter defining stars. On the other hand, their sobriquet ``vermin of the sky'' is well-earned, due to the complications they present to both observers and theoreticians. These range from non-linear proper motions to stray light in detectors, to confusion in pointing of instruments due to non-symmetric point spread functions, to angular momentum conservation in multiple stars which results in binaries closer than allowed by evolution of two single stars. This proposal is an effort to address both their positive and negative aspects, through speckle interferometric observations, targeting ~1200 systems where useful information can be obtained with only a single additional observation. The proposed work will refine current statistics regarding duplicity (chance alignments of nearby point sources) and binarity (actual physical relationships), and improve the precisions and accuracies of stellar masses. Several targets support Raghavan's Ph.D. thesis, which is a comprehensive survey aimed at determining the multiplicity fraction among solar-type stars.

  14. Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity

    USDA-ARS?s Scientific Manuscript database

    We have expanded upon a previously reported comparative genomics approach using a read-depth (JaRMs) and a hybrid read-pair, split-read (RAPTR-SV) copy number variation (CNV) detection method that uses read alignments to the cattle reference genome in order to identify species-specific genomic rearr...

  15. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean

    USDA-ARS?s Scientific Manuscript database

    Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean (Glycine max (L.) Merrill) pl...

  16. Large national series of patients with Xq28 duplication involving MECP2: Delineation of brain MRI abnormalities in 30 affected patients.

    PubMed

    El Chehadeh, Salima; Faivre, Laurence; Mosca-Boidron, Anne-Laure; Malan, Valérie; Amiel, Jeanne; Nizon, Mathilde; Touraine, Renaud; Prieur, Fabienne; Pasquier, Laurent; Callier, Patrick; Lefebvre, Mathilde; Marle, Nathalie; Dubourg, Christèle; Julia, Sophie; Sarret, Catherine; Francannet, Christine; Laffargue, Fanny; Boespflug-Tanguy, Odile; David, Albert; Isidor, Bertrand; Le Caignec, Cédric; Vigneron, Jacqueline; Leheup, Bruno; Lambert, Laetitia; Philippe, Christophe; Cuisset, Jean-Marie; Andrieux, Joris; Plessis, Ghislaine; Toutain, Annick; Goldenberg, Alice; Cormier-Daire, Valérie; Rio, Marlène; Bonnefont, Jean-Paul; Thevenon, Julien; Echenne, Bernard; Journel, Hubert; Afenjar, Alexandra; Burglen, Lydie; Bienvenu, Thierry; Addor, Marie-Claude; Lebon, Sébastien; Martinet, Danièle; Baumann, Clarisse; Perrin, Laurence; Drunat, Séverine; Jouk, Pierre-Simon; Devillard, Françoise; Coutton, Charles; Lacombe, Didier; Delrue, Marie-Ange; Philip, Nicole; Moncla, Anne; Badens, Catherine; Perreton, Nathalie; Masurel, Alice; Thauvin-Robinet, Christel; Des Portes, Vincent; Guibaud, Laurent

    2016-01-01

    Xq28 duplications encompassing MECP2 have been described in male patients with a severe neurodevelopmental disorder associated with hypotonia and spasticity, severe learning disability, stereotyped movements, and recurrent pulmonary infections. We report on standardized brain magnetic resonance imaging (MRI) data of 30 affected patients carrying an Xq28 duplication involving MECP2 of various sizes (228 kb to 11.7 Mb). The aim of this study was to seek recurrent malformations and attempt to determine whether variations in imaging features could be explained by differences in the size of the duplications. We showed that 93% of patients had brain MRI abnormalities such as corpus callosum abnormalities (n = 20), reduced volume of the white matter (WM) (n = 12), ventricular dilatation (n = 9), abnormal increased hyperintensities on T2-weighted images involving posterior periventricular WM (n = 6), and vermis hypoplasia (n = 5). The occipitofrontal circumference varied considerably between >+2SD in five patients and <-2SD in four patients. Among the nine patients with dilatation of the lateral ventricles, six had a duplication involving L1CAM. The only patient harboring bilateral posterior subependymal nodular heterotopia also carried an FLNA gene duplication. We could not demonstrate a correlation between periventricular WM hyperintensities/delayed myelination and duplication of the IKBKG gene. We thus conclude that patients with an Xq28 duplication involving MECP2 share some similar but non-specific brain abnormalities. These imaging features, therefore, could not constitute a diagnostic clue. The genotype-phenotype correlation failed to demonstrate a relationship between the presence of nodular heterotopia, ventricular dilatation, WM abnormalities, and the presence of FLNA, L1CAM, or IKBKG, respectively, in the duplicated segment.

  17. Gastric duplication cyst: A cause of rectal bleeding in a young child.

    PubMed

    Surridge, Clare A; Goodier, Matthew D

    2014-01-01

    Gastric duplication cysts are an uncommon congenital anomaly and rectal bleeding is a rare presentation of a complicated gastric duplication cyst. This case report describes the radiological findings in a child with a complicated gastric duplication cyst.

  18. The "Bilhaut-Cloquet" technique for treatment of thumb duplication.

    PubMed

    Samson, P; Salazard, B; Magalon, G

    2004-01-01

    The presentation of thumb duplication is variable depending on the level of bifurcation, the relative sizes of the two thumbs and their possible symmetry along a longitudinal axis. Resection of the supernumerary thumb often leads to disappointing results when both thumbs are hypoplastic. The principle of the "Bilhaut-Cloquet" procedure involves central resection of the duplication followed by fusion of the remaining lateral portions, in order to obtain a thumb of satisfactory volume. Thirteen children with unilateral thumb duplication were treated using the "Bilhaut-Cloquet" procedure. Nine cases involved duplication of the distal phalanx (Wassel type II). Five of these duplications were symmetrical and four were asymmetrical with an associated proximal delta phalanx. In these cases, a corrective osteotomy of the delta phalanx was performed at the same time. Four cases involved symmetrical duplications of both proximal and distal phalanges (Wassel type IV). The mean age at time of surgery was 11.5 months. Patients were reviewed with a mean follow-up of four years. The aesthetic aspect of the nail was judged as good in 12 cases. In one case, the aesthetic aspect of the nail was judged as fair due to a prominent longitudinal ridge. Bony fusion was obtained in all cases but one. The alignment was corrected in all cases but four, involving asymmetrical duplications. Joint mobility was limited in all patients. The "Bilhaut-Cloquet" technique leads to a satisfactory volume of the thumb in selected cases. Good correction of preoperative angular deformity is obtained in symmetrical cases. A precise technique of bone and nail approximation yields good functional and aesthetic results. The "Bilhaut-Cloquet" technique is indicated in balanced and symmetrical duplications, when the two thumbs are severely hypoplastic. It can be used either in the distal or proximal phalangeal types of thumb duplication.

  19. The probability of preservation of a newly arisen gene duplicate.

    PubMed

    Lynch, M; O'Hely, M; Walsh, B; Force, A

    2001-12-01

    Newly emerging data from genome sequencing projects suggest that gene duplication, often accompanied by genetic map changes, is a common and ongoing feature of all genomes. This raises the possibility that differential expansion/contraction of various genomic sequences may be just as important a mechanism of phenotypic evolution as changes at the nucleotide level. However, the population-genetic mechanisms responsible for the success vs. failure of newly arisen gene duplicates are poorly understood. We examine the influence of various aspects of gene structure, mutation rates, degree of linkage, and population size (N) on the joint fate of a newly arisen duplicate gene and its ancestral locus. Unless there is active selection against duplicate genes, the probability of permanent establishment of such genes is usually no less than 1/(4N) (half of the neutral expectation), and it can be orders of magnitude greater if neofunctionalizing mutations are common. The probability of a map change (reassignment of a key function of an ancestral locus to a new chromosomal location) induced by a newly arisen duplicate is also generally >1/(4N) for unlinked duplicates, suggesting that recurrent gene duplication and alternative silencing may be a common mechanism for generating microchromosomal rearrangements responsible for postreproductive isolating barriers among species. Relative to subfunctionalization, neofunctionalization is expected to become a progressively more important mechanism of duplicate-gene preservation in populations with increasing size. However, even in large populations, the probability of neofunctionalization scales only with the square of the selective advantage. Tight linkage also influences the probability of duplicate-gene preservation, increasing the probability of subfunctionalization but decreasing the probability of neofunctionalization.

