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Sample records for analysis chromosomal localization

  1. IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus.

    Directory of Open Access Journals (Sweden)

    Ishita Mehta

    Full Text Available The alteration in the location of the chromosomes within the nucleus upon action of internal or external stimuli has been implicated in altering genome function. The effect of stimuli at a whole genome level is studied by using two-dimensional fluorescence in situ hybridization (FISH to delineate whole chromosome territories within a cell nucleus, followed by a quantitative analysis of the spatial distribution of the chromosome. However, to the best of our knowledge, open access software capable of quantifying spatial distribution of whole chromosomes within cell nucleus is not available. In the current work, we present a software package that computes localization of whole chromosomes - Image Analysis of Chromosomes for computing localization (IMACULAT. We partition the nucleus into concentric elliptical compartments of equal area and the variance in the quantity of any chromosome in these shells is used to determine its localization in the nucleus. The images are pre-processed to remove the smudges outside the cell boundary. Automation allows high throughput analysis for deriving statistics. Proliferating normal human dermal fibroblasts were subjected to standard a two-dimensional FISH to delineate territories for all human chromosomes. Approximately 100 images from each chromosome were analyzed using IMACULAT. The analysis corroborated that these chromosome territories have non-random gene density based organization within the interphase nuclei of human fibroblasts. The ImageMagick Perl API has been used for pre-processing the images. The source code is made available at www.sanchak.com/imaculat.html.

  2. Porcine UCHL1: genomic organization, chromosome localization and expression analysis

    DEFF Research Database (Denmark)

    Larsen, Knud; Madsen, Lone Bruhn; Bendixen, Christian

    2012-01-01

    to and protection from Parkinson’s disease. Here we report cloning, characterization, expression analysis and mapping of porcine UCHL1. The UCHL1 cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine cDNA codes...... for a protein of 223 amino acids which shows a very high similarity to human (98%) and to mouse (97%) UCHL1. In addition, the genomic organization of the porcine UCHL1 gene was determined. The porcine UCHL1 gene was mapped to chromosome 8(½p21)–p23. Three SNPs were found in the porcine UCHL1 sequence....... Expression analysis by quantitative real time RT-PCR demonstrated that porcine UCHL1 mRNA is differentially expressed in various organs and tissues and similar to its human counterpart. UCHL1 transcript is most abundant in brain tissues and in the spinal cord. The UCHL1 mRNA expression was also investigated...

  3. Chromosome Analysis

    Science.gov (United States)

    1998-01-01

    Perceptive Scientific Instruments, Inc., provides the foundation for the Powergene line of chromosome analysis and molecular genetic instrumentation. This product employs image processing technology from NASA's Jet Propulsion Laboratory and image enhancement techniques from Johnson Space Center. Originally developed to send pictures back to earth from space probes, digital imaging techniques have been developed and refined for use in a variety of medical applications, including diagnosis of disease.

  4. The murine ufo receptor: molecular cloning, chromosomal localization and in situ expression analysis.

    Science.gov (United States)

    Faust, M; Ebensperger, C; Schulz, A S; Schleithoff, L; Hameister, H; Bartram, C R; Janssen, J W

    1992-07-01

    We have cloned the mouse homologue of the ufo oncogene. It encodes a novel tyrosine kinase receptor characterized by a unique extracellular domain containing two immunoglobulin-like and two fibronectin type III repeats. Comparison of the predicted ufo amino acid sequences of mouse and man revealed an overall identity of 87.6%. The ufo locus maps to mouse chromosome 7A3-B1 and thereby extends the known conserved linkage group between mouse chromosome 7 and human chromosome 19. RNA in situ hybridization analysis established the onset of specific ufo expression in the late embryogenesis at day 12.5 post coitum (p.c.) and localized ufo transcription to distinct substructures of a broad spectrum of developing tissues (e.g. subepidermal cells of the skin, mesenchymal cells of the periosteum). In adult animals ufo is expressed in cells forming organ capsules as well as in connective tissue structures. ufo may function as a signal transducer between specific cell types of mesodermal origin.

  5. cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Finocchiaro, G.; Taroni, F.; Martin, A.L.; Colombo, I.; Tarelli, G.T.; DiDonato, S. (Istituto Nazionale Neurologico C. Besta, Milan (Italy)); Rocchi, M. (Istituto G. Gaslini, Genoa (Italy))

    1991-01-15

    The authors have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA encoding such a peptide. A 60-base-pair (bp) oligonucleotide synthesized on the basis of the sequence from this fragment was used for the screening of a cDNA library from human liver and hybridized to a cDNA insert of 2255 bp. This cDNA contains an open reading frame of 1974 bp that encodes a protein of 658 amino acid residues including 25 residues of an NH{sub 2}-terminal leader peptide. The assignment of this open reading frame to human liver CPTase is confirmed by matches to seven different amino acid sequences of tryptic peptides derived from pure human CPTase and by the 82.2% homology with the amino acid sequence of rat CPTase. The NH{sub 2}-terminal region of CPTase contains a leucine-proline motif that is shared by carnitine acetyl- and octanoyltransferases and by choline acetyltransferase. The gene encoding CPTase was assigned to human chromosome 1, region 1q12-1pter, by hybridization of CPTase cDNA with a DNA panel of 19 human-hanster somatic cell hybrids.

  6. Fetal chromosome analysis: screening for chromosome disease?

    DEFF Research Database (Denmark)

    Philip, J; Tabor, Ann; Bang, J

    1983-01-01

    The aim of the study was to investigate the rationale of the current indications for fetal chromosome analysis. 5372 women had 5423 amniocentesis performed, this group constituting a consecutive sample at the chromosome laboratory, Rigshospitalet, Copenhagen from March 1973 to September 1980 (Group...... to women having amniocentesis, although considered not to have any increased risk of fetal chromosome abnormality (1390 pregnancies, group B). They were also compared with 750 consecutive pregnancies in women 25-34 years of age, in whom all heritable diseases were excluded (group C). The risk of unbalanced...... with women without elevated risk. Spontaneous abortion rate and prematurity rate did not differ from rates expected without amniocentesis. It is concluded that current indications may be characterized as a mixture of evident high risk factors and factors with only a minor influence on risk. Indications...

  7. Cloning, chromosomal localization, SNP detection and association analysis of the porcine IRS-1 gene.

    Science.gov (United States)

    Niu, P-X; Huang, Z; Li, C-C; Fan, B; Li, K; Liu, B; Yu, M; Zhao, S-H

    2009-11-01

    Insulin receptor substrate-1(IRS-1) gene is one member of the Insulin receptor substrate (IRS) gene family, which plays an important role in mediating the growth of skeletal muscle and the molecular metabolism of type 2 diabetes. Here, we cloned a 3,573 bp fragment of the partial CDS sequence of porcine IRS-1 gene by in silicon cloning strategy and RT-PCR method. The porcine IRS-1 gene was assigned to SSC15q25 by using IMpRH. Sequencing of PCR products from Duroc and Tibetan pig breeds identified one SNP in exon 1 of porcine IRS-1 gene (C3257A polymorphisms). Association analysis of genotypes with the growth traits, anatomy traits, meat quality traits and physiological biochemical indexes traits showed that different genotypes at locus 3,257 of IRS-1 have significant differences in carcass straight length in pigs (P = 0.0102 \\ 0.05).

  8. Porcine gamma-synuclein: molecular cloning, expression analysis, chromosomal localization and functional expression

    DEFF Research Database (Denmark)

    Frandsen, Pernille Munk; Madsen, Lone Bruhn; Bendixen, Christian

    2009-01-01

    which shows a high similarity to bovine (90%), human (87%) and mouse (83%) γ-synuclein. A genomic clone containing the entire porcine SNCG gene was isolated and its genomic organization determined. The gene is composed of five exons, the general structure being observed to be very similar...... reports the cloning and characterization of the porcine (Sus scrofa) γ-synuclein cDNA (SNCG). The SNCG cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine SNCG cDNA codes for a protein of 126 amino acids...... to that of the human SNCG gene. Expression analysis by quantitative real-time RT-PCR revealed the presence of SNCG transcripts in all examined organs and tissues. Differential expression was observed, with very high levels of SNCG mRNA in fat tissue and high expression levels in spleen, cerebellum, frontal cortex...

  9. Localization, by linkage analysis, of the cystinuria type III gene to chromosome 19q13.1

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    Bisceglia, L.; Totaro, A.; Melchionda, S. [and others

    1997-03-01

    Cystinuria is an autosomal recessive aminoaciduria in which three urinary phenotypes (I, II, and III) have been described. An amino acid transporter gene, SLC3A1 (formerly rBAT), was found to be responsible for this disorder. Mutational and linkage analysis demonstrated the presence of genetic heterogeneity in which the SLC3A1 gene is responsible for type I cystinuria but not for type II or type III. In this study, we report the identification of the cystinuria type III locus on the long arm of chromosome 19 (19q13.1), obtained after a genomewide search. Pairwise linkage analysis in a series of type III or type II families previously excluded from linkage to the cystinuria type I locus (SLC3A1 gene) revealed a significant maximum LOD score (Z{sub max}) of 13.11 at a maximum recombination fraction ({theta}{sub max}) of .00, with marker D19S225. Multipoint linkage analysis performed with the use of additional markers from the region placed the cystinuria type III locus between D19S414 and D19S220. Preliminary data on type II families also seem to place the disease locus for this rare type of cystinuria at 19q13.1 (significant Z{sub max} = 3.11 at {theta}{sub max} of .00, with marker D19S225). 33 refs., 2 figs., 1 tab.

  10. Refining the localization of the PKD2 locus on chromosome 4q by linkage analysis in Spanish families with autosomal dominant polycystic kidney disease type 2

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    San Millan, J.L.; Viribay, M.; Peral, B.; Moreno, F. [Unidad de Genetica Molecular, Madrid (Spain); Martinez, I. [Hospital de Galdacano (Spain); Weissenbach, J. [Genethon, Evry (France)

    1995-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is a genetically heterogeneous disorder. At least two distinct forms of ADPKD are now well defined. In {approximately}86% of affected European families, a gene defect localized to 16p13.3 was responsible for ADPKD, while a second locus has been recently localized to 4q13-q23 as candidate for the disease in the remaining families. We present confirmation of linkage to microsatellite markers on chromosome 4q in eight Spanish families with ADPKD, in which the disease was not linked to 16p13.3. By linkage analysis with marker D4S423, a maximum lod score of 9.03 at a recombination fraction of .00 was obtained. Multipoint linkage analysis, as well as a study of recombinant haplotypes, placed the PKD2 locus between D4S1542 and D4S1563, thereby defining a genetic interval of {approximately}1 cM. The refined map will serve as a genetic framework for additional genetic and physical mapping of the region and will improve the accuracy of presymptomatic diagnosis of PKD2. 25 refs., 4 figs., 1 tab.

  11. Chromosomal localization of the human and mouse hyaluronan synthase genes

    Energy Technology Data Exchange (ETDEWEB)

    Spicer, A.P.; McDonald, J.A. [Mayo Clinic Scottsdale, AZ (United States); Seldin, M.F. [Univ. of California Davis, CA (United States)] [and others

    1997-05-01

    We have recently identified a new vertebrate gene family encoding putative hyaluronan (HA) synthases. Three highly conserved related genes have been identified, designated HAS1, HAS2, and HAS3 in humans and Has1, Has2, and Has3 in the mouse. All three genes encode predicted plasma membrane proteins with multiple transmembrane domains and approximately 25% amino acid sequence identity to the Streptococcus pyogenes HA synthase, HasA. Furthermore, expression of any one HAS gene in transfected mammalian cells leads to high levels of HA biosynthesis. We now report the chromosomal localization of the three HAS genes in human and in mouse. The genes localized to three different positions within both the human and the mouse genomes. HAS1 was localized to the human chromosome 19q13.3-q13.4 boundary and Has1 to mouse Chr 17. HAS2 was localized to human chromosome 8q24.12 and Has2 to mouse Chr 15. HAS3 was localized to human chromosome 16q22.1 and Has3 to mouse Chr 8. The map position for HAS1 reinforces the recently reported relationship between a small region of human chromosome 19q and proximal mouse chromosome 17. HAS2 mapped outside the predicted critical region delineated for the Langer-Giedion syndrome and can thus be excluded as a candidate gene for this genetic syndrome. 33 refs., 2 figs.

  12. Local adaptation and the evolution of chromosome fusions.

    Science.gov (United States)

    Guerrero, Rafael F; Kirkpatrick, Mark

    2014-10-01

    We use forward and coalescent models of population genetics to study chromosome fusions that reduce the recombination between two locally adapted loci. Under a continent-island model, a fusion spreads and reaches a polymorphic equilibrium when it causes recombination between locally adapted alleles to be less than their selective advantage. In contrast, fusions in a two-deme model always spread; whether it reaches a polymorphic equilibrium or becomes fixed depends on the relative recombination rates of fused homozygotes and heterozygotes. Neutral divergence around fusion polymorphisms is markedly increased, showing peaks at the point of fusion and at the locally adapted loci. Local adaptation could explain the evolution of many of chromosome fusions, which are some of the most common chromosome rearrangements in nature.

  13. Identification of Local Melon (Cucumis melo L. var. Bartek Based on Chromosomal Characters

    Directory of Open Access Journals (Sweden)

    BUDI SETIADI DARYONO

    2011-12-01

    Full Text Available Bartek is one of local melon varieties mainly cultivated in Pemalang, Central Java. Bartek has three variations of fruits; Long-Green, Ellips-Green, and Yellow. Chromosome characterization of the Bartek was investigated to determine the genetic variation. The main purpose of this research was to determine the genetic characters of Bartek including chromosome number, mitosis, cell cycle, and karyotype. Squash method was used for chromosome preparation. The results showed that all of Bartek observed in this study have similar diploid (2n chromosome number = 24. According to the total number of chromosome, Bartek is closer to melon than cucumber. The mitotic analysis exhibited that the Bartek has similar karyotype formula, 2n = 2x = 24m. Based on the R value of the three kinds of Bartek (R < 0.27, it indicated that three kinds of Bartek were considered to be originated from similar species and one of melon varieties (Cucumis melo L. var. Bartek.

  14. Chromosomal localization of ribosomal DNA sequences in an apple rootstock using a digoxygenin detection system

    Institute of Scientific and Technical Information of China (English)

    ZHUJIMEI; SEGARDINER

    1995-01-01

    A 6kb rDNA probe comprising the 18S coding plus spacer sequences has been hybridized to the metaphase chromosomes of apple rootstock cultivar MM106 demonstrating the localization of ribosomal gene arrays in the vicinity of the telomeric regions of the short arms of chromosomes 6 and 14.The in situ results using digoxygenin labelling coupled to an alkaline phosphatase immunoassay were confirmed by silver staining for NORs and nucleoli.This study demonstrates the feasibility of molecular cytogenetic analysis of very small chromosomes(1.0-2.7μm) of apple.

  15. Chromosome banding and gene localizations support extensive conservation of chromosome structure between cattle and sheep.

    Science.gov (United States)

    Hediger, R; Ansari, H A; Stranzinger, G F

    1991-01-01

    By using three gene probes, one derived from the porcine major histocompatibility complex (MHC) and two from bovine cytokeratin genes, type I (KRTA) and type II (KRTB), the hypothesis of conservation of genome structure in two members of the family Bovidae was examined. Gene mapping data revealed the MHC to be in chromosome region 23q15----q23 in cattle (BOLA) and 20q15----q23 in sheep (OLA). KRTA was localized to chromosome region 19q25----q29 in cattle and 11q25----q29 in sheep and KRTB to 5q14----q22 in cattle and 3q14----q22 in sheep. The banding patterns of the chromosome arms to which the loci were assigned were identical in both species. Moreover, the resemblances of GTG- or QFQ-banding patterns between the cattle and sheep karyotypes illustrated further chromosome homologies. These studies, based on gene mapping comparisons and comparative cytogenetics, document that within bovid chromosomes, homology of banding patterns corresponds to a homologous genetic structure. Hence, we propose that gene assignments on identified chromosomal segments in one species of the Bovidae can be extrapolated, in general, to other bovid species based on the banding homologies presented here.

  16. Chromosome analysis of arsenic affected cattle

    Directory of Open Access Journals (Sweden)

    S. Shekhar

    2014-10-01

    Full Text Available Aim: The aim was to study the chromosome analysis of arsenic affected cattle. Materials and Methods: 27 female cattle (21 arsenic affected and 6 normal were selected for cytogenetical study. The blood samples were collected, incubated, and cultured using appropriate media and specific methods. The samples were analyzed for chromosome number and morphology, relative length of the chromosome, arm ratio, and centromere index of X chromosome and chromosomal abnormalities in arsenic affected cattle to that of normal ones. Results: The diploid number of metaphase chromosomes in arsenic affected cattle as well as in normal cattle were all 2n=60, 58 being autosomes and 2 being sex chromosomes. From the centromeric position, karyotyping studies revealed that all the 29 pair of autosomes was found to be acrocentric or telocentric, and the sex chromosomes (XX were submetacentric in both normal and arsenic affected cattle. The relative length of all the autosome pairs and sex chrosomosome pair was found to be higher in normal than that of arsenic affected cattle. The mean arm ratio of X-chromosome was higher in normal than that of arsenic affected cattle, but it is reverse in case of centromere index value of X-chromosome. There was no significant difference of arm ratio and centromere index of X-chromosomes between arsenic affected and normal cattle. No chromosomal abnormalities were found in arsenic affected cattle. Conclusion: The chromosome analysis of arsenic affected cattle in West Bengal reported for the first time in this present study which may serve as a guideline for future studies in other species. These reference values will also help in comparison of cytological studies of arsenic affected cattle to that of various toxicants.

  17. Inherited unbalanced structural chromosome abnormalities at prenatal chromosome analysis are rarely ascertained through recurrent miscarriage

    NARCIS (Netherlands)

    Franssen, M. T. M.; Korevaar, J. C.; Tjoa, W. M.; Leschot, N. J.; Bossuyt, P. M. M.; Knegt, A. C.; Suykerbuyk, R. F.; Hochstenbach, R.; van der Veen, F.; Goddijn, M.

    2008-01-01

    Objective To determine the mode of ascertainment of inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis. Methods From the databases of three centres for clinical genetics in the Netherlands, all cases of inherited unbalanced structural chromosome abnorma

  18. Analysis of plant meiotic chromosomes by chromosome painting.

    Science.gov (United States)

    Lysak, Martin A; Mandáková, Terezie

    2013-01-01

    Chromosome painting (CP) refers to visualization of large chromosome regions, entire chromosome arms, or entire chromosomes via fluorescence in situ hybridization (FISH). For CP in plants, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the target species or from a closely related species (comparative chromosome painting, CCP) are typically applied as painting probes. Extended pachytene chromosomes provide the highest resolution of CP in plants. CP enables identification and tracing of particular chromosome regions and/or entire chromosomes throughout all meiotic stages as well as corresponding chromosome territories in premeiotic interphase nuclei. Meiotic pairing and structural chromosome rearrangements (typically inversions and translocations) can be identified by CP. Here, we describe step-by-step protocols of CP and CCP in plant species including chromosome preparation, BAC DNA labeling, and multicolor FISH.

  19. Chromosomal localization of the gonadotropin-releasing hormone receptor gene to human chromosome 4q13. 1-q21. 1 and mouse chromosome 5

    Energy Technology Data Exchange (ETDEWEB)

    Kaiser, U.B.; Dushkin, H.; Beier, D.R.; Chin, W.W. (Harvard Medical School, Boston, MA (United States)); Altherr, M.R. (Los Alamos National Lab., NM (United States))

    1994-04-01

    The gonadotropin-releasing hormone receptor (GRHR) is a G-protein-coupled receptor on the cell surface of pituitary gonadotropes, where it serves to transduce signals from the extracellular ligand, the hypothalamic factor gonadotropin-releasing hormone, and to modulate the synthesis and secretion of luteinizing hormone and follicle-stimulating hormone. The authors have localized the GRHR gene to the q13.1-q21.1 region of the human chromosome 4 using mapping panels of human/rodent somatic cell hybrids containing different human chromosomes or different regions of human chromosome 4. Furthermore, using linkage analysis of single-strand conformational polymorphisms, the murine GRHR gene was localized to mouse chromosome 5, linked to the endogenous retroviral marker Pmv-11. This is consistent with the evolutionary conservation of homology between these two regions, as has been previously suggested from comparative mapping of several other loci. The localization of the GRHR gene may be useful in the study of disorders of reproduction. 22 refs., 2 figs.

  20. Research on automatic human chromosome image analysis

    Science.gov (United States)

    Ming, Delie; Tian, Jinwen; Liu, Jian

    2007-11-01

    Human chromosome karyotyping is one of the essential tasks in cytogenetics, especially in genetic syndrome diagnoses. In this thesis, an automatic procedure is introduced for human chromosome image analysis. According to different status of touching and overlapping chromosomes, several segmentation methods are proposed to achieve the best results. Medial axis is extracted by the middle point algorithm. Chromosome band is enhanced by the algorithm based on multiscale B-spline wavelets, extracted by average gray profile, gradient profile and shape profile, and calculated by the WDD (Weighted Density Distribution) descriptors. The multilayer classifier is used in classification. Experiment results demonstrate that the algorithms perform well.

  1. Globally Divergent but Locally Convergent X- and Y-Chromosome Influences on Cortical Development.

    Science.gov (United States)

    Raznahan, Armin; Lee, Nancy Raitano; Greenstein, Deanna; Wallace, Gregory L; Blumenthal, Jonathan D; Clasen, Liv S; Giedd, Jay N

    2016-01-01

    Owing to their unique evolutionary history, modern mammalian X- and Y-chromosomes have highly divergent gene contents counterbalanced by regulatory features, which preferentially restrict expression of X- and Y-specific genes. These 2 characteristics make opposing predictions regarding the expected dissimilarity of X- vs. Y-chromosome influences on biological structure and function. Here, we quantify this dissimilarity using in vivo neuroimaging within a rare cohort of humans with diverse sex chromosome aneuploidies (SCAs). We show that X- and Y-chromosomes have opposing effects on overall brain size but exert highly convergent influences on local brain anatomy, which manifest across biologically distinct dimensions of the cerebral cortex. Large-scale online meta-analysis of functional neuroimaging data indicates that convergent sex chromosome dosage effects preferentially impact centers for social perception, communication, and decision-making. Thus, despite an almost complete lack of sequence homology, and opposing effects on overall brain size, X- and Y-chromosomes exert congruent effects on the proportional size of cortical systems involved in adaptive social functioning. These convergent X-Y effects (i) track the dosage of those few genes that are still shared by X- and Y-chromosomes, and (ii) may provide a biological substrate for the link between SCA and increased rates of psychopathology.

  2. Chromosome analysis of three species of Myoxidae

    Directory of Open Access Journals (Sweden)

    Maria Vittoria Civitelli

    1995-05-01

    Full Text Available Abstract Karyotype analysis was carried out on three species of dormice: Myoxus glis, 4 populations from Northern and Southern Italy and from Turkey; Dryomys nitedula, 4 populations from Northern and Southern Italy, from Israel and from Turkey; Myomimus roachi, 1 specimen from Turkey. Myoxus glis shows 2n=62; comparison of our specimens from different localities shows complete correspondence between karyotypes, both for the autosomes and the heterochromosomes. Dryomys nitedula shows 2n=48. All populations we studied, show the same karyotypic pattern, except for the NOR-bearing chromosomes. Myomimus roachi, here studied for the first time, shows 2n=44. All the autosomes are biarmed of decreasing size. The X-chromosome is a medium size metacentric, while the Y-chromosome is the smallest one. All the three species we studied, show one pair of NOR-bearing chromosomes, Ag-NORs always correspond to the secondary constriction. Differences in the fundamental number and in heterochromosome morphology, have been observed by other authors, in different European populations. This variability is analysed and discussed. Riassunto Analisi cromosomica in tre specie di Myoxidae - L'analisi cromosomica è stata condotta su popolazioni europee di tre specie di Myoxidae: Myoxus glis, 4 popolazioni provenienti dal Nord e Sud Italia, e dalla Turchia; Dryomys nitedula, 4 popolazioni provenienti dal Nord e Sud Italia, da Israele e dalla Turchia; Myomimus roachi, 1 esemplare, proveniente dalla Turchia. Myoxus glis presenta 2n=62. Gli esemplari, provenienti dalle diverse popolazioni, mostrano corrispondenza nella morfologia sia degli autosomi che degli eterocromosomi. Dryomys nitedula presenta 2n=48. La morfologia dei cromosomi nei cariotipi appare corrispondente mentre diversa è la localizzazione degli Ag-NOR.

  3. Thermolabile phenol sulfotransferase gene (STM): Localization to human chromosome 16p11.2

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    Aksoy, I.A.; Her, C.; Weinshilboum, M. [Mayo Medical School, Rochester, MN (United States)] [and others

    1994-09-01

    Thermolabile (TL) phenol sulfotransferase (PST) catalyzes the sulfate conjugation of phenolic monoamine neurotransmitters such as dopamine and serotonin. We recently cloned a cDNA for human liver TL PST and expressed it in COS-1 cells. We now report the chromosomal localization of the human TL PST gene (STM) as well as its partial sequence. DNA from NIGMS Human/Rodent Somatic Cell Hybrid Mapping Panels 1 and 2 was screened by use of the PCR, and the STM gene was mapped to chromosome 16. Regional localization to 16p11.2 was performed by PCR analysis of a high-resolution mouse/human somatic cell hybrid panel that contained defined portions of human chromosome 16. 15 refs., 2 figs.

  4. The gene for human glutaredoxin (GLRX) is localized to human chromosome 5q14

    Energy Technology Data Exchange (ETDEWEB)

    Padilla, C.A.; Holmgren, A. [Karolinska Inst., Stockholm (Sweden); Bajalica, S.; Lagercrantz, J. [Karolinska Hospital, Stockholm (Sweden)

    1996-03-05

    Glutaredoxin is a small protein (12 kDa) catalyzing glutathione-dependent disulfide oxidoreduction reactions in a coupled system with NADPH, GSH, and glutathione reductase. A cDNA encoding the human glutaredoxin gene (HGMW-approved symbol GLRX) has recently been isolated and cloned from a human fetal spleen cDNA library. The screening of a human fetal spleen cDNA library. The screening of a human genomic library in Charon 4A led to the identification of three genomic clones. Using fluorescence in situ hybridization to metaphase chromosomes with one genomic clone as a probe, the human glutaredoxin gene was localized to chromosomal region 5q14. This localization at chromosome 5 was in agreement with the somatic cell hybrid analysis, using DNA from a human-hamster and a human-mouse hybrid panel and using a human glutaredoxin cDNA as a probe. 13 refs., 2 figs.

  5. Structure and chromosomal localization of the human thrombospondin gene.

    Science.gov (United States)

    Wolf, F W; Eddy, R L; Shows, T B; Dixit, V M

    1990-04-01

    Thrombospondin (THBS1) is a large modular glycoprotein component of the extracellular matrix and contains a variety of distinct domains, including three repeating subunits (types I, II, and III) that share homology to an assortment of other proteins. Determination of THBS1 gene structure has revealed that the type I repeat modules are encoded by symmetrical exons and that the heparin-binding domain is encoded by a single exon. To further elucidate the higher level organization of THBS1, the gene was localized to the q11-qter region of chromosome 15.

  6. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

    Science.gov (United States)

    Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J

    2011-09-01

    The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

  7. Structure, tissue distribution, and chromosomal localization of the prepronociceptin gene.

    Science.gov (United States)

    Mollereau, C; Simons, M J; Soularue, P; Liners, F; Vassart, G; Meunier, J C; Parmentier, M

    1996-08-01

    Nociceptin (orphanin FQ), the newly discovered natural agonist of opioid receptor-like (ORL1) receptor, is a neuropeptide that is endowed with pronociceptive activity in vivo. Nociceptin is derived from a larger precursor, prepronociceptin (PPNOC), whose human, mouse, and rat genes we have now isolated. The PPNOC gene is highly conserved in the three species and displays organizational features that are strikingly similar to those of the genes of preproenkephalin, preprodynorphin, and preproopiomelanocortin, the precursors to endogenous opioid peptides, suggesting the four genes belong to the same family-i.e., have a common evolutionary origin. The PPNOC gene encodes a single copy of nociceptin as well as of other peptides whose sequence is strictly conserved across murine and human species; hence it is likely to be neurophysiologically significant. Northern blot analysis shows that the PPNOC gene is predominantly transcribed in the central nervous system (brain and spinal cord) and, albeit weakly, in the ovary, the sole peripheral organ expressing the gene. By using a radiation hybrid cell line panel, the PPNOC gene was mapped to the short arm of human chromosome 8 (8p21), between sequence-tagged site markers WI-5833 and WI-1172, in close proximity of the locus encoding the neurofilament light chain NEFL. Analysis of yeast artificial chromosome clones belonging to the WC8.4 contig covering the 8p21 region did not allow to detect the presence of the gene on these yeast artificial chromosomes, suggesting a gap in the coverage within this contig.

  8. Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes.

    Science.gov (United States)

    Kitada, Kunio; Taima, Akira; Ogasawara, Kiyomoto; Metsugi, Shouichi; Aikawa, Satoko

    2011-04-01

    Analysis of structural rearrangements at the individual chromosomal level is still technologically challenging. Here we optimized a chromosome isolation method using fluorescent marker-assisted laser-capture and laser-beam microdissection and applied it to structural analysis of two aberrant chromosomes found in a lung cancer cell line. A high-density array-comparative genomic hybridization (array-CGH) analysis of DNA samples prepared from each of the chromosomes revealed that these two chromosomes contained 296 and 263 segments, respectively, ranging from 1.5 kb to 784.3 kb in size, derived from different portions of chromosome 8. Among these segments, 242 were common in both aberrant chromosomes, but 75 were found to be chromosome-specific. Sequences of 263 junction sites connecting the ends of segments were determined using a PCR/Sanger-sequencing procedure. Overlapping microhomologies were found at 169 junction sites. Junction partners came from various portions of chromosome 8 and no biased pattern in the positional distribution of junction partners was detected. These structural characteristics suggested the occurrence of random fragmentation of the entire chromosome 8 followed by random rejoining of these fragments. Based on that, we proposed a model to explain how these aberrant chromosomes are formed. Through these structural analyses, it was demonstrated that the optimized chromosome isolation method described here can provide high-quality chromosomal DNA for high resolution array-CGH analysis and probably for massively parallel sequencing analysis.

  9. Structure and chromosomal localization of the gene encoding the human myelin protein zero (MPZ)

    Energy Technology Data Exchange (ETDEWEB)

    Hayasaka, Kiyoshi; Himoro, Masato; Takada, Goro (Akita Univ. School of Medicine, Akita (Japan)); Wang, Yimin; Takata, Mizuho; Minoshima, Shinsei; Shimizu, Nobuyoshi; Miura, Masayuki; Uyemura, Keiichi (Keio Univ. School of Medicine, Tokyo (Japan))

    1993-09-01

    The authors describe the cloning, characterization, and chromosomal mapping of the human myelin protein zero (MPZ) gene (a structural protein of myelin and an adhesive glycoprotein of the immunoglobulin superfamily). The gene is about 7 kb long and consists of six exons corresponding of the functional domains. All exon-intron junction sequences conform to the GT/AG rule. The 5[prime]-flanking region of the gene has a TA-rich element (TATA-like box), two CAAT boxes, and a single defined transcription initiation site detected by the primer extension method. The gene for human MPZ was assigned to chromosome 1q22-q23 by spot blot hybridization of flow-sorted human chromosomes and fluorescence in situ hybridization. The localization of the MPZ gene coincides with the locus for Charcot-Marie-Tooth disease type 1B, determined by linkage analysis. 20 refs., 3 figs., 1 tab.

  10. Chromosome analysis and sorting using flow cytometry.

    Science.gov (United States)

    Doležel, Jaroslav; Kubaláková, Marie; Cíhalíková, Jarmila; Suchánková, Pavla; Simková, Hana

    2011-01-01

    Chromosome analysis and sorting using flow cytometry (flow cytogenetics) is an attractive tool for fractionating plant genomes to small parts. The reduction of complexity greatly simplifies genetics and genomics in plant species with large genomes. However, as flow cytometry requires liquid suspensions of particles, the lack of suitable protocols for preparation of solutions of intact chromosomes delayed the application of flow cytogenetics in plants. This chapter outlines a high-yielding procedure for preparation of solutions of intact mitotic chromosomes from root tips of young seedlings and for their analysis using flow cytometry and sorting. Root tips accumulated at metaphase are mildly fixed with formaldehyde, and solutions of intact chromosomes are prepared by mechanical homogenization. The advantages of the present approach include the use of seedlings, which are easy to handle, and the karyological stability of root meristems, which can be induced to high degree of metaphase synchrony. Chromosomes isolated according to this protocol have well-preserved morphology, withstand shearing forces during sorting, and their DNA is intact and suitable for a range of applications.

  11. Sequence and chromosomal localization of the mouse brevican gene

    DEFF Research Database (Denmark)

    Rauch, U; Meyer, H; Brakebusch, C

    1997-01-01

    Brevican is a brain-specific proteoglycan belonging to the aggrecan family. Phage clones containing the complete mouse brevican open reading frame of 2649 bp and the complete 3'-untranslated region of 341 bp were isolated from a mouse brain cDNA library, and cosmid clones containing the mouse bre...... to an alternative brevican cDNA, coding for a GPI-linked isoform. Single strand conformation polymorphism analysis mapped the brevican gene (Bcan) to chromosome 3 between the microsatellite markers D3Mit22 and D3Mit11....

  12. Human estrogen sulfotransferase gene (STE): Cloning, structure, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Her, Chengtao; Aksoy, I.A.; Weinshilboum, M. [Mayo Foundation, Rochester, MI (United States)] [and others

    1995-09-01

    Sulfation is an important pathway in the metabolism of estrogens. We recently cloned a human liver estrogen sulfotransferase (EST) cDNA. We have now determined the structure and chromosomal localization of the EST gene, STE, as a step toward molecular genetic studies of the regulation of EST in humans. STE spans approximately 20 kb and consists of 8 exons, ranging in length from 95 to 181 bp. The locations of most exon-intron splice junctions within STE are identical to those found in a human phenol ST (PST) gene, STM, and in a rat PST gene. In addition, the locations of five STE introns are also conserved in the human dehydroepiandrosterone (DBEA) ST gene, STD. The 5{prime} flanking region of STE contains one CCAAT and two TATA sequences. The location of one of the TATA box elements is in excellent agreement with the site of transcription initiation as determined by 5{prime}-rapid amplification of cDNA ends. STE was mapped to human chromosome 4q13.1 by fluorescence in situ hybridization. Cloning and structural characterization of STE will now make it possible to study potential molecular genetic mechanisms involved in the regulation of EST in human tissues. 50 refs., 6 figs., 1 tab.

  13. Localization of introduced genes on the chromosomes of transgenic barley, wheat and triticale by fluorescence in situ hybridization

    DEFF Research Database (Denmark)

    Pedersen, C.; Zimny, J.; Becker, D.

    1997-01-01

    transformant showed a totally different integration pattern. Southern analysis confirmed that the inserted genes were segregating independently, resulting in different integration patterns among the progeny lines. The application of the FISH technique for the analysis of transgenic plants is discussed.......Using fluorescence in situ hybridization (FISH) we localized introduced genes on metaphase chromosomes of barley, wheat, and triticale transformed by microprojectile bombardment of microspores and scutellar tissue with the pDB1 plasmid containing the uidA and bar genes. Thirteen integration sites...... of single-copy integrations. There was a slight tendency towards the localization of transgenes in distal chromosome regions. Using the GAA-satellite sequence for chromosome banding, the chromosomes containing the inserted genes were identified in most cases. Two barley lines derived from the same...

  14. DETECTION OF CHROMOSOME ABERRATIONS IN TWELVE PRIMARY GASTRIC CANCERS BY DIRECT CHROMOSOME ANALYSIS AND FISH

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Direct chromosome analysis and FISH were performed on twelve primary gastric carcinomas. Two of them had simple chromosome changes: 48,XX, +8, +20, and 49, XY, +2, +8, +9, and the others had complicated chromosome changes, which includes much more numerical and structural chromosome aberrations. Frequent structural changes in the complicated types involved chromosome 7, 3, 1, 5 and 12 etc. The del 7q was noted in eight cases. The del (3p) and del (1p) were noted in six and five cases, respectively. The results provide some important clues for isolation of the genes related to gastric cancer.

  15. [Physical localization of ribosomal genes and chromosome DAPI banding by in situ hybridization in Medicago sativa L].

    Science.gov (United States)

    Chen, Jian-Min; Hong, Yi-Huan; Wang, You-Ping; Bowley, Steve; Wan, Jian-Min

    2006-02-01

    Physical localization of ribosomal genes in diploid and tetraploid alfalfa (Medicago. sativa) was studied using fluorescent in situ hybridization (FISH). It was revealed that 45s gene was only located at nucleolus organizer region (NOR) with a single locus in both diploid and tetraploid alfalfa, while 5s gene had 2-3 loci on chromosomes. Using the genomic DNA from M. coerulea and M. falcata as probe to hybridize with tetraploid species in alfalfa, both diploid species were successfully hybridized with tetraploid chromosomes, only showing the difference in hybridization signals in different numbers of chromosomes. Chromosomes of alfalfa exhibited DAPI banding by FISH analysis. In general, the patterns of distribution of DAPI banding were consistent with C-banding for M. coerulea. The possible origination of tetraploid alfalfa was discussed based on DAPI banding patterns and FISH analysis for ribosomal genes .

  16. A novel allelic variant of the human TSG-6 gene encoding an amino acid difference in the CUB module. Chromosomal localization, frequency analysis, modeling, and expression.

    Science.gov (United States)

    Nentwich, Hilke A; Mustafa, Zehra; Rugg, Marilyn S; Marsden, Brian D; Cordell, Martin R; Mahoney, David J; Jenkins, Suzanne C; Dowling, Barbara; Fries, Erik; Milner, Caroline M; Loughlin, John; Day, Anthony J

    2002-05-03

    Tumor necrosis factor-stimulated gene-6 (TSG-6) encodes a 35-kDa protein, which is comprised of contiguous Link and CUB modules. TSG-6 protein has been detected in the articular joints of osteoarthritis (OA) patients, with little or no constitutive expression in normal adult tissues. It interacts with components of cartilage matrix (e.g. hyaluronan and aggrecan) and thus may be involved in extracellular remodeling during joint disease. In addition, TSG-6 has been found to have anti-inflammatory properties in models of acute and chronic inflammation. Here we have mapped the human TSG-6 gene to 2q23.3, a region of chromosome 2 linked with OA. A single nucleotide polymorphism was identified that involves a non-synonymous G --> A transition at nucleotide 431 of the TSG-6 coding sequence, resulting in an Arg to Gln alteration in the CUB module (at residue 144 in the preprotein). Molecular modeling of the CUB domain indicated that this amino acid change might lead to functional differences. Typing of 400 OA cases and 400 controls revealed that the A(431) variant identified here is the major TSG-6 allele in Caucasians (with over 75% being A(431) homozygotes) but that this polymorphism is not a marker for OA susceptibility in the patients we have studied. Expression of the Arg(144) and Gln(144) allotypes in Drosophila Schneider 2 cells, and functional characterization, showed that there were no significant differences in the ability of these full-length proteins to bind hyaluronan or form a stable complex with inter-alpha-inhibitor.

  17. Chromosome

    Science.gov (United States)

    Chromosomes are structures found in the center (nucleus) of cells that carry long pieces of DNA. DNA ... is the building block of the human body. Chromosomes also contain proteins that help DNA exist in ...

  18. The oxytocin receptor gene (OXTR) localizes to human chromosome 3p25 by fluorescence in situ hybridization and PCR analysis of somatic cell hybrids

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, C.F. Jr.; Clancy, T.E.; Quan, R. [Children`s Hospital, Boston, MA (United States)] [and others

    1995-04-10

    The human oxytocin receptor regulates parturition and myometrial contractility, breast milk let-down, and reproductive behaviors in the mammalian central nervous system. Kimura et al. recently identified a human oxytocin receptor cDNA by means of expression cloning from a human myometrial cDNA library. To elucidate further the molecular mechanisms that regulate oxytocin receptor gene expression and to define the expected Mendelian inheritance of possible human disease states, we must determine the number of genes, their localization, and their organization and structure. We summarize below our data indicating that the human oxytocin receptor gene is localized to 3p25 and exists as a single copy in the haploid genome. 9 refs., 2 figs.

  19. Chromosomes in the flow to simplify genome analysis.

    Science.gov (United States)

    Doležel, Jaroslav; Vrána, Jan; Safář, Jan; Bartoš, Jan; Kubaláková, Marie; Simková, Hana

    2012-08-01

    Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.

  20. Cloning, chromosome localization and features of a novel human gene, MATH2

    Indian Academy of Sciences (India)

    Lingchen Guo; Min Jiang; Yushu Ma; Haipeng Cheng; Xiaohua Ni; Yangsheng Jin; Yi Xie; Yumin Mao

    2002-04-01

    We report cloning and some features of a novel human gene, MATH2, which encodes a protein of 337 amino acid residues with a basic helix–loop–helix domain and exhibits 98% similarity to mouse Math2. Results of Northern blot analysis revealed two transcripts of the MATH2 gene of 1.7 kb and 2.4 kb in human brain. We localized MATH2 to chromosome 7 at 7p14–15 by matching with the Human Genome Sequence Database. Human MATH2 and mouse Math2 may have the same functions in the nervous system.

  1. Localization to Chromosomes of Structural Genes for the Major Protease Inhibitors of Barley Grains

    DEFF Research Database (Denmark)

    Hejgaard, Jørn; Bjørn, S.E.; Nielsen, Gunnar Gissel

    1984-01-01

    Wheat-barley chromosome addition lines were compared by isoelectric focusing of protein extracts to identify chromosomes carrying loci for the major immunochemically distinct protease inhibitors of barley grains. Structural genes for the following inhibitors were localized: an inhibitor of both...

  2. Computerized prototypes of DAPI-stained chromosomes for FISH analysis

    Energy Technology Data Exchange (ETDEWEB)

    Baldini, A.; Smith, L.C.; Knapp, R.D. [Baylor College of Medicine, Houston, TX (United States)

    1994-09-01

    DAPI is fluorescent dye widely used in chromosome counterstaining for fluorescence in situ hybridization (FISH) experiments. It produces a Q-banding pattern that allows chromosomes to be identified and permits molecular probes to be assigned to specific cytogenetic bands. Using a statistical procedure based on eigenanalysis, we have extracted features from digital images of DAPI-stained chromosomes and constructed prototypes of each of the 24 human chromosomes. The features of prototypes are directly proportional, in intensity profile and band location, to those of real chromosomes. The prototype`s intensity profile can be translated into cytogenetic bands to provide a computer-based strategy for chromosome mapping and analysis amenable to automation. Data have been obtained using images from the 24 human chromosomes and mouse X chromosome. Moreover, the same procedure is general and can be used for the analysis of chromosomes from other species, as well as with banding techniques other than those using DAPI. Images of hybridization patterns produced by complex probes are also suitable for this analysis. The speed and flexibility of the procedure opens the way to application so far unexplored, such as computer-assisted chromosome band assignment of probe; combined analysis of multiple, geometrically distorted chromosomes; and the direct comparison of raw data from different experiments. The applications will not be limited to mapping experiments but will include analysis of chromosome structure, variability and analysis of the pattern of chromosome distribution of repetitive sequences. The results from such analysis is suitable for objective statistical evaluation and, eventually, for autonomous machine interpretation.

  3. Persistent chromosome damage induced by localized radiotherapy for lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Zaslav, A.L.; Stamberg, J.; Shende, A.

    1988-02-01

    A fibroblast culture was established from a lymph node biopsy of a patient with non-Hodgkin lymphoma, 9 months after chemotherapy and intensive therapeutic x-irradiation of the area. In contrast with blood and bone marrow, which were chromosomally normal, all cells of the lymph node were chromosomally abnormal, with numerous clones having multiple structural abnormalities. Numerical abnormalities (trisomies and monosomies) were not found. Structural abnormalities included translocations, terminal deletions, and pericentric inversions, with an excess of centromeric breakpoints being the only apparent deviation from a random distribution of breakpoints. None of the rearrangements associated with malignant lymphoma were seen, indicating that the chromosome abnormalities in the lymph stroma were radiation-associated, not disease-associated. These acquired changes may be a cause of additional malignant transformation.

  4. The mouse Fau gene: genomic structure, chromosomal localization, and characterization of two retropseudogenes.

    Science.gov (United States)

    Casteels, D; Poirier, C; Guénet, J L; Merregaert, J

    1995-01-01

    The Fau gene is the cellular homolog of the fox sequence of the Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV). FBR-MuSV acquired the Fau gene by transduction in a transcriptional orientation opposite to that of the genomic Fau gene. The genomic structure of the mouse Fau gene (MMFAU) and its upstream elements have been determined and are similar to those of the human FAU gene. The gene consists of five exons and is located on chromosome 19. The first exon is not translated. The promoter region has no well-defined TATA box but contains the polypyrimidine initiator flanked by regions of high GC content (65%) and shows all of the characteristics of a housekeeping gene. The 5' end of the mRNA transcript was determined by 5' RACE analysis and is located, as expected, in the polypyrimidine initiator site. Furthermore, the sequences of two retropseudogenes (Fau-ps1 and Fau-ps2) are reported. Both pseudogenes are approximately 75% identical to the Fau cDNA, but both are shorter due to a deletion at the 5' end and do not encode a functional protein. Fau-prs is interrupted by an AG-rich region of about 350 bp within the S30 region of the Fau cDNA. Fau-ps1 was localized on chromosome 1 and Fau-ps2 on chromosome 7.

  5. Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

    Directory of Open Access Journals (Sweden)

    Ben Beheshti

    2003-01-01

    Full Text Available Conventional comparative genomic hybridization (CGH profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1 no amplifications evident, 2 a small MYCN amplicon as the only detectable imbalance, and 3 a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.

  6. Localization of a gene for autosomal dominant amelogenesis imperfecta (ADAI) to chromosome 4q

    Energy Technology Data Exchange (ETDEWEB)

    Forsman, K.; Lind. L.; Westermark, E. [Univ. of Umea (Sweden)] [and others

    1994-09-01

    Amelogenesis imperfecta (AI), a disorder affecting the formation of enamel, is significantly more common in Northern Sweden than in other parts of the world. The disease is genetically and clinically heterogenous, and autosomal dominant, autosomal recessive and X-linked inheritance patterns have been recognized. Linkage analysis has identified two different loci for X-linked AI, one of which is identical to the gene encoding the enamel protein amelogenin. However, in families with an autosomal inheritance pattern for AI, the genetic basis of the disease still remains unknown. We report a linkage analysis study performed on three Swedish families where the affected members had an autosomal dominant variant of AI (ADAI) clinically characterized as local hypoplastic. Significant linkage to microsatellite markers on chromosome 4q were obtained, with a maximum lod score of 5.55 for the marker D4S428. Recombinations in the family localized the ADAI locus to the interval between D4S392 and D4S395. This chromosome region contains both a locus for the dental disorder dentinogenesis imperfecta and the albumin gene. Serum albumin has been suggested to play a role in enamel formation, and the albumin gene is therefore a candidate gene for this genetic disease.

  7. Gene expression meta-analysis identifies chromosomal regions involved in ovarian cancer survival

    DEFF Research Database (Denmark)

    Thomassen, Mads; Jochumsen, Kirsten M; Mogensen, Ole;

    2009-01-01

    the relation of gene expression and chromosomal position to identify chromosomal regions of importance for early recurrence of ovarian cancer. By use of *Gene Set Enrichment Analysis*, we have ranked chromosomal regions according to their association to survival. Over-representation analysis including 1......Ovarian cancer cells exhibit complex karyotypic alterations causing deregulation of numerous genes. Some of these genes are probably causal for cancer formation and local growth, whereas others are causal for metastasis and recurrence. By using publicly available data sets, we have investigated......-4 consecutive cytogenetic bands identified regions with increased expression for chromosome 5q12-14, and a very large region of chromosome 7 with the strongest signal at 7p15-13 among tumors from short-living patients. Reduced gene expression was identified at 4q26-32, 6p12-q15, 9p21-q32, and 11p14-11. We...

  8. Localization of latency-associated nuclear antigen (LANA) on mitotic chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Rahayu, Retno; Ohsaki, Eriko [Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871 (Japan); Omori, Hiroko [Central Instrumentation Laboratory Research Institute for Microbial Diseases (BIKEN), Osaka University, Osaka 565-0871 (Japan); Ueda, Keiji, E-mail: kueda@virus.med.osaka-u.ac.jp [Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871 (Japan)

    2016-09-15

    In latent infection of Kaposi's sarcoma-associated herpesvirus (KSHV), viral gene expression is extremely limited and copy numbers of viral genomes remain constant. Latency-associated nuclear antigen (LANA) is known to have a role in maintaining viral genome copy numbers in growing cells. Several studies have shown that LANA is localized in particular regions on mitotic chromosomes, such as centromeres/pericentromeres. We independently examined the distinct localization of LANA on mitotic chromosomes during mitosis, using super-resolution laser confocal microscopy and correlative fluorescence microscopy–electron microscopy (FM-EM) analyses. We found that the majority of LANA were not localized at particular regions such as telomeres/peritelomeres, centromeres/pericentromeres, and cohesion sites, but at the bodies of condensed chromosomes. Thus, LANA may undergo various interactions with the host factors on the condensed chromosomes in order to tether the viral genome to mitotic chromosomes and realize faithful viral genome segregation during cell division. - Highlights: • This is the first report showing LANA dots on mitotic chromosomes by fluorescent microscopy followed by electron microscopy. • LANA dots localized randomly on condensed chromosomes other than centromere/pericentromere and telomere/peritelomre. • Cellular mitotic checkpoint should not be always involved in the segregation of KSHV genomes in the latency.

  9. Cytogenetic analysis of chromosomal abnormalities in Sri Lankan children

    Institute of Scientific and Technical Information of China (English)

    Colombo; Sri Lanka

    2015-01-01

    Background: Cytogenetic analysis is a valuable investigation in the diagnostic work up of children with suspected chromosomal disorders. The objective of this study was to describe the prevalence of various types of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis. Methods: Cytogenetic reports of 1554 consecutive children with suspected chromosomal disorders who underwent karyotyping in two genetic centers in Sri Lanka from January 2006 to December 2011 were reviewed retrospectively. Results: A total of 1548 children were successfully karyotyped. Abnormal karyotypes were found in 783 (50.6%) children. Numerical and structural abnormalities accounted for 90.8% and 9.2%, respectively. Down syndrome was the commonest aneuploidy identifi ed. Other various autosomal and sex chromosomal aneuploidies as well as micro-deletion syndromes were also detected. Conclusions: The prevalence of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis for suspected chromosomal disorders was relatively higher than that in Caucasian and other Asian populations.

  10. Uniparental disomy analysis in carriers of balanced chromosome rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    May, K.M.; Pettay, D.; Muralidharan, K. [Emory Univ. School of Medicine, Atlanta, GA (United States)] [and others

    1994-09-01

    Although most individuals who carry a balanced familial chromosome rearrangement are phenotypically normal, those who are clinically abnormal raise the question of whether or not the rearrangement plays a causative role. One possible mechanism involves meiotic segregation of a normal homolog along with the rearranged chromosome(s) such that a trisomic conception occurs. Subsequent loss by mitotic nondisjunction of the structurally normal chromosome contributed by the non-carrier parent would then result in uniparental disomy (UPD) in a conceptus carrying a balanced rearrangement. UPD for chromosomes 14 and 15 has been demonstrated in several clinically abnormal individuals who carry a familial Robertsonian translocation. We have extended this type of analysis to include other forms of balanced chromosome rearrangements. We report the results of UPD analysis of 14 families who have a phenotypically abnormal child with an apparently balanced rearrangement. The series includes 4 reciprocal translocations, 4 Robertsonian translocations, 2 X;autosome translocations, and 4 inversions. High resolution chromosomes were used to compare breakpoints between parent and offspring to exclude the possibility of further rearrangements. Parental origin of the chromosome(s) involved was determined by DNA polymorphism analysis using PCR or Southern blotting techniques. We found no evidence of UPD in any of the 14 cases. Our data suggest that UPD is not a common explanation for phenotypically abnormal carriers of balanced chromosome rearrangements.

  11. Cytogenetic Analysis for Suspected Chromosomal Abnormalities; A Five Years Experience

    Science.gov (United States)

    Karra, Vijay Kumar; Jindal, Ankur; Puppala, Madhavi; Singh, Pratiksha; Rawat, Kanchan; Kapoor, Seema

    2016-01-01

    Introduction Chromosomal abnormalities are the results of alterations in the number or structure of chromosomes causing significant human morbidity and mortality. They are responsible for a large proportion of miscarriages, developmental delay, disorders of sexual development, congenital malformations and mental retardation. Aim The aim of this study was to describe the prevalence of different chromosomal abnormalities in North Indian patients referred for cytogenetic analysis. Materials and Methods Total of 859 patients ranging from newborn to 37 years of age were referred to the division of genetics, Department of Paediatrics between 2010 and 2015, with a variety of clinical disorders; Down syndrome (DS), Turner’s syndrome (TS) and Klinefelter syndrome; amenorrhea; ambiguous sex and multiple congenital malformations. Chromosomal analysis was performed on lymphocyte culture according to standard methods. Results Of the 859 cases studied, 371 (43.1%) had chromosomal abnormalities. The most common autosomal abnormalities were DS 302 (81.4%) and sex chromosomal abnormalities were TS 51 (13.7%). Numerical abnormalities were accounted for 353 (41.0%) and structural abnormalities 18 (2.0%), respectively. Various other chromosomal anomalies were also reported. Conclusion We have reviewed the incidence and distribution of chromosomal abnormalities and found higher rate of chromosomal abnormalities 43.1% in the referred cases. Our data suggest that chromosomal analysis is important tool in the evaluation of genetic disorders and helps clinicians to provide accurate diagnosis and proper genetic counselling. PMID:27790464

  12. Dynamic in situ chromosome immobilisation and DNA extraction using localized poly(N-isopropylacrylamide) phase transition

    DEFF Research Database (Denmark)

    Eriksen, Johan; Thilsted, Anil Haraksingh; Marie, Rodolphe

    2011-01-01

    A method of in situ chromosome immobilisation and DNA extraction in a microfluidic polymer chip was presented. Light-induced local heating was used to induce poly(N-isopropylacrylamide) phase transition in order to create a hydrogel and embed a single chromosome such that it was immobilised....... This was achieved with the use of a near-infrared laser focused on an absorption layer integrated in the polymer chip in close proximity to the microchannel. It was possible to proceed to DNA extraction while holding on the chromosome at an arbitrary location by introducing protease K into the microchannel. © 2011...

  13. Chromosomal localization of murine and human oligodendrocyte-specific protein genes

    Energy Technology Data Exchange (ETDEWEB)

    Bronstein, J.M.; Wu, S.; Korenberg, J.R. [UCLA School of Medicine, Los Angeles, CA (United States)] [and others

    1996-06-01

    Oligodendrocyte-specific protein (OSP) is a recently described protein present only in myelin of the central nervous system. Several inherited disorders of myelin are caused by mutations in myelin genes but the etiology of many remain unknown. We mapped the location of the mouse OSP gene to the proximal region of chromosome 3 using two sets of multilocus crosses and to human chromosome 3 using somatic cell hybrids. Fine mapping with fluorescence in situ hybridization placed the OSP gene at human chromosome 3q26.2-q26.3. To date, there are no known inherited neurological disorders that localize to these regions. 24 refs., 2 figs.

  14. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, Donna M; Scherer, Steven E; Kaul, Rajinder

    2006-01-01

    After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chr...

  15. Should the indications for prenatal chromosome analysis be changed?

    DEFF Research Database (Denmark)

    Philip, J; Bang, J; Madsen, Mette

    1977-01-01

    Amniocentesis for chromosome analysis was performed in 1086 pergnant women, 739 of whom had an increased risk of giving birth to a child with chromosome abnormalities. Such abnormalities were found in almost identical proportions among the fetuses with an increased risk (1.2%) and among those...

  16. Quickscan dicentric chromosome analysis for radiation biodosimetry.

    Science.gov (United States)

    Flegal, F N; Devantier, Y; McNamee, J P; Wilkins, R C

    2010-02-01

    The dicentric chromosome assay (DCA) is the gold-standard assay for accurately estimating unknown radiological doses to individuals following radiological or nuclear accidents. However in a mass-casualty scenario, this assay is not well suited for providing timely dose estimates due to its time- and expertise-intensive nature. In Canada, two approaches are being developed in an attempt to increase triage-quality biological dosimetry throughput. These are 1) increasing the number of trained personnel capable of conducting the DCA, and 2) evaluating alternative biodosimetry approaches or DCA variations. In a recent exercise, a new scoring technique (termed DCA QuickScan) was evaluated as an alternative rapid-scoring approach. Triage-quality conventional DCA and DCA QuickScan analysis were based upon scoring a minimum of 50 metaphase cells or 30 dicentrics by 9-15 scorers across four laboratories. Dose estimates for the conventional DCA were found to be within 0.5 Gy of the actual dose for 83% of the unknown samples, while DCA QuickScan dose estimates were within 0.5 Gy for 80% of the samples. Of the dose estimates falling 0.5 Gy or more outside the actual dose, the majority were dose over-estimates. It was concluded that the DCA QuickScan approach can provide critical dose information at a much faster rate than the conventional DCA without sacrificing accuracy. Future studies will further evaluate the accuracy of the DCA QuickScan method.

  17. Expression and chromosomal localization of the Requiem gene.

    Science.gov (United States)

    Gabig, T G; Crean, C D; Klenk, A; Long, H; Copeland, N G; Gilbert, D J; Jenkins, N A; Quincey, D; Parente, F; Lespinasse, F; Carle, G F; Gaudray, P; Zhang, C X; Calender, A; Hoeppener, J; Kas, K; Thakker, R V; Farnebo, F; Teh, B T; Larsson, C; Piehl, F; Lagercrantz, J; Khodaei, S; Carson, E; Weber, G

    1998-08-01

    Apoptosis in murine myeloid cell lines requires the expression of the Requiem gene, which encodes a putative zinc finger protein. We detected the protein in both cytoplasmic and nuclear subcellular fractions of murine myeloid cells and human K562 leukemia cells, which suggests that the protein might have a function distinct from a transcription factor. This distribution did not alter upon apoptosis induction by IL-3 deprivation. As an approach to investigate its role in development, we determined the spatio-temporal expression pattern in the mouse. Expression was detected in various tissues in earlier gestational age; however, confined to testes, spleen, thymus, and part of the hippocampus in the adult mouse. The expression profile is consistent with a functional role during rapid growth and cell turnover, and in agreement with a regulatory function for hematopoietic cells. The human cDNA clone sequenced showed high homology to its murine counterpart and extended the open reading frame by 20 codons upstream. The gene is located in the proximal region of mouse Chromosome (Chr) 19. In the homologous human region at 11q13, it is located at about 150 kb centromeric from MLK3.

  18. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution.

    Science.gov (United States)

    Paesold, Susanne; Borchardt, Dietrich; Schmidt, Thomas; Dechyeva, Daryna

    2012-11-01

    We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA.

  19. Major chromosomal breakpoint intervals in breast cancer tumors co-localize with differentially methylated regions.

    Directory of Open Access Journals (Sweden)

    Man-Hung Eric eTang

    2012-12-01

    Full Text Available Solid tumors exhibit chromosomal rearrangements resulting in gain or loss of multiple loci (copy number variation and translocations that occasionally result in the creation of novel chimeric genes. In the case of breast cancer, although most individual tumors each have unique CNV landscape the breakpoints, as measured over large datasets, appear to be non-randomly distributed in the genome. Breakpoints show a significant regional concentration at genomic loci spanning perhaps several megabases. The proximal cause of these breakpoint concentrations is a subject of speculation but is, as yet, largely unknown. To shed light on this issue, we have performed a bio-statistical analysis on our previously published data for a set of 119 breast tumors and normal controls, where each sample has both high resolution CNV and methylation data. The method examined the distribution of closeness of breakpoint regions with differentially methylated regions, coupled with additional genomic parameters, such as repeat elements and designated fragile sites in the reference genome. Through this analysis, we have identified a set of 91 regional loci called breakpoint enriched differentially methylated regions (BEDMRs characterized by altered DNA methylation in cancer compared to normal cells that are associated with frequent breakpoint concentrations within a distance of 1Mb. BEDMR loci are further associated with local hypomethylation (66% concentrations of the Alu SINE repeats within 3Mb and tend to occur near a number of cancer related genes such as the protocadherins, AKT1, DUB3, GAB2. BEDMRs seem to deregulate members of the histone gene family and chromatin remodeling factors e.g JMJD1B which might affect the chromatin structure and disrupt coordinate signaling and repair. From this analysis we propose that preference for chromosomal breakpoints is related to genome structure coupled with alterations in DNA methylation and hence chromatin structure associated

  20. MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics.

    Science.gov (United States)

    Meguro-Horike, Makiko; Horike, Shin-Ichi

    2015-01-01

    Recent evidence implicated several long noncoding RNA (lncRNA) in gene expression in cis or trans through regulating the local chromosomal architecture. However, the mechanisms underlying the lncRNA mediated silencing of multiple genes remain unknown. We believe that Microcell Mediated Chromosome Transfer (MMCT) is a suitable approach for functional analysis of lncRNAs and nuclear dynamics. MMCT is a unique research technique that can be generally used to transfer a single chromosome from one mammalian cell to another. Transferred chromosomes can be stably maintained as functioning in the recipient cells. Since there is no size limit to introducing genomic locus, an approach using the chromosome transfer technique is suitable for functional analysis of a large chromosomal domain. Here we describe a general strategy of MMCT, applications of which have potential to be an alternative tool of existing gene delivery system.