  20. The probability of preservation of a newly arisen gene duplicate.

    PubMed Central

    Lynch, M; O'Hely, M; Walsh, B; Force, A

    2001-01-01

    Newly emerging data from genome sequencing projects suggest that gene duplication, often accompanied by genetic map changes, is a common and ongoing feature of all genomes. This raises the possibility that differential expansion/contraction of various genomic sequences may be just as important a mechanism of phenotypic evolution as changes at the nucleotide level. However, the population-genetic mechanisms responsible for the success vs. failure of newly arisen gene duplicates are poorly understood. We examine the influence of various aspects of gene structure, mutation rates, degree of linkage, and population size (N) on the joint fate of a newly arisen duplicate gene and its ancestral locus. Unless there is active selection against duplicate genes, the probability of permanent establishment of such genes is usually no less than 1/(4N) (half of the neutral expectation), and it can be orders of magnitude greater if neofunctionalizing mutations are common. The probability of a map change (reassignment of a key function of an ancestral locus to a new chromosomal location) induced by a newly arisen duplicate is also generally >1/(4N) for unlinked duplicates, suggesting that recurrent gene duplication and alternative silencing may be a common mechanism for generating microchromosomal rearrangements responsible for postreproductive isolating barriers among species. Relative to subfunctionalization, neofunctionalization is expected to become a progressively more important mechanism of duplicate-gene preservation in populations with increasing size. However, even in large populations, the probability of neofunctionalization scales only with the square of the selective advantage. Tight linkage also influences the probability of duplicate-gene preservation, increasing the probability of subfunctionalization but decreasing the probability of neofunctionalization. PMID:11779815

  1. Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

    PubMed Central

    2011-01-01

    Background Dlx (Distal-less) genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development. PMID:21846345

  2. Foregut duplication cysts of the stomach with respiratory epithelium

    PubMed Central

    Theodosopoulos, Theodosios; Marinis, Athanasios; Karapanos, Konstantinos; Vassilikostas, Georgios; Dafnios, Nikolaos; Samanides, Lazaros; Carνounis, Εleni

    2007-01-01

    Gastrointestinal duplication is a congenital rare disease entity. Gastric duplication cysts seem to appear even more rarely. Herein, two duplications cysts of the stomach in a 46 year-old female patient are presented. Abdominal computed tomography demonstrated a cystic lesion attached to the posterior aspect of the gastric fundus, while upper gastrointestinal endoscopy was negative. An exploratory laparotomy revealed a non-communicating cyst and a smaller similar cyst embedded in the gastrosplenic ligament. Excision of both cysts along with the spleen was performed and pathology reported two smooth muscle coated cysts with a pseudostratified ciliated epithelial lining (respiratory type). PMID:17451215

  3. Foregut duplication cysts of the stomach with respiratory epithelium.

    PubMed

    Theodosopoulos, Theodosios; Marinis, Athanasios; Karapanos, Konstantinos; Vassilikostas, Georgios; Dafnios, Nikolaos; Samanides, Lazaros; Carvounis, Eleni

    2007-02-28

    Gastrointestinal duplication is a congenital rare disease entity. Gastric duplication cysts seem to appear even more rarely. Herein, two duplications cysts of the stomach in a 46 year-old female patient are presented. Abdominal computed tomography demonstrated a cystic lesion attached to the posterior aspect of the gastric fundus, while upper gastrointestinal endoscopy was negative. An exploratory laparotomy revealed a non-communicating cyst and a smaller similar cyst embedded in the gastrosplenic ligament. Excision of both cysts along with the spleen was performed and pathology reported two smooth muscle coated cysts with a pseudostratified ciliated epithelial lining (respiratory type).

  4. Methods, apparatus and system for selective duplication of subtasks

    DOEpatents

    Andrade Costa, Carlos H.; Cher, Chen-Yong; Park, Yoonho; Rosenburg, Bryan S.; Ryu, Kyung D.

    2016-03-29

    A method for selective duplication of subtasks in a high-performance computing system includes: monitoring a health status of one or more nodes in a high-performance computing system, where one or more subtasks of a parallel task execute on the one or more nodes; identifying one or more nodes as having a likelihood of failure which exceeds a first prescribed threshold; selectively duplicating the one or more subtasks that execute on the one or more nodes having a likelihood of failure which exceeds the first prescribed threshold; and notifying a messaging library that one or more subtasks were duplicated.

  5. Benchmarks for measurement of duplicate detection methods in nucleotide databases.

    PubMed

    Chen, Qingyu; Zobel, Justin; Verspoor, Karin

    2017-01-08

    Duplication of information in databases is a major data quality challenge. The presence of duplicates, implying either redundancy or inconsistency, can have a range of impacts on the quality of analyses that use the data. To provide a sound basis for research on this issue in databases of nucleotide sequences, we have developed new, large-scale validated collections of duplicates, which can be used to test the effectiveness of duplicate detection methods. Previous collections were either designed primarily to test efficiency, or contained only a limited number of duplicates of limited kinds. To date, duplicate detection methods have been evaluated on separate, inconsistent benchmarks, leading to results that cannot be compared and, due to limitations of the benchmarks, of questionable generality. In this study, we present three nucleotide sequence database benchmarks, based on information drawn from a range of resources, including information derived from mapping to two data sections within the UniProt Knowledgebase (UniProtKB), UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. Each benchmark has distinct characteristics. We quantify these characteristics and argue for their complementary value in evaluation. The benchmarks collectively contain a vast number of validated biological duplicates; the largest has nearly half a billion duplicate pairs (although this is probably only a tiny fraction of the total that is present). They are also the first benchmarks targeting the primary nucleotide databases. The records include the 21 most heavily studied organisms in molecular biology research. Our quantitative analysis shows that duplicates in the different benchmarks, and in different organisms, have different characteristics. It is thus unreliable to evaluate duplicate detection methods against any single benchmark. For example, the benchmark derived from UniProtKB/Swiss-Prot mappings identifies more diverse types of duplicates, showing the importance of expert curation, but

  6. Four segment piezo based micropump

    NASA Astrophysics Data System (ADS)

    Haldkar, Rakesh Kumar; Sheorey, Tanuja; Gupta, Vijay Kumar; Ansari, M. Zahid

    2017-06-01

    In recent years, micropumps have been investigated by various researchers as drug delivery and disease diagnostic devices. Many of these micropumps have been designed, considering available micro fabrication technologies rather than appropriate pump performance analysis. Piezoelectric based micro pumps are more popular as compared to other smart materials being explored. In this paper, four segment piezoelectric bimorph actuator (FSPB) are compared with circular disc piezoelectric bimorph actuator (CDPB) based pump. The static and transient behaviors under various electric fields have been analyzed by using ANSYS 12.1(R) finite element software. Simulation results show that dividing the actuator in segment can amplify the deflection and improve the performance of the pump.

  7. Surface-Based Morphometry of Cortical Thickness and Surface Area Associated with Heschl's Gyri Duplications in 430 Healthy Volunteers

    PubMed Central

    Marie, Damien; Maingault, Sophie; Crivello, Fabrice; Mazoyer, Bernard; Tzourio-Mazoyer, Nathalie

    2016-01-01

    We applied Surface-Based Morphometry to assess the variations in cortical thickness (CT) and cortical surface area (CSA) in relation to the occurrence of Heschl's gyrus (HG) duplications in each hemisphere. 430 healthy brains that had previously been classified as having a single HG, Common Stem Duplication (CSD) or Complete Posterior Duplication (CPD) in each hemisphere were analyzed. To optimally align the HG area across the different groups of gyrification, we computed a specific surface-based template composed of 40 individuals with a symmetrical HG gyrification pattern (20 single HG, 10 CPD, 10 CSD). After normalizing the 430 participants' T1 images to this specific template, we separately compared the groups constituted of participants with a single HG, CPD, and CSD in each hemisphere. The occurrence of a duplication in either hemisphere was associated with an increase in CT posterior to the primary auditory cortex. This may be the neural support of expertise or great abilities in either speech or music processing domains that were related with duplications by previous studies. A decrease in CSA in the planum temporale was detected in cases with duplication in the left hemisphere. In the right hemisphere, a medial decrease in CSA and a lateral increase in CSA were present in HG when a CPD occurred together with an increase in CSA in the depth of the superior temporal sulcus (STS) in CSD compared to a single HG. These variations associated with duplication might be related to the functions that they process jointly within each hemisphere: temporal and speech processing in the left and spectral and music processing in the right. PMID:27014013

  8. Surface-Based Morphometry of Cortical Thickness and Surface Area Associated with Heschl's Gyri Duplications in 430 Healthy Volunteers.