  1. Isolation, expression, and chromosomal localization of the human mitochondrial capsule selenoprotein gene (MCSP)

    Energy Technology Data Exchange (ETDEWEB)

    Aho, Hanne; Schwemmer, M.; Tessmann, D.; Murphy, D. [Institut fuer Humangenetik der Universitaet, Goettingen (Germany)] [and others

    1996-03-01

    The mitochondrial capsule selenoprotein (MCS) (HGMW-approved symbol MCSP) is one of three proteins that are important for the maintenance and stabilization of the crescent structure of the sperm mitochondria. We describe here the isolation of a cDNA, the exon-intron organization, the expression, and the chromosomal localization of the human MCS gene. Nucleotide sequence analysis of the human and mouse MCS cDNAs reveals that the 5{prime}- and 3{prime}-untranslated sequences are more conserved (71%) than the coding sequences (59%). The open reading frame encodes a 116-amino-acid protein and lacks the UGA codons, which have been reported to encode the selenocysteines in the N-terminal of the deduced mouse protein. The deduced human protein shows a low degree of amino acid sequence identity to the mouse protein. The deduced human protein shows a low degree of amino acid sequence identity to the mouse protein (39%). The most striking homology lies in the dicysteine motifs. Northern and Southern zooblot analyses reveal that the MCS gene in human, baboon, and bovine is more conserved than its counterparts in mouse and rat. The single intron in the human MCS gene is approximately 6 kb and interrupts the 5{prime}-untranslated region at a position equivalent to that in the mouse and rat genes. Northern blot and in situ hybridization experiments demonstrate that the expression of the human MCS gene is restricted to haploid spermatids. The human gene was assigned to q21 of chromosome 1. 30 refs., 9 figs.

  2. Localization of the human fibromodulin gene (FMOD) to chromosome 1q32 and completion of the cDNA sequence

    Energy Technology Data Exchange (ETDEWEB)

    Sztrolovics, R.; Grover, J.; Roughley, P.J. [McGill Univ., Montreal (Canada)] [and others

    1994-10-01

    This report describes the cloning of the 3{prime}-untranslated region of the human fibromodulin cDNA and its use to map the gene. For somatic cell hybrids, the generation of the PCR product was concordant with the presence of chromosome 1 and discordant with the presence of all other chromosomes, confirming that the fibromodulin gene is located within region q32 of chromosome 1. The physical mapping of genes is a critical step in the process of identifying which genes may be responsible for various inherited disorders. Specifically, the mapping of the fibromodulin gene now provides the information necessary to evaluate its potential role in genetic disorders of connective tissues. The analysis of previously reported diseases mapped to chromosome 1 reveals two genes located in the proximity of the fibromodulin locus. These are Usher syndrome type II, a recessive disorder characterized by hearing loss and retinitis pigmentosa, and Van der Woude syndrome, a dominant condition associated with abnormalities such as cleft lip and palate and hyperdontia. The genes for both of these disorders have been projected to be localized to 1q32 of a physical map that integrates available genetic linkage and physical data. However, it seems improbable that either of these disorders, exhibiting restricted tissue involvement, could be linked to the fibromodulin gene, given the wide tissue distribution of the encoded proteoglycan, although it remains possible that the relative importance of the quantity and function of the proteoglycan may avry between tissues. 11 refs., 1 fig.

  3. Human oocyte chromosome analysis: complicated cases and major pitfalls

    Indian Academy of Sciences (India)

    Bernd Rosenbusch; Michael Schneider; Hans Wilhelm Michelmann

    2008-08-01

    Human oocytes that remained unfertilized in programmes of assisted reproduction have been analysed cytogenetically for more than 20 years to assess the incidence of aneuploidy in female gametes. However, the results obtained so far are not indisputable as a consequence of difficulties in evaluating oocyte chromosome preparations. Because of the lack of guidelines, we decided to summarize for the first time, the possible pitfalls in human oocyte chromosome analysis. Therefore, we screened the material from our previous studies and compiled representative, complicated cases with recommendations for their cytogenetic classification. We point out that maturity and size of the oocyte are important parameters and that fixation artefacts, as well as the particular structure of oocyte chromosomes, may predispose one to misinterpretations. Moreover, phenomena related to oocyte activation and fertilization are illustrated and explained. This compilation may help to avoid major problems in future studies and contribute to a more precise, and uniform assessment of human oocyte chromosomes.

  4. Usp16 regulates kinetochore localization of Plk1 to promote proper chromosome alignment in mitosis.

    Science.gov (United States)

    Zhuo, Xiaolong; Guo, Xiao; Zhang, Xiaoyan; Jing, Guihua; Wang, Yao; Chen, Qiang; Jiang, Qing; Liu, Junjun; Zhang, Chuanmao

    2015-08-31

    During the G2 to M phase transition, a portion of mitotic regulator Plk1 localizes to the kinetochores and regulates the initiation of kinetochore-microtubule attachments for proper chromosome alignment. Once kinetochore-microtubule attachment is achieved, this portion of Plk1 is removed from the kinetochores as a result of ubiquitination. However, the crucial molecular mechanism that promotes the localization and the maintenance of Plk1 on the kinetochores until metaphase is still unclear. We report that ubiquitin-specific peptidase 16 (Usp16) plays a key role during this process. Usp16 deubiquitinates Plk1, resulting in an enhanced interaction with kinetochore-localized proteins such as BubR1, and thereby retains Plk1 on the kinetochores to promote proper chromosome alignment in early mitosis. Down-regulation of Usp16 causes increased ubiquitination and decreased kinetochore localization of Plk1. Thus, our data unveil a unique mechanism by which Usp16 promotes the localization and maintenance of Plk1 on the kinetochores for proper chromosome alignment.

  5. Structure, sequence, expression, and chromosomal localization of the human V{sub 1a} vasopressin receptor gene

    Energy Technology Data Exchange (ETDEWEB)

    Thibonnier, M.; Graves, M.K.; Wagner, M.S. [Case Western Reserve Univ. School of Medicine, Cleveland, OH (United States)] [and others

    1996-02-01

    We recently reported the structure and functional expression of a human V{sub 1a} vasopressin receptor (V{sub 1a}R) cDNA isolated from human liver cDNA libraries. To understand further the expression and regulation of the V{sub 1a}R, we now describe the genomic characteristics, tissue expression, chromosomal localization, and regional mapping of the human V{sub 1a}R gene, AVPR1A. Tissue distribution of the human V{sub 1a}R mRNA explored by Northern blot analysis of various human tissues or organs revealed the presence of a 5.5-kb mRNA transcript expressed in the liver and to a lesser degree in the heart, the kidney, and skeletal muscle. Screening of human genomic libraries revealed that the human AVPR1A gene is included entirely within a 6.4-kb rated by a 2.2-kb intron located before the corresponding seventh transmembrane domain of the receptor sequence. The first exon also contains 2 kb of 5{prime}-untranslated region, and the second exon includes 1 kb of 3{prime}-untranslated region. 5{prime}-RACE analysis of human liver mRNA by PCR localized the V{sub 1a}R mRNA transcription start site 1973 bp upstream of the translation the intron sequence were used as primers in polymerase chain reaction (PCR) analysis of human/rodent somatic cell hybrids. AVPR1A was localized by PCR analysis of a somatic cell hybrid panel to chromosome 12. Fluorescence in situ hybridization using a yeast artificial chromosome physically mapped AVPR1A to region 12q14-q15. 34 refs., 4 figs.

  6. Systematic analysis of human protein complexes identifies chromosome segregation proteins.

    Science.gov (United States)

    Hutchins, James R A; Toyoda, Yusuke; Hegemann, Björn; Poser, Ina; Hériché, Jean-Karim; Sykora, Martina M; Augsburg, Martina; Hudecz, Otto; Buschhorn, Bettina A; Bulkescher, Jutta; Conrad, Christian; Comartin, David; Schleiffer, Alexander; Sarov, Mihail; Pozniakovsky, Andrei; Slabicki, Mikolaj Michal; Schloissnig, Siegfried; Steinmacher, Ines; Leuschner, Marit; Ssykor, Andrea; Lawo, Steffen; Pelletier, Laurence; Stark, Holger; Nasmyth, Kim; Ellenberg, Jan; Durbin, Richard; Buchholz, Frank; Mechtler, Karl; Hyman, Anthony A; Peters, Jan-Michael

    2010-04-30

    Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization, and tandem-affinity purification-mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or had only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex and the gamma-tubulin ring complex--large complexes that are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high-throughput follow-up analyses of phenotypic screens in mammalian cells.

  7. Molecular karyotype and chromosomal localization of genes encoding ß-tubulin, cysteine proteinase, hsp 70 and actin in Trypanosoma rangeli

    Directory of Open Access Journals (Sweden)

    CB Toaldo

    2001-01-01

    Full Text Available The molecular karyotype of nine Trypanosoma rangeli strains was analyzed by contour-clamped homogeneous electric field electrophoresis, followed by the chromosomal localization of ß-tubulin, cysteine proteinase, 70 kDa heat shock protein (hsp 70 and actin genes. The T. rangeli strains were isolated from either insects or mammals from El Salvador, Honduras, Venezuela, Colombia, Panama and southern Brazil. Also, T. cruzi CL-Brener clone was included for comparison. Despite the great similarity observed among strains from Brazil, the molecular karyotype of all T. rangeli strains analyzed revealed extensive chromosome polymorphism. In addition, it was possible to distinguish T. rangeli from T. cruzi by the chromosomal DNA electrophoresis pattern. The localization of ß-tubulin genes revealed differences among T. rangeli strains and confirmed the similarity between the isolates from Brazil. Hybridization assays using probes directed to the cysteine proteinase, hsp 70 and actin genes discriminated T. rangeli from T. cruzi, proving that these genes are useful molecular markers for the differential diagnosis between these two species. Numerical analysis based on the molecular karyotype data revealed a high degree of polymorphism among T. rangeli strains isolated from southern Brazil and strains isolated from Central and the northern South America. The T. cruzi reference strain was not clustered with any T. rangeli strain.

  8. Cytosolic phospholipase A{sub 2} gene in human and rat: Chromosomal localization and polymorphic markers

    Energy Technology Data Exchange (ETDEWEB)

    Tay, A.; Simon, J.S.; Jacob, H.J. [Univ. of Toronto (Canada)] [and others

    1995-03-01

    The authors report the chromosomal localization and a simple sequence repeat (SSR) in the cytosolic phospholipase A{sub 2} (cPLA{sub 2}) gene in both human and rat. A (CA){sub 18} repeat in the promoter of the rat gene was determined to exhibit length polymorphism when analyzed using the polymerase chain reaction (PCR) in 19 different inbred rat strains. Genotyping for this marker in 234 F{sub 2} progeny of a SHRXBN intercross mapped the gene to rat chromosome 13. Using a PCR strategy, a fragment of the promoter for the human gene was isolated, and a (CA){sub 18} repeat was identified. Since this marker displayed a low heterozygosity index, they also identified a mononucleotide repeat in the promoter for cPLA{sub 2} that displayed a polymorphism information content value of 0.76. The human gene was mapped using fluorescence in situ hybridization (FISH) to chromosome 1q25. Of interest, the gene encoding the enzyme prostaglandin-endoperoxide synthase 2 (cyclooxygenase-2), which acts on the arachidonic acid product of cPLA{sub 2}, was previously localized to this same chromosomal region, raising the possibility of coordinate regulation. Identification of intragenic markers may facilitate studies of polymorphic variants of these genes as candidates for disorders in which perturbations of the eicosanoid cascade may play a role. 20 refs., 3 figs., 2 tabs.

  9. Analysis of chromosome damage for biodosimetry using imaging flow cytometry.

    Science.gov (United States)

    Beaton, L A; Ferrarotto, C; Kutzner, B C; McNamee, J P; Bellier, P V; Wilkins, R C

    2013-08-30

    The dicentric chromosome assay (DCA), which involves counting the frequency of dicentric chromosomes in mitotic lymphocytes and converting it to a dose-estimation for ionizing radiation exposure, is considered to be the gold standard for radiation biodosimetry. Furthermore, for emergency response, the DCA has been adapted for triage by simplifying the scoring method [1]. With the development of new technologies such as the imaging flow cytometer, it may now be possible to adapt this microscope-based method to an automated cytometry method. This technology allows the sensitivity of microscopy to be maintained while adding the increased throughput of flow cytometry. A new protocol is being developed to adapt the DCA to the imaging cytometer in order to further increase the rapid determination of a biological dose. Peripheral blood mononuclear cells (PBMC) were isolated from ex vivo irradiated whole blood samples using a density gradient separation method and cultured with PHA and Colcemid. After 48h incubation, the chromosomes were isolated, stained for DNA content with propidium iodide (PI) and labelled with a centromere marker. Stained chromosomes were then analyzed on the ImageStream(×) (EMD-Millipore, Billerica, MA). Preliminary results indicate that individual chromosomes can be identified and mono- and dicentric chromosomes can be differentiated by imaging cytometry. A dose response curve was generated using this technology. The details of the method and the dose response curve are presented and compared to traditional microscope scoring. Imaging cytometry is a new technology which enables the rapid, automated analysis of fluorescently labelled chromosomes. Adapting the dicentric assay to this technology has the potential for high throughput analysis for mass casualty events.

  10. Cultivation and differentiation change nuclear localization of chromosome centromeres in human mesenchymal stem cells.

    Science.gov (United States)

    Voldgorn, Yana I; Adilgereeva, Elmira P; Nekrasov, Evgeny D; Lavrov, Alexander V

    2015-01-01

    Chromosome arrangement in the interphase nucleus is not accidental. Strong evidences support that nuclear localization is an important mechanism of epigenetic regulation of gene expression. The purpose of this research was to identify differences in the localization of centromeres of chromosomes 6, 12, 18 and X in human mesenchymal stem cells depending on differentiation and cultivating time. We analyzed centromere positions in more than 4000 nuclei in 19 mesenchymal stem cell cultures before and after prolonged cultivation and after differentiation into osteogenic and adipogenic directions. We found a centromere reposition of HSAX at late passages and after differentiation in osteogenic direction as well as of HSA12 and HSA18 after adipogenic differentiation. The observed changes of the nuclear structure are new nuclear characteristics of the studied cells which may reflect regulatory changes of gene expression during the studied processes.

  11. Cultivation and differentiation change nuclear localization of chromosome centromeres in human mesenchymal stem cells.

    Directory of Open Access Journals (Sweden)

    Yana I Voldgorn

    Full Text Available Chromosome arrangement in the interphase nucleus is not accidental. Strong evidences support that nuclear localization is an important mechanism of epigenetic regulation of gene expression. The purpose of this research was to identify differences in the localization of centromeres of chromosomes 6, 12, 18 and X in human mesenchymal stem cells depending on differentiation and cultivating time. We analyzed centromere positions in more than 4000 nuclei in 19 mesenchymal stem cell cultures before and after prolonged cultivation and after differentiation into osteogenic and adipogenic directions. We found a centromere reposition of HSAX at late passages and after differentiation in osteogenic direction as well as of HSA12 and HSA18 after adipogenic differentiation. The observed changes of the nuclear structure are new nuclear characteristics of the studied cells which may reflect regulatory changes of gene expression during the studied processes.

  12. Chromosomal and regional localization of the loci for IGKC, IGGC, ALDB, HOXB, GPT, and PRNP in the American mink (Mustela vison): comparisons with human and mouse

    DEFF Research Database (Denmark)

    Khlebodarova, TM; Malchenko, Sergey; Matveeva, NM;

    1995-01-01

    Chromosomal localization of the genes for gamma- and kappa-immunoglobulins (IGGC and IGKC, respectively), aldolase B (ALDB), prion protein (PRNP), homeo box B (HOXB), and glutamate pyruvate transaminase (GPT) were determined with the use of mink-rodent hybrid cells. Analysis of segregation...

  13. Karyotyping and in situ chromosomal localization of rDNA sites in black cumin Bunium persicum (Boiss B. Fedtsch,1915 (Apiaceae

    Directory of Open Access Journals (Sweden)

    R. K. Chahota

    2011-11-01

    Full Text Available The fluorescent in situ hybridization (FISH technique has been applied to somatic chromosomes in the medicinally important species, Bunium persicum, to elucidate its karyotypes. The bicolour FISH technique involving 18S-5.8S-26S and 5S ribosomal RNA genes as probes was used to assign physical localization and measurement of rDNA sites on homologous pairs of chromosomes. The two 18S-5.8S-26S rRNA gene sites were at the terminal regions of the short arms of the chromosomes 1 and 2 involving NOR region of chromosome 1. The 5S rDNA sites were found on subtelomeric region of the long arm of the chromosome number 5 and at interstitial regions of the short arm of chromosome 7. Based on direct visual analysis of chromosome length, morphology and position of FISH signals, a pioneer attempt has been made to construct metaphase karyotype in B. persicum, an endangered medicinal plant of North Western Himalayas.

  14. Localization of the kappa opioid receptor gene to human chromosome band 8q11. 2

    Energy Technology Data Exchange (ETDEWEB)

    Yasuda, Kazuki; Takeda, Jun; Bell, G.I.; Espinosa, R.; Le Beau, M.M. (Univ. of Chicago, IL (United States))

    1994-02-01

    Using the cloned mouse kappa opioid receptor cDNA clone as a probe, screened a human genomic library and isolated a clone containing part of the human kappa opioid receptor gene (OPRK1), designated [lambda]hSR4-1. To determine the chromosomal localization of OPRK1, [lambda]hSR4-1 DNA was labeled with biotin by nick-translation in the presence of bio-11-dUTP and hybridized to human metaphase cells prepared from phytohemagglutinin-stimulated peripheral blood lymphocytes as described previously. Hybridization of the OPRK1-specific probe [lambda]hSR4-1 DNA to normal human metaphase chromosomes resulted in specific labeling only of chromosome 8. Specific labeling of 8q11 was observed on all 4 (6 cells), 3 (9 cells), 2 (9 cells), or 1 (1 cell) chromatid of the chromosome 8 homologs in 25 cells examined. Of 72 signals observed, 70 were located at 8q11. 1 signal was located at 7q11 and at 12p11. In most cells, the signal on 8q was located at 8q11.2. 7 refs., 1 fig.

  15. Genomic analysis of plant chromosomes based on meiotic pairing

    Directory of Open Access Journals (Sweden)

    Lisete Chamma Davide

    2007-12-01

    Full Text Available This review presents the principles and applications of classical genomic analysis, with emphasis on plant breeding. The main mathematical models used to estimate the preferential chromosome pairing in diploid or polyploid, interspecific or intergenera hybrids are presented and discussed, with special reference to the applications and studies for the definition of genome relationships among species of the Poaceae family.

  16. Human gene encoding prostacyclin synthase (PTGIS): Genomic organization, chromosomal localization, and promoter activity

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Chieko; Yabuki, Tomoko; Inoue, Hiroyasu [National Cardiovascular Center Research Institute, Osaka (Japan)] [and others

    1996-09-01

    The prostacyclin synthase gene isolated from human genomic libraries (PTGIS) consists of 10 exons spanning approximately 60 kb. All the splice donor and acceptor sites conform to the GT/AG rule. Genomic Southern blot and fluorescence in situ hybridization analyses revealed that the human prostacyclin synthase gene is present as a single copy per haploid genome and is localized on chromosome 20q13.11-q13.13. The 1.5-kb sequence of the 5{prime} of the translational initiation site contained both GC-rich and pyrimidine-rich regions and consensus sequences of the transcription factor recognition sites such as Sp1, AP-2, the interferon-{gamma} response element, GATA, NF-{kappa}B, the CACCC box, and the glucocorticoid response element. The core binding sequence (GAGACC) of the shear stress responsive element was also found in the 5{prime}-flanking region of the gene. The major product of the primer extension analysis suggested that the transcription of the gene started from the positions around 49 bp upstream of the translational initiation codon. Transient transfection experiments using human aortic and bovine arterial endothelial cells demonstrated that the GC-rich region (positions -145 to -10) possessed a significant promoter activity. The 6-kb downstream sequence of the translational termination codon contained multiple polyadenylation signals, Alu repeat sequences, and the consensus sequence of the primate-repetitive DNA element, MER1. Two sizes of the prostacyclin synthase mRNAs (approximately 6 and 3.3 kb) were detected with the human aorta and lung. RNA blot hybridization analysis using the 3{prime}-untranslated region as probe indicated that the sizes of the 3{prime}-flanking regions were different in the major 6-kb and minor 3.3-kb mRNAs. 54 refs., 7 figs.

  17. Chromosomal localization of the [delta] opioid receptor gene to human 1p34. 3-36. 1 and mouse 4D bands by in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Befort, K.; Kieffer, B. (Ecole Superieure de Biotechnologie de Strasbourg (France)); Mattei, M.G.; Roeckel, N. (Hopital d' Enfants de la Timone, Marseille (France))

    1994-03-01

    The aim of the present study is to determine the precise localization of this gene in the murine as well as human genome by in situ hybridization. Southern analysis, using the noncoding part of the cDNA as a probe (NotI-BamHI fragment, 1040 bp) under high-stringency conditions, shows the existence of a single-copy gene in the murine genome. In a similar analysis performed on human genomic DNA, the coding part of the cDNA (PstI-NotI fragment, 976 bp) clearly detected a single gene in the human genome (not shown). The authors therefore used these two probes for the chromosomal localization of the murine gene and its human counterpart, respectively. Chromosome spread preparations from concanavalin A (mouse) or phytohemagglutinin (human)-stimulated lymphocytes were hybridized with tritium-labeled cDNAs, exposed for 15 days, and developed, as described previously. For the murine assignment, a total of 100 metaphase cells were examined, and 149 silver grains were found. Forty-two grains were associated with chromosome 4, and 73.8% of them mapped to the D1-D3 region of the chromosome. In the 120 metaphase human cells analyzed, 197 silver grains were found, 25.8% of which were located on chromosome 1. The distribution of grains allowed mapping of the human [delta] opioid receptor gene to the p34.3-p36.1 region of the short arm with a maximum in the p35 band.

  18. Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection.

    Science.gov (United States)

    Zavattari, P; Deidda, E; Whalen, M; Lampis, R; Mulargia, A; Loddo, M; Eaves, I; Mastio, G; Todd, J A; Cucca, F

    2000-12-12

    Linkage disequilibrium (LD) mapping of disease genes is complicated by population- and chromosome-region-specific factors. We have analysed demographic factors by contrasting intermarker LD results obtained in a large cosmopolitan population (UK), a large genetic isolate (Sardinia) and a subisolate (village of Gavoi) for two regions of the X chromosome. A dramatic increase of LD was found in the subisolate. Demographic history of populations therefore influences LD. Chromosome-region-specific effects, namely the pattern and frequency of homologous recombination, were next delineated by the analysis of chromosome 6p21, including the HLA region. Patterns of global LD in this region were very similar in the UK and Sardinian populations despite their entirely distinct demographies, and correlate well with the pattern of recombinations. Nevertheless, haplotypes extend across recombination hot spots indicative of selection of certain haplotypes. Subisolate aside, chromosome-region-specific differences in LD patterns appear to be more important than the differences in intermarker LD between distinct populations.

  19. Comparative analysis by chromosome painting of the sex chromosomes in arvicolid rodents.

    Science.gov (United States)

    Acosta, M J; Romero-Fernández, I; Sánchez, A; Marchal, J A

    2011-01-01

    Sex chromosome evolution in mammals has been extensively investigated through chromosome-painting analyses. In some rodent species from the subfamily Arvicolinae the sex chromosomes contain remarkable features such as giant size, a consequence of heterochromatic enlargement, or asynaptic behaviour during male meiosis. Here, we have made a comparative study of the sex chromosomes in 6 arvicolid species using different probes from the X and Y chromosomes of 3 species, in order to gain knowledge about intra- or interspecific preservation of euchromatic regions. Our results clearly reveal poor conservation of the euchromatic region of the Y chromosome within these species, while the euchromatin on the X chromosome is extremely well preserved. Furthermore, we detected no clear correlation between the synaptic/asynaptic behaviour of the sex chromosomes, and the presence or absence of sequence homology within their euchromatic regions. Notably, our study has shown a new relationship between the giant sex chromosomes of 2 species, Microtus agrestis and Microtus cabrerae, that is, both X and Y share a novel region of common sequences in the euchromatin that is not present in the other species analysed. This interspecific euchromatic conservation, limited to the giant sex chromosomes, could point towards a common evolutionary origin for the heterochromatic enlargement process that has characterized the evolution of the sex chromosomes in some arvicolid species.

  20. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes).

    Science.gov (United States)

    Silva, Duílio M Z de A; Pansonato-Alves, José Carlos; Utsunomia, Ricardo; Araya-Jaime, Cristian; Ruiz-Ruano, Francisco J; Daniel, Sandro Natal; Hashimoto, Diogo Teruo; Oliveira, Cláudio; Camacho, Juan Pedro M; Porto-Foresti, Fábio; Foresti, Fausto

    2014-01-01

    Supernumerary (B) chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH) is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.

  1. Cloning, structural characterization, and chromosomal localization of the gene encoding the human prostaglandin E(2) receptor EP2 subtype.

    Science.gov (United States)

    Smock, S L; Pan, L C; Castleberry, T A; Lu, B; Mather, R J; Owen, T A

    1999-09-17

    Northern blot analysis of human placental RNA using a probe to the 5' end of the human prostaglandin E(2) (PGE(2)) EP2 receptor subtype coding region revealed the existence of a high abundance, low molecular weight transcript. To investigate the origin of this transcript, and its possible relationship to the human EP2 mRNA, we have cloned and characterized the gene encoding the human PGE(2) EP2 receptor subtype, identified transcriptional initiation and termination sites in two tissues (spleen and thymus), and determined its chromosomal localization. The human EP2 gene consists of two exons separated by a large intron, utilizes a common initiation site in both spleen and thymus at 1113 bp upstream of the translation initiation site, and has 3' transcript termini at 1140 bp and 1149 bp downstream of the translation stop site in spleen and thymus respectively. Southern and fluorescence in situ hybridization analysis demonstrated the human EP2 gene to be a single copy gene located in band 22 of the long arm of chromosome 14 (14q22). Though our initial interest in this gene was to investigate potential differential splicing of the human EP2 gene in placenta, this work demonstrates that the atypical transcript observed in placenta probably arises from a distinct, yet related, gene. Knowledge of the sequence, structure, and transcription events associated with the human EP2 gene will enable a broader understanding of its regulation and potential role in normal physiology and disease.

  2. Analysis of chromosome conservation in Lemur catta studied by chromosome paints and BAC/PAC probes.

    Science.gov (United States)

    Cardone, Maria Francesca; Ventura, Mario; Tempesta, Sergio; Rocchi, Mariano; Archidiacono, Nicoletta

    2002-12-01

    A panel of human chromosome painting probes and bacterial and P1 artificial chromosome (BAC/PAC) clones were used in fluorescence in situ hybridization (FISH) experiments to investigate the chromosome conservation of the ring-tailed lemur (Lemur catta, LCA) with respect to human. Whole chromosome paints specific for human chromosomes 7, 9, 11, 13, 14, 17, 18, 20, 21, and X were found to identify a single chromosome or an uninterrupted chromosomal region in LCA. A large set of partial chromosome paints and BAC/PAC probes were then used to refine the characterization of the rearrangements differentiating the two karyotypes. The results were also used to reconstruct the ancestral Lemuridae karyotype. Lemur catta, indeed, can be used as an outgroup, allowing symplesiomorphic (ancestral) rearrangements to be distinguished from apomorphic (derived) rearrangements in lemurs. Some LCA chromosomes are difficult to distinguish morphologically. The 'anchorage' of most LCA chromosomes to specific probes will contribute to the standardization of the karyotype of this species.

  3. In situ hybridization analysis of isodicentric X-chromosomes with short arm fusion

    DEFF Research Database (Denmark)

    Koch, J E; Kølvraa, S; Hertz, Jens Michael;

    1990-01-01

    We present here an alternative approach to the study of mosaic cell lines containing dicentric chromosomes. The approach is based on chromosome-specific non-radioactive in situ hybridization with centromere (alpha satellite DNA) probes. The hybridization analysis may be used as an alternative...... it for the analysis of two cases of isodicentric X-chromosomes. The approach is expected to be generally applicable, so that it may be applied to the scoring of other types of chromosomal mosaicism as well....

  4. Bivariate linkage analysis of the insulin resistance syndrome phenotypes on chromosome 7q.

    Science.gov (United States)

    Lehman, Donna M; Arya, Rector; Blangero, John; Almasy, Laura; Puppala, Sobha; Dyer, Thomas D; Leach, Robin J; O'Connell, Peter; Stern, Michael P; Duggirala, Ravindranath

    2005-04-01

    Metabolic abnormalities of the insulin resistance syndrome (IRS) have been shown to aggregate in families and to exhibit trait-pair correlations, suggesting a common genetic component. A broad region on chromosome 7q has been implicated in several studies to contain loci that cosegregate with IRS-related traits. However, it is not clear whether such loci have any common genetic (pleiotropic) influences on the correlated traits. Also, it is not clear whether the chromosomal regions contain more than one locus influencing the IRS-related phenotypes. In this study we present evidence for linkage of five IRS-related traits [body mass index (BMI), waist circumference (WC), In split proinsulin (LSPI), In triglycerides (LTG), and high-density lipoprotein cholesterol (HDLC)] to a region at 7q11.23. Subsequently, to gain further insight into the genetic component(s) mapping to this region, we explored whether linkage of these traits is due to pleiotropic effects using a bivariate linkage analytical technique, which has been shown to localize susceptibility regions with precision. Four hundred forty individuals from 27 Mexican American families living in Texas were genotyped for 19 highly polymorphic markers on chromosome 7. Multipoint variance component linkage analysis was used to identify genetic location(s) influencing IRS-related traits of obesity (BMI and WC), dyslipidemia (LTG and HDLC), and insulin levels (LSPI); the analysis identified a broad chromosomal region spanning approximately 24 cM. To gain more precision in localization, we used a bivariate linkage approach for each trait pair. These analyses suggest localization of most of these bivariate traits to an approximately 6-cM region near marker D7S653 [7q11.23, 103-109 cM; a maximum bivariate LOD of 4.51 was found for the trait pair HDLC and LSPI (the LODeq score is 3.94)]. We observed evidence of pleiotropic effects in this region on obesity and insulin-related trait pairs.

  5. Molecular-Cytological Identification and Chromosome Behavior Analysis of Telotetrasomic in Rice

    Institute of Scientific and Technical Information of China (English)

    GONG Zhi-yun; GAO Qing-song; YU Heng-xiu; YI Chuan-deng; GU Ming-hong

    2008-01-01

    From the progenies of a telotrisomic of chromosome 9 short arm of an indica rice variety, Zhongxian 3037, a phenotypical variant was selected. The variant plant had rolled leaves, dispersed plant type, as well as a low seed-setting rate. Cytological and molecular cytological investigations revealed two extra chromosomes, which were the shortest in somatic cells of the variant. Fluorescent in situ hybridization (FISH) analysis using a rice centromere specific DNA (RCS2) and a DNA sequence specific for chromosome 9 on premetaphase and pachytene chromosomes showed that these two chromosomes were the short arms of chromosome 9. That is to say, the variant was a telotetrasomic of chromosome 9. Among the 25 pachytene cells, the two telosomic chromosomes paired each other to form a bivalent and didn't pair with other normal chromosome 9 as multivalents in 96% cells. However, the bivalent was easy to disassociate in advance.

  6. Local real analysis in locally homogeneous spaces

    CERN Document Server

    Bramanti, Marco

    2011-01-01

    We introduce the concept of locally homogeneous space, and prove in this context L^p and Holder estimates for singular and fractional integrals, as well as L^p estimates on the commutator of a singular or fractional integral with a BMO or VMO function. These results are motivated by local a-priori estimates for subelliptic equations.

  7. Local Component Analysis

    CERN Document Server

    Roux, Nicolas Le

    2011-01-01

    Kernel density estimation, a.k.a. Parzen windows, is a popular density estimation method, which can be used for outlier detection or clustering. With multivariate data, its performance is heavily reliant on the metric used within the kernel. Most earlier work has focused on learning only the bandwidth of the kernel (i.e., a scalar multiplicative factor). In this paper, we propose to learn a full Euclidean metric through an expectation-minimization (EM) procedure, which can be seen as an unsupervised counterpart to neighbourhood component analysis (NCA). In order to avoid overfitting with a fully nonparametric density estimator in high dimensions, we also consider a semi-parametric Gaussian-Parzen density model, where some of the variables are modelled through a jointly Gaussian density, while others are modelled through Parzen windows. For these two models, EM leads to simple closed-form updates based on matrix inversions and eigenvalue decompositions. We show empirically that our method leads to density esti...

  8. Chromosomal localization of 5S rDNA in Chinese shrimp (Fenneropenaeus chinensis):a chromosome-specific marker for chromosome identification

    Institute of Scientific and Technical Information of China (English)

    郇聘; 张晓军; 李富花; 赵翠; 张成松; 相建海

    2010-01-01

    Chinese shrimp(Fenneropenaeus chinensis)is an economically important aquaculture species in China.However,cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze.In this study,fluorescence in-situ hybridization(FISH) was used to identify the chromosomes of F.chinensis.The 5S ribosomal RNA gene(rDNA)of F. chinensis was isolated,cloned and then used as a hybridization probe.The results show that the 5S rDNA was located on one pair of homologo...

  9. Analysis of repetitive DNA in chromosomes by flow cytometry.

    Science.gov (United States)

    Brind'Amour, Julie; Lansdorp, Peter M

    2011-06-01

    We developed a flow cytometry method, chromosome flow fluorescence in situ hybridization (FISH), called CFF, to analyze repetitive DNA in chromosomes using FISH with directly labeled peptide nucleic acid (PNA) probes. We used CFF to measure the abundance of interstitial telomeric sequences in Chinese hamster chromosomes and major satellite sequences in mouse chromosomes. Using CFF we also identified parental homologs of human chromosome 18 with different amounts of repetitive DNA.

  10. Chromosomal localization of three repair genes: The xeroderma pigmentosum group C gene and two human homologs of yeast RAD23

    Energy Technology Data Exchange (ETDEWEB)

    Spek, P.J. van der; Smit, E.M.E.; Beverloo, H.B. [Erasmus Univ., Rotterdam (Netherlands)] [and others

    1994-10-01

    The nucleotide excision repair (NER) disorder xeroderma pigmentosum (XP) is characterized by sun (UV) sensitivity, predisposition to skin cancer, and extensive genetic heterogeneity. Recently, we reported the cloning and analysis of three human NER genes, XPC, HHR23A, and HHR23B. The previously cloned XPC gene is involved in the common XP complementation group C, which is defective in excision repair of nontranscribed sequences in the genome. The XPC protein was found to be complexed with the product of HHR23B, one of the two human homologs of the Saccharomyes cerevisiae NER gene RAD23. Here we present the chromosomal localization by in situ hybridization using haptenized probes of all three genes. The HHR23A gene was assigned to chromosome 19p13.2. Interestingly, the HHR23B and XPC genes, the product of which forms a tight complex, were found to colocalize on band 3p25.1. Pulsed-field gel electrophoresis revealed that the HHR23B and XPC genes possibly share a MluI restriction fragment of about 625 kb. Potential involvement of the HHR23 genes in human genetic disorders is discussed. 53 refs., 4 figs., 2 tabs.

  11. Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) by primed in situ labeling.

    Science.gov (United States)

    Wang, Y; Wang, J F; Yin, H; Gao, H Q; Zhuang, N S; Liu, J P

    2015-07-28

    Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) were achieved using primed in situ labeling. Amplified signals for both the EST507-1 and SSRY13-5 markers were consistently observed in different stages of cell division. A comparison of the length, arm ratio, and other morphological characteristics of somatic metaphase chromosomes in karyotype analysis indicated that the EST507-1 and SSRY13-5 markers were localized on the short and long arm of cassava chromosome 11 with the relative map positions of 41.67 and 23.07, respectively. The physical localization of the 2 markers on chromosome 11 of the karyotype corresponds to their positions on the 15th linkage group in cassava.

  12. Human phenol sulfotransferase STP2 gene: Molecular cloning, structural characterization, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Her, C.; Raftogianis, R.; Weinshilboum, R.M. [Mayo Foundation, Rochester, MN (United States)

    1996-05-01

    Sulfonation is an important pathway in the biotransformation of many drugs, xenobiotics, neurotransmitters, and steroid hormones. The thermostable (TS) form of phenol sulfotransferase (PST) preferentially catalyzes the sulfonation of {open_quotes}simple{close_quotes} planar phenols, and levels of activity of TS PST in human tissues are controlled by inheritance. Two different human liver TS PST cDNAs have been cloned that encode proteins with amino acid sequences that are 96% identical. We have determined the structure and chromosomal localization of the gene for one of these two cDNAs, STP2, as a step toward understanding molecular genetic mechanisms involved in the regulation of this enzyme activity in humans. STP2 spans approximately 5.1 kb and contains nine exons that range in length from 74 to 347 bp. The locations of most STP2 exon-intron splice junctions are identical to those of a gene for the thermolabile form of PST in humans, STM; a rat PST gene; a human estrogen ST (EST) gene, STE; and a guinea pig EST gene. The two initial STP2 exons, IA and IB, were identified by performing 5{prime}-rapid amplification of cDNA ends with human liver cDNA as template. Exons IA and IB are noncoding and represent two different human liver TS PST cDNA 5{prime}untranslated region sequences. The two apparent 5{prime}-ons IA and IB, contain no canonical TATA boxes, but do contain CCAAT elements. STP2 was localized to human chromosome 16 by performing the PCR with DNA from NIGMS human/rodent somatic cell hybrids as template. Structural characterization of STP2 will make it possible to begin to study molecular genetic mechanisms involved in the regulation of TS PST activity in human tissues. 63 refs., 7 figs., 1 tab.

  13. Transcript analysis of 250 novel yeast genes from chromosome XIV.

    Science.gov (United States)

    Planta, R J; Brown, A J; Cadahia, J L; Cerdan, M E; de Jonge, M; Gent, M E; Hayes, A; Kolen, C P; Lombardia, L J; Sefton, M; Oliver, S G; Thevelein, J; Tournu, H; van Delft, Y J; Verbart, D J; Winderickx, J

    1999-03-15

    The European Functional Analysis Network (EUROFAN) is systematically analysing the function of novel Saccharomyces cerevisiae genes revealed by genome sequencing. As part of this effort our consortium has performed a detailed transcript analysis for 250 novel ORFs on chromosome XIV. All transcripts were quantified by Northern analysis under three quasi-steady-state conditions (exponential growth on rich fermentative, rich non-fermentative, and minimal fermentative media) and eight transient conditions (glucose derepression, glucose upshift, stationary phase, nitrogen starvation, osmo-stress, heat-shock, and two control conditions). Transcripts were detected for 82% of the 250 ORFs, and only one ORF did not yield a transcript of the expected length (YNL285w). Transcripts ranged from low (62%), moderate (16%) to high abundance (2%) relative to the ACT1 mRNA. The levels of 73% of the 206 chromosome XIV transcripts detected fluctuated in response to the transient states tested. However, only a small number responded strongly to the transients: eight ORFs were induced upon glucose upshift; five were repressed by glucose; six were induced in response to nitrogen starvation; three were induced in stationary phase; five were induced by osmo-stress; four were induced by heat-shock. These data provide useful clues about the general function of these ORFs and add to our understanding of gene regulation on a genome-wide basis.

  14. Localization of Sry gene on Y chromosome of Muntjac munticus vaginalis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The chromosomes 1, Y1, Y2 of Muntjac munticus vaginalis were isolated by fluorescence activated chromosome sorting and amplified by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR). A primer pair within human Sry HMG box was designed and the Sry gene of the male M. m vaginalis was amplified. The product was cloned and sequenced. The result proved that Sry is located on chromosome Y2, which is the sex-determining chromosome in the male M. m vaginalis.

  15. Chromosomal localization of rDNA genes and genomic organization of 5S rDNA in Oreochromis mossambicus, O. urolepis hornorum and their hybrid

    Indian Academy of Sciences (India)

    Hua Ping Zhu; Mai Xin Lu; Feng Ying Gao; Zhang Han Huang; Li Ping Yang; Jain Fang Gui

    2010-08-01

    In this study, classical and molecular cytogenetic analyses were performed in tilapia fishes, Oreochromis mossambicus (XX/XY sex determination system), O. urolepis hornorum (WZ/ZZ sex determination system) and their hybrid by crossing O. mossambicus female × O. u. hornorum male. An identical karyotype (($2n = 44$, NF (total number of chromosomal arms) = 50) was obtained from three examined tilapia samples. Genomic organization analysis of 5S rDNA revealed two different types of 5S rDNA sequences, 5S type I and 5S type II. Moreover, fluorescence in situ hybridization (FISH) with 5S rDNA probes showed six positive fluorescence signals on six chromosomes of all the analysed metaphases from the three tilapia samples. Subsequently, 45S rDNA probes were also prepared, and six positive fluorescence signals were observed on three chromosome pairs in all analysed metaphases of the three tilapia samples. The correlation between 45 rDNA localization and nucleolar organizer regions (NORs) was confirmed by silver nitrate staining in tilapia fishes. Further, different chromosomal localizations of 5S rDNA and 45S rDNA were verified by two different colour FISH probes. Briefly, the current data provide an insights for hybridization projects and breeding improvement of tilapias.

  16. Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. & Zucc.

    Science.gov (United States)

    Hizume, M; Shibata, F; Maruyama, Y; Kondo, T

    2001-09-01

    Japanese red pine, Pinus densiflora, has 2n=24 chromosomes, of which most carry chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) bands at their centromere-proximal regions. It was proposed that these regions contain highly repetitive DNA. The DNA localized in the proximal fluorescent bands was isolated and characterized. In P. densiflora, centromeric and neighboring segments of the somatic chromosomes were dissected with a manual micromanipulator. The centromeric DNA was amplified from the DNA contained in dissected centromeric segments by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) and a cloned DNA library was constructed. Thirty-one clones carrying highly repetitive DNA were selected by colony hybridization using Cot-1 DNA from this species as a probe, and their chromosomal localization was determined by fluorescent in situ hybridization (FISH). Clone PDCD501 was localized to the proximal CMA band of 20 chromosomes. This clone contained tandem repeats, comprising a 27 bp repeat unit, which was sufficient to provide the proximal FISH signal, with a 52.3% GC content. The repetitive sequence was named PCSR (proximal CMA band-specific repeat). Clone PDCD159 was 1700 bp in length, with a 61.7% AT content, and produced FISH signals at the proximal DAPI band of the remaining four chromosomes. Four clones hybridized strongly to the secondary constriction and gave weak signals at the centromeric region of several chromosomes. Clone PDCD537, one of the four clones, was homologous to the 26S rRNA gene. A PCR experiment using microdissected centromeric regions suggested that the centromeric region contains 18S and 26S rDNA. Another 24 clones hybridized to whole chromosome arms, with varying intensities and might represent dispersed repetitive DNA.

  17. Localization of the Laevigatum powdery mildew resistance gene to barley chromosome 2 by the use of RFLP markers

    DEFF Research Database (Denmark)

    Giese, H.; Holm-Jensen, A.G.; Jensen, H.P.;

    1993-01-01

    The powdery mildew disease resistance gene Ml(La) was found to belong to a locus on barely chromosome 2. We suggest that this locus be designated MlLa. Linkage analysis was carried out on 72 chromosome-doubled, spring-type progeny lines from a cross between the winter var 'Vogelsanger Gold' and t......' and the spring var 'Alf'. A map of chromosome 2 spanning 119 cM and flanked by two peroxidase gene loci was constructed. In addition to the Laevigatum resistance locus the map includes nine RFLP markers, the two peroxidase gene loci and the six-row locus in barley....

  18. Chromosomal localization of a novel repetitive sequence in the Chenopodium quinoa genome.

    Science.gov (United States)

    Kolano, Bozena; Plucienniczak, Andrzej; Kwasniewski, Miroslaw; Maluszynska, Jolanta

    2008-01-01

    In this study, a novel repetitive sequence pTaq10 was isolated from the Taq I digest of the genomic DNA of the pseudocereal Chenopodium quinoa. Sequence analysis indicated that this 286-bp monomer is not homologous to any known retroelement sequence. FISH and Southern blot analysis showed that this sequence is characterized by an interspersed genomic organization. After FISH, hybridization signals were observed as small dots spread throughout all of the chromosomes. pTaq hybridization signals were excluded from 45S rRNA gene loci, but they partly overlapped with 5S rDNA loci. pTaq10 is not a species-specific sequence, as it was also detected in C. berlandieri.

  19. Genomic structure and refined chromosomal localization of the mouse Ptch2 gene.

    Science.gov (United States)

    Fröhlich, L; Liu, Z; Beier, D R; Lanske, B

    2002-01-01

    The vertebrate Patched 2 (Ptch2) gene encodes a putative membrane-embedded protein which may have roles in Hedgehog signaling during development and in tumorigenesis. We determined the genomic structure of the mouse Ptch2 gene and show that Ptch2 is composed of 22 exons spanning approximately 18 kb of genomic DNA. The exon-intron boundaries were found to be conserved within the human and mouse Ptch2 genes. Analysis of the 5' flanking region revealed a CpG island, the putative promoter region and the transcriptional start site while a polyadenylation signal as well as a mRNA destabilizing motif were identified in the 3' flanking region. Single-strand conformation polymorphism analysis was used to map mouse Ptch2 to chromosome 4 between the microsatellite markers D4Mit20 and D4Mit334.

  20. Localization of a human homolog of the mouse pericentrin gene (PCNT) to chromosome 21qter

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Haiming [Univ. of Geneva Medical School (Switzerland); Gos, A.; Morris, M.A. [Cantonal Hospital, Geneva (Switzerland)] [and others

    1996-08-01

    Exon trapping was used to identify portions of genes from cosmid DNA of a human chromosome 21-specific library LL21NC02-Q. More than 650 potential exons have been cloned and characterized to date. Among these, 3 trapped {open_quotes}exons{close_quotes} showed strong homology to different regions of the cDNA for the mouse pericentrin (Pcnt) gene, indicating that these 3 exons are portions of a human homolog of the mouse pericentrin gene. With PCR amplification, Southern blot analysis, and FISH, we have mapped this presumed human pericentrin gene (PCNT) to the long arm of chromosome 21 between marker PFKL and 21qter. Pericentrin is a conserved protein component of the filamentous matrix of the centrosome involved in the initial establishment of the organized microtubule array. No candidate hereditary disorder for pericentrin deficiency/abnormality has yet been mapped in the most distal region of 21q; in addition the role of triplication of the pericentrin gene in the pathophysiology or etiology of trisomy 21 is currently unknown. 16 refs., 3 figs.

  1. Transcript variations, phylogenetic tree and chromosomal localization of porcine aryl hydrocarbon receptor (AhR) and AhR nuclear translocator (ARNT) genes

    Indian Academy of Sciences (India)

    AGNIESZKA SADOWSKA; LUKASZ PAUKSZTO; ANNA NYNCA; IZABELA SZCZERBAL; KARINA ORLOWSKA; SYLWIA SWIGONSKA; MONIKA RUSZKOWSKA; TOMASZ MOLCAN; JAN P. JASTRZEBSKI; GRZEGORZ PANASIEWICZ; RENATA E. CIERESZKO

    2017-03-01

    Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor best known for mediating xenobiotic-induced toxicity. AhR requires aryl hydrocarbon receptor nuclear translocator (ARNT) to form an active transcription complex and promote the activation of genes which have dioxin responsive element in their regulatory regions. The present study was performed to determine the complete cDNA sequences of porcine AhR and ARNT genes and their chromosomal localization. Total RNA from porcine livers were used to obtain the sequence of the entire porcine transcriptome by next-generation sequencing (NGS;lllumina HiSeq2500). In addition, both, in silico analysis and fluorescence in situ hybridization (FISH) were used to determine chromosomal localization of porcine AhR and ARNT genes. In silico analysis of nucleotide sequences showed that there were two transcript variants of AhR and ARNT genes in the pig. In addition, computer analysis revealed that AhR gene in the pig is located on chromosome 9 and ARNT on chromosome 4. The results of FISH experiment confirmed the localization of porcine AhR and ARNT genes. In the present study, for the first time, the full cDNAs of AhR and ARNT were demonstrated in the pig.In future, it would be interesting to determine the tissue distribution of AhR and ARNT transcript variants in the pig and to test whether these variants are associated with different biological functions and/or different activation pathways.

  2. Essential functions of Sds22p in chromosome stability and nuclear localization of PP1.

    Science.gov (United States)

    Peggie, Mark W; MacKelvie, Sarah H; Bloecher, Andrew; Knatko, Elena V; Tatchell, Kelly; Stark, Michael J R

    2002-01-01

    Sds22p is a conserved, leucine-rich repeat protein that interacts with the catalytic subunit of protein phosphatase 1 (PP1(C)) and which has been proposed to regulate one or more functions of PP1(C) during mitosis. Here we show that Saccharomyces cerevisiae Sds22p is a largely nuclear protein, most of which is present as a sTable 1:1 complex with yeast PP1(C) (Glc7p). Temperature-sensitive (Ts(-)) S. cerevisiae sds22 mutants show profound chromosome instability at elevated growth temperatures but do not confer a cell cycle stage-specific arrest. In the sds22-6 Ts(-) mutant, nuclear Glc7p is both reduced in level and aberrantly localized at 37 degrees C and the interaction between Glc7p and Sds22p in vitro is reduced at higher temperatures, consistent with the in vivo Ts(-) growth defect. Like some glc7 mutations, sds22-6 can suppress the Ts(-) growth defect associated with ipl1-2, a loss of function mutation in a protein kinase that is known to work in opposition to PP1 on at least two nuclear substrates. This, together with reciprocal genetic interactions between GLC7 and SDS22, suggests that Sds22p functions positively with Glc7p to promote dephosphorylation of nuclear substrates required for faithful transmission of chromosomes during mitosis, and this role is at least partly mediated by effects of Sds22p on the nuclear distribution of Glc7p

  3. Condensation and localization of the partitioning protein ParB on the bacterial chromosome.

    Science.gov (United States)

    Broedersz, Chase P; Wang, Xindan; Meir, Yigal; Loparo, Joseph J; Rudner, David Z; Wingreen, Ned S

    2014-06-17

    The ParABS system mediates chromosome segregation and plasmid partitioning in many bacteria. As part of the partitioning mechanism, ParB proteins form a nucleoprotein complex at parS sites. The biophysical basis underlying ParB-DNA complex formation and localization remains elusive. Specifically, it is unclear whether ParB spreads in 1D along DNA or assembles into a 3D protein-DNA complex. We show that a combination of 1D spreading bonds and a single 3D bridging bond between ParB proteins constitutes a minimal model for a condensed ParB-DNA complex. This model implies a scaling behavior for ParB-mediated silencing of parS-flanking genes, which we confirm to be satisfied by experimental data from P1 plasmids. Furthermore, this model is consistent with experiments on the effects of DNA roadblocks on ParB localization. Finally, we show experimentally that a single parS site is necessary and sufficient for ParB-DNA complex formation in vivo. Together with our model, this suggests that ParB binding to parS triggers a conformational switch in ParB that overcomes a nucleation barrier. Conceptually, the combination of spreading and bridging bonds in our model provides a surface tension ensuring the condensation of the ParB-DNA complex, with analogies to liquid-like compartments such as nucleoli in eukaryotes.

  4. Molecular cloning and chromosomal localization of the ADH7 gene encoding human class IV ({sigma}) ADH

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Hirokazu; Baraona, E.; Lieber, C.S. [Mount Sinai School of Medicine, Bronx, NY (United States)

    1996-01-15

    The ADH7 gene encoding human Class IV ({sigma}) alcohol dehydrogenase (ADH) was cloned from a Caucasian genomic DNA library and characterized. It has nine exons and eight introns that span about 22 kb, and its intron insertion is identical to that of the other ADH genes (ADH1 to ADH5). The nucleotide sequences of the exons encoding 374 amino acids are identical to the previously reported cDNA sequence of {sigma} ADH. Fluorescence in situ hybridization analysis showed that ADH7 is located on human chromosome 4q23-q24, close to the ADH cluster locus (4q21-q25). These data are consistent with the view that Class IV ADH is a member of the ADH family and is phylogenetically close to the other ADHs. 15 refs., 2 figs., 1 tab.

  5. Structure, expression pattern and chromosomal localization of the rice Osgrp-2 gene

    Institute of Scientific and Technical Information of China (English)

    LIU; Zongzhi; (刘宗旨); WANG; Jianlong; (王建龙); WANG; Qun; (王群); HUANG; Xun; (黄勋); XU; Weihui; (徐卫辉); ZHU; Lihuang; (朱立煌); HE; Ping; (何平); FANG; Rongxiang; (方荣祥)

    2003-01-01

    Glycine-rich proteins (GRPs) belong to a kind of important structural proteins of plant cell walls. The expression of GRP genes is regulated spatially and developmentally as well as by various environmental stresses, thus providing a good model for the study of plant gene expression. We obtained the genomic sequence of a new GRP gene (Osgrp-2) from a rice genomic library. The transcription start site of Osgrp-2 was determined by 5'-rapid amplification of cDNA ends (RACE) and a 2.4-kb promoter sequence was thus delimited. The spatial and developmental expression pattern as well as the wound-inducible character of Osgrp-2 in rice plants was analyzed in detail. Furthermore, the gene was mapped onto rice chromosome 10 by analysis of restriction fragment length polymorphism (RFLP).

  6. The cryptomonad histone H4-encoding gene: structure and chromosomal localization.

    Science.gov (United States)

    Müller, S B; Rensing, S A; Maier, U G

    1994-12-15

    Cryptomonads are unicellular flagellates whose plastids are surrounded by four membranes. A periplastidal compartment, containing eukaryote-type ribosomes, starch grains and a so-called nucleomorph, is located between the inner and outer membrane pairs. The nucleomorph has been shown to be the vestigial nucleus of a eukaryotic endosymbiont. In order to obtain more information about the chromatin structure of the nucleomorph and the host nuclear chromosomes, we studied the distribution of the histone, H4. H4 was not detectable in the nucleomorph by immunolocalization, thus supporting earlier findings by Gibbs [In: Wiesner et al. (Eds.), Experimental Phycology 1, 1990, pp. 145-157]. Likewise, no H4 DNA was demonstrable in the nucleomorph by Southern hybridization. Sequence analysis, and Southern and Northern blot data of a cryptomonad gene, H4, indicate an intermediate position for these genes between animals and plants.

  7. Tropomyosin is localized in the nuclear matrix and chromosome scaffold of physarum polycephalum

    Institute of Scientific and Technical Information of China (English)

    ZENGXIANLU; XIAOGUANGWANG; 等

    1999-01-01

    The nuclei and chromosomes were isolated from plasmodia of Physarum polycephalum.The nuclear matrix and chromosome scaffold were obtained after the DNA and most of the proteins were extracted with DNase I and 2 M NaCl.SD-PAGE analyses revealed that the nuclear matrix and chromosome scaffold contained a 37 kD polypeptide which is equivalent to tropomyosin in molecular weight.Immunofluorescence observations upon slide preparations labeled with anti-tropomyosin antibody showed that the nuclear matrix and chromosome scaffold emanated bright fluorescence,suggesting the presence of the antigen in them.Immunodotting results confirmed the presence of tropomyosin in the nuclear matrix and chromosome scaffold.Immunoelectron microscopic observations further demonstrated that tropomyosin was dispersively distributed in the interphase nuclei and metaphase chromosomes.

  8. Patterns of rDNA chromosomal localization in Palearctic Cephalota and Cylindera (Coleoptera: Carabidae: Cicindelini with different numbers of X-chromosomes

    Directory of Open Access Journals (Sweden)

    Sonia J. R. Proença

    2011-05-01

    Full Text Available The ribosomal clusters of six Paleartic taxa belonging to the tiger beetle genera Cephalota Dokhtourow, 1883 and Cylindera Westwood, 1831, with multiple sex chromosomes (XXY, XXXY and XXXXY have been localised on mitotic and meiotic cells by fluorescence in situ hybridization (FISH, using a PCR-amplified 18S rDNA fragment as a probe. Four patterns of rDNA localization in these tiger beetles were found: 1. Two clusters located in one autosomal pair; 2. Two clusters located in one autosomal pair and one in an X chromosome; 3. Three clusters located in three heterosomes (XXY; 4. Two clusters located in one autosomal pair and two in the heterosomes (one of the Xs and the Y. These results illustrate that ribosomal cistrons have changed their number and localization during the evolution of these genera, showing a dynamic rather than a conservative pattern. These changes in rDNA localization are uncoupled with changes in the number of autosomes and/or heterosomes. A mechanism that involves transposable elements that carry ribosomal cistrons appears to be the most plausible explanation for these dynamics that involve jumping from one location in the genome to another, in some cases leaving copies in the original location.

  9. Physical mapping and YAC contig analysis of the region surrounding Xist on the mouse X chromosome.

    Science.gov (United States)

    Heard, E; Simmler, M C; Larin, Z; Rougeulle, C; Courtier, B; Lehrach, H; Avner, P

    1993-03-01

    The Xist sequence has been proposed as a potential candidate for the X-inactivation center based both on its localization within the candidate region for the X-inactivation center in man and mouse and on its unique pattern of expression from the inactive X chromosome. We have cloned 550 kb of DNA surrounding the mouse Xist sequence in contiguously overlapping YAC clones and have developed a long-range restriction map that spans almost 1 Mb of this region and includes this YAC contig. The detailed restriction map we have established provides a framework for the identification of expressed sequences other than Xist that may equally exhibit unusual expression characteristics associated with X inactivation. The presence of possible structural or methylation differences within this region between the active and inactive X chromosomes has been investigated through comparative analysis of male and female genomic DNA, and we report here the identification of certain CpG-containing restriction sites around Xist that have an interesting differential methylation status on the inactive and active X chromosomes.

  10. Localization of a gene for an autosomal recessive form of juvenile Parkinsonism to chromosome 6q25.2-27

    Energy Technology Data Exchange (ETDEWEB)

    Matsumine, Hiroto; Shimoda-Matsubayashi, Satoe; Nakagawa-Hattori, Yuko [Tokyo Metropolitan Ebara Hospital (Japan)] [and others

    1997-03-01

    An autosomal recessive form of juvenile Parkinsonism (AR-JP) (MIM 600116) is a levodopa-responsive Parkinsonism whose pathological finding is a highly selective degeneration of dopaminergic neurons in the zona compacta of the substantia nigra. By linkage analysis of diallelic polymorphism of the Mn-superoxide dismutase gene (SOD2), we found a family with AR-JP showing perfect segregation of the disease with the SOD2 locus. By extending the linkage analysis to 13 families with AR-JP, we discovered strong evidence for the localization of the AR-JP gene at chromosome 6q25.2-27, including the SOD2 locus, with the maximal cumulative pairwise LOD scores of 7.26 and 7.71 at D6S305 ({theta} = .03) and D6S253 ({theta} = .02), respectively. Observation of obligate recombination events, as well as multipoint linkage analysis, placed the AR-JP gene in a 17-cM interval between D6S437 and D6S264. Delineation of the AR-JP gene will be an important step toward our understanding of the molecular mechanism underlying selective degeneration of the nigral neurons. 38 refs., 4 figs., 1 tab.

  11. Chromosomal localization of a tandemly repeated DNA sequence in Trifilium repens L.

    Institute of Scientific and Technical Information of China (English)

    ZHUJM; NWELLISON; 等

    1996-01-01

    A karyotype of Trifolium repens constructed from mitotic cells revealed 13 pairs of metacentric and 3 pairs of submetacentric chromosomes including a pair of satellites located at the end of the short arm of chromosome 16.C-bands were identified around the centromeric regions of 8 pairs of chromosomes.A 350 bp tandemly repeated DNAsequence from T.repens labelled with digoxygenin hybridized to the proximal centromeric regions of 12 chromosome pairs.Some correlation between the distribution of the repeat sequence and the distribution of C-banding was demonstrated.

  12. Hematoxylin: a simple, multiple-use dye for chromosome analysis

    Directory of Open Access Journals (Sweden)

    Guerra Marcelo

    1999-01-01

    Full Text Available A staining mixture of hematoxylin-iron alum combined with a strong hydrochloric hydrolysis was successfully applied for chromosome observation of several kinds of plants and some animals. Slightly different procedures were developed for different materials and objectives. For plant cells, the most important technical aspect was the use of 5 N HCl hydrolysis, which resulted in a very transparent cytoplasm, combined with an intense, specific hematoxylin stain. This technique is recommended for cytogenetical analysis in general, and it is especially indicated for practical classes, due to its simplicity and high reproducibility of results. Moreover, the deep contrast observed makes this technique very useful for sequential staining of cells previously analyzed with other stains, as well as for materials with fixation problems.

  13. Linkage analysis on chromosome 2 in essential hypotension pedigrees

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    It is a new approach to study the important genes related to the control of blood pressure by probing into hypotension and hypertension at the same time. Genome scanning on whole chromosome 2 in 8 hypotension pedigrees has been done and parameter (LOD score) and non-pa- rameter (NPL score) were used in the linkage analysis by GENEHUNTER software. The results show the evidence of linkage between D2S112 and D2S117, indicating a number of critical genes may lie in thisregion and contribute to the mechanism of blood pressure regulation. Also this region has been found in the previous study in hypertension pedigrees. These genes may play an important role in the regulation of blood pressure and can also be the important candidate genes in hypertension studies.

  14. Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae.

    Science.gov (United States)

    Hizume, Masahiro; Shibata, Fukashi; Matsumoto, Ayako; Maruyama, Yukie; Hayashi, Eiji; Kondo, Teiji; Kondo, Katsuhiko; Zhang, Shozo; Hong, Deyuan

    2002-08-01

    Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.0-3.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.

  15. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis.

    Science.gov (United States)

    Melters, Daniël P; Paliulis, Leocadia V; Korf, Ian F; Chan, Simon W L

    2012-07-01

    In most eukaryotes, the kinetochore protein complex assembles at a single locus termed the centromere to attach chromosomes to spindle microtubules. Holocentric chromosomes have the unusual property of attaching to spindle microtubules along their entire length. Our mechanistic understanding of holocentric chromosome function is derived largely from studies in the nematode Caenorhabditis elegans, but holocentric chromosomes are found over a broad range of animal and plant species. In this review, we describe how holocentricity may be identified through cytological and molecular methods. By surveying the diversity of organisms with holocentric chromosomes, we estimate that the trait has arisen at least 13 independent times (four times in plants and at least nine times in animals). Holocentric chromosomes have inherent problems in meiosis because bivalents can attach to spindles in a random fashion. Interestingly, there are several solutions that have evolved to allow accurate meiotic segregation of holocentric chromosomes. Lastly, we describe how extensive genome sequencing and experiments in nonmodel organisms may allow holocentric chromosomes to shed light on general principles of chromosome segregation.

  16. Chromosome Aberrations in Human Epithelial Cells Exposed Los Alamos High-Energy Secondary Neutrons: M-BAND Analysis

    Science.gov (United States)

    Hada, M.; Saganti, P. B.; Gersey, B.; Wilkins, R.; Cucinotta, F. A.; Wu, H.