    PubMed

    Marie, Damien; Maingault, Sophie; Crivello, Fabrice; Mazoyer, Bernard; Tzourio-Mazoyer, Nathalie

    2016-01-01

    We applied Surface-Based Morphometry to assess the variations in cortical thickness (CT) and cortical surface area (CSA) in relation to the occurrence of Heschl's gyrus (HG) duplications in each hemisphere. 430 healthy brains that had previously been classified as having a single HG, Common Stem Duplication (CSD) or Complete Posterior Duplication (CPD) in each hemisphere were analyzed. To optimally align the HG area across the different groups of gyrification, we computed a specific surface-based template composed of 40 individuals with a symmetrical HG gyrification pattern (20 single HG, 10 CPD, 10 CSD). After normalizing the 430 participants' T1 images to this specific template, we separately compared the groups constituted of participants with a single HG, CPD, and CSD in each hemisphere. The occurrence of a duplication in either hemisphere was associated with an increase in CT posterior to the primary auditory cortex. This may be the neural support of expertise or great abilities in either speech or music processing domains that were related with duplications by previous studies. A decrease in CSA in the planum temporale was detected in cases with duplication in the left hemisphere. In the right hemisphere, a medial decrease in CSA and a lateral increase in CSA were present in HG when a CPD occurred together with an increase in CSA in the depth of the superior temporal sulcus (STS) in CSD compared to a single HG. These variations associated with duplication might be related to the functions that they process jointly within each hemisphere: temporal and speech processing in the left and spectral and music processing in the right.

  9. 7 CFR 91.29 - Issuance of duplicate certificates or reissuance of an analysis report.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE... initial analysis report shall be shown on the duplicate form. (e) Duplicate certificates or...

  10. Phasing piston error in segmented telescopes.

    PubMed

    Jiang, Junlun; Zhao, Weirui

    2016-08-22

    To achieve a diffraction-limited imaging, the piston errors between the segments of the segmented primary mirror telescope should be reduced to λ/40 RMS. We propose a method to detect the piston error by analyzing the intensity distribution on the image plane according to the Fourier optics principle, which can capture segments with the piston errors as large as the coherence length of the input light and reduce these to 0.026λ RMS (λ = 633nm). This method is adaptable to any segmented and deployable primary mirror telescope. Experiments have been carried out to validate the feasibility of the method.

  11. Nature and management of duplicate medication alerts.

    PubMed

    Heringa, Mette; Floor, Annemieke; Meijer, Willemijn M; De Smet, Peter A G M; Bouvy, Marcel L

    2015-07-01

    To investigate the nature of duplicate medication (DM) alerts, their management by community pharmacists, and potential characteristics of DM alerts that lead to interventions by pharmacists. Observational study in 53 community pharmacies. Each pharmacist registered the nature and management of 24 DM alerts on a structured form. On average, the clinical decision support systems generated 20.4 DM alerts per 100 dispensed drugs. In half of the 1272 registered alerts, the pharmacists judged that there was no risk for concurrent use of both prescriptions. In 32% of the alerts, the DM alert was generated for an intentional combination. In 17% of the alerts, there was a risk for unintentional concurrent use. In 32% of the alerts the pharmacists decided that one or more actions were needed: the electronic patient record was updated in 15% of the alerts and in 19% of the alerts the pharmacists performed an external action-for example, informing the patient or modifying the prescription (including 5 therapeutic prescription modifications and 22 logistic prescription modifications). Alerts concerning first dispensing were more likely to be followed by an external action than alerts concerning refills (40% vs 14%, P < .001). In community pharmacy, prescription modifications based on DM alerts are rare, but DM alerts lead with some regularity to other actions-for example, patient instruction and update of the electronic patient record. As the current DM alerts are diverse and nonspecific in detecting situations where external action is considered relevant, other ways of alerting should therefore be considered. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Duplications of the Y-chromosome specific loci P25 and 92R7 and forensic implications.

    PubMed

    Sanchez, Juan J; Brión, Maria; Parson, Walther; Blanco-Verea, Alejandro J; Børsting, Claus; Lareu, Maviki; Niederstätter, Harald; Oberacher, Herbert; Morling, Niels; Carracedo, Angel

    2004-03-10

    In the present study, we demonstrate that two commonly used Y-chromosome single nucleotide polymorphisms (SNPs), P25 and 92R7, are paralogous sequence variants (PSVs) originating from segmental duplications and that at least one of the sequence variants in each group of loci is polymorphic. Several methodologies were used in order to detect the SNP alleles and the PSVs of the loci. All results obtained with the various typing techniques supported the conclusion. The allele distributions of the binary markers were analysed in more than 600 males with seven different haplogroups. For P25, the ancestral allele C was found in several samples from different haplogroups. The derived allele A was always present with an additional C variant. Haplogroup P was defined by the derived allele A at the 92R7 locus. However, the ancestral allele G was always associated with an A variant due to the duplication.

  13. The PTAP sequence duplication in HIV-1 subtype C Gag p6 in drug-naive subjects of India and South Africa.

    PubMed

    Sharma, Shilpee; Aralaguppe, Shambhu G; Abrahams, Melissa-Rose; Williamson, Carolyn; Gray, Clive; Balakrishnan, Pachamuthu; Saravanan, Shanmugam; Murugavel, Kailapuri G; Solomon, Suniti; Ranga, Udaykumar

    2017-01-24

    HIV-1 subtype C demonstrates several biological properties distinct from other viral subtypes. One such variation is the duplication of PTAP motif in p6 Gag. PTAP motif is a key player in viral budding. Here, we studied the prevalence of PTAP motif duplication in subtype C viral strains in a longitudinal study. In a prospective follow-up study, 65 HIV-1 seropositive drug-naive subjects were monitored in two different clinical cohorts of India for 2 years with repeated sampling at 6-month intervals. The viral RNA was extracted from plasma, the gag segment was amplified and sequenced. From a subset of viral isolates the sequences of pol, env and LTR were sequenced. Using HIV-1 gag amino acid sequences available from public databases and additional sequences derived from the Indian and South-African cohorts, we examined the nature of PTAP motif duplication in subtype C. In 16% (8 of 50) of the primary viral strains of India, we identified a sequence duplication of the PTAP motif in Gag p6. The length of the sequence duplication varied from 6 to 14 amino acids in the viral isolates but remained fixed within a subject over a period of 24-36 month follow-up. In the duplicated motif, the core PTAP motif was invariable, but the flanking residues were highly variable. In an acute phase clinical cohort of South Africa, in a subset of 75 subjects, we found the presence of the PTAP duplication at a frequency of 29.3%. An analysis of the gag sequences from the extant databases showed that unlike other subtypes of HIV-1, subtype C has a natural propensity to generate the PTAP motif duplication at a significantly higher frequency and of greater length. Additionally, the global prevalence of PTAP duplication in subtype C appears to be increasing progressively over the past 30 years. We showed that in subtype C, the duplication of the PTAP motif in p6 Gag involves sequence stretches of greater length, and at a much higher frequency as compared to other HIV-1 subtypes. Given that

  14. Massively Scalable Near Duplicate Detection in Streams of Documents using MDSH

    SciTech Connect

    Bogen, Paul Logasa; Symons, Christopher T; McKenzie, Amber T; Patton, Robert M; Gillen, Rob

    2013-01-01

    In a world where large-scale text collections are not only becoming ubiquitous but also are growing at increasing rates, near duplicate documents are becoming a growing concern that has the potential to hinder many different information filtering tasks. While others have tried to address this problem, prior techniques have only been used on limited collection sizes and static cases. We will briefly describe the problem in the context of Open Source Intelligence (OSINT) along with our additional constraints for performance. In this work we propose two variations on Multi-dimensional Spectral Hash (MDSH) tailored for working on extremely large, growing sets of text documents. We analyze the memory and runtime characteristics of our techniques and provide an informal analysis of the quality of the near-duplicate clusters produced by our techniques.

  15. 30. Duplicate view of the south end of the west ...

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

    30. Duplicate view of the south end of the west wall with light illuminating the dirt floor and showing the condition of the brick masonry, with scale - Kiskiack, Naval Mine Depot, State Route 238 vicinity, Yorktown, York County, VA

  16. Duplicate of the historic view showing the exterior of the ...

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

    Duplicate of the historic view showing the exterior of the library from approximately the same vantage point as MD-1109-Q-16 - National Park Seminary, Miller Library, 2801 Woodstock Avenue, Silver Spring, Montgomery County, MD

  17. Dietary intakes of pesticides based on community duplicate diet samples

    EPA Science Inventory

    The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from...