    2007-01-01

    High-energy secondary neutrons, produced by the interaction of galactic cosmic rays (GCR) with the atmosphere, spacecraft structure and planetary surfaces, contribute a significant fraction to the dose equivalent radiation measurement in crew members and passengers of commercial aviation travel as well as astronauts in space missions. The Los Alamos Nuclear Science Center (LANSCE) neutron facility's 30L beam line (4FP30L-A/ICE House) is known to generate neutrons that simulate the secondary neutron spectrum of the Earth's atmosphere at high altitude. The neutron spectrum is also similar to that measured onboard spacecrafts like the MIR and the International Space Station (ISS). To evaluate the biological damage, we exposed human epithelial cells in vitro to the LANSCE neutron beams with an entrance dose rate of 2.5 cGy/hr, and studied the induction of chromosome aberrations that were identified with multicolor-banding in situ hybridization (mBAND) technique. With this technique, individually painted chromosomal bands on one chromosome allowed the identification of inter-chromosomal aberrations (translocation to unpainted chromosomes) and intra-chromosomal aberrations (inversions and deletions within a single painted chromosome). Compared to our previous results with gamma-rays and 600 MeV/nucleon Fe ions of high dose rate at NSRL (NASA Space Radiation Laboratory at Brookhaven National Laboratory), the neutron data from the LANSCE experiments showed significantly higher frequency of chromosome aberrations. However, detailed analysis of the inversion type revealed that all of the three radiation types in the study induced a low incidence of simple inversions. Most of the inversions in gamma-ray irradiated samples were accompanied by other types of intrachromosomal aberrations but few inversions were accompanied by interchromosomal aberrations. In contrast, neutrons and Fe ions induced a significant fraction of inversions that involved complex rearrangements of both

  17. Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

    Science.gov (United States)

    Godler, David E; Inaba, Yoshimi; Schwartz, Charles E; Bui, Quang M; Shi, Elva Z; Li, Xin; Herlihy, Amy S; Skinner, Cindy; Hagerman, Randi J; Francis, David; Amor, David J; Metcalfe, Sylvia A; Hopper, John L; Slater, Howard R

    2015-07-01

    Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility.

  18. Direct ChromOSOme Analysis and FISH Detection of Primary Gastric cancer

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective: To investigate chromosome aberrations and their role in the genesis and development of primary gastric cancer. Methods: An improved, direct chromosome preparation from solid tumors was adopted for G-banding analysis followed by FISH on decolored G-banding chromosomes so that chromosome aberrations could be confirmed at DNA level. Results: A total of 28 primary gastric cancer specimens were studies. Case 1 and case 2 had simple chromosome numerical changes: 49, XY, +2, +8, +9 and 48, +8, +20, respectively. All but case 1 and 2 had complicated chromosome abnormalities. Chromosome structural of frequent occurrence involved del(7q)(21/26), del(3p)(14/26), del(lp)(l1/26) and del(17p)(10/26). The chromosome abnormalities could be simple and complicated. In former, numerical changes involving 1 to 3 chromosome could be observed. Trisomies 8 and 9 might represent a cytogenetic subgroup of primary gastric cancer. In the later, the del(7q) was the most consistent aberration. 7q32-qter was the commonly lost segment. Conclusion: Numerical and structural alterations of chromosomes are present in primary gastric cancer. Del(7q) is one of the structural change characteristic of primary gastric cancer. In the 7q32-qter fragment, a tumor suppressor gene probably exists and it may have close relation to the genesis and progression of gastric cancer.

  19. Mammalian DNA ligase III: Molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jingwen; Danehower, S.; Besterman, J.M.; Husain, I. [Glaxo Research Inst., Research Triangle Park, NC (United States)] [and others

    1995-10-01

    Three biochemically distinct DNA ligase activities have been identified in mammalian cell extracts. We have recently purified DNA ligase II and DNA ligase III to near homogeneity from bovine liver and testis tissue, respectively. Amino acid sequencing studies indicated that these enzymes are encoded by the same gene. In the present study, human and murine cDNA clones encoding DNA ligase III were isolated with probes based on the peptide sequences. The human DNA ligase III cDNA encodes a polypeptide of 862 amino acids, whose sequence is more closely related to those of the DNA ligases encoded by poxviruses than to replicative DNA ligases, such as human DNA ligase I. In vitro transcription and translation of the cDNA produced a catalytically active DNA ligase similar in size and substrate specificity to the purified bovine enzyme. The DNA ligase III gene was localized to human chromosome 17, which eliminated this gene as a candidate for the cancer-prone disease Bloom syndrome that is associated with DNA joining abnormalities. DNA ligase III is ubiquitously expressed at low levels, except in the testes, in which the steady-state levels of DNA ligase III mRNA are at least 10-fold higher than those detected in other tissues and cells. Since DNA ligase I mRNA is also present at high levels in the testes, we examined the expression of the DNA ligase genes during spermatogenesis. DNA ligase I mRNA expression correlated with the contribution of proliferating supermatogonia cells to the testes, in agreement with the previously defined role of this enzyme in DNA replications. In contrast, elevated levels of DNA ligase III mRNA were observed in primary supermatocytes undergoing recombination prior to the first meiotic division. Therefore, we suggest that DNA ligase III seals DNA strand breaks that arise during the process of meiotic recombination in germ cells and as a consequence of DNA damage in somatic cells. 62 refs., 7 figs.

  20. Chromosomal localization of the major ribosomal RNA genes in scallop Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    HUANG Xiaoting; BAO Zhenmin; BI Ke; HU Jingjie; ZHANG Can; ZHANG Quanqi; HU Xiaoli

    2006-01-01

    The chromosomes of Chlamys farreri were analyzed by means of silver staining and fluorescence in situ hybridization ( FISH ) with 18S-28S rDNA probe. Probe was made by PCR amplification of a DNA fragment containing internal transcribed spacers ITS1 between 18S and 5.8S ribosomal RNA gene, ITS2 between 5.8S and 28S ribosomal RNA gene and 5.8S rRNA gene, and labeled by PCR incorporation of bio-16-dUTP. FISH signals were located on the short arm of subtelocentric chromosome 10. After silverstaining, nucleolus organizer regions (NORs) could be observed on the telomere of the short arm of chromosome 10. However,one metaphase spread displayed an additional silver spot on the short arm of subtelocentric chromosome 12.

  1. Localization of a novel gene for congenital nonsyndromic simple microphthalmia to chromosome 2q11-14.

    Science.gov (United States)

    Li, Hui; Wang, Jia-Xin; Wang, Cheng-Ye; Yu, Ping; Zhou, Qiang; Chen, Yong-Gang; Zhao, Lu-Hang; Zhang, Ya-Ping

    2008-01-01

    Microphthalmia is a clinically and genetically heterogeneous disorder of eye development. The genetic basis of nonsyndromic microphthalmia is not yet fully understood. Previous studies indicated that disease pedigrees from different genetic backgrounds could be attributed to completely different gene loci. To investigate the etiology in a large autosomal-dominant inherited simple microphthalmia (nanophthalmia) pedigree, which is the first genetically analyzed Chinese microphthalmia pedigree, we performed a whole-genome scan using 382 micro-satellite DNA markers after the exclusion of reported candidates associated with microphthalmia. Strong evidence indicated that microphthalmia in this family was mapped to an unreported new locus on chromosome 2q. A significantly positive two-point LOD score was obtained with a maximum 3.290 at a recombination fraction of 0.00 for marker D2S2265. Subsequent haplotype analysis and recombination data further confined the disease-causing gene to a 15-cM interval between D2S1890 and D2S347 on 2q11-14. Our results further underlined the degree of heterogeneity in microphthalmia from Chinese background and localized a novel gene which regulates eye embryogenesis.

  2. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation.

    Directory of Open Access Journals (Sweden)

    David B Lowry

    Full Text Available The role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and reproductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift, and

  3. Chromosomal localization and partial sequencing of the 18S and 28S ribosomal genes from Bradysia hygida (Diptera: Sciaridae).

    Science.gov (United States)

    Gaspar, V P; Shimauti, E L T; Fernandez, M A

    2014-03-26

    In insects, ribosomal genes are usually detected in sex chromosomes, but have also or only been detected in autosomal chromosomes in some cases. Previous results from our research group indicated that in Bradysia hygida, nucleolus organizer regions were associated with heterochromatic regions of the autosomal C chromosome, using the silver impregnation technique. The present study confirmed this location of the ribosomal genes using fluorescence in situ hybridization analysis. This analysis also revealed the partial sequences of the 18S and 28S genes for this sciarid. The sequence alignment showed that the 18S gene has 98% identity to Corydalus armatus and 91% identity to Drosophila persimilis and Drosophila melanogaster. The partial sequence analysis of the 28S gene showed 95% identity with Bradysia amoena and 93% identity with Schwenckfeldina sp. These results confirmed the location of ribosomal genes of B. hygida in an autosomal chromosome, and the partial sequence analysis of the 18S and 28S genes demonstrated a high percentage of identity among several insect ribosomal genes.

  4. cDNA cloning, tissue distribution, and chromosomal localization of myelodysplasia/Myeloid Leukemia Factor 2 (MLF2)

    Energy Technology Data Exchange (ETDEWEB)

    Kuefer, M.U.; Valentine, V.; Behm, F.G. [St. Jude Children`s Research Hospital, Memphis, TN (United States)] [and others

    1996-07-15

    A fusion gene between nucleophosmin (NPM) and myelodysplasia/myeloid leukemia factor 1 (MLF1) and myelodysplasia/myeloid leukemia factor 1 (MLF1) is formed by a recurrent t(3;5)(q25.1;q34) in myelodysplastic syndrome and acute myeloid leukemia. Here we report the identification of a novel gene, MLF2, which contains an open reading frame of 744 bp encoding a 248-amino-acid protein highly related to the previously identified MLF1 protein (63% similarity, 40% identity). In contrast to the tissue-restricted expression pattern of MLF1, and MLF2 messenger RNA is expressed ubiquitously. The MLF2 gene locus was mapped by fluorescence in situ hybridization to human chromosome 12p13, a chromosomal region frequently involved in translocations and deletions in acute leukemias of lymphoid or myeloid lineage. In a physical map of chromosome 12, MLF2 was found to reside on the yeast artificial chromosome clone 765b9. Southern blotting analysis of malignant cell DNAs prepared from a series of acute lymphoblastic leukemia cases with translocations involving chromosome arm 12p, as well as a group of acute myeloid leukemias with various cytogenetic abnormalities, failed to reveal MLF2 gene rearrangements. 19 refs., 2 figs.

  5. Analysis of chromosome translocation frequency after a single CT scan in adults.

    Science.gov (United States)

    Abe, Yu; Miura, Tomisato; Yoshida, Mitsuaki A; Ujiie, Risa; Kurosu, Yumiko; Kato, Nagisa; Katafuchi, Atsushi; Tsuyama, Naohiro; Kawamura, Fumihiko; Ohba, Takashi; Inamasu, Tomoko; Shishido, Fumio; Noji, Hideyoshi; Ogawa, Kazuei; Yokouchi, Hiroshi; Kanazawa, Kenya; Ishida, Takashi; Muto, Satoshi; Ohsugi, Jun; Suzuki, Hiroyuki; Ishikawa, Tetsuo; Kamiya, Kenji; Sakai, Akira

    2016-06-01

    We recently reported an increase in dicentric chromosome (DIC) formation after a single computed tomography (CT) scan (5.78-60.27 mSv: mean 24.24 mSv) and we recommended analysis of 2000 metaphase cells stained with Giemsa and centromere-FISH for dicentric chromosome assay (DCA) in cases of low-dose radiation exposure. In the present study, we analyzed the frequency of chromosome translocations using stored Carnoy's-fixed lymphocyte specimens from the previous study; these specimens were from 12 patients who were subject to chromosome painting of Chromosomes 1, 2 and 4. Chromosomes 1, 2 and 4 were analyzed in ∼5000 cells, which is equivalent to the whole-genome analysis of almost 2000 cells. The frequency of chromosome translocation was higher than the number of DICs formed, both before and after CT scanning. The frequency of chromosome translocations tended to be higher, but not significantly higher, in patients with a treatment history compared with patients without such a history. However, in contrast to the results for DIC formation, the frequency of translocations detected before and after the CT scan did not differ significantly. Therefore, analysis of chromosome translocation may not be a suitable assay for detecting chromosome aberrations in cases of low-dose radiation exposure from a CT scan. A significant increase in the frequency of chromosome translocations was not likely to be detected due to the high baseline before the CT scan; the high and variable frequency of translocations was probably due to multiple confounding factors in adults.

  6. Systematic analysis of S. cerevisiae chromosome VIII genes.

    Science.gov (United States)

    Niedenthal, R; Riles, L; Güldener, U; Klein, S; Johnston, M; Hegemann, J H

    1999-12-01

    To begin genome-wide functional analysis, we analysed the consequences of deleting each of the 265 genes of chromosome VIII of Saccharomyces cerevisiae. For 33% of the deletion strains a growth phenotype could be detected: 18% of the genes are essential for growth on complete glucose medium, and 15% grow significantly more slowly than the wild-type strain or exhibit a conditional phenotype when incubated under one of 20 different growth conditions. Two-thirds of the mutants that exhibit conditional phenotypes are pleiotropic; about one-third of the mutants exhibit only one phenotype. We also measured the level of expression directed by the promoter of each gene. About half of the promoters direct detectable transcription in rich glucose medium, and most of these exhibited only low or medium activity. Only 1% of the genes are expressed at about the same level as ACT1. The number of active promoters increased to 76% upon growth on a non-fermentable carbon source, and to 93% in minimal glucose medium. The majority of promoters fluctuated in strength, depending on the medium.

  7. Laboratory intercomparison of the dicentric chromosome analysis assay.

    Science.gov (United States)

    Beinke, C; Barnard, S; Boulay-Greene, H; De Amicis, A; De Sanctis, S; Herodin, F; Jones, A; Kulka, U; Lista, F; Lloyd, D; Martigne, P; Moquet, J; Oestreicher, U; Romm, H; Rothkamm, K; Valente, M; Meineke, V; Braselmann, H; Abend, M

    2013-08-01

    The study design and obtained results represent an intercomparison of various laboratories performing dose assessment using the dicentric chromosome analysis (DCA) as a diagnostic triage tool for individual radiation dose assessment. Homogenously X-irradiated (240 kVp, 1 Gy/min) blood samples for establishing calibration data (0.25-5 Gy) as well as blind samples (0.1-6.4 Gy) were sent to the participants. DCA was performed according to established protocols. The time taken to report dose estimates was documented for each laboratory. Additional information concerning laboratory organization/characteristics as well as assay performance was collected. The mean absolute difference (MAD) was calculated and radiation doses were merged into four triage categories reflecting clinical aspects to calculate accuracy, sensitivity and specificity. The earliest report time was 2.4 days after sample arrival. DCA dose estimates were reported with high and comparable accuracy, with MAD values ranging between 0.16-0.5 Gy for both manual and automated scoring. No significant differences were found for dose estimates based either on 20, 30, 40 or 50 cells, suggesting that the scored number of cells can be reduced from 50 to 20 without loss of precision of triage dose estimates, at least for homogenous exposure scenarios. Triage categories of clinical significance could be discriminated efficiently using both scoring procedures.

  8. Chromosomal localization of the human V3 pituitary vasopressin receptor gene (AVPR3) to 1q32

    Energy Technology Data Exchange (ETDEWEB)

    Rousseau-Merck, M.F.; Derre, J.; Berger, R. [INSERM, Paris (France)] [and others

    1995-11-20

    Vasopressin exerts its physiological effects on liver metabolism, fluid osmolarity, and corticotrophic response to stress through a set of at least three receptors, V1a, V2, and V3 (also called V1b), respectively. These receptors constitute a distinct group of the superfamily of G-protein-coupled cell surface receptors. When bound to vasopressin, they couple to G proteins activating phospholipase C for the V1a and V3 types and adenylate cyclase for the V2. The vasopressin receptor subfamily also includes the receptor for oxytocin, a structurally related hormone that signals through the activation of phospholipase C. The chromosomal position of the V2 receptor gene has been assigned to Xq28-qter by PCR-based screening of somatic cell hybrids, whereas the oxytocin receptor gene has been mapped to chromosome 3q26.2 by fluorescence in situ hybridization (FISH). The chromosomal location of the V1a gene is currently unknown. We recently cloned the cDNA and the gene coding for the human pituitary-specific V3 receptor (HGMW-approved symbol AVPR3). We report here the chromosomal localization of this gene by two distinct in situ hybridization techniques using radioactive and fluorescent probes. 11 refs., 1 fig.

  9. Localization of a human homolog of the mouse Tiam-1 gene to chromosome 21q22.1

    Energy Technology Data Exchange (ETDEWEB)

    Haiming Chen; Antonarakis, S.E. [Univ. of Geneva Medical School (Switzerland)

    1995-11-01

    Exon trapping was applied to genomic DNA from a chromosome 21-specific cosmid library (LL21NC02-Q) to clone portions of genes from this chromosome. Among a large number of trapped exons, three showed striking homology to different regions of the cDNA for the mouse T-lymphoma invasion and metastasis gene (Tiam-1) at both nucleotide and predicted amino acid sequence levels, suggesting that these three exons are part of a human homolog of the mouse Tiam-1 gene. We mapped this presumed human TIAM1 gene to chromosome 21 by using appropriate somatic cell hybrids, YACs, and cosmids. The TIAM1 gene localizes to YAC 760H5 of the I. Chumakov et al. YAC contig between markers D21S298 and D21S404 in band 21q22.1. This human gene (which is a member of the group of guanine nucleotide-dissociation stimulators that modulate the activity of Rho-like proteins) may be important in the development or metastasis of malignancies that are associated with abnormalities on chromosome 21, including the various forms of leukemia frequent in trisomy 21. 25 refs., 2 figs.

  10. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  11. Chromosomal localization of the human apolipoprotein B gene and detection of homologous RNA in monkey intestine

    Energy Technology Data Exchange (ETDEWEB)

    Deeb, S.S.; Disteche, C.; Motulsky, A.G.; Lebo, R.V.; Kan, Y.W.

    1986-01-01

    A cDNA clone of the human apolipoprotein B-100 was used as a hybridization probe to detect homologous sequences in both flow-sorted and in situ metaphase chromosomes. The results indicate that the gene encoding this protein is on the distal end of the short arm of chromosome 2 (2p23-2p24). RNA isolated from monkey small intestine contained sequences (6.5 and 18 kilobases) homologous to the cDNA of apolipoprotein B-100. These results are consistent with the hypothesis that one gene codes for both the intestinal (B-48) and the hepatic (B-100) forms.

  12. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Directory of Open Access Journals (Sweden)

    Sehgal Sunish K

    2012-05-01

    Full Text Available Abstract Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4% was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from

  13. The DNA Sequence And Comparative Analysis Of Human Chromosome5

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy; Martin, Joel; Terry, Astrid; Couronne, Olivier; Grimwood, Jane; Lowry, Steve; Gordon, Laurie A.; Scott, Duncan; Xie,Gary; Huang, Wayne; Hellsten, Uffe; Tran-Gyamfi, Mary; She, Xinwei; Prabhakar, Shyam; Aerts, Andrea; Altherr, Michael; Bajorek, Eva; Black,Stacey; Branscomb, Elbert; Caoile, Chenier; Challacombe, Jean F.; Chan,Yee Man; Denys, Mirian; Detter, John C.; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Israni, Sanjay; Jett, Jamie; Kadner,Kristen; Kimball, Heather; Kobayashi, Arthur; Lopez, Frederick; Lou,Yunian; Martinez, Diego; Medina, Catherine; Morgan, Jenna; Nandkeshwar,Richard; Noonan, James P.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Priest, James; Ramirez, Lucia; Retterer, James; Rodriguez, Alex; Rogers,Stephanie; Salamov, Asaf; Salazar, Angelica; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wheeler, Jeremy; Wu, Kevin; Yang,Joan; Dickson, Mark; Cheng, Jan-Fang; Eichler, Evan E.; Olsen, Anne; Pennacchio, Len A.; Rokhsar, Daniel S.; Richardson, Paul; Lucas, SusanM.; Myers, Richard M.; Rubin, Edward M.

    2004-08-01

    Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Chromosomal evolution in the Drosophila cardini group (Diptera: Drosophilidae): photomaps and inversion analysis.

    Science.gov (United States)

    Cordeiro, Juliana; De Toni, Daniela Cristina; da Silva, Gisele de Souza; Valente, Vera Lucia da Silva

    2014-10-01

    Detailed chromosome photomaps are the first step to develop further chromosomal analysis to study the evolution of the genetic architecture in any set of species, considering that chromosomal rearrangements, such as inversions, are common features of genome evolution. In this report, we analyzed inversion polymorphisms in 25 different populations belonging to six neotropical species in the cardini group: Drosophila cardini, D. cardinoides, D. neocardini, D. neomorpha, D. parthenogenetica and D. polymorpha. Furthermore, we present the first reference photomaps for the Neotropical D. cardini and D. parthenogenetica and improved photomaps for D. cardinoides, D. neocardini and D. polymorpha. We found 19 new inversions for these species. An exhaustive pairwise comparison of the polytene chromosomes was conducted for the six species in order to understand evolutionary patterns of their chromosomes.

  16. [Chromosomal localization of the hormone-sensitive lipase gene (Hsl) in rice field eel].

    Science.gov (United States)

    Ji, Fu-Yun; Yu, Qi-Xing; Pan, Pei-Wen

    2003-03-01

    Adipose tissue triacylglycerols are the quantitatively most important source of stored energy in animals. Hormone-sensitive lipase encoded by hormone-sensitive lipase gene (Hsl) is a multifunctional enzyme that catalyzes the hydrolysis of triacylglycerol stored in adipose tissue and cholesterol esters in the adrenals, ovaries, testes and macrophages. Using pig Hsl gene inserted into pBS labeled by the radioactive isotope and the digoxigenin as the probes respectively one band, 11.5kb, has been shown to hybridized with total DNA of rice field eel digested with Pst I by Southern blotting and Hsl gene has been assigned to metaphase chromosome 5, at the position of 78.35+/-1.26 from the centromere in rice field eel by fluorescent in situ hybridization (FISH). The mapping results are corresponding to that of "specific-chromosomal DNA pool" obtained by chromosome microisolation used to map gene and the mapping result is more accurate. The results of the study further illustrate the importance of the presence of Hsl gene in rice field eel genome and provide the first FISH mapping data for rice field eel chromosome 5. The current studies would advance the addition of known genetic markers and the construction of high resolution genetic map in rice field eel genome.

  17. Cytogenetic analysis of Aegilops chromosomes, potentially usable in triticale (X Triticosecale Witt.) breeding.

    Science.gov (United States)

    Kwiatek, M; Wiśniewska, H; Apolinarska, B

    2013-05-01

    Chromosome identification using fluorescence in situ hybridization (FISH) is widely used in cytogenetic research. It is a diagnostic tool helpful in chromosome identification. It can also be used to characterize alien introgressions, when exercised in a combination with genomic in situ hybridization (GISH). This work aims to find chromosome identification of Aegilops species and Aegilops × Secale amphiploids, which can be used in cereal breeding as a source of favourable agronomic traits. Four diploid and two tetraploid Aegilops species and three Aegilops × Secale hybrids were analysed using FISH with pSc119.2, pAs1, 5S rDNA and 25S rDNA clones to differentiate the U-, M-, S(sh)- and D-subgenome chromosomes of Aegilops genus. Additionally, GISH for chromosome categorization was carried out. Differences in the hybridization patterns allowed to identify all U-, M-, S(sh)- and D-subgenome chromosomes. Some differences in localization of the rDNA, pSc119.2 and pAs1 sequences between analogue subgenomes in diploid and tetraploid species and Aegilops × Secale hybrids were detected. The hybridization pattern of the M and S genome was more variable than that of the U and D genome. An importance of the cytogenetic markers in plant breeding and their possible role in chromosome structure, function and evolution is discussed.

  18. Novel Integrated Lab-on-Chip System for Chromosome Translocations Analysis

    DEFF Research Database (Denmark)

    Svendsen, Winnie Edith; Lange, Jacob Moresco; Shah, Pranjul Jaykumar

    2009-01-01

    This presentation will focus on the development of a chromosome total analysis system (C-TAS) starting from the design strategy and simulations to the integration into a final monolithic plug and play device. Individual modules which perform the sample preprocessing and analysis tasks like - cell...... isolation, cell culture, cell lysing, chromosome extraction and Fluorescence In-Situ Hybridization will be presented. How we solved connecting the individual chips and adjusting the microfluidic flows, by using simulations will be discussed....

  19. Prenatal diagnosis and molecular cytogenetic analysis of a de novo isodicentric chromosome 18

    Science.gov (United States)

    Zhang, Yanliang; Dai, Yong; Ren, Jinghui; Wang, Linqian

    2010-01-01

    Isodicentric chromosome 18 [idic(18)] is rare structural aberration. We report on a prenatal case described by conventional and molecular cytogenetic analyses. The sonography at 24 weeks of gestation revealed multiple fetal anomalies; radial aplasia and ventricular septal defect were significant features. Routine karyotyping showed a derivative chromosome replacing one normal chromosome 18. The parental karyotypes were normal, indicating that the derivative chromosome was de novo. Array comparative genomic hybridization (array-CGH) revealed 18p11.21→qter duplication and 18p11.21→pter deletion for genomic DNA of the fetus. The breakpoint was located at 18p11.21 (between 12104527 bp and 12145199 bp from the telomere of 18p). Thus, the derivative chromosome was ascertained as idic(18)(qter→p11.21::p11.21→qter). Fluorescent in situ hybridization (FISH) confirmed that the derivative chromosome was idic(18). Our report describes a rare isodicentric chromosome 18 and demonstrates that array-CGH is a useful complementary tool to cytogenetic analysis for reliable identifying derivative chromosome. PMID:20864786

  20. Characterization of cDNAs encoding human leukosialin and localization of the leukosialin gene to chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Pallant, A.; Eskenazi, A.; Frelinger, J.G. (Univ. of Rochester Medical Center, NY (USA)); Mattei, M.G. (Hopital d' Enfants de la Timone, Marseille (France)); Fournier, R.E.K. (Fred Hutchinson Cancer Research Center, Seattle, WA (USA)); Carlsson, S.R.; Fukuda, M. (La Jolla Center Research Foundation, CA (USA))

    1989-02-01

    The authors describe the isolation and characterization of cDNA clones encoding human leukosialin, a major sialoglycoprotein of human leukocytes. Leukosialin is very closely related or identical to the sialophorin molecule, which is involved in T-cell proliferation and whose expression is altered in Wiskott-Aldrich syndrome (WAS), an X-chromosome-linked immunodeficiency disease. Using a rabbit antiserum to leukosialin, a cDNA clone was isolated from a {lambda}gt11 cDNA library constructed from human peripheral blood cells. The {lambda}gt11 clone was used to isolate longer cDNA clones that correspond to the entire coding sequence of leukosialin. DNA sequence analysis reveals three domains in the predicted mature protein. The extracellular domain is enriched for Ser, Thr, and Pro and contains four contiguous 18-amino acid repeats. The transmembrane and intracellular domains of the human leukosialin molecule are highly homologous to the rat W3/13 molecule. RNA gel blot analysis reveals two polyadenylylated species of 2.3 and 8 kilobases. Southern blot analysis suggests that human leukosialin is a single-copy gene. Analysis of monochromosomal cell hybrids indicates that the leukosialin gene is not X chromosome linked and in situ hybridization shows leukosialin is located on chromosome 16. These findings demonstrate that the primary mutation in WAS is not a defect in the structural gene for leukosialin.

  1. Cloning, tissue expression pattern characterization and chromosome localization of human peptide methionine sulfoxide reductase cDNA

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Oxidation and reduction of some amino acids are one of the molecular mechanisms for regulating the function of proteins. The oxidation of methionine (Met) to methionine sulfoxide (Met(O)) results in decreasing or loss of the biological activity of related proteins. It was found that peptide methionine sulfoxide reductase (msrA) can reduce Met(O) to Met and therefore restored the biological function of the oxidized proteins. To reveal the methionine oxidation-reduction mechanism in human body, in this study, the cDNA sequence of bovine msrA was used as an information-probe to screen the human EST database. Based on a contig assembled from homologous ESTs, a 1 256-bp human MSRA cDNA was cloned from several human cDNA libraries. The cDNA contains an open reading frame (ORF) of 705 bp in length, which encodes 235 amino acid residues. Homology comparison revealed that human MSRA shares 88% and 61% identities with bovine and Escherichia coli msrA protein respectively. Expression pattern analysis revealed a single 1.6-kb transcript of human MSRA in most human tissues and with highest expression in kidney. By radiation hybrid panel mapping, the gene was localized to human chromosome 8p22-23 between markers D8S518 and D8S550. There are 2 human inherited diseases Keratolytic Winter Erythema and Microcephaly related genes in this region, it is inferred that human MSRA might be the candidate of the two diseases.

  2. Polo kinase regulates the localization and activity of the chromosomal passenger complex in meiosis and mitosis in Drosophila melanogaster.

    Science.gov (United States)

    Carmena, Mar; Lombardia, Miguel Ortiz; Ogawa, Hiromi; Earnshaw, William C

    2014-11-01

    Cell cycle progression is regulated by members of the cyclin-dependent kinase (CDK), Polo and Aurora families of protein kinases. The levels of expression and localization of the key regulatory kinases are themselves subject to very tight control. There is increasing evidence that crosstalk between the mitotic kinases provides for an additional level of regulation. We have previously shown that Aurora B activates Polo kinase at the centromere in mitosis, and that the interaction between Polo and the chromosomal passenger complex (CPC) component INCENP is essential in this activation. In this report, we show that Polo kinase is required for the correct localization and activity of the CPC in meiosis and mitosis. Study of the phenotype of different polo allele combinations compared to the effect of chemical inhibition revealed significant differences in the localization and activity of the CPC in diploid tissues. Our results shed new light on the mechanisms that control the activity of Aurora B in meiosis and mitosis.

  3. Analysis of chromosome aberration data by hybrid-scale models

    Energy Technology Data Exchange (ETDEWEB)

    Indrawati, Iwiq [Research and Development on Radiation and Nuclear Biomedical Center, National Nuclear Energy Agency (Indonesia); Kumazawa, Shigeru [Nuclear Technology and Education Center, Japan Atomic Energy Research Institute, Honkomagome, Tokyo (Japan)

    2000-02-01

    This paper presents a new methodology for analyzing data of chromosome aberrations, which is useful to understand the characteristics of dose-response relationships and to construct the calibration curves for the biological dosimetry. The hybrid scale of linear and logarithmic scales brings a particular plotting paper, where the normal section paper, two types of semi-log papers and the log-log paper are continuously connected. The hybrid-hybrid plotting paper may contain nine kinds of linear relationships, and these are conveniently called hybrid scale models. One can systematically select the best-fit model among the nine models by among the conditions for a straight line of data points. A biological interpretation is possible with some hybrid-scale models. In this report, the hybrid scale models were applied to separately reported data on chromosome aberrations in human lymphocytes as well as on chromosome breaks in Tradescantia. The results proved that the proposed models fit the data better than the linear-quadratic model, despite the demerit of the increased number of model parameters. We showed that the hybrid-hybrid model (both variables of dose and response using the hybrid scale) provides the best-fit straight lines to be used as the reliable and readable calibration curves of chromosome aberrations. (author)

  4. Molecular cytogenetic analysis of dicentric chromosomes in acute myeloid leukemia.

    Science.gov (United States)

    Sarova, Iveta; Brezinova, Jana; Zemanova, Zuzana; Ransdorfova, Sarka; Izakova, Silvia; Svobodova, Karla; Pavlistova, Lenka; Berkova, Adela; Cermak, Jaroslav; Jonasova, Anna; Siskova, Magda; Michalova, Kyra

    2016-04-01

    Dicentric chromosomes (DCs) have been described in many hematological diseases, including acute myeloid leukemia (AML). They are markers of cancer and induce chromosomal instability, leading to the formation of other chromosomal aberrations and the clonal evolution of pathological cells. Our knowledge of the roles and behavior of human DCs is often derived from studies of induced DCs and cell lines. It is difficult to identify all the DCs in the karyotypes of patients because of the limitations of metaphase cytogenetic methods. The aim of this study was to revise the karyotypes of 20 AML patients in whom DCs were found with conventional G-banding or multicolor fluorescence in situ hybridization (mFISH) with (multi)centromeric probes and to characterize the DCs at the molecular cytogenetic level. FISH analyses confirmed 23 of the 29 expected DCs in 18 of 20 patients and identified 13 others that had not been detected cytogenetically. Fourteen DCs were altered by other chromosomal changes. In conclusion, karyotypes with DCs are usually very complex, and we have shown that they often contain more than one DC, which can be missed with conventional or mFISH methods. Our study indicates an association between number of DCs in karyotype and very short survival of patients.

  5. Analysis of chromosomal alterations induced by asbestos and ceramic fibers.

    Science.gov (United States)

    Dopp, E; Schiffmann, D

    1998-08-01

    Asbestos and other mineral fibers have long been known as carcinogenic agents. However, the primary mechanisms of fiber-induced carcinogenesis still remain unclear. We have investigated mitotic disturbances caused by amosite, crocidolite, and chrysotile in Syrian hamster embryo (SHE) fibroblasts. We also analyzed micronucleus formation as a result of mitotic disturbances, and carried out a characterization of the induced micronucleus population by kinetochore staining. In addition, the spindle fiber morphology was examined. Supravital UV-microscopy was used to analyze changes in chromatin structure, impaired chromatid separation and blocked cytokinesis. All three fiber types induced micronuclei in SHE cells with a high frequency (up to 200 MN/2000 cells; dose range: 0.1-5.0 microg/cm2) in a dose-dependent manner with a maximum between 48 and 66 h. Kinetochore staining revealed that 48% of fiber-induced micronuclei reacted positively. Furthermore, spindle deformation was observed in cells with disturbed meta- and anaphases while the spindle fiber morphology appeared unchanged. Our results show that asbestos fibers may cause both loss as well as breakage of chromosomes in the absence of direct interaction with spindle fibers. In addition, we analyzed the induction of micronuclei, hyperdiploidy and chromosome breakage in human amniotic fluid cells (AFC) in vitro by amosite, chrysotile and crocidolite asbestos and ceramic fibers. The response of human (AFC) and rodent (SHE) cells to fiber treatment was compared using the micronucleus assay. AFC were much less susceptible than SHE cells to the induction of micronuclei by mineral fibers. The application of fluorescence in situ hybridization (FISH) with tandem DNA probes yielded more detailed informations about specific structural chromosome aberrations in the 1(cen-q12) and 9(cen-q12) regions and about abnormal numbers of chromosomes in interphase AFC. Using this FISH approach we found a statistically significant

  6. Cyclin B1 is localized to unattached kinetochores and contributes to efficient microtubule attachment and proper chromosome alignment during mitosis

    Institute of Scientific and Technical Information of China (English)

    Qiang Chen; Xiaoyan Zhang; Qing Jiang; Paul R Clarke; Chuanmao Zhang

    2008-01-01

    Cyclin Bl is a key regulatory protein controlling cell cycle progression in vertebrates. Cyclin Bl binds CDK1, a cyclin-dependent kinase catalytic subunit, forming a complex that orchestrates mitosis through phosphorylation of key proteins. Cyclin Bl regulates both the activation of CDK1 and its subcellular localization, which may be critical for substrate selection. Here, we demonstrate that cyclin Bl is concentrated on the outer plate of the kinetochore during prometaphase. This localization requires the cyclin box region of the protein. Cyclin Bl is displaced from individual kinetochores to the spindle poles by microtubule attachment to the kinetochores, and this displacement is dependent on the dynein/dynactin complex. Depletion of cyclin Bl by vector-based siRNA causes inefficient attachment between kinetochores and microtubules, and chromosome alignment defects, and delays the onset of anaphase. We conclude that cyclin Bl accumulates at kinetochores during prometaphase, where it contributes to the correct attachment of microtubules to kinetochores and efficient alignment of the chromosomes, most likely through localized phosphorylation of specific substrates by cyclin B1-CDK1. Cyclin Bl is then transported from each kinetochore as microtubule attachment is completed, and this relocalization may redirect the activity of cyclin B1-CDK1 and contribute to inactivation of the spindle assembly checkpoint.

  7. Autosomal dominant polycystic kidney disease: Localization of the second gene to chromosome 4q13-q23

    Energy Technology Data Exchange (ETDEWEB)

    Kimberling, W.J.; Kumar, S.; Kenyon, J.B.; Connolly, C.J. (Creighton Univ. Medical School, Omaha, NE (United States)); Gabow, P.A. (Colorado Univ. Health Sciences Center, Denver, CO (United States)); Somlo, S. (Albert Einstein School of Medicine, Bronx, NY (United States))

    1993-12-01

    At least two loci are known to exist for autosomal dominant polycystic kidney disease (ADPKD). One was localized to 16p, but the second less common locus has remained unlinked. Over 100 microsatellite markers, distributed across all chromosomes, have been typed on informative family members from the large Sicilian kindred in which the genetic heterogeneity was first discovered. Both the affected and the unaffected status of every family member used in the study were consulted in the successful localization of a second ADPKD gene to chromosome 4q. It was found to be flanked by the markers D4S231 and D4S414, defining a segment that spans about 9 cM. The new locus has been designated PKD4. This second localization will allow researchers to target another ADPKD gene for isolation in an effort to understand the pathogenesis of this common disorder. Furthermore, when flanking markers for the second ADPKD gene are used in conjunction with flanking markers for PKD1, the accuracy of the diagnosis of the subtype of ADPKD present in any particular family will be enhanced. This will improve the accuracy of linkage-based presymptomatic diagnoses by reducing the error due to genetic heterogeneity. 42 refs., 3 figs., 1 tab.

  8. Human nicotinamide N-methyltransferase gene: Molecular cloning, structural characterization and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Aksoy, S.; Weinshilboum, R.M. [Mayo Medical School/Mayo Clinic/Mayo Foundation, Rochester, MN (United States); Brandriff, B.F. [Lawrence Livermore National Lab., CA (United States); Ward, A.; Little, P.F.R. [Imperial College of Science, Technology and Medicine, London (United Kingdom)

    1995-10-10

    Genomic DNA clones for nicotinamide N-methyltransferase (NNMT), an enzyme that catalyzes drug and xenobiotic metabolism, were isolated from a human chromosome 11-specific DNA library. Study of one of those clones, when combined with PCR-based experiments performed with human genomic DNA, made it possible to determine the structure of the human NNMT gene. The gene was approximately 16.5 kb in length and consisted of 3 exons and 2 introns. Transcription initiation for the NNMT gene occurred 105-109 nucleotides 5{prime}-upstream from the cDNA translation initiation codon on the basis of the results of both primer extension and 5{prime}-rapid amplification of cDNA ends. NNMT mapped to chromosome band 11q23.1 by fluorescence in situ hybridization.

  9. Genomic Imbalances in Neonates With Birth Defects: High Detection Rates by Using Chromosomal Microarray Analysis

    Science.gov (United States)

    Lu, Xin-Yan; Phung, Mai T.; Shaw, Chad A.; Pham, Kim; Neil, Sarah E.; Patel, Ankita; Sahoo, Trilochan; Bacino, Carlos A.; Stankiewicz, Pawel; Lee Kang, Sung-Hae; Lalani, Seema; Chinault, A. Craig; Lupski, James R.; Cheung, Sau W.; Beaudet, Arthur L.

    2009-01-01

    OBJECTIVES Our aim was to determine the frequency of genomic imbalances in neonates with birth defects by using targeted array-based comparative genomic hybridization, also known as chromosomal microarray analysis. METHODS Between March 2006 and September 2007, 638 neonates with various birth defects were referred for chromosomal microarray analysis. Three consecutive chromosomal microarray analysis versions were used: bacterial artificial chromosome-based versions V5 and V6 and bacterial artificial chromosome emulated oligonucleotide-based version V6 Oligo. Each version had targeted but increasingly extensive genomic coverage and interrogated >150 disease loci with enhanced coverage in genomic rearrangement-prone pericentromeric and subtelomeric regions. RESULTS Overall, 109 (17.1%) patients were identified with clinically significant abnormalities with detection rates of 13.7%, 16.6%, and 19.9% on V5, V6, and V6 Oligo, respectively. The majority of these abnormalities would not be defined by using karyotype analysis. The clinically significant detection rates by use of chromosomal microarray analysis for various clinical indications were 66.7% for “possible chromosomal abnormality” ± “others” (other clinical indications), 33.3% for ambiguous genitalia ± others, 27.1% for dysmorphic features + multiple congenital anomalies ± others, 24.6% for dysmorphic features ± others, 21.8% for congenital heart disease ± others, 17.9% for multiple congenital anomalies ± others, and 9.5% for the patients referred for others that were different from the groups defined. In all, 16 (2.5%) patients had chromosomal aneuploidies, and 81 (12.7%) patients had segmental aneusomies including common microdeletion or microduplication syndromes and other genomic disorders. Chromosomal mosaicism was found in 12 (1.9%) neonates. CONCLUSIONS Chromosomal microarray analysis is a valuable clinical diagnostic tool that allows precise and rapid identification of genomic imbalances

  10. Cell cycle coordination and regulation of bacterial chromosome segregation dynamics by polarly localized proteins.

    Science.gov (United States)

    Schofield, Whitman B; Lim, Hoong Chuin; Jacobs-Wagner, Christine

    2010-09-15

    What regulates chromosome segregation dynamics in bacteria is largely unknown. Here, we show in Caulobacter crescentus that the polarity factor TipN regulates the directional motion and overall translocation speed of the parS/ParB partition complex by interacting with ParA at the new pole. In the absence of TipN, ParA structures can regenerate behind the partition complex, leading to stalls and back-and-forth motions of parS/ParB, reminiscent of plasmid behaviour. This extrinsic regulation of the parS/ParB/ParA system directly affects not only division site selection, but also cell growth. Other mechanisms, including the pole-organizing protein PopZ, compensate for the defect in segregation regulation in ΔtipN cells. Accordingly, synthetic lethality of PopZ and TipN is caused by severe chromosome segregation and cell division defects. Our data suggest a mechanistic framework for adapting a self-organizing oscillator to create motion suitable for chromosome segregation.

  11. Structural comparison and chromosomal localization of the human and mouse IL-13 genes

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, A.N.J.; Sato, A.; Doyle, E.L.; Zurawski, G. (DNAX Research Institute of Cellular and Molecular Biology, Palo Alto, CA (United States)); Li, X.; Milatovich, A.; Francke, U. (Stanford Univ. Medical School, CA (United States)); Largaespada, D.A.; Copeland, N.G.; Jenkins, N.A. (National Cancer Institute, Frederick, MD (United States))

    1993-06-15

    The genomic structure of the recently described cytokine IL-13 has been determined for both human and mouse genes. The nucleotide sequence of a 4.6-kb DNA segment of the human gene is described. The human IL-13 gene (IL 13) occurs as a single copy in the haploid genome and maps to human chromosome 5. A 4.3-kb DNA fragment of the mouse IL-13 gene (Il 13) has been sequenced and found to occur as a single copy, mapping to mouse chromosome 11. Intrachromosomal mapping studies revealed that both genes contain four exons and three introns and show a high degree of sequence identify throughout their length. Potential recognition sequences for transcription factors that are present in the 5'-flanking region and are conserved between both genes include IFN-responsive elements, binding sites for AP-1, AP-2, and AP-3, an NF-lL 6 site, and a TATA-like sequence. Both genes map to chromosomal locations adjacent to genes encoding other cytokines, including IL-3, GM-CSF, IL-5, and IL-4 suggesting that IL-13 is another member of this cytokine gene family that may have arisen by gene duplication. 26 refs., 5 figs., 3 tabs.

  12. Insights into the evolution of mammalian telomerase: Platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes

    Directory of Open Access Journals (Sweden)

    Hrdličková Radmila

    2012-06-01

    Full Text Available Abstract Background The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT ortholog, and provide a comparison with genes of other vertebrates. Results The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.

  13. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.

    Science.gov (United States)

    Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen

    2013-10-15

    We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Analysis of Recombination and Chromosome Structure during Yeast Meiosis.

    Science.gov (United States)

    Börner, G Valentin; Cha, Rita S

    2015-11-02

    Meiosis is a diploid-specific differentiation program that consists of a single round of genome duplication followed by two rounds of chromosome segregation. These events result in halving of the genetic complement, which is a requirement for formation of haploid reproductive cells (i.e., spores in yeast and gametes in animals and plants). During meiosis I, homologous maternal and paternal chromosomes (homologs) pair and separate, whereas sister chromatids remain connected at the centromeres and separate during the second meiotic division. In most organisms, accurate homolog disjunction requires crossovers, which are formed as products of meiotic recombination. For the past two decades, studies of yeast meiosis have provided invaluable insights into evolutionarily conserved mechanisms of meiosis.

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

    Science.gov (United States)

    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.

  17. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques

    Science.gov (United States)

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-11-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  18. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques.

    Science.gov (United States)

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-01-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  19. A new chromosome fluorescence banding technique combining DAPI staining with image analysis in plants.

    Science.gov (United States)

    Liu, Jing Yu; She, Chao Wen; Hu, Zhong Li; Xiong, Zhi Yong; Liu, Li Hua; Song, Yun Chun

    2004-08-01

    In this study, a new chromosome fluorescence banding technique was developed in plants. The technique combined 4',6-diamidino-2-phenylindole (DAPI) staining with software analysis including three-dimensional imaging after deconvolution. Clear multiple and adjacent DAPI bands like G-bands were obtained by this technique in the tested species including Hordeum vulgare L., Oryza officinalis, Wall & Watt, Triticum aestivum L., Lilium brownii, Brown, and Vicia faba L. During mitotic metaphase, the numbers of bands for the haploid genomes of these species were about 185, 141, 309, 456 and 194, respectively. Reproducibility analysis demonstrated that banding patterns within a species were stable at the same mitotic stage and they could be used for identifying specific chromosomes and chromosome regions. The band number fluctuated: the earlier the mitotic stage, the greater the number of bands. The technique enables genes to be mapped onto specific band regions of the chromosomes by only one fluorescence in situ hybridisation (FISH) step with no chemical banding treatments. In this study, the 45S and 5S rDNAs of some tested species were located on specific band regions of specific chromosomes and they were all positioned at the interbands with the new technique. Because no chemical banding treatment was used, the banding patterns displayed by the technique should reflect the natural conformational features of chromatin. Thus it could be expected that this technique should be suitable for all eukaryotes and would have widespread utility in chromosomal structure analysis and physical mapping of genes.

  20. Local models for spatial analysis

    CERN Document Server

    Lloyd, Christopher D

    2010-01-01

    Focusing on solutions, this second edition provides guidance to a wide variety of real-world problems. The text presents a complete introduction to key concepts and a clear mapping of the methods discussed. It also explores connections between methods. New chapters address spatial patterning in single variables and spatial relations. In addition, every chapter now includes links to key related studies. The author clearly distinguishes between local and global methods and provides more detailed coverage of geographical weighting, image texture measures, local spatial autocorrelation, and multic

  1. Correlation between localization, age, and chromosomal imbalances in ependymal tumours as detected by CGH.

    Science.gov (United States)

    Jeuken, Judith W M; Sprenger, Sandra H E; Gilhuis, Job; Teepen, Hans L J M; Grotenhuis, Andre J; Wesseling, Pieter

    2002-06-01

    Ependymal tumours (ETs) are gliomas that arise from the ependymal lining of the cerebral ventricles and from the remnants of the central canal of the spinal cord. Both clinical and genetic studies suggest that distinct genetic subtypes of ETs exist, the subtypes being correlated with patient age and/or tumour site. In the present study, the tumour genome of 20 ETs (15 adult and five paediatric cases) was screened for chromosomal imbalances by comparative genomic hybridization (CGH). The most frequently detected imbalances were -22q (75%), -10q (65%), -21 (50%), -16p (50%), -1p (45%), +4q (45%), -10p (45%), -2q (40%), -6 (40%), -19 (40%), -2p (35%), -3p (35%), and -16q (35%). Comparison of the chromosomal imbalances detected in ETs with those previously reported in oligodendroglial and astrocytic tumours revealed that in this respect ETs show similarities to these other gliomas. By combining these results with those of a recent study of Zheng et al. and Hirose et al., it was found that although ETs from different sites and from adult and paediatric patients show overlap at the CGH level, some chromosomal imbalances occur predominantly in a certain category. In adult patients, spinal ETs relatively often showed +2, +7, +12, and -14q; infratentorial ETs -22; and supratentorial ETs -9. In addition, in posterior fossa ETs, -6 and +9 were much more frequent in adults than in children. It is concluded that the genetic background of ETs is complex and partly determined by tumour site, histopathological subtype, and age of the patient.

  2. Chromosomal localization of a novel retinoic acid induced gene RA28 and the protein distribution of its encoded protein

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Gene RA28 is a retinoic acid induced novel gene isolated in our laboratory previously. All-trans retinoic acid (ATRA) was used to induce lung adenocarcinoma cell line GLC-82, and RA28 was obtained by subtractive hybridization. Green fluorescent protein (GFP) has emerged as a unique tool for examining introcellular phenomena in living cells. GFP possesses an intrinsic fluorescence at 488 nm that does not require other co-factors. In this report, an eukaryotic expression plasmid pEGFP-C1-RA28 was constructed and transfected with parental cell line GLC-82 to analyze protein expression and its distribution in living cells. Moreover, radiation hybrid (RH) technique was used to localize RA28 to the chromosome. The results show that gene RA28 is mapped to the chromosome 19q13.1 region, its encoded protein is distributed on cell membrane. All the results further demonstrate that GFP and RH techniques are accurate, fast, repetitive, and will be powerful methods for investigating the gene and protein localization.

  3. Replication timing of human telomeres is chromosome arm-specific, influenced by subtelomeric structures and connected to nuclear localization.

    Directory of Open Access Journals (Sweden)

    Nausica Arnoult

    2010-04-01

    Full Text Available The mechanisms governing telomere replication in humans are still poorly understood. To fill this gap, we investigated the timing of replication of single telomeres in human cells. Using in situ hybridization techniques, we have found that specific telomeres have preferential time windows for replication during the S-phase and that these intervals do not depend upon telomere length and are largely conserved between homologous chromosomes and between individuals, even in the presence of large subtelomeric segmental polymorphisms. Importantly, we show that one copy of the 3.3 kb macrosatellite repeat D4Z4, present in the subtelomeric region of the late replicating 4q35 telomere, is sufficient to confer both a more peripheral localization and a later-replicating property to a de novo formed telomere. Also, the presence of beta-satellite repeats next to a newly created telomere is sufficient to delay its replication timing. Remarkably, several native, non-D4Z4-associated, late-replicating telomeres show a preferential localization toward the nuclear periphery, while several early-replicating telomeres are associated with the inner nuclear volume. We propose that, in humans, chromosome arm-specific subtelomeric sequences may influence both the spatial distribution of telomeres in the nucleus and their replication timing.

  4. Karyotype analysis of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae) reveals a large X chromosome with rRNA and histone gene families.

    Science.gov (United States)

    Novotná, Jana; Havelka, Jan; Starý, Petr; Koutecký, Petr; Vítková, Magda

    2011-03-01

    The Russsian wheat aphid (RWA), Diuraphis noxia (Kurdjumov), is a worldwide pest of cereals. Despite its economic importance, little is known about its genome. Here we investigated physical genomic features in RWA by karyotype analysis using differential staining with AgNO(3), CMA(3), and DAPI, by chromosomal localization of ribosomal DNA (rDNA), H3 and H4 histone genes, and the "arthropod" telomeric sequence (TTAGG)(n) using fluorescence in situ hybridization (FISH), and by measuring the RWA genome size using flow cytometry. The female karyotype, 2n = 10, is composed of four autosome pairs and a pair of X chromosomes, whereas the male karyotype, 2n = 9, has a single X. The X chromosome is the largest element in the karyotype. All three molecular markers used, i.e., 18S rRNA and both H3 and H4 probes are co-localized at one end of the X chromosome. The FISH probes revealed that the AgNO(3)-positive bridge between two prometaphase X chromosomes of females, which is believed to be responsible for the elimination of one X chromosome in aphid oocytes determined to undergo male development, contains clusters of both histone genes, in addition to an rDNA cluster. Interestingly, RWA lacks the (TTAGG)(n) telomeric sequence in its genome, in contrast to several previously investigated aphid species. Additionally, we compared female and male genome sizes. The female genome size is 2C = 0.86 pg, whereas the male genome size is 2C = 0.70 pg. The difference between the DNA content in the two genders suggests that the RWA X chromosome occupies about 35% of the female haploid genome (1C = 0.43 pg), which makes it one of the largest sex chromosomes in the animal kingdom.

  5. Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba.

    Science.gov (United States)

    Maggini, F; Cremonini, R; Zolfino, C; Tucci, G F; D'Ovidio, R; Delre, V; DePace, C; Scarascia Mugnozza, G T; Cionini, P G

    1991-05-01

    Subrepeating sequences of 325 bp found in the ribosomal intergenic spacer (IGS) of Vicia faba and responsible for variations in the length of the polycistronic units for rRNA were isolated and used as probes for in situ hybridization. Hybridization occurs at many regions of the metaphase chromosomes besides those bearing rRNA genes, namely chromosome ends and all the heterochromatic regions revealed by enhanced fluorescence after quinacrine staining. The DNA homologous to the 325 bp repeats that does not reside in the IGS was isolated, cloned and sequenced. It is composed of tandemly arranged 336 bp elements, each comprising two highly related 168 bp sequences. This structure is very similar to that of the IGS repeats and ca. 75% nucleotide sequence identity can be observed between these and the 168 bp doublets. The most obvious difference lies in the deletion, in the former, of a 14 bp segment from one of the two related sequences. It is hypothesized that the IGS repeats are derived from the 336 bp elements and have been transposed to ribosomal cistrons from other genome fractions. The possible relations between these sequences and others with similar structural features found in other species are discussed.

  6. PCR-based panel for regional localization of genes on chromosome 15

    Energy Technology Data Exchange (ETDEWEB)

    McDaniel, L.D.; Zhang, B.; Schultz, R.A. [Univ. of Texas Southwestern Medical Center, Dallas (United States)

    1994-09-01

    As the number of genes mapped to specific human chromosomes continues to increase, the feasibility of identifying the gene involved in a human genetic disease via a `candidate gene` approach will continue to improve. Although fluorescence in situ hybridization offers one approach to achieve refined mapping, results are dependent on the size of the probe used, which is not optimal for cDNAs or ESTs. In contrast, a PCR-based approach can achieve mapping for clones <100 bp in size. Through the use of a previously described deletion of chromosome 15 and the 15/17 translocation common to acute promyelocytic leukemia, we have assembled a small panel of somatic cell hybrids that can be used to assign probes to the regions 15p-q15, 15q15-q22, and 15q22-ter. Primers specific for unique cDNA sequences were used to amplify genomic DNA through the polymerase chain reaction. With this approach, we have assigned hexosaminidase A and aggrecan1 to 15q22-qter and leukocyte tyrosine kinase to 15q15-22.

  7. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

    Indian Academy of Sciences (India)

    Irfan A Ghazi; Prem S Srivastava; Vivek Dalal; Kishor Gaikwad; Ashok K Singh; Tilak R Sharma; Nagendra K Singh; Trilochan Mohapatra

    2009-06-01

    Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

  8. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.

    OpenAIRE

    Kejnovský, E; Vrána, J; Matsunaga, S.; Soucek, P.; Siroký, J; Dolezel, J; Vyskot, B

    2001-01-01

    The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that ...

  9. Chromosome region-specific libraries for human genome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kao, Fa-Ten.

    1991-01-01

    We have made important progress since the beginning of the current grant year. We have further developed the microdissection and PCR- assisted microcloning techniques using the linker-adaptor method. We have critically evaluated the microdissection libraries constructed by this microtechnology and proved that they are of high quality. We further demonstrated that these microdissection clones are useful in identifying corresponding YAC clones for a thousand-fold expansion of the genomic coverage and for contig construction. We are also improving the technique of cloning the dissected fragments in test tube by the TDT method. We are applying both of these PCR cloning technique to human chromosomes 2 and 5 to construct region-specific libraries for physical mapping purposes of LLNL and LANL. Finally, we are exploring efficient procedures to use unique sequence microclones to isolate cDNA clones from defined chromosomal regions as valuable resources for identifying expressed gene sequences in the human genome. We believe that we are making important progress under the auspices of this DOE human genome program grant and we will continue to make significant contributions in the coming year. 4 refs., 4 figs.

  10. Phosphorylation of Sli15 by Ipl1 is important for proper CPC localization and chromosome stability in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Vasso Makrantoni

    Full Text Available The chromosomal passenger complex (CPC is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15 and two additional proteins (Survivin/Bir1 and Borealin/Nbl1. Here we have identified multiple sites of CPC autophosphorylation on yeast Sli15 that are located within its central microtubule-binding domain and examined the functional significance of their phosphorylation by Ipl1 through mutation of these sites, either to non-phosphorylatable alanine (sli15-20A or to acidic residues to mimic constitutive phosphorylation (sli15-20D. Both mutant sli15 alleles confer chromosome instability, but this is mediated neither by changes in the capacity of Sli15 to activate Ipl1 kinase nor by decreased efficiency of chromosome biorientation, a key process in cell division that requires CPC function. Instead, we find that mimicking constitutive phosphorylation of Sli15 on the Ipl1 phosphorylation sites causes delocalization of the CPC in metaphase, whereas blocking phosphorylation of Sli15 on the Ipl1 sites drives excessive localization of Sli15 to the mitotic spindle in pre-anaphase cells. Consistent with these results, direct interaction of Sli15 with microtubules in vitro is greatly reduced either following phosphorylation by Ipl1 or when constitutive phosphorylation at the Ipl1-dependent phosphorylation sites is mimicked by aspartate or glutamate substitutions. Furthermore, we find that mimicking Ipl1 phosphorylation of Sli15 interferes with the 'tension checkpoint'--the CPC-dependent mechanism through which cells activate the spindle assembly checkpoint to delay anaphase in the absence of tension on kinetochore-microtubule attachments. Ipl1-dependent phosphorylation of Sli15 therefore inhibits its association with microtubules both in vivo and in vitro and may negatively regulate the tension checkpoint mechanism.

  11. Localization of the human indoleamine 2,3-dioxygenase (IDO) gene to the pericentromeric region of human chromosome 8

    Energy Technology Data Exchange (ETDEWEB)

    Burkin, D.J.; Jones, C. (Eleanor Roosevelt Institute for Cancer Research, Denver, CO (United States)); Kimbro, K.S.; Taylor, M.W. (Indiana Univ., Bloomington, IN (United States)); Barr, B.L.; Gupta, S.L. (Hipple Cancer Research Center, Dayton, OH (United States))

    1993-07-01

    Indoleamine 2,3-dioxygenase (IDO) is the first enzyme in the catabolic pathway for tryptophan. This extrahepatic enzyme differs from the hepatic enzyme, tryptophan 2,3-dioxygenase (TDO), in molecular as well as enzymatic characteristics, although both enzymes catalyze the same reaction: cleavage of tryptophan into N-formylkynurenine. The induction of IDO by IFN-[gamma] plays a role in the antigrowth effect of IFN-[gamma] in cell cultures and in the inhibition of intracellular pathogens, e.g., Toxoplasma gondii and Chlamydia psittaci. Tryptophan is also the precursor for the synthesis of serotonin, and reduced levels of tryptophan and serotonin found in AIDS patients have been correlated with the presence of IFN-[gamma] and consequent elevation of IDO activity. The IDO enzyme has been purified and characterized, and its cDNA and genomic DNA clones have been isolated and analyzed. DNA from hybrid cells containing fragments of human chromosome 8 was used to determine the regional localization of the IDO gene on chromosome 8. The hybrids R30-5B and R30-2A contain 8p11 [yields] qter and 8q13 [yields] qter, respectively. Hybrid 229-3A contains the 8pter [yields] q11. The hybrid R30-2A was negative for the IDO gene, whereas R30-5B and 229-3A were positive as analyzed by PCR and verified by Southern blotting. Only the region close to the centromere is shared by R30-5B and 229-3A hybrids. The results indicate that the IDO gene is located on chromosome 8p11 [yields] q11.

  12. Uroporphyrinogen-III synthase: Molecular cloning, nucleotide sequence, expression of a mouse full-length cDNA, and its localization on mouse chromosome 7

    Energy Technology Data Exchange (ETDEWEB)

    Xu, W.; Desnick, R.J. [Mount Sinai School of Medicine, New York, NY (United States); Kozak, C.A. [National Institute of Health, Bethesda, MD (United States)

    1995-04-10

    Uroporphyrinogen-III synthase, the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an autosomal recessive disorder. For the generation of a mouse model of CEP, the human URO-S cDNA was used to screen 2 X 10{sup 6} recombinants from a mouse adult liver cDNA library. Ten positive clones were isolated, and dideoxy sequencing of the entire 1.6-kb insert of clone pmUROS-1 revealed 5{prime} and 3{prime} untranslated sequences of 144 and 623 bp, respectively, and an open reading frame of 798 bp encoding a 265-amino-acid polypeptide with a predicted molecular mass of 28,501 Da. The mouse and human coding sequences had 80.5 and 77.8% nucleotide and amino acid identity, respectively. The authenticity of the mouse cDNA was established by expression of the active monomeric enzyme in Escherichia coli. In addition, the analysis of two multilocus genetic crosses localized the mouse gene on chromosome 7, consistent with the mapping of the human gene to a position of conserved synteny on chromosome 10. The isolation, expression, and chromosomal mapping of this full-length cDNA should facilitate studies of the structure and organization of the mouse genomic sequence and the development of a mouse model of CEP for characterization of the disease pathogenesis and evaluation of gene therapy. 38 refs., 1 tab.

  13. Cloning, tissue expression pattern, and chromosome localization of human protein kinase Bγ gene

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Protein kinase B (PKB) is a member of the second messenger-regulated subfamily of protein kinases, and plays a key role in cell-cycle regulation, glucose uptake and promotion of cell differentiation. Evidence shows that PKB undergoes activation in some human tumors and is involved in Ras pathway, which implies that PKB can trigger a pathway to induce oncogenic transformation. A nucleotide sequence of mouse Pkb? was used as a probe to screen homolog in a human liver cDNA library. A fragment of 1998 bp containing a 1440 bp ORF encoding 479 amino acid residues was obtained. Then the 3'-terminal of this fragment was extended to 2788 bp by 'electronic walking' screening, and the extended fragment was confirmed by PCR amplification. The protein deduced by the gene had a high identity of 83% and 78% to the human PKBγ and γ, respectively, and was designated as human PKB?. Northern hybridization detected two equally expressed transcripts of 8.5 and 6.5 kb in length in all 16 human tissues tested, with the highest expression level in brain, and lower levels with variation in the other tissues. By RH mapping, the PKBγ was placed on chromosome 1q43, between markers D1S304 and D1S2693. It is a valuable clue for cloning the candidate genes related to prostate cancer; Arrhythmogenic Right Ventricular Dysplasia (ARVD); Chediak-Higashi, NK cell Deficiency (CHS); and Hypoparathyrodism with Short Stature, Mental Retardation and Seizures which have already been mapped in this chromosomal region.