  18. 40 CFR 25.13 - Coordination and non-duplication.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... PROGRAMS UNDER THE RESOURCE CONSERVATION AND RECOVERY ACT, THE SAFE DRINKING WATER ACT, AND THE CLEAN WATER ACT § 25.13 Coordination and non-duplication. The public participation activities and materials...

  19. 40 CFR 25.13 - Coordination and non-duplication.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... PROGRAMS UNDER THE RESOURCE CONSERVATION AND RECOVERY ACT, THE SAFE DRINKING WATER ACT, AND THE CLEAN WATER ACT § 25.13 Coordination and non-duplication. The public participation activities and materials...

  20. Genetics Home Reference: 22q11.2 duplication

    MedlinePlus

    ... same family. Affected individuals may have developmental delay, intellectual disability, slow growth leading to short stature, and weak ... with the duplication have no apparent physical or intellectual disabilities. Related Information What does it mean if a ...

  1. Dietary intakes of pesticides based on community duplicate diet samples

    EPA Science Inventory

    The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from...

  2. 33. Duplicate view, detail of the stair and baluster on ...

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

    33. Duplicate view, detail of the stair and baluster on the southwest balcony (Note: The anchor is the symbol of the state of Rhode Island) - Cranston Street Armory, Cranston Street, Providence, Providence County, RI

  3. Proximal 10q duplication in a child with severe central hypotonia characterized by array-comparative genomic hybridization: A case report and review of the literature

    PubMed Central

    MANOLAKOS, EMMANOUIL; VETRO, ANNALISA; GARAS, ANTONIOS; THOMAIDIS, LORETTA; KEFALAS, KONSTANTINOS; KITSOS, GEORGE; ZIEGLER, MONIKA; LIEHR, THOMAS; ZUFFARDI, ORSETTA; PAPOULIDIS, IOANNIS

    2014-01-01

    Proximal 10q duplication is a well-defined but rare genetic syndrome. Duplication of proximal segments of the long arm of chromosome 10 results in a pattern of malformations, which are distinct from those of the more common distal 10q trisomy syndrome. The present study describes the case of a boy with phenotypic abnormalities (severe central hypotonia, mild ataxia, moderate developmental delay and mild dysmorphic features), due to duplication of chromosome region, 10q11.21→q11.22, which was characterized by the array-comparative genomic hybridization (CGH) technique. The phenotypic findings were compared with those in eight additional similar published cases. Major similarities have emerged, suggesting a likely minimal critical region. However, only detailed characterization of additional cases may provide firm conclusions. PMID:24669257

  4. Urethral duplication II-A Y type with rectal urethra: ASTRA approach and tunica vaginalis flap for first stage repair.

    PubMed

    Macedo, Antonio; Rondon, Atila; Bacelar, Herick; Ottoni, Sergio; Liguori, Riberto; Garrone, Gilmar; Ortiz, Valdemar

    2012-01-01

    Urethral duplication is a rare congenital anomaly affecting mainly boys. Generally, the duplication develops on the sagittal plane; the accessory urethra may run dorsally or ventrally to the orthotopic one. We present a patient with urethral duplication in which the orthotopic urethra was patent in the penile segment but atresic in the bulbar and prostatic segment. The patient had urinary flow from the rectum and the ectopic urethra could be well identified by anal examination. Age at surgery was 13 months. The procedure consisted of an ASTRA (anterior sagittal trans-ano-rectal) approach for dividing the urethra and rectum and was successful to move the urethra up to the perineal area. The rectum was reconstructed and the patient placed into a lithotomy position. A urethral catheter inserted in the penile urethra oriented us were the atresic urethra in bulbar area started. The scrotum was opened in the middle and the distance between the two urethral stumps proximal and distal defined the extension of no urethral tissue that consisted of 5 cm. We opened the right scrotal space and a tunica vaginalis flap was obtained and attached to the bulbar tissue for a two-stage urethroplasty strategy. Patient had a nice healing and the tunica vaginalis was nicely incorporated to the adjacent tissue, having the two urethral stumps well delineated. ASTRA approach in combination with a two-stage urethroplasty with tunica vaginalis dorsal flap proved to be an excellent combination for a rare case of urethral Y duplication having the main urethra into the rectum.

  5. A Challenge for Cochlear Implantation: Duplicated Internal Auditory Canal.

    PubMed

    Binnetoğlu, Adem; Bağlam, Tekin; Sarı, Murat; Gündoğdu, Yavuz; Batman, Çağlar

    2016-08-01

    Duplication of the internal auditory canal is an uncommon, congenital malformation that can be associated with sensorineural hearing loss owing to aplasia/hypoplasia of the vestibulocochlear nerve. Only 14 such cases have been reported to date. We report the case of a 13-month-old girl with bilateral, congenital, sensorineural hearing loss caused by narrow, duplicated internal auditory canals and discuss the challenges encountered in the diagnosis and treatment of this condition.

  6. Thoracoabdominal foregut duplication cyst with respiratory epithelium and alimentary epithelium.

    PubMed

    Zhang, Juan; Zhang, Ke Ren; Bai, Yu Zuo; Song, Dan; Wang, Weilin

    2010-05-01

    Thoracoabdominal foregut duplication is a rare congenital abnormality. The authors report a case of thoracoabdominal foregut duplication cyst in a 13-year-old male patient. The pathologic report revealed that a thoracic mass with a pseudostratified, ciliated, columnar epithelial lining (respiratory tract epithelium), an abdominal mass with gastric mucosa (alimentary tract epithelium), and the cyst originated from the foregut. Copyright 2010 Elsevier Inc. All rights reserved.

  7. Tessier 30 Facial Cleft with Duplication of Tongue

    PubMed Central

    Goswami, Jayanta Kumar

    2017-01-01

    A case of midline cleft of the lower lip, mandible, and the neck with complete duplication of the tongue repaired at neonatal period is reported here. Median cleft of the lower lip, mandible, and bifid tongue with ankyloglossia is reported in the literature, but cleft of the neck with complete duplication of the tongue as a part of the Tessier 30 cleft is very rare. We could not find such report in the available English literature. PMID:28082778

  8. Sibs lacking characteristic features of duplication of distal 17q.

    PubMed Central

    Ohdo, S; Madokoro, H; Sonoda, T; Ohba, K

    1989-01-01

    Two brothers with karyotype 46,XY,-16,+der(16),t(16;17)(q24.3;q25.1)pat are presented. It is commonly thought that duplication of distal 17q results in a clinically recognisable syndrome. Although our cases had several features often seen in patients with autosomal chromosome aberrations, they did not have any of the specific features found in other patients with this duplication. Images PMID:2664178

  9. [Respiratory insufficiency due to duplications of the oesophagus].

    PubMed

    Luoma, Reijo

    2015-01-01

    Duplications of the oesophagus are uncommon congenital malformations with possible occurrence in any part of the gastrointestinal tract. The duplications may be cysts, diverticula or tubular-shaped. Cysts may even occur further away from the gastrointestinal tract, not necessarily having contact with it. I present a patient case, in which a 13-month-old child was brought to the emergency room due to gradually increasing dyspnea. The child made a full recovery after the surgical procedure.

  10. Effect of removal of duplicate isolates on cumulative susceptibility reports.

    PubMed

    White, R L; Friedrich, L V; Burgess, D S; Brown, E W; Scott, L E

    2001-04-01

    The objective of our study is to assess the impact of different methods of duplicate isolate removal on cumulative susceptibility reports. Over a 1-year period, we studied the effect of 3 methods of duplicate isolate removal on the cumulative percentage susceptibility of 9 Gram-negative bacilli to 15 antimicrobials. Raw data from which no duplicate isolates were removed (NR) were generated by the Sensititre breakpoint susceptibility testing system. D3 and D7 were methods of duplicate isolate removal defined as follows: same patient, bacterial species, irrespective of susceptibility within either three (D3) or seven (D7) calendar days of the date of the previous culture. The third method evaluated was an algorithm utilized by Cerner, a laboratory management program that defines duplicate isolates as follows: same patient, bacterial species, and NCCLS susceptibility category to an individual antimicrobial. Differences in percentage susceptibility between the three methods of duplicate isolate removal and NR were assessed. The number of isolates studied ranged from 80 (E. aerogenes) to 681 (P. aeruginosa). Of the methods of duplicate isolate removal, the highest percentage susceptibility occurred most frequently with Cerner followed by D7 and D3. Differences in percentage susceptibility between methods of removal and NR ranged from -11 to 25%, -5 to 8%, and -3 to 10%, with Cerner, D3, and D7, respectively. The percentage susceptibility was at least 5% higher than NR with a method of removal for 15 individual organism/antimicrobial combinations in which susceptibility was > or = 70% by at least one of the methods. These occurred most frequently with Enterobacter species and Cerner. Although there is no consensus on the ideal method of duplicate isolate removal, one should be cognizant that these manipulations may produce different cumulative susceptibility reports.