  14. Chromosomal localization of the gene for the human Theta class glutathione transferase (GSTT1)

    Energy Technology Data Exchange (ETDEWEB)

    Webb, G.; Vaska, V. [Queen Elizabeth Hospital, Adelaide (Australia); Goggan, M.; Board, P. [Australian National Univ., Canberra (Australia)

    1996-04-01

    Two loci encoding Theta class glutathione transferases (GSTs) have been identified in humans. In situ hybridization studies have localized the GSTT1 gene to 22q11.2. This is the same band to which we previously localized the GSTT2 gene. This finding confirms the trend for human GST genes to be found in class-specific clusters. 20 refs., 1 fig.

  15. Chromosomal imbalances in nasopharyngeal carcinoma: a meta-analysis of comparative genomic hybridization results

    Directory of Open Access Journals (Sweden)

    Jin Ping

    2006-01-01

    Full Text Available Abstract Nasopharyngeal carcinoma (NPC is a highly prevalent disease in Southeast Asia and its prevalence is clearly affected by genetic background. Various theories have been suggested for its high incidence in this geographical region but to these days no conclusive explanation has been identified. Chromosomal imbalances identifiable through comparative genomic hybridization may shed some light on common genetic alterations that may be of relevance to the onset and progression of NPC. Review of the literature, however, reveals contradictory results among reported findings possibly related to factors associated with patient selection, stage of disease, differences in methodological details etc. To increase the power of the analysis and attempt to identify commonalities among the reported findings, we performed a meta-analysis of results described in NPC tissues based on chromosomal comparative genomic hybridization (CGH. This meta-analysis revealed consistent patters in chromosomal abnormalities that appeared to cluster in specific "hot spots" along the genome following a stage-dependent progression.

  16. Chromosomes and karyotype analysis of a liver fluke, Opisthorchis viverrini, by scanning electron microscopy.

    Science.gov (United States)

    Kaewkong, Worasak; Choochote, Wej; Kanla, Pipatpong; Maleewong, Wanchai; Intapan, Pewpan M; Wongkham, Sopit; Wongkham, Chaisiri

    2012-09-01

    Opisthorchis viverrini, a human liver fluke, has been categorized as the carcinogenic organism according to the strong association with carcinogenesis of cholangiocarcinoma (CCA). The infection of this food-borne parasite is a major impact on the health of humans, especially CCA patients in the northeast of Thailand. Taxonomy, morphology, epidemiology and molecular study of O. viverrini have been publicized increasingly but the precise karyotypic study is still incomplete. In this study, the chromosomes of O. viverrini were prepared from the testes of adult worms retrieved from metacercariae infected-hamsters. The chromosomes of O. viverrini were identified in haploid (n=6) meiotic metaphase and in diploid (2n=12) mitotic metaphase by light microscopy. The chromosome number, length and nomenclature of each chromosome were determined by scanning electron microscopy. The six chromosomes consist of one large-sized metacentric, one medium-sized metacentric, two small-sized metacentric, one small-sized submetacentric and one small-sized acrocentric chromosomes with the lengths of 2.84±0.03, 2.12±0.10, 1.71±0.13, 1.44±0.04, 1.23±0.03 and 0.84±0.13 μm, respectively. This is the first karyotype analysis of O. viverrini with defined complete nomenclature.

  17. High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes.

    Science.gov (United States)

    Krasikova, Alla; Fukagawa, Tatsuo; Zlotina, Anna

    2012-12-01

    Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes.

  18. Modified C-band technique for the analysis of chromosome abnormalities in irradiated human lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Akifumi; Akiyama, Miho; Yamada, Yuji [Biodosimetry Section, Department of Radiation Dosimetry, Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Yoshida, Mitsuaki A., E-mail: myoshida@cc.hirosaki-u.ac.jp [Biodosimetry Section, Department of Radiation Dosimetry, Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

    2011-10-15

    A modified C-band technique was developed in order to analyze more accurately dicentric, tricentric, and ring chromosomes in irradiated human peripheral lymphocytes. Instead of the original method relying on treatment with barium hydroxide Ba(OH){sub 2}, C-bands were obtained using a modified form of heat treatment in formamide followed with DAPI staining. This method was tentatively applied to the analysis of dicentric chromosomes in irradiated human lymphocytes to examine its availability. The frequency of dicentric chromosome was almost the same with conventional Giemsa staining and the modified C-band technique. In the analysis using Giemsa staining, it is relatively difficult to identify the centromere on the elongated chromosomes, over-condensed chromosomes, fragment, and acentric ring. However, the modified C-band method used in this study makes it easier to identify the centromere on such chromosomes than with the use of Giemsa staining alone. Thus, the modified C-band method may give more information about the location of the centromere. Therefore, this method may be available and more useful for biological dose estimation due to the analysis of the dicentric chromosome in human lymphocytes exposed to the radiation. Furthermore, this method is simpler and faster than the original C-band protocol and fluorescence in situ hybridization (FISH) method with the centromeric DNA probe. - Highlights: > The dicentric (dic) assay is the most effective for the radiation biodosimetry. > It is important to recognize the centromere of the dic. > We improved a C-band technique based on heat denaturation. > This technique enables the accurate detection of a centromere. > This method may be available and more useful for biological dose estimation.

  19. Mammalian E-type cyclins control chromosome pairing, telomere stability and CDK2 localization in male meiosis.

    Directory of Open Access Journals (Sweden)

    Laetitia Martinerie

    2014-02-01

    Full Text Available Loss of function of cyclin E1 or E2, important regulators of the mitotic cell cycle, yields viable mice, but E2-deficient males display reduced fertility. To elucidate the role of E-type cyclins during spermatogenesis, we characterized their expression patterns and produced additional deletions of Ccne1 and Ccne2 alleles in the germline, revealing unexpected meiotic functions. While Ccne2 mRNA and protein are abundantly expressed in spermatocytes, Ccne1 mRNA is present but its protein is detected only at low levels. However, abundant levels of cyclin E1 protein are detected in spermatocytes deficient in cyclin E2 protein. Additional depletion of E-type cyclins in the germline resulted in increasingly enhanced spermatogenic abnormalities and corresponding decreased fertility and loss of germ cells by apoptosis. Profound meiotic defects were observed in spermatocytes, including abnormal pairing and synapsis of homologous chromosomes, heterologous chromosome associations, unrepaired double-strand DNA breaks, disruptions in telomeric structure and defects in cyclin-dependent-kinase 2 localization. These results highlight a new role for E-type cyclins as important regulators of male meiosis.

  20. Assignment of human sprouty 4 gene to chromosome segment 5q32∼33 and analysis of its pattern of expression

    Indian Academy of Sciences (India)

    Hua Liu; Jin-Zhong Chen; Shao-Hua Gu; Jian-Liang Dai; En-Pang Zhao; Lu Huang; Wang-Xiang Xu; Yi Xie; Yu-Min Mao

    2003-04-01

    The human sprouty 4 (SPYR4) gene was localized to chromosome band 5q32∼33 by screening the Stanford radiation hybrid G3 panel using a SPRY4-specific primer pair for PCR. Northern blot analysis revealed two different mRNAs (5 kb and 2 kb) in liver, skeletal muscle, heart, lung, kidney, spleen, placenta and small intestine. Reverse transcriptase-PCR analysis showed that SPYR4 was expressed in all tested tissues to different levels.

  1. Sequence and expression analysis of gaps in human chromosome 20

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan;

    2012-01-01

    The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and....../or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing...... and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum...

  2. A Semi-Closed Device for Chromosome Spreading for Cytogenetic Analysis

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Mednova, Olga; Vedarethinam, Indumathi;

    2014-01-01

    Metaphase chromosome spreading is the most crucial step required for successful karyotyping and FISH analysis. These two techniques are routinely used in cytogenetics to assess the chromosome abnormalities. The spreading process has been studied for years but it is still considered an art more than......, and thus allow for better quality spreads. Further cytogenetic analysis depends on the quality of the spreads, which is dependent on the skills of the personnel and is thus limited to laboratory settings. Here, we present a semi-closed microfluidic chip for preparation of the metaphase spreads on a glass...

  3. Molecular cloning and chromosomal localization of human genes encoding three closely related G protein-coupled receptors

    Energy Technology Data Exchange (ETDEWEB)

    Zhao-Hui Song; Bonner, T.I. [NIMH National Inst. of Health, Bethesda, MD (United States); Modi, W. [Frederick Cancer Research and Development Center, Frederick, MD (United States)

    1995-07-20

    Cosmids containing human genes for orphan G protein-coupled receptors, GPR12, GPR6, and GPR3, were isolated using their rat homologs as probes. Previous studies of the mouse and rat cDNAs have shown the receptors to be expressed primarily in brain but have failed to identify their ligands. The three receptor proteins of 334, 363, and 330 amino acids, respectively, are encoded by a single exon in each gene. Excluding the divergent sequences preceding the first transmembrane domain, they have {approximately}60% amino acid identity with each other. Flurorescence in situ hybridization of GPR12, GPR6, and GPR3 localized these three genes to human chromosomal regions 13q12, 6q21, and 1p34.3-p36.1, respectively. 9 refs., 2 figs.

  4. Gonadoblastomas in 45,X/46,XY mosaicism: analysis of Y chromosome distribution by fluorescence in situ hybridization.

    Science.gov (United States)

    Iezzoni, J C; Von Kap-Herr, C; Golden, W L; Gaffey, M J

    1997-08-01

    Gonadoblastomas are composed of nests of neoplastic germ cells and sex cord derivatives surrounded by ovarian-type stroma. These tumors are found almost exclusively in persons with gonadal dysgenesis associated with a Y chromosome or Y chromosome fragment, and accordingly, the Y chromosome has been implicated in gonadoblastoma oncogenesis. To evaluate this association, we used two-color fluorescence in situ hybridization with chromosome-specific probes to determine the distribution of the X and Y chromosomes in the tumor nests and surrounding stromal cells in paraffin tissue sections of three gonadoblastomas in two patients with gonadal dysgenesis and 45,X/46,XY mosaicism. Statistical analysis of the data from the fluorescence in situ hybridization demonstrated that in all three gonadoblastomas, the proportion of nuclei with a Y chromosome signal was significantly higher in the tumor cells than in the nontumoral cells of the surrounding stroma (P<.001). These results suggest that Y chromosome material participates in gonadoblastoma tumorigenesis.

  5. Fine localization of the locus for autosomal dominant retinitis pigmentosa on chromosome 17p

    Energy Technology Data Exchange (ETDEWEB)

    Goliath, R.; Janssens, P.; Beighton, P. [Univ. of Cape Town (South Africa)] [and others

    1995-10-01

    The term {open_quotes}retintis pigmentosa{close_quotes} (RP) refers to a group of inherited retinal degenerative disorders. Clinical manifestations include night-blindness, with variable age of onset, followed by constriction of the visual field that may progress to total loss of sight in later life. Previous studies have shown that RP is caused by mutations within different genes and may be inherited as an X-linked recessive (XLRRP), autosomal recessive (ARRP), or autosomal dominant (ADRP) trait. The AD form of this group of conditions has been found to be caused by mutations within the rhodopsin gene in some families and the peripherin/RDS gene in others. In addition, some ADRP families have been found to be linked to anonymous markers on 8cen, 7p, 7q,19q, and, more recently, 17p. The ADRP gene locus on the short arm of chromosome 17 was identified in a large South African family (ADRP-SA) of British origin. The phenotypic expression of the disorder, which has been described elsewhere is consistent in the pedigree with an early onset of disease symptoms. In all affected subjects in the family, onset of symptoms commenced before the age of 10 years. 16 refs., 3 figs., 1 tab.

  6. Linkage analysis of chromosome 14 and essential hypertension in Chinese population

    Institute of Scientific and Technical Information of China (English)

    ZHAO Wei-yan; HUANG Jian-feng; GE Dong-liang; SU Shao-yong; LI Biao; GU Dong-feng

    2005-01-01

    Background Hypertension is a complex biological trait that influenced by multiple factors. The encouraging results for hypertension research showed that the linkage analysis can be used to replicate other studies and discover new genetic risk factors. Previous studies linked human chromosome 14 to essential hypertension or blood pressure traits. With a Chinese population, we tried to replicate these findings. Methods A linkage scan was performed on chromosome 14 with 14-microsatellite markers with a density of about 10 centi Morgen (cM) in 147 Chinese hypertensive nuclear families. Multipoint non-parametric linkage analysis and exclusion mapping were performed with the GENEHUNTER software, whereas quantitative analysis was performed with the variance component method integrated in the SOLAR package. Results In the qualitative analysis, the highest non-parametric linkage score is 1.0 (P=0.14) at D14S261 in the single point analysis, and no loci achieved non-parametric linkage score more than 1.0 in the multipoint analysis. Maximum-likelihood mapping showed no significant results, either. Subsequently the traditional exclusion criteria of the log-of-the-odds score-2 were adopted, and the chromosome 14 with λs≥2.4 was excluded. In the quantitative analysis of blood pressure with the SOLAR software, two-point analysis and multipoint analysis suggested no evidence for linkage occurred on chromosome 14 for systolic and diastolic blood pressure. Conclusion There was no substantial evidence to support the linkage of chromosome 14 and essential hypertension or blood pressure trait in Chinese hypertensive subjects in this study.

  7. Fourier analysis on local fields (MN-15)

    CERN Document Server

    Taibleson, M H

    2015-01-01

    This book presents a development of the basic facts about harmonic analysis on local fields and the n-dimensional vector spaces over these fields. It focuses almost exclusively on the analogy between the local field and Euclidean cases, with respect to the form of statements, the manner of proof, and the variety of applications. The force of the analogy between the local field and Euclidean cases rests in the relationship of the field structures that underlie the respective cases. A complete classification of locally compact, non-discrete fields gives us two examples of connected fields (rea

  8. In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.

    2006-02-01

    The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

  9. The Utility of Chromosomal Microarray Analysis in Developmental and Behavioral Pediatrics

    Science.gov (United States)

    Beaudet, Arthur L.

    2013-01-01

    Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism…

  10. Diagnostic Yield of Chromosomal Microarray Analysis in an Autism Primary Care Practice: Which Guidelines to Implement?

    Science.gov (United States)

    McGrew, Susan G.; Peters, Brittany R.; Crittendon, Julie A.; Veenstra-VanderWeele, Jeremy

    2012-01-01

    Genetic testing is recommended for patients with ASD; however specific recommendations vary by specialty. American Academy of Pediatrics and American Academy of Neurology guidelines recommend G-banded karyotype and Fragile X DNA. The American College of Medical Genetics recommends Chromosomal Microarray Analysis (CMA). We determined the yield of…

  11. Economic analysis of chromosome testing in couples with recurrent miscarriage to prevent handicapped offspring.

    NARCIS (Netherlands)

    Leeuwen, M. van; Vansenne, F.; Korevaar, J.C.; Veen, F. van der; Goddijn, M.; Mol, B.W.J.

    2013-01-01

    Study Question: Which strategy is least expensive to prevent the birth of a handicapped child in couples with recurrent miscarriage (RM); parental chromosome analysis followed by amniocentesis in case of carrier status of one of the parents, or amniocentesis in all ongoing pregnancies without the kn

  12. 40 CFR 798.5385 - In vivo mammalian bone marrow cytogenetics tests: Chromosomal analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 31 2010-07-01 2010-07-01 true In vivo mammalian bone marrow cytogenetics tests: Chromosomal analysis. 798.5385 Section 798.5385 Protection of Environment ENVIRONMENTAL... used. Examples of commonly used rodent species are rats, mice, and hamsters. (ii) Age. Healthy...

  13. Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species.

    Science.gov (United States)

    Ulloa, M; Wang, C; Saha, S; Hutmacher, R B; Stelly, D M; Jenkins, J N; Burke, J; Roberts, P A

    2016-04-01

    Chromosome substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with chromosome or chromosome segment substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease

  14. Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

    Directory of Open Access Journals (Sweden)

    Lei Fang

    Full Text Available Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes, glycolysis/gluconeogenesis (122 genes, phenylpropanoid biosynthesis (101 genes, and oxidative phosphorylation (87 genes, etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.

  15. Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

    Science.gov (United States)

    Fang, Lei; Tian, Ruiping; Chen, Jiedan; Wang, Sen; Li, Xinghe; Wang, Peng; Zhang, Tianzhen

    2014-01-01

    Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes), glycolysis/gluconeogenesis (122 genes), phenylpropanoid biosynthesis (101 genes), and oxidative phosphorylation (87 genes), etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.

  16. Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

    Directory of Open Access Journals (Sweden)

    Sanchez-Alberola Neus

    2012-02-01

    Full Text Available Abstract Background The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the Vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. Here we combine in silico and in vitro techniques to perform a comparative genomics analysis of the SOS regulon in the Vibrionaceae, and we extend the methodology to map this transcriptional network in other bacterial species harboring multiple chromosomes. Results Our analysis provides the first comprehensive description of the SOS response in a family (Vibrionaceae that includes major human pathogens. It also identifies several previously unreported members of the SOS transcriptional network, including two proteins of unknown function. The analysis of the SOS response in other bacterial species with multiple chromosomes uncovers additional regulon members and reveals that there is a conserved core of SOS genes, and that specialized additions to this basic network take place in different phylogenetic groups. Our results also indicate that across all groups the main elements of the SOS response are always found in the large chromosome, whereas specialized additions are found in the smaller chromosomes and plasmids. Conclusions Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and dissemination of antibiotic resistance, and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an

  17. Localization of a gene (CMT2A) for autosomal dominant Charcot-Marie-Tooth disease type 2 to chromosome 1p and evidence of genetic heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Othmane, K.B.; Loprest, L.J.; Wilkinson, K.M. (Duke Univ. Medical Center, Durham, NC (United States)); Middleton, L.T. (Cyprus Institute of Neurology and Genetics, Nicosia (Cyprus)) (and others)

    1993-08-01

    Charcot-Marie-Tooth (CMT) disease type 2 (CMT2) is an inherited peripheral neuropathy characterized by variable age of onset and normal or slightly diminished nerve conduction velocity. CMT2 is pathologically and genetically distinct from CMT type 1 (CMT1). While CMT1 has been shown to be genetically heterogeneous, no chromosomal localization has been established for CMT2. The authors have performed pedigree linkage analysis in six large autosomal dominant CMT2 families and have demonstrated linkage and heterogeneity to a series of microsatellites (D1S160, D1S170, D1S244, D1S228 and D1S199) in the distal region of the short arm of chromosome 1. Significant evidence for heterogeneity was found using admixture analyses and the two-point lod scores. Admixture analyses using the multipoint results for the markers D1S244, D1S228, and D1S199 supported the two-point findings. Three families, DUK662, DUK1241, and 1523 gave posterior probabilities of 1.0, 0.98, and 0.88 of being of the linked type. Multipoint analysis examining the [open quotes]linked[close quotes] families showed that the most favored location for the CMT2A gene is within the interval flanked by D1S244 and D1S228 (odds approximately 70:1 of lying within versus outside that interval). These findings suggest that the CMT2 phenotype is secondary to at least two different genes and demonstrate further heterogeneity in the CMT phenotype.

  18. Chromosomal localization of the murine RFC-1 gene encoding a folate transporter and its amplification in an antifolate resistant variant overproducing the transporter.

    Science.gov (United States)

    Roy, K; Chiao, J H; Spengler, B A; Tolner, B; Yang, C H; Biedler, J L; Sirotnak, F M

    1998-08-01

    A variant of the L1210 cell (L1210/R83) selected in the presence of the lipophilic antifolate, metoprine, and a concentration of the natural diastereoisomer of 5-formyltetrahydrofolate, lL5CHO-folateH4, suboptimum for growth exhibited a 35-fold increase compared to parental L1210 cells in one-carbon, reduced folate transport. This was evidenced by the increase in Vmax for [3H]MTX (methotrexate) influx and a commensurate increase in the amount of the 46 kilodalton (kDa) transport protein and reduced folate carrier (RFC-1) mRNA. The variant is resistant to lipophilic antifolates, but shows collateral sensitivity to classical folate analogues. Karyotype analysis of L1210/R83 cells revealed the presence of several new chromosome abnormalities. One of these was a large, submetacentric marker chromosome comprising a normal #10 and a longer, abnormally banded arm of uncertain origin which exhibited an interstitial, palely staining, HSR-like segment. The results of Southern and Northern blotting showed that the RFC-1 gene copy number and RNA transcript level were markedly increased (30-35 fold) in L1210/R83 cells. Fluorescence in situ hybridization (FISH) analysis revealed that the HSR-like segment in these cells was the site of amplified RFC-1 genes. Independent revertant subclones, obtained following growth in the absence of selection pressure, showed four- to 12-fold decreases in [3H]MTX influx Vmax and in amount of NHS (N-hydroxysuccinimide)-[3H]MTX affinity labeled one-carbon, reduced folate transporter compared to L1210/R83 cells. RFC-1 gene copy number also decreased, and the mean length of the HSR in these revertants declined 1.6- to 5-fold. Based upon genomic nucleotide sequencing, the RFC-1 gene in the normal mouse genome was localized to chromosome 10 in close association with the alpha 1 (Col18a1) collagen gene at 10B3(locus 41cM). The close association of these genes was confirmed by other data showing that the alpha 1 collagen gene was co-amplified in L1210/R

  19. X chromosome-linked and mitochondrial gene control of Leber hereditary optic neuropathy: Evidence from segregation analysis for dependence on X chromosome inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Xiangdong Bu; Rotter, J.I. (Cedars-Sinai Medical Center, Los Angeles, CA (United States) Univ. of California, Los Angeles (United States))

    1991-09-15

    Leber hereditary optic neuropathy (LHON) has been shown to involve mutation(s) of mitochondrial DNA, yet there remain several confusing aspects of its inheritance not explained by mitochondrial inheritance alone, including male predominance, reduced penetrance, and a later age of onset in females. By extending segregation analysis methods to disorders that involve both a mitochondrial and a nuclear gene locus, the authors show that the available pedigree data for LHON are most consistent with a two-locus disorder, with one responsible gene being mitochondrial and the other nuclear and X chromosome-linked. Furthermore, they have been able to extend the two-locus analytic method and demonstrate that a proportion of affected females are likely heterozygous at the X chromosome-linked locus and are affected due to unfortunate X chromosome inactivation, thus providing an explanation for the later age of onset in females. The estimated penetrance for a heterozygous female is 0.11{plus minus}0.02. The calculated frequency of the X chromosome-linked gene for LHON is 0.l08. Among affected females, 60% are expected to be heterozygous, and the remainder are expected to be homozygous at the responsible X chromosome-linked locus.

  20. The molecular characterization of maize B chromosome specific AFLPs

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The origin and evolution of B chromosomes could be explained by the specific DNA sequence on them.But the specific sequences known were quite limited. To investigate maize B chromosome sqicific DNA sequeces, maize genomes with and without B chromosomes were analyzed by AFLP. Only 5 markers were found specific to genomes with B chromosomes among about 2000 AFLP markers. Southern hybridization and sequence analysis revealed that only the sequence of M8-2D was a B chromosome specific sequence.This sequence contained the telomeric repeat unit AGGGTTT conserved in plant chromosome telomeres.In addition, the sequence of M8-2D shared low homology to clones from maize chromosome 4 centromere as well. M8-2D were localized to B chromosome centromeric and telomeric regions.

  1. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

    Directory of Open Access Journals (Sweden)

    Thomas George H

    2006-01-01

    Full Text Available Abstract Background A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes, microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity. SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. Results We have developed SNPscan, a web-accessible tool to analyze and visualize high density SNP data. It enables researchers (1 to visually and quantitatively assess the quality of user-generated SNP data relative to a benchmark data set derived from a control population, (2 to display SNP intensity and allelic call data in order to detect chromosomal copy number anomalies (duplications and deletions, (3 to display uniparental isodisomy based on loss of heterozygosity (LOH across genomic regions, (4 to compare paired samples (e.g. tumor and normal, and (5 to generate a file type for viewing SNP data in the University of California, Santa Cruz (UCSC Human Genome Browser. SNPscan accepts data exported from Affymetrix Copy Number Analysis Tool as its input. We validated SNPscan using data generated from patients with known deletions, duplications, and uniparental disomy. We also inspected previously generated SNP data from 90 apparently normal individuals from the Centre d'Étude du Polymorphisme Humain (CEPH collection, and identified three cases of uniparental isodisomy, four females having an apparently mosaic X chromosome, two mislabelled SNP data sets, and one microdeletion on chromosome 2 with mosaicism from an apparently normal female. These previously unrecognized abnormalities were all detected using SNPscan. The microdeletion was independently

  2. Human sulfotransferase SULT1C1: cDNA cloning, tissue-specific expression, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Her, Chengtao; Weinshilboum, R.M. [Mayo Foundation, Rochester, MN (United States); Kaur, G.P. [Temple Univ. Medical School, Philadelphia, PA (United States)] [and others

    1997-05-01

    We have isolated and sequenced a cDNA that encodes an apparent human orthologue of a rat sulfotransferase (ST) cDNA that has been referred to as {open_quotes}ST1C1{close_quotes} - although it was recently recommended that sulfotransferase proteins and cDNAs be abbreviated {open_quotes}SULT.{close_quotes} The new human cDNA was cloned from a fetal liver-spleen cDNA library and had an 888-bp open reading frame. The amino acid sequence of the protein encoded by the cDNA was 62% identical with that encoded by the rat ST1C1 cDNA and included signature sequences that are conserved in all cytosolic SULT enzymes. Dot blot analysis of mRNA from 50 human tissues indicated that the cDNA was expressed in adult human stomach, kidney, and thyroid, as well as fetal kidney and liver. Northern blot analyses demonstrated that the major SULT1C1 mRNA in those same tissues was 1.4 kb in length. We next determined the partial human SULT1C1 gene sequence for a portion of the 5{prime}-terminus of one intron. That sequence was used to design SULT1C1 gene-specific primers that were used to perform the PCR with DNA from human/rodent somatic cell hybrids to demonstrate that the gene was located on chromosome 2. PCR amplifications performed with human chromosome 2/rodent hybrid cell DNA as template sublocalized SULT1C1 to a region between bands 2q11.1 and 2q11.2. 14 refs., 2 figs.

  3. Gene-rich chromosomal regions are preferentially localized in the lamin B deficient nuclear blebs of atypical progeria cells.

    Science.gov (United States)

    Bercht Pfleghaar, Katrin; Taimen, Pekka; Butin-Israeli, Veronika; Shimi, Takeshi; Langer-Freitag, Sabine; Markaki, Yolanda; Goldman, Anne E; Wehnert, Manfred; Goldman, Robert D

    2015-01-01

    More than 20 mutations in the gene encoding A-type lamins (LMNA) cause progeria, a rare premature aging disorder. The major pathognomonic hallmarks of progeria cells are seen as nuclear deformations or blebs that are related to the redistribution of A- and B-type lamins within the nuclear lamina. However, the functional significance of these progeria-associated blebs remains unknown. We have carried out an analysis of the structural and functional consequences of progeria-associated nuclear blebs in dermal fibroblasts from a progeria patient carrying a rare point mutation p.S143F (C428T) in lamin A/C. These blebs form microdomains that are devoid of major structural components of the nuclear envelope (NE)/lamina including B-type lamins and nuclear pore complexes (NPCs) and are enriched in A-type lamins. Using laser capture microdissection and comparative genomic hybridization (CGH) analyses, we show that, while these domains are devoid of centromeric heterochromatin and gene-poor regions of chromosomes, they are enriched in gene-rich chromosomal regions. The active form of RNA polymerase II is also greatly enriched in blebs as well as nascent RNA but the nuclear co-activator SKIP is significantly reduced in blebs compared to other transcription factors. Our results suggest that the p.S143F progeria mutation has a severe impact not only on the structure of the lamina but also on the organization of interphase chromatin domains and transcription. These structural defects are likely to contribute to gene expression changes reported in progeria and other types of laminopathies.

  4. An Allometric Analysis of Sex and Sex Chromosome Dosage Effects on Subcortical Anatomy in Humans.

    Science.gov (United States)

    Reardon, Paul Kirkpatrick; Clasen, Liv; Giedd, Jay N; Blumenthal, Jonathan; Lerch, Jason P; Chakravarty, M Mallar; Raznahan, Armin

    2016-02-24

    Structural neuroimaging of humans with typical and atypical sex-chromosome complements has established the marked influence of both Yand X-/Y-chromosome dosage on total brain volume (TBV) and identified potential cortical substrates for the psychiatric phenotypes associated with sex-chromosome aneuploidy (SCA). Here, in a cohort of 354 humans with varying karyotypes (XX, XY, XXX, XXY, XYY, XXYY, XXXXY), we investigate sex and SCA effects on subcortical size and shape; focusing on the striatum, pallidum and thalamus. We find large effect-size differences in the volume and shape of all three structures as a function of sex and SCA. We correct for TBV effects with a novel allometric method harnessing normative scaling rules for subcortical size and shape in humans, which we derive here for the first time. We show that all three subcortical volumes scale sublinearly with TBV among healthy humans, mirroring known relationships between subcortical volume and TBV among species. Traditional TBV correction methods assume linear scaling and can therefore invert or exaggerate sex and SCA effects on subcortical anatomy. Allometric analysis restricts sex-differences to: (1) greater pallidal volume (PV) in males, and (2) relative caudate head expansion and ventral striatum contraction in females. Allometric analysis of SCA reveals that supernumerary X- and Y-chromosomes both cause disproportionate reductions in PV, and coordinated deformations of striatopallidal shape. Our study provides a novel understanding of sex and sex-chromosome dosage effects on subcortical organization, using an allometric approach that can be generalized to other basic and clinical structural neuroimaging settings.

  5. Cloning of genomic DNA of rice 5-enolpyruvylshikimate 3-phosphate synthase gene and chromosomal localization of the gene

    Institute of Scientific and Technical Information of China (English)

    徐军望; 冯德江; 李旭刚; 常团结; 朱祯

    2002-01-01

    The shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSPs) is the target of nonselective herbicide glyphosate. A partial rice epsps cDNA was generated by RT-PCR with primers designed according to EST sequence in GenBank and used as probe for rice genomic library screening. In a screen of approximately 8.0×104 clones from the rice genomic library, sixteen positive clones were obtained, which strongly hybridized to the probe. One clone, E11, was selected for further analysis and the full-length 3661 bp rice epsps genomic sequence was obtained. Sequence analysis and homologous comparison revealed that epsps gene is composed of 8 exons and 7 introns. Analysis by restriction fragment length polymorphism with the probe of rice epsps cDNA fragment confirmed that rice epsps is located on chromosome 6 with an indica-japonica (ZYQ8-JX17) double-haploid (DH) population. This is the first report on the EPSP synthase from monocotyledons.