  11. Anal Canal Duplication in an 11-Year-Old-Child

    PubMed Central

    Van Biervliet, S.; Maris, E.; Vande Velde, S.; Vande Putte, D.; Meerschaut, V.; Herregods, N.; De Bruyne, R.; Van Winckel, M.; Van Renterghem, K.

    2013-01-01

    Anal canal duplication (ACD) is the least frequent digestive duplication. Symptoms are often absent but tend to increase with age. Recognition is, however, important as almost half of the patients with ACD have concomitant malformations. We present the clinical history of an eleven-year-old girl with ACD followed by a review of symptoms, diagnosis, treatment, and prognosis based on all the reported cases in English literature. PMID:24151565

  12. [Intestinal cystic duplication in infants and the etiology of intussusception].

    PubMed

    Kasis, A; Sabo, E; Mogilner, J G; Boss, J

    1993-11-15

    2 infants, 3 months old and 8 months, respectively, with restlessness and vomiting were each found to have ileocolic intussusception with barium filling defects. Laparotomy disclosed in each a dome-shaped structure, 2 cm and 0.6 cm in greatest diameter, respectively, on the antimesenteric side of the ileal wall. Histological examination showed cystic duplication of the ileum. It is suggested that manual reduction generally fails when cystic duplication is an etiological factor, and surgery is then mandatory.

  13. Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model.

    PubMed

    Zhang, Yun; Jiang, Wen-kai; Gao, Li-zhi

    2011-01-01

    The origin and evolution of microRNA (miRNA) genes, which are of significance in tuning and buffering gene expressions in a number of critical cellular processes, have long attracted evolutionary biologists. However, genome-wide perspectives on their origins, potential mechanisms of their de novo generation and subsequent evolution remain largely unsolved in flowering plants. Here, genome-wide analyses of Oryza sativa and Arabidopsis thaliana revealed apparently divergent patterns of miRNA gene origins. A large proportion of miRNA genes in O. sativa were TE-related and MITE-related miRNAs in particular, whereas the fraction of these miRNA genes much decreased in A. thaliana. Our results show that the majority of TE-related and pseudogene-related miRNA genes have originated through inverted duplication instead of segmental or tandem duplication events. Based on the presented findings, we hypothesize and illustrate the four likely molecular mechanisms to de novo generate novel miRNA genes from TEs and pseudogenes. Our rice genome analysis demonstrates that non-MITEs and MITEs mediated inverted duplications have played different roles in de novo generating miRNA genes. It is confirmed that the previously proposed inverted duplication model may give explanations for non-MITEs mediated duplication events. However, many other miRNA genes, known from the earlier proposed model, were rather arisen from MITE transpositions into target genes to yield binding sites. We further investigated evolutionary processes spawned from de novo generated to maturely-formed miRNA genes and their regulatory systems. We found that miRNAs increase the tunability of some gene regulatory systems with low gene copy numbers. The results also suggest that gene balance effects may have largely contributed to the evolution of miRNA regulatory systems.

  14. Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy.

    PubMed

    Guo, Hai-Song; Zhang, Yan-Mei; Sun, Xiao-Qin; Li, Mi-Mi; Hang, Yue-Yu; Xue, Jia-Yu

    2016-04-01

    Very long-chain fatty acids (VLCFAs) play an important role in the survival and development of plants, and VLCFA synthesis is regulated by β-ketoacyl-CoA synthases (KCSs), which catalyze the condensation of an acyl-CoA with malonyl-CoA. Here, we present a genome-wide survey of the genes encoding these enzymes, KCS genes, in 28 species (26 genomes and two transcriptomes), which represents a large phylogenetic scale, and also reconstruct the evolutionary history of this gene family. KCS genes were initially single-copy genes in the green plant lineage; duplication resulted in five ancestral copies in land plants, forming five fundamental monophyletic groups in the phylogenetic tree. Subsequently, KCS genes duplicated to generate 11 genes of angiosperm origin, expanding up to 20-30 members in further-diverged angiosperm species. During this process, tandem duplications had only a small contribution, whereas polyploidy events and large-scale segmental duplications appear to be the main driving force. Accompanying this expansion were variations that led to the sub- and neofunctionalization of different members, resulting in specificity that is likely determined by the 3-D protein structure. Novel functions involved in other physiological processes emerged as well, though redundancy is also observed, largely among recent duplications. Conserved sites and variable sites of KCS proteins are also identified by statistical analysis. The variable sites are likely to be involved in the emergence of product specificity and catalytic power, and conserved sites are possibly responsible for the preservation of fundamental function.

  15. Heterogeneous Duplications in Patients with Pelizaeus-Merzbacher Disease Suggest a Mechanism of Coupled Homologous and Nonhomologous Recombination

    PubMed Central

    Woodward, Karen J.; Cundall, Maria; Sperle, Karen; Sistermans, Erik A.; Ross, Mark; Howell, Gareth; Gribble, Susan M.; Burford, Deborah C.; Carter, Nigel P.; Hobson, Donald L.; Garbern, James Y.; Kamholz, John; Heng, Henry; Hodes, M. E.; Malcolm, Sue; Hobson, Grace M.

    2005-01-01

    We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1–6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability. PMID:16380909

  16. Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination.

    PubMed

    Woodward, Karen J; Cundall, Maria; Sperle, Karen; Sistermans, Erik A; Ross, Mark; Howell, Gareth; Gribble, Susan M; Burford, Deborah C; Carter, Nigel P; Hobson, Donald L; Garbern, James Y; Kamholz, John; Heng, Henry; Hodes, M E; Malcolm, Sue; Hobson, Grace M

    2005-12-01

    We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1-6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability.

  17. Evolution in action: following function in duplicated floral homeotic genes.

    PubMed

    Causier, Barry; Castillo, Rosa; Zhou, Junli; Ingram, Richard; Xue, Yongbiao; Schwarz-Sommer, Zsuzsanna; Davies, Brendan

    2005-08-23

    Gene duplication plays a fundamental role in evolution by providing the genetic material from which novel functions can arise. Newly duplicated genes can be maintained by subfunctionalization (the duplicated genes perform different aspects of the original gene's function) and/or neofunctionalization (one of the genes acquires a novel function). PLENA in Antirrhinum and AGAMOUS in Arabidopsis are the canonical C-function genes that are essential for the specification of reproductive organs. These functionally equivalent genes encode closely related homeotic MADS-box transcription factors. Using genome synteny, we confirm phylogenetic analyses showing that PLENA and AGAMOUS are nonorthologous genes derived from a duplication in a common ancestor. Their respective orthologs, SHATTERPROOF in Arabidopsis and FARINELLI in Antirrhinum, have undergone independent subfunctionalization via changes in regulation and protein function. Surprisingly, the functional divergence between PLENA and FARINELLI, is morphologically manifest in both transgenic Antirrhinum and Arabidopsis. This provides a clear illustration of a random evolutionary trajectory for gene functions after a duplication event. Different members of a duplicated gene pair have retained the primary homeotic functions in different lineages, illustrating the role of chance in evolution. The differential ability of the Antirrhinum genes to promote male or female development provides a striking example of subfunctionalization at the protein level.

  18. Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

    PubMed Central

    Gout, Jean-Francois; Lynch, Michael

    2015-01-01

    Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints are major factors opposing post-WGD gene loss in several Paramecium species that share a common ancestral WGD. We propose a model where a majority of WGD-derived duplicates preserve their ancestral function and are retained to produce enough of the proteins performing this same ancestral function. Under this model, the expression level of individual duplicated genes can evolve neutrally as long as they maintain a roughly constant summed expression, and this allows random genetic drift toward uneven contributions of the two copies to total expression. Our analysis suggests that once a high level of imbalance is reached, which can require substantial lengths of time, the copy with the lowest expression level contributes a small enough fraction of the total expression that selection no longer opposes its loss. Extension of our analysis to yeast species sharing a common ancestral WGD yields similar results, suggesting that duplicated-gene retention for dosage constraints followed by divergence in expression level and eventual deterministic gene loss might be a universal feature of post-WGD evolution. PMID:25908670

  19. Phylogenomics: Gene Duplication, Unrecognized Paralogy and Outgroup Choice

    PubMed Central

    Roy, Scott William

    2009-01-01

    Comparative genomics has revealed the ubiquity of gene and genome duplication and subsequent gene loss. In the case of gene duplication and subsequent loss, gene trees can differ from species trees, thus frequent gene duplication poses a challenge for reconstruction of species relationships. Here I address the case of multi-gene sets of putative orthologs that include some unrecognized paralogs due to ancestral gene duplication, and ask how outgroups should best be chosen to reduce the degree of non-species tree (NST) signal. Consideration of expected internal branch lengths supports several conclusions: (i) when a single outgroup is used, the degree of NST signal arising from gene duplication is either independent of outgroup choice, or is minimized by use of a maximally closely related post-duplication (MCRPD) outgroup; (ii) when two outgroups are used, NST signal is minimized by using one MCRPD outgroup, while the position of the second outgroup is of lesser importance; and (iii) when two outgroups are used, the ability to detect gene trees that are inconsistent with known aspects of the species tree is maximized by use of one MCRPD, and is either independent of the position of the second outgroup, or is maximized for a more distantly related second outgroup. Overall, these results generalize the utility of closely-related outgroups for phylogenetic analysis. PMID:19234600

  20. A novel duplicate images detection method based on PLSA model

    NASA Astrophysics Data System (ADS)

    Liao, Xiaofeng; Wang, Yongji; Ding, Liping; Gu, Jian

    2012-01-01

    Web image search results usually contain duplicate copies. This paper considers the problem of detecting and clustering duplicate images contained in web image search results. Detecting and clustering the duplicate images together facilitates users' viewing. A novel method is presented in this paper to detect and cluster duplicate images by measuring similarity between their topics. More specifically, images are viewed as documents consisting of visual words formed by vector quantizing the affine invariant visual features. Then a statistical model widely used in text domain, the PLSA(Probabilistic Latent Semantic Analysis) model, is utilized to map images into a probabilistic latent semantic space. Because the main content remains unchanged despite small digital alteration, duplicate images will be close to each other in the derived semantic space. Based on this, a simple clustering process can successfully detect duplicate images and cluster them together. Comparing to those methods based on comparison between hash value of visual words, this method is more robust to the visual feature level alteration posed on the images. Experiments demonstrates the effectiveness of this method.

  1. A novel duplicate images detection method based on PLSA model

    NASA Astrophysics Data System (ADS)

    Liao, Xiaofeng; Wang, Yongji; Ding, Liping; Gu, Jian

    2011-12-01

    Web image search results usually contain duplicate copies. This paper considers the problem of detecting and clustering duplicate images contained in web image search results. Detecting and clustering the duplicate images together facilitates users' viewing. A novel method is presented in this paper to detect and cluster duplicate images by measuring similarity between their topics. More specifically, images are viewed as documents consisting of visual words formed by vector quantizing the affine invariant visual features. Then a statistical model widely used in text domain, the PLSA(Probabilistic Latent Semantic Analysis) model, is utilized to map images into a probabilistic latent semantic space. Because the main content remains unchanged despite small digital alteration, duplicate images will be close to each other in the derived semantic space. Based on this, a simple clustering process can successfully detect duplicate images and cluster them together. Comparing to those methods based on comparison between hash value of visual words, this method is more robust to the visual feature level alteration posed on the images. Experiments demonstrates the effectiveness of this method.

  2. Structure and expression analysis of rice paleo duplications.

    PubMed

    Throude, Mickael; Bolot, Stéphanie; Bosio, Mickael; Pont, Caroline; Sarda, Xavier; Quraishi, Umar Masood; Bourgis, Fabienne; Lessard, Philippe; Rogowsky, Peter; Ghesquiere, Alain; Murigneux, Alain; Charmet, Gilles; Perez, Pascual; Salse, Jérôme

    2009-03-01

    Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

  3. Structure and expression analysis of rice paleo duplications

    PubMed Central

    Throude, Mickael; Bolot, Stéphanie; Bosio, Mickael; Pont, Caroline; Sarda, Xavier; Quraishi, Umar Masood; Bourgis, Fabienne; Lessard, Philippe; Rogowsky, Peter; Ghesquiere, Alain; Murigneux, Alain; Charmet, Gilles; Perez, Pascual; Salse, Jérôme

    2009-01-01

    Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution. PMID:19136467

  4. Duplicate publication rate decline in Korean medical journals.

    PubMed

    Kim, Soo Young; Bae, Chong-Woo; Hahm, Chang Kok; Cho, Hye Min

    2014-02-01

    The purpose of this study was to examine trends in duplicate publication in Korean medical articles indexed in the KoreaMed database from 2004 to 2009, before and after a campaign against scientific misconduct launched by the Korean Association of Medical Journal Editors in 2006. The study covered period from 2007 to 2012; and 5% of the articles indexed in KoreaMed were retrieved by random sampling. Three authors reviewed full texts of the retrieved articles. The pattern of duplicate publication, such as copy, salami slicing (fragmentation), and aggregation (imalas), was also determined. Before the launching ethics campaign, the national duplication rate in medical journals was relatively high: 5.9% in 2004, 6.0% in 2005, and 7.2% in 2006. However, duplication rate steadily declined to 4.5% in 2007, 2.8% in 2008, and 1.2 % in 2009. Of all duplicated articles, 53.4% were classified as copies, 27.8% as salami slicing, and 18.8% as aggregation (imalas). The decline in duplicate publication rate took place as a result of nationwide campaigns and monitoring by KoreaMed and KoreaMed Synapse, starting from 2006.

  5. A 15 Mb large paracentric chromosome 21 inversion identified in Czech population through a pair of flanking duplications.

    PubMed

    Drabova, Jana; Trkova, Marie; Hancarova, Miroslava; Novotna, Drahuse; Hejtmankova, Michaela; Havlovicova, Marketa; Sedlacek, Zdenek

    2014-01-01

    Inversions are balanced structural chromosome rearrangements, which can influence gene expression and the risk of unbalanced chromosome constitution in offspring. Many examples of inversion polymorphisms exist in human, affecting both heterochromatic regions and euchromatin. We describe a novel, 15 Mb long paracentric inversion, inv(21)(q21.1q22.11), affecting more than a third of human 21q. Despite of its length, the inversion cannot be detected using karyotyping due to similar band patterns on the normal and inverted chromosomes, and is therefore likely to escape attention. Its identification was aided by the repeated observation of the same pair of 150 kb long duplications present in cis on chromosome 21 in three Czech families subjected to microarray analysis. The finding prompted us to hypothesise that this co-occurrence of two remote duplications could be associated with an inversion of the intervening segment, and this speculation turned out to be right. The inversion was confirmed in a series of FISH experiments which also showed that the second copy of each of the duplications was always located at the opposite end of the inversion. The presence of the same pair of duplications in additional individuals reported in public databases indicates that the inversion may also be present in other populations. Three out of the total of about 4000 chromosomes 21 examined in our sample carried the duplications and were inverted, corresponding to carrier frequency of about 1/660. Although the breakpoints affect protein-coding genes, the occurrence of the inversion in normal parents and siblings of our patients and the occurrence of the duplications in unaffected controls in databases indicate that this rare variant is rather non-pathogenic. The inverted segment carried an identical shared haplotype in the three families studied. The haplotypes, however, diverged very rapidly in the flanking regions, possibly pointing to an ancient founder event at the origin of the

  6. Efficient edit distance with duplications and contractions

    PubMed Central

    2013-01-01

    We propose three algorithms for string edit distance with duplications and contractions. These include an efficient general algorithm and two improvements which apply under certain constraints on the cost function. The new algorithms solve a more general problem variant and obtain better time complexities with respect to previous algorithms. Our general algorithm is based on min-plus multiplication of square matrices and has time and space complexities of O (|Σ|MP (n)) and O (|Σ|n2), respectively, where |Σ| is the alphabet size, n is the length of the strings, and MP (n) is the time bound for the computation of min-plus matrix multiplication of two n × n matrices (currently, MP(n)=On3log3lognlog2n due to an algorithm by Chan). For integer cost functions, the running time is further improved to O|Σ|n3log2n. In addition, this variant of the algorithm is online, in the sense that the input strings may be given letter by letter, and its time complexity bounds the processing time of the first n given letters. This acceleration is based on our efficient matrix-vector min-plus multiplication algorithm, intended for matrices and vectors for which differences between adjacent entries are from a finite integer interval D. Choosing a constant 1log|D|n<λ<1, the algorithm preprocesses an n × n matrix in On2+λ|D| time and On2+λ|D|λ2log|D|2n space. Then, it may multiply the matrix with any given n-length vector in On2λ2log|D|2n time. Under some discreteness assumptions, this matrix-vector min-plus multiplication algorithm applies to several problems from the domains of context-free grammar parsing and RNA folding and, in particular, implies the asymptotically fastest On3log2n time algorithm for single-strand RNA folding with discrete cost functions. Finally, assuming a different constraint on the cost function, we present another version of the algorithm that exploits the run-length encoding of the strings and runs in O|Σ|nMP(ñ)ñ time and O