  6. Fine genetic mapping of the Batten disease locus (CLN3) by haplotype analysis and demonstration of allelic association with chromosome 16p microsatellite loci

    Energy Technology Data Exchange (ETDEWEB)

    Mitchison, H.M.; McKay, T.R. [Univ. College London Medical School (United Kingdom); Thompson, A.D.; Mulley, J.C.; Kozman, H.M.; Richards, R.I.; Callen, D.F. [Women and Children`s Hospital, Adelaide (Australia); Stallings, R.L.; Doggett, N.A. [Los Alamos National Lab., NM (United States); Attwood, J. [Galton Lab., London (United Kingdom)] [and others

    1993-05-01

    Batten disease, juvenile onset neuronal ceroid lipofuscinosis, is an autosomal recessive neurodegenerative disorder characterized by accumulation of autofluorescent lipopigment in neurons and other cell types. The disease locus (CLN3) has previously been assigned to chromosome 16p. The genetic localization of CLN3 has been refined by analyzing 70 families using a high-resolution map of 15 marker loci encompassing the CLN3 region on 16p. Crossovers in three maternal meioses allowed localization of CLN3 to the interval between D16S297 and D16S57. Within that interval alleles at three highly polymorphic dinucleotide repeat loci (D16S288, D16S298, D16S299) were found to be in strong linkage disequilibrium with CLN3. Analysis of haplotypes suggests that a majority of CLN3 chromosomes have arisen from a single founder mutation. 15 refs., 2 figs., 5 tabs.

  7. Chromosomal damage and apoptosis analysis in exfoliated oral epithelial cells from mouthwash and alcohol users

    Science.gov (United States)

    Rocha, Rodrigo dos Santos; Meireles, José Roberto Cardoso; de Moraes Marcílio Cerqueira, Eneida

    2014-01-01

    Chromosomal damage and apoptosis were analyzed in users of mouthwash and/or alcoholic beverages, using the micronucleus test on exfoliated oral mucosa cells. Samples from four groups of 20 individuals each were analyzed: three exposed groups (EG1, EG2 and EG3) and a control group (CG). EG1 comprised mouthwash users; EG2 comprised drinkers, and EG3 users of both mouthwashes and alcoholic beverages. Cell material was collected by gently scraping the insides of the cheeks. Then the cells were fixed in a methanol/acetic acid (3:1) solution and stained and counterstained, respectively, with Schiff reactive and fast green. Endpoints were computed on 2,000 cells in a blind test. Statistical analysis showed that chromosomal damage and apoptosis were significantly higher in individuals of groups EG1 and EG3 than in controls (p < 0.005 and p < 0.001, respectively). No significant difference in chromosomal damage and apoptosis was observed between the exposed groups. In EG2, only the occurrence of apoptosis was significantly higher than in the controls. These results suggest that mouthwashes alone or in association with alcoholic drinks induce genotoxic effects, manifested as chromosomal damage and apoptosis. They also suggest that alcoholic drinks are effective for stimulating the process of apoptosis. However, these data need to be confirmed in larger samples. PMID:25505845

  8. The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis.

    Science.gov (United States)

    McEvoy, Brian; Brady, Claire; Moore, Laoise T; Bradley, Daniel G

    2006-12-01

    The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800-1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.

  9. Molecular analysis of sex chromosome-linked mutants in the silkworm Bombyx mori

    Indian Academy of Sciences (India)

    Tsuguru Fujii; Hiroaki Abe; Toru Shimada

    2010-09-01

    In Bombyx mori, the W chromosome determines the female sex. A few W chromosome-linked mutations that cause masculinization of the female genitalia have been found. In female antennae of a recently isolated mutant, both female-type and male-type Bmdsx mRNAs were expressed, and BmOr1 (bombykol receptor) and BmOr3 (bombykal receptor), which are predominantly expressed in the antennae of male moths, were expressed about 50 times more abundantly in the antennae of mutant females than in those of normal females. These mutants are valuable resources for the molecular analysis of the sex-determination system. Besides the Fem gene, the quantitative egg size-determining gene Esd is thought to be present on the W chromosome, based on the observation that ZWW triploid moths produce larger eggs than ZZW triploids. The most recently updated B. mori genome assembly comprises 20.5 Mb of Z chromosome sequence. Using these sequence data, responsible genes or candidate genes for four Z-linked mutants have been reported. The od (distinct oily) and spli (soft and pliable) are caused by mutation in BmBLOS2 and Bmacj6, respectively. Bmap is a candidate gene for $V_g$ (vestigial). Similarly, Bmprm is a candidate gene for Md (muscle dystrophy), causing abnormal development of indirect flight muscle.

  10. Chromosomal localization of 45S rDNA, sex-specific C values, and heterochromatin distribution in Coccinia grandis (L.) Voigt.

    Science.gov (United States)

    Bhowmick, Biplab Kumar; Yamamoto, Masashi; Jha, Sumita

    2016-01-01

    Coccinia grandis is a widely distributed dioecious cucurbit in India, with heteromorphic sex chromosomes and X-Y sex determination mode. The present study aids in the cytogenetic characterization of four native populations of this plant employing distribution patterns of 45S rDNA on chromosomes and guanine-cytosine (GC)-rich heterochromatin in the genome coupled with flow cytometric determination of genome sizes. Existence of four nucleolar chromosomes could be confirmed by the presence of four telomeric 45S rDNA signals in both male and female plants. All four 45S rDNA sites are rich in heterochromatin evident from the co-localization of telomeric chromomycin A (CMA)(+ve) signals. The size of 45S rDNA signal was found to differ between the homologues of one nucleolar chromosome pair. The distribution of heterochromatin is found to differ among the male and female populations. The average GC-rich heterochromatin content of male and female populations is 23.27 and 29.86 %, respectively. Moreover, the male plants have a genome size of 0.92 pg/2C while the female plants have a size of 0.73 pg/2C, reflecting a huge genomic divergence between the genders. The great variation in genome size is owing to the presence of Y chromosome in the male populations, playing a multifaceted role in sexual divergence in C. grandis.

  11. Karyotype evolution in Tilapia: mitotic and meiotic chromosome analysis of Oreochromis karongae and O. niloticus x O. karongae hybrids.

    Science.gov (United States)

    Harvey, S C; Campos-Ramos, R; Kennedy, D D; Ezaz, M T; Bromage, N R; Griffin, D K; Penman, D J

    2002-06-01

    The karyotype of Oreochromis species is considered to be highly conserved, with a diploid chromosome complement of 2n = 44. Here we show, by analysis of mitotic and meiotic chromosomes, that the karyotype of O. karongae, one of the Lake Malawi 'chambo' species, is 2n = 38. This difference in chromosome number does not prevent the production of inter-specific hybrids between O. niloticus (2n = 44) and O. karongae (2n = 38). Analysis of the meiotic chromosomes of the O. niloticus x O. karongae hybrids indicates that three separate chromosome fusion events have occurred in O. karongae. Comparison of the O. karongae and O. niloticus karyotypes suggests that these consist of one Robertsonian fusion and two fusions of a more complex nature.

  12. Chromosome analysis in the Kruger National Park - the chromosomes of the saddle-backed jackal Canis Mesomelas

    Directory of Open Access Journals (Sweden)

    C. Wallace

    1977-08-01

    Full Text Available Among the present-day members of the Canidae family are included the dogs and foxes (Wurster and Benirschke 1968. The genus Canis is represented in Africa by four species of jackal (Bigaike 1972. This paper presents the chromosome Findings in a male saddle-backed jackal Canis mesomelas studied in the Kruger National Park, Republic of South Africa.

  13. Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome

    Directory of Open Access Journals (Sweden)

    Vibranovski Maria D

    2012-06-01

    Full Text Available Abstract Background Meiotic sex chromosome inactivation (MSCI during spermatogenesis has been proposed as one of the evolutionary driving forces behind both the under-representation of male-biased genes on, and the gene movement out of, the X chromosome in Drosophila. However, the relevance of MSCI in shaping sex chromosome evolution is controversial. Here we examine two aspects of a recent study on testis gene expression (Mikhaylova and Nurminsky, BMC Biol 2011, 9:29 that failed to support the MSCI in Drosophila. First, Mikhaylova and Nurminsky found no differences between X-linked and autosomal genes based on the transcriptional profiling of the early testis development, and thus concluded that MSCI does not occur in D. melanogaster. Second, they also analyzed expression data from several D. melanogaster tissues and concluded that under-representation on the X chromosome is not an exclusive property of testis-biased genes, but instead, a general property of tissue-specific genes. Results By re-analyzing the Mikhaylova and Nurminsky's testis data and the expression data on several D. melanogaster tissues, we made two major findings that refuted their original claims. First, the developmental testis data has generally greater experimental error than conventional analyses, which reduced significantly the power to detect chromosomal differences in expression. Nevertheless, our re-analysis observed significantly lower expression of the X chromosome in the genomic transcriptomes of later development stages of the testis, which is consistent with the MSCI hypothesis. Second, tissue-specific genes are also in general enriched with genes more expressed in testes than in ovaries, that is testis-biased genes. By completely excluding from the analyses the testis-biased genes, which are known to be under-represented in the X, we found that all the other tissue-specific genes are randomly distributed between the X chromosome and the autosomes. Conclusions

  14. Refined localization of the Escherichia coli F4ab/F4ac receptor locus on pig chromosome 13.

    Science.gov (United States)

    Joller, D; Jørgensen, C B; Bertschinger, H U; Python, P; Edfors, I; Cirera, S; Archibald, A L; Bürgi, E; Karlskov-Mortensen, P; Andersson, L; Fredholm, M; Vögeli, P

    2009-10-01

    Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207-S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207-MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb.

  15. Isolation of a novel G protein-coupled receptor (GPR4) localized to chromosome 19q13.3

    Energy Technology Data Exchange (ETDEWEB)

    Mahadevan, M.S.; Baird, S.; Bailly, J.E. [Univ. of Ottawa, Ontario (Canada)] [and others

    1995-11-01

    We present the cloning and sequencing of the human gene for a novel G-protein coupled receptor (GPR4), from the critical myotonic dystrophy (DM) region on chromosome 19q13.3. The homologous porcine gene was isolated and sequenced as well. The genes of both species are intronless and contain an open reading frame encoding a protein of 362 amino acids. In human, two isoforms of GPR4 are expressed, differing in their 3{prime} untranslated region due to the use of alternate polyadenylation signals and measuring approximately 2.8 and 1.8 kb, respectively. Northern blot analysis showed that GPR4 is widely expressed, with higher levels in kidney, heart, and especially lung, where it is at least fivefold greater than in other tissues. Sequence analysis suggests that GPR4 is a peptide receptor and shares strongest homologies with purinergic receptors and receptors for angiotensin II, platelet activating factor, thrombin, and bradykinin. 25 refs., 3 figs., 1 tab.

  16. Chromosome analysis of nuclear power plant workers using fluorescence in situ hybridization and Giemsa assay.

    Science.gov (United States)

    Hristova, Rositsa; Hadjidekova, Valeria; Grigorova, Mira; Nikolova, Teodora; Bulanova, Minka; Popova, Ljubomira; Staynova, Albena; Benova, Donka

    2013-09-01

    The aim of this study was to evaluate the genotoxic effects of ionizing radiation in vivo in exposed Bulgarian nuclear power plant workers by using classical cytogenetic and molecular cytogenetic analyses of peripheral lymphocytes. Chromosome analysis using fluorescence in situ hybrydization (FISH) and Giemsa techniques was undertaken on 63 workers and 45 administrative staff controls from the Bulgarian Nuclear Power Plant. Using the Giemsa method, the frequencies of cells studied with chromosome aberrations, dicentrics plus rings and chromosome fragments in the radiation workers were significantly higher compared with the control group (P = 0.044, P = 0.014, and P = 0.033, respectively). A significant association between frequencies of dicentrics plus rings and accumulated doses was registered (P < 0.01). In the present study, a FISH cocktail of whole chromosome paints for chromosomes 1, 4 and 11 was used. A significant association between frequency of translocations and accumulated doses was also observed (P < 0.001). Within the control group, a correlation was found between age and the spontaneous frequency of translocations. No correlation was found between smoking status and frequency of translocations. When compared with the control group, workers with accumulated doses up to 100 mSv showed no increase in genome translocation frequency, whereas workers with accumulated doses from 101 to 200 mSv showed a statistically significant doubling of genome translocation frequency (P = 0.009). Thus, in cases of chronic exposure and for purposes of retrospective dosimetry, the genome frequency of translocations is a more useful marker for evaluation of genotoxic effects than dicentric frequency.

  17. Chromosome analysis of nuclear power plant workers using fluorescence in situ hybridization and Giemsa assay

    Science.gov (United States)

    Hristova, Rositsa; Hadjidekova, Valeria; Grigorova, Mira; Nikolova, Teodora; Bulanova, Minka; Popova, Ljubomira; Staynova, Albena; Benova, Donka

    2013-01-01

    The aim of this study was to evaluate the genotoxic effects of ionizing radiation in vivo in exposed Bulgarian nuclear power plant workers by using classical cytogenetic and molecular cytogenetic analyses of peripheral lymphocytes. Chromosome analysis using fluorescence in situ hybrydization (FISH) and Giemsa techniques was undertaken on 63 workers and 45 administrative staff controls from the Bulgarian Nuclear Power Plant. Using the Giemsa method, the frequencies of cells studied with chromosome aberrations, dicentrics plus rings and chromosome fragments in the radiation workers were significantly higher compared with the control group (P = 0.044, P = 0.014, and P = 0.033, respectively). A significant association between frequencies of dicentrics plus rings and accumulated doses was registered (P < 0.01). In the present study, a FISH cocktail of whole chromosome paints for chromosomes 1, 4 and 11 was used. A significant association between frequency of translocations and accumulated doses was also observed (P < 0.001). Within the control group, a correlation was found between age and the spontaneous frequency of translocations. No correlation was found between smoking status and frequency of translocations. When compared with the control group, workers with accumulated doses up to 100 mSv showed no increase in genome translocation frequency, whereas workers with accumulated doses from 101 to 200 mSv showed a statistically significant doubling of genome translocation frequency (P = 0.009). Thus, in cases of chronic exposure and for purposes of retrospective dosimetry, the genome frequency of translocations is a more useful marker for evaluation of genotoxic effects than dicentric frequency. PMID:23536543

  18. Analysis of human chromosome 21 for a locus conferring susceptibility to Hirschsprung Disease

    Energy Technology Data Exchange (ETDEWEB)

    Bolk, S.; Duggan, D.J.; Chakravarti, A. [Case Western Reserve Univ., Cleveland, OH (United States)

    1994-09-01

    It has been estimated that approximately 5% of patients diagnosed with Hirschsprung disease (HSCR), or aganglionic megacolon, have trisomy 21. Since the incidence of Hirschsprung disease is 1/5000 live births and the incidence of trisomy 21 is approximately 1/1000 live births, the observed occurrence of HSCR in trisomy 21 is fifty times higher than expected. We propose that at least one locus on chromosome 21 predisposes to HSCR. Although at fifty times elevated risk, only 1% of Down Syndrome cases have HSCR. Thus additional genes or genetic events are necessary for HSCR to manifest in patients with trisomy 21. Based on segregation analysis, Badner et al. postulated that recessive genes may be responsible for up to 80% of HSCR. We postulate that at least one such gene is on chromosome 21 and increased homozygosity for common recessive HSCR mutations may be one cause for the elevated risk of HSCR in cases of trisomy 21. To map such a chromosome 21 locus, we are searching for segments of human chromosome 21 which are identical by descent from the parent in whom non-disjunction occurred. These segments will arise either from meiosis I (followed by a crossover between the centromere and the locus) or from meiosis II (followed by no crossovers). Nine nuclear families with a proband diagnosed with HSCR and Down Syndrome have been genotyped for 18 microsatellite markers spanning human chromosome 21q. In all nine cases analyzed thus far, trisomy 21 resulted from maternal non-disjunction at meiosis I. At this point no single IBD region is apparent. Therefore, additional families are being ascertained and additional markers at high density are being genotyped to map the HSCR locus.

  19. Linkage between stature and a region on chromosome 20 and analysis of a candidate gene, bone morphogenetic protein 2

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, D.B.; Ossowski, V.; Janssen, R.C.; Knowler, W.C.; Bogardus, C. [National Inst. of Health, Phoenix, AZ (United States)

    1995-12-04

    Sib-pair linkage analysis of the quantitative trait, stature, in over 500 Pima Indians indicates that a genetic determinant of governing stature is located on chromosome 20. Analysis of 10 short tandem repeat polymorphisms localized this linkage to a 3. cM region that includes D20S98 and D20S66. Using all possible sib-pair combinations, linkage was detected to both stature (P = 0.0001) and to leg length (P = 0.001), but not to sitting height. Single-strand conformational polymorphism analysis of exon 3 of the bone morphogenetic protein 2 (BMP2) gene, a candidate gene in this region, in genomic DNA of 20 of the tallest and 20 of the shortest individuals did not show any consistent differences associated with leg length or height. Sequence analysis of the region encoding the mature protein revealed a single nucleotide substitution, a T to G transversion, not detected by single-strand conformational polymorphism (SSCP) analysis. This transversion results in a conservative amino acid substitution of glycine for valine at codon 80 of BMP2. The frequency of this allele was 0.23 in the sample. No significant differences in height were noted in persons carrying either allele. This indicates that this structural alteration in the mature BMP2 protein does not contribute to the differences in stature observed in the Pima Indians, nor is this structural change in the mature protein likely to be responsible for the linkage observed with stature on chromosome 20. 33 refs., 2 figs., 2 tabs.

  20. Genomic and expression analysis of multiple Sry loci from a single Rattus norvegicus Y chromosome

    Directory of Open Access Journals (Sweden)

    Farkas Joel

    2007-04-01

    Full Text Available Abstract Background Sry is a gene known to be essential for testis determination but is also transcribed in adult male tissues. The laboratory rat, Rattus norvegicus, has multiple Y chromosome copies of Sry while most mammals have only a single copy. DNA sequence comparisons with other rodents with multiple Sry copies are inconsistent in divergence patterns and functionality of the multiple copies. To address hypotheses of divergence, gene conversion and functional constraints, we sequenced Sry loci from a single R. norvegicus Y chromosome from the Spontaneously Hypertensive Rat strain (SHR and analyzed DNA sequences for homology among copies. Next, to determine whether all copies of Sry are expressed, we developed a modification of the fluorescent marked capillary electrophoresis method to generate three different sized amplification products to identify Sry copies. We applied this fragment analysis method to both genomic DNA and cDNA prepared from mRNA from testis and adrenal gland of adult male rats. Results Y chromosome fragments were amplified and sequenced using primers that included the entire Sry coding region and flanking sequences. The analysis of these sequences identified six Sry loci on the Y chromosome. These are paralogous copies consistent with a single phylogeny and the divergence between any two copies is less than 2%. All copies have a conserved reading frame and amino acid sequence consistent with function. Fragment analysis of genomic DNA showed close approximations of experimental with predicted values, validating the use of this method to identify proportions of each copy. Using the fragment analysis procedure with cDNA samples showed the Sry copies expressed were significantly different from the genomic distribution (testis p Sry transcript expression, analyzed by real-time PCR, showed significantly higher levels of Sry in testis than adrenal gland (p, 0.001. Conclusion The SHR Y chromosome contains at least 6 full length

  1. DNA Ploidy and Chromosome (FISH Pattern Analysis of Peripheral Nerve Sheath Tumors

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    Anett Hruska

    2004-01-01

    Full Text Available Background and methods: 44 peripheral nerve sheath tumors (PNST (27 schwannomas, 9 neurofibromas and 8 malignant peripheral nerve sheath tumors (MPNST were analyzed to determine DNA ploidy pattern and to clarify the conflicting data in the literature concerning this topic (whether benign PNSTs are aneuploid or not. For further insight we analyzed 6 schwannomas, one atypical neurofibroma and five MPNSTs by fluorescence in situ hybridization (FISH technique using centromeric chromosome probes (7, 17 and 18 and automatic image analysis station, Metafer 4. Results: Benign schwannomas (including the problematic variants as ancient, cellular, neuroblastoma like and multiplex schwannomas could be characterized by euploid‐polyploidisation and by their 4c peak height value which was usually more than 10% of total cell number measured. These characters were not found among neurofibromas and MPNST‐s. FISH analysis revealed and confirmed that the ‘normal’ euploid–polyploid cells are mainly eusomic–polysomic containing two, four, eight or sixteen signals for each chromosomes examined, but in a small proportion aneusomy was found among tumor cells of benign schwannomas (average: 2.58; range 1.33–3.44. In contrast, the atypical neurofibroma displayed marked aneusomy (18.44% but it contained normal eusomic and polysomic cells too. Two diploid MPNSTs proved to be clearly aneusomic with trisomy of chromosome 17 and monosomy of chromosome 18. Conclusions: All these data suggest that ploidy pattern determination combined with FISH analysis may be a very useful supplementary tool for making a right diagnosis (to differentiate benign versus malignant schwannomas in problematic variants and to understand better the malignant transformation in PNSTs.

  2. Combined fluorescent-chromogenic in situ hybridization for identification and laser microdissection of interphase chromosomes.

    Directory of Open Access Journals (Sweden)

    Nerea Paz

    Full Text Available Chromosome territories constitute the most conspicuous feature of nuclear architecture, and they exhibit non-random distribution patterns in the interphase nucleus. We observed that in cell nuclei from humans with Down Syndrome two chromosomes 21 frequently localize proximal to one another and distant from the third chromosome. To systematically investigate whether the proximally positioned chromosomes were always the same in all cells, we developed an approach consisting of sequential FISH and CISH combined with laser-microdissection of chromosomes from the interphase nucleus and followed by subsequent chromosome identification by microsatellite allele genotyping. This approach identified proximally positioned chromosomes from cultured cells, and the analysis showed that the identity of the chromosomes proximally positioned varies. However, the data suggest that there may be a tendency of the same chromosomes to be positioned close to each other in the interphase nucleus of trisomic cells. The protocol described here represents a powerful new method for genome analysis.

  3. Cloning, sequencing, and analysis of inv8 chromosome breakpoints associated with recombinant 8 syndrome.

    Science.gov (United States)

    Graw, S L; Sample, T; Bleskan, J; Sujansky, E; Patterson, D

    2000-03-01

    Rec8 syndrome (also known as "recombinant 8 syndrome" and "San Luis Valley syndrome") is a chromosomal disorder found in individuals of Hispanic descent with ancestry from the San Luis Valley of southern Colorado and northern New Mexico. Affected individuals typically have mental retardation, congenital heart defects, seizures, a characteristic facial appearance, and other manifestations. The recombinant chromosome is rec(8)dup(8q)inv(8)(p23.1q22.1), and is derived from a parental pericentric inversion, inv(8)(p23.1q22.1). Here we report on the cloning, sequencing, and characterization of the 8p23.1 and 8q22 breakpoints from the inversion 8 chromosome associated with Rec8 syndrome. Analysis of the breakpoint regions indicates that they are highly repetitive. Of 6 kb surrounding the 8p23.1 breakpoint, 75% consists of repetitive gene family members-including Alu, LINE, and LTR elements-and the inversion took place in a small single-copy region flanked by repetitive elements. Analysis of 3.7 kb surrounding the 8q22 breakpoint region reveals that it is 99% repetitive and contains multiple LTR elements, and that the 8q inversion site is within one of the LTR elements.

  4. Autosomal dominant familial spastic paraplegia; Linkage analysis and evidence for linkage to chromosome 2p

    Energy Technology Data Exchange (ETDEWEB)

    Figlewicz, D.A. [Univ. of Rochester, NY (United States); Dube, M.P.; Rouleau, G.A. [McGill Univ., Montreal (Canada)] [and others

    1994-09-01

    Familial spastic paraplegia (FSP) is a degenerative disorder of the motor system characterized by progressive weakness and spasticity of the lower limbs. Little is known about the pathophysiology of this disorder. FSP can be inherited as an autosomal dominant (AD), autosomal recessive, or X-linked trait. We have undertaken linkage analysis for a group of 36 AD FSP families from which we have collected blood samples from 427 individuals, including 148 affected individuals. Typing of polymorphic markers has allowed us to exclude more than 50% of the genome. Recently, linkage for AD FSP to a locus on chromosome 14q was reported. Our AD FSP kindreds were tested for linkage to markers spanning the 20 cM region between D14S69 and D14S66; however, we were not able to establish linkage for any of our families to chromosome 14. Lod scores suggestive of linkage for some AD FSP kindreds have been obtained for markers on chromosome 2p. We have tested seven polymorphic markers spanning the region between D2S405 and D2S177. Our highest aggregate lod score, including all families tested, was obtained at the locus D2S352: 2.4 at 20 cM. Results from HOMOG analysis for linkage heterogeneity will be reported.

  5. Molecular cloning and chromosomal localization of the human cyclin C (CCNC) and cyclin E (CCNE) genes: Deletion of the CCNC gene in human tumors

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haimin; Lahti, J.M.; Kidd, V.J. [St. Jude Children`s Research Hospital, Memphis, TN (United States)] [and others

    1996-03-01

    The human G1-phase cyclins are important regulators of cell cycle progression that interact with various cyclin-dependent kinases and facilitate entry into S-phase. We have confirmed the localization of the human cyclin C (CCNC) gene to chromosome 6q21 and of human cyclin E (CCNE to 19q12). The CCNC gene structure was also determined, and we have shown that it is deleted in a subset of acute lymphoblastic leukemias, including a patient sample containing a t(2;6)(p21;q15), with no apparent cytogenetic deletion. Single-strand conformational polymorphism analysis of the remaining CCNC allele from patients with a deletion of one allele established that there were no further mutations within the exons or the flanking intronic sequences. These results suggest either that haploinsufficiency of the cyclin C protein is sufficient to promote tumorigenesis or that the important tumor suppressor gene is linked to the CCNC locus. 48 refs., 4 figs., 1 tab.

  6. Molecular cloning and chromosomal localization of the nucleic acid sequences encoding the cerebrovascular and plaque amyloid peptide

    Energy Technology Data Exchange (ETDEWEB)

    Robakis, N.K.; Ramakrishna, N.; Wolfe, G.; Wisniewski, H.M.

    1987-05-01

    Amyloid deposits in vessels and neuritic plaques are found in large numbers in the brains of Alzheimer's Disease (AD) and adult Downs Syndrome (DS) patients. The partial amino acid sequence of the amyloid peptide has been determined. They used this amino acid sequence to synthesize an oligonucleotide probe specific for the amyloid peptide gene. Screening of a human brain cDNA library with this probe, yielded a clone which contained an insert 1.8 kb. This clone contains a long open reading frame including a region which encodes the 28 amino acids of the amyloid peptide. Northern blots of human brain mRNA detected a transcript of 3.3 kb long which hybridized to their cDNA clone. A similar mRNA was detected in the hamster, mouse, sheep and rabbit brains. Southern blots under stringent hybridization conditions detected sequences homologous to the amyloid gene in the genomes of hamster, mouse, sheep and rabbit suggesting that this gene has been conserved during mammalian evolution. Hybridization under reduced stringency revealed the presence of additional sequences related to the amyloid gene in the genome of the above organisms. Hybridization analysis of human x chinese hamster cell lines DNA showed that the gene encoding the amyloid peptide is located on chromosome 21, suggesting a genetic relationship between AD and DS.

  7. Refined localization of twenty-one genes in subregion p13.1 of human chromosome 1.

    Science.gov (United States)

    Chelala, C; Imbeaud, S; Devignes, M D; Zoorob, R; Auffray, C

    2001-01-01

    In this report, we describe a refinement of the human transcript map of chromosome 1p13.1, a subregion undergoing many aberrations in various types of human cancers. Publicly available genetic linkage, radiation hybrid and physical maps, as well as cytogenetic and sequence data were used to establish the relative order and orientation of ten known intragenic markers. The complete sequence of genomic clones of the region, available at the Sanger Centre, provided the tool for further studies performed by BLAST analysis against all cDNA sequences registered in the Genexpress Index2. This allowed us to assign to subband 1p13.1 nine of the ten known genes, an additional member of the gene family of one of these genes and eleven new transcripts. The remaining known gene and one additional new transcript map at the 1p13.1 and 1p13.2 boundary. The corresponding genes may be responsible for disorders related to this region. The resulting transcript map of 1p13.1 is presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/CARTO.

  8. Construction of BAC-based physical map and analysis of chromosome rearrangement in Chinese hamster ovary cell lines.

    Science.gov (United States)

    Cao, Yihua; Kimura, Shuichi; Itoi, Takayuki; Honda, Kohsuke; Ohtake, Hisao; Omasa, Takeshi

    2012-06-01

    Chinese hamster ovary (CHO) cells have frequently been used in biotechnology for many years as a mammalian host cell platform for cloning and expressing genes of interest. A detailed physical chromosomal map of the CHO DG44 cell line was constructed by fluorescence in situ hybridization (FISH) imaging using randomly selected 303 BAC clones as hybridization probes (BAC-FISH). The two longest chromosomes were completely paired chromosomes; other chromosomes were partly deleted or rearranged. The end sequences of 624 BAC clones, including 287 mapped BAC clones, were analyzed and 1,119 informative BAC end sequences were obtained. Among 303 mapped BAC clones, 185 clones were used for BAC-FISH analysis of CHO K1 chromosomes and 94 clones for primary Chinese hamster lung cells. Based on this constructed physical map and end sequences, the chromosome rearrangements between CHO DG44, CHO K1, and primary Chinese hamster cells were investigated. Among 20 CHO chromosomes, eight were conserved without large rearrangement in CHO DG44, CHO K1, and primary Chinese hamster cells. This result suggested that these chromosomes were stable and essential in CHO cells and supposedly conserved in other CHO cell lines.

  9. Patterns of association in the human metaphase complement: ring analysis and estimation of associativity of specific chromosome regions.

    Science.gov (United States)

    Rodman, T C; Flehinger, B J; Squire, R D

    1978-02-23

    The pattern of metaphase chromosome association in the human complement was studied by two methods of statistical analysis of interchromosomal distances. Those methods included ring analysis in which a characteristic position of the centromere of each chromosome relative to the center of a two dimensional representation of a metaphase complement was defined, and estimation of the capacity for associativity of each of three regions of each chromosome: the centromere (c) and the ends of each arm (p, q). The following information was obtained: 1. In general, the distance from the center is directly related to chromosome size. 2. The most notable deviation from that size-related progression is displayed by the X chromosomes. The markedly peripheral position of the X is characteristic of both X's of the female and the single X of the male. 3. The relative associativity of each chromosome of the complement is, in general, inversely related to size with an additional preferential capacity of associativity displayed by the acrocentric chromosomes. Analyses of the different inter-regional classes established that the supplementary associativity factor of the acrocentric chromosomes was inherent in their pericentromeric and p-arm regions and excluded the ends of the q arms from participation in that factor. 4. Those analyses demonstrated that the specific morphology or 'geometry' of the acrocentric chromosomes contributes little to their high relative associativity. In addition to the tendency for the c/p regions of the acrocentric chromosomes to associate with each other, presumably because of their common function in nucleolar organization, those regions also displayed a propensity to associate with the distal regions of the arms of other chromosomes. A molecular basis for that propensity other than that of ribosomal DNA is postulated to be that of other fractions of highly reiterated DNA sequences. 5. Analysis of the relative associativities of each of the three regions

  10. Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma.

    Science.gov (United States)

    Barra, Gustavo Barcelos; Santa Rita, Ticiane Henriques; Chianca, Camilla Figueiredo; Velasco, Lara Francielle Ribeiro; de Sousa, Claudia Ferreira; Nery, Lídia Freire Abdalla; Costa, Sandra Santana Soares

    2015-03-01

    The aim of this study is to determine the fetus Y-STR haplotype in maternal plasma during pregnancy and estimate, non-invasively, if the alleged father and fetus belong to the same male lineage. The