  7. Segmented trapped vortex cavity

    NASA Technical Reports Server (NTRS)

    Grammel, Jr., Leonard Paul (Inventor); Pennekamp, David Lance (Inventor); Winslow, Jr., Ralph Henry (Inventor)

    2010-01-01

    An annular trapped vortex cavity assembly segment comprising includes a cavity forward wall, a cavity aft wall, and a cavity radially outer wall there between defining a cavity segment therein. A cavity opening extends between the forward and aft walls at a radially inner end of the assembly segment. Radially spaced apart pluralities of air injection first and second holes extend through the forward and aft walls respectively. The segment may include first and second expansion joint features at distal first and second ends respectively of the segment. The segment may include a forward subcomponent including the cavity forward wall attached to an aft subcomponent including the cavity aft wall. The forward and aft subcomponents include forward and aft portions of the cavity radially outer wall respectively. A ring of the segments may be circumferentially disposed about an axis to form an annular segmented vortex cavity assembly.

  8. Station Tour: Russian Segment

    NASA Image and Video Library

    Expedition 33 Commander Suni Williams concludes her tour of the International Space Station with a visit to the Russian segment, which includes Zarya, the first segment of the station launched in 1...

  9. Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

    PubMed Central

    2010-01-01

    Background Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (Gossypium spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (G. herbaceum, G. raimondii) or allotetraploid (G. hirsutum, G. barbadense) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton. Results We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the PHYA, PHYB/D, PHYC and PHYE gene sub-families from A- and D-genome diploid and AD-genome allotetraploid Gossypium species. We identified two paralogous PHYA genes (designated PHYA1 and PHYA2) in diploid cottons, the result of a Malvaceae-specific PHYA gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of PHYB, PHYC, and PHYE in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four PHYA genes and two genes encoding PHYB, PHYC and PHYE in the AD-genomes. We did not identify a PHYD gene in any cotton genomes examined. Conclusions Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via

  10. Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom

    PubMed Central

    2010-01-01

    Background The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive drug rapamycin, which in complex with the prolyl isomerase FKBP12 inhibits Tor functions. Rapamycin is a gold standard drug for organ transplant recipients that was approved by the FDA in 1999 and is finding additional clinical indications as a chemotherapeutic and antiproliferative agent. Capitalizing on the plethora of recently sequenced genomes we have conducted comparative genomic studies to annotate the Tor pathway throughout the fungal kingdom and related unicellular opisthokonts, including Monosiga brevicollis, Salpingoeca rosetta, and Capsaspora owczarzaki. Results Interestingly, the Tor signaling cascade is absent in three microsporidian species with available genome sequences, the only known instance of a eukaryotic group lacking this conserved pathway. The microsporidia are obligate intracellular pathogens with highly reduced genomes, and we hypothesize that they lost the Tor pathway as they adapted and streamlined their genomes for intracellular growth in a nutrient-rich environment. Two TOR paralogs are present in several fungal species as a result of either a whole genome duplication or independent gene/segmental duplication events. One such event was identified in the amphibian pathogen Batrachochytrium dendrobatidis, a chytrid responsible for worldwide global amphibian declines and extinctions. Conclusions The repeated independent duplications of the TOR gene in the fungal kingdom might reflect selective pressure acting upon this kinase that populates two proteinaceous complexes with different cellular roles. These comparative genomic analyses illustrate the evolutionary trajectory of a central nutrient-sensing cascade that enables diverse eukaryotic organisms to respond to their natural environments. PMID:20863387

  11. Assessing duplication and loss of APETALA1/FRUITFULL homologs in Ranunculales

    PubMed Central

    Pabón-Mora, Natalia; Hidalgo, Oriane; Gleissberg, Stefan; Litt, Amy

    2013-01-01

    Gene duplication and loss provide raw material for evolutionary change within organismal lineages as functional diversification of gene copies provide a mechanism for phenotypic variation. Here we focus on the APETALA1/FRUITFULL MADS-box gene lineage evolution. AP1/FUL genes are angiosperm-specific and have undergone several duplications. By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades. Functional characterization of several euAP1 and euFUL genes has shown that both function in proper floral meristem identity, and axillary meristem repression. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth, compound leaf morphogenesis and fruit development. Significant functional variation has been detected in the function of pre-duplication basal-eudicot FUL-like genes, but the underlying mechanisms for change have not been identified. FUL-like genes in the Papaveraceae encode all functions reported for euAP1 and euFUL genes, whereas FUL-like genes in Aquilegia (Ranunculaceae) function in inflorescence development and leaf complexity, but not in flower or fruit development. Here we isolated FUL-like genes across the Ranunculales and used phylogenetic approaches to analyze their evolutionary history. We identified an early duplication resulting in the RanFL1 and RanFL2 clades. RanFL1 genes were present in all the families sampled and are mostly under strong negative selection in the MADS, I and K domains. RanFL2 genes were only identified from Eupteleaceae, Papaveraceae s.l., Menispermaceae and Ranunculaceae and show relaxed purifying selection at the I and K domains. We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes

  12. High fitness costs and instability of gene duplications reduce rates of evolution of new genes by duplication-divergence mechanisms.

    PubMed

    Adler, Marlen; Anjum, Mehreen; Berg, Otto G; Andersson, Dan I; Sandegren, Linus

    2014-06-01

    An important mechanism for generation of new genes is by duplication-divergence of existing genes. Duplication-divergence includes several different submodels, such as subfunctionalization where after accumulation of neutral mutations the original function is distributed between two partially functional and complementary genes, and neofunctionalization where a new function evolves in one of the duplicated copies while the old function is maintained in another copy. The likelihood of these mechanisms depends on the longevity of the duplicated state, which in turn depends on the fitness cost and genetic stability of the duplications. Here, we determined the fitness cost and stability of defined gene duplications/amplifications on a low copy number plasmid. Our experimental results show that the costs of carrying extra gene copies are substantial and that each additional kilo base pairs of DNA reduces fitness by approximately 0.15%. Furthermore, gene amplifications are highly unstable and rapidly segregate to lower copy numbers in absence of selection. Mathematical modeling shows that the fitness costs and instability strongly reduces the likelihood of both sub- and neofunctionalization, but that these effects can be offset by positive selection for novel beneficial functions.

  13. Deletions or duplications in the BtuB protein affect its level in the outer membrane of Escherichia coli.

    PubMed Central

    Köster, W; Gudmundsdottir, A; Lundrigan, M D; Seiffert, A; Kadner, R J

    1991-01-01

    The Escherichia coli btuB product is an outer membrane protein that mediates the TonB-coupled active transport of cobalamins and the uptake of the E colicins and bacteriophage BF23. The roles of various segments of the BtuB protein in its function or cellular localization were investigated by analysis of several genetic constructs. Hybrid proteins in which various lengths from the amino terminus of BtuB were linked to alkaline phosphatase (btuB::phoA genes) were all secreted across the cytoplasmic membrane. The BtuB-PhoA proteins that carried up to 327 amino acids of BtuB appeared to reside in the periplasmic space, whereas hybrid proteins containing at least 399 amino acids of BtuB were associated with the outer membrane. Eleven in-frame internal deletion mutations that spanned more than half of the mature sequence were prepared by combining appropriate restriction fragments from btuB variants with 6-bp linker insertions. None of the deleted proteins was able to complement any BtuB functions, and only three of them were detectable in the outer membrane, suggesting that most of the deletions affected sequences needed for stable association with the outer membrane. Duplications covering the same portions of BtuB were prepared in the same manner. All of these partial duplication variants complemented all BtuB functions, although some gave substantially reduced levels of activity. These proteins were found in the outer membrane, although some were subject to proteolytic cleavage within or near the duplicated segment. These results indicate that the insertion of BtuB into the outer membrane requires the presence of several regions of teh BtuB protein and that the presence of extra or redundant segments of the protein can be tolerated during its insertion and function. Images PMID:1885541

  14. Molecular analyses of unrelated Charcot-Marie-Tooth (CMT) disease patients suggest a high frequency of the CMT1A duplication

    SciTech Connect

    Wise, C.A.; Davis, S.N.; Heju, Z.; Pentao, L.; Patel, P.I.; Lupski, J.R. ); Garcia, C.A. )

    1993-10-01

    Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. One form of CMT, CMT type 1A, is characterized by uniformly decreased nerve conduction velocities, usually shows autosomal dominant inheritance, and is associated with a large submicroscopic duplication of the p11.2-p12 region of chromosome 17. A cohort of 75 unrelated patients diagnosed clinically with CMT and evaluated by electrophysiological methods were analyzed molecularly for the presence of the CMT1A DNA duplication. Three methodologies were used to assess the duplication: Measurement of dosage differences between RFLP alleles, analysis of polymorphic (GT)[sub n] repeats, and detection of a junction fragment by pulsed-field gel electrophoresis. The CMT1A duplication was found in 68% of the 63 unrelated CMT patients with electrophysiological studies consistent with CMT type 1 (CMT1). The CMT1A duplication was detected as a de novo event in two CMT1 families. Twelve CMT patients who did not have decreased nerve conduction velocities consistent with a diagnosis of CMT type 2 (CMT2) were found not to have the CMT1A duplication. The most informative molecular method was the detection of the CMT1A duplication-specific junction fragment. Given the high frequency of the CMT1A duplication in CMT patients and the high frequency of new mutations, the authors conclude that a molecular test for the CMT1A DNA duplication is very useful in the differential diagnosis of patients with peripheral neuropathies. 61 refs., 4 figs.

  15. The origin of the 5S ribosomal RNA molecule could have been caused by a single inverse duplication: strong evidence from its sequences.

    PubMed

    Branciamore, Sergio; Di Giulio, Massimo

    2012-04-01

    The secondary structure of the 5S ribosomal RNA (5S rRNA) molecule shows a high degree of symmetry. In order to explain the origin of this symmetry, it has been conjectured that one half of the 5S rRNA molecule was its precursor and that an indirect duplication of this precursor created the other half and thus the current symmetry of the molecule. Here, we have subjected to an empirical test both the indirect duplication model, analysing a total of 684 5S rRNA sequences for complementarity between the two halves of the 5S rRNA, and the direct duplication model analysing in this case the similarity between the two halves of this molecule. In intra- and inter-molecule and intra- and inter-domain comparisons, we find a high statistical support to the hypothesis of a complementarity relationship between the two halves of the 5S rRNA molecule, denying vice versa the hypothesis of similarity between these halves. Therefore, these observations corroborate the indirect duplication model at the expense of the direct duplication model, as reason of the origin of the 5S rRNA molecule. More generally, we discuss and favour the hypothesis that all RNAs and proteins, which present symmetry, did so through gene duplication and not by gradualistic accumulation of few monomers or segments of molecule into a gradualistic growth process. This would be the consequence of the very high propensity that nucleic acids have to be subjected to duplications.

  16. A de novo 22q11.22q11.23 interchromosomal tandem duplication in a boy with developmental delay, hyperactivity, and epilepsy.

    PubMed

    Shimojima, Keiko; Imai, Katsumi; Yamamoto, Toshiyuki

    2010-11-01

    The recent development of high-throughput analysis for genomic copy numbers has enabled to identify microscopic chromosomal duplications that had never been recognized before. Microarray-based comparative genomic hybridization (aCGH) identified a de novo 2.1-Mb microduplication in the 22q11.22q11.23 region surrounded by low copy repeats (LCRs) LCR22E and LCR22H in a 5-year-old boy with developmental delay, hyperactivity, epilepsy, and distinctive facial features, which were within the wide range of the clinical manifestations of the patients with the same duplication pattern. Fiber-fluorescent in situ hybridization (FISH) analysis confirmed that the duplicated segments were aligned in a tandem configuration. Familial single nucleotide polymorphism (SNP) typing determined that the duplication was derived from paternal interchromosomal non-allelic homologous recombination (NAHR) during the first meiotic process of spermatogenesis. Although no patient with the deletions of the distal 22q11.2 has been reported as showing epilepsy, at least five patients including the presenting patient having the duplication between LCR22E and LCR22G showed epilepsy. Thus, the gain of the genomic copy number of this region may have epileptogenesis. © 2010 Wiley-Liss, Inc.

  17. Duplicate origin of the right vertebral artery in which both channels arose from the extreme proximal right subclavian artery: a case report.

    PubMed

    Uchino, Akira; Kurita, Hiroki

    2016-11-08

    Rarely, two channels of the right vertebral artery (VA) arise from the right subclavian artery (SA) and fuse at the level of the C5 or C4 transverse foramen, a variation of the artery termed duplicate origin. Usually, one channel arises from the normal position, and the second arises from the extreme proximal segment of the SA. We report a case of duplicate origin of the right VA in which both channels arose from the extreme proximal segment of the SA, which we diagnosed by computed tomography (CT) angiography. The smaller channel entered the C5 transverse foramen and the larger channel, the C4 transverse foramen, and they fused at the level of the C4. Careful scrutiny of CT angiographic source images is important to detect rare arterial variations, especially to identify the level at which the VA enters the transverse foramen.

  18. TECHNIQUES OF TAPE PREPARATION AND DUPLICATION, WITH SUGGESTIONS FOR A LANGUAGE LABORATORY.

    ERIC Educational Resources Information Center

    Kansas State Dept. of Public Instruction, Topeka.

    PART ONE OF THIS BULLETIN PROVIDES HELP IN THE TWO CRITICAL AREAS OF MASTER TAPE PREPARATION AND DUPLICATION. SUPPLEMENTED BY NUMEROUS PHOTOGRAPHS AND DIAGRAMS OF EQUIPMENT AND DUPLICATION TECHNIQUES, THE BULLETIN DESCRIBES MASTER PROGRAM DUPLICATION USING LANGUAGE LABORATORY EQUIPMENT, A PROFESSIONAL MASS DUPLICATOR, A TAPE RECORDER, A RECORD…

  19. Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

    NASA Astrophysics Data System (ADS)

    Peng, Qian; Alekseyev, Max A.; Tesler, Glenn; Pevzner, Pavel A.

    The existing synteny block reconstruction algorithms use anchors (e.g., orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes. This approach, while efficient for a few genomes, cannot be scaled to address the need to construct synteny blocks in many mammalian genomes that are currently being sequenced. The problem is that the number of anchors shared among all genomes quickly decreases with the increase in the number of genomes. Another problem is that many genomes (plant genomes in particular) had extensive duplications, which makes decoding of genomic architecture and rearrangement analysis in plants difficult. The existing synteny block generation algorithms in plants do not address the issue of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution history of duplications. We present a new algorithm based on the A-Bruijn graph framework that overcomes these difficulties and provides a unified approach to synteny block reconstruction for multiple genomes, and for genomes with large duplications.

  20. Behavioral and neuroanatomical analyses in a genetic mouse model of 2q13 duplication.

    PubMed

    Kishimoto, Keiko; Nomura, Jun; Ellegood, Jacob; Fukumoto, Keita; Lerch, Jason P; Moreno-De-Luca, Daniel; Bourgeron, Thomas; Tamada, Kota; Takumi, Toru

    2017-03-29

    Duplications of human chromosome 2q13 have been reported in patients with neurodevelopmental disorder including autism spectrum disorder. Nephronophthisis-1 (NPHP1) was identified as a causative gene in the minimal deletion on chromosome 2q13 for familial juvenile type 1 nephronophthisis and Joubert syndrome, an autosomal recessive neurodevelopmental disorder characterized by a cerebellar and brain stem malformation, hypotonia, developmental delay, ataxia, and sometimes associated with cognitive impairment. NPHP1 encodes a ciliary protein, nephrocystin-1, which is expressed in the brain, yet its function in the brain remains largely unknown. In this study, we generated bacterial artificial chromosome-based transgenic mice, called 2q13 dup, that recapitulate human chromosome 2q13 duplication and contain one extra copy of the Nphp1 transgene. To analyze any behavioral alterations in 2q13 dup mice, we conducted a battery of behavioral tests. Although 2q13 dup mice show no significant differences in social behavior, they show deficits in spontaneous alternation behavior and fear memory. We also carried out magnetic resonance imaging to confirm whether copy number gain in this locus affects the neuroanatomy. There was a trend toward a decrease in the cerebellar paraflocculus of 2q13 dup mice. This is the first report of a genetic mouse model for human 2q13 duplication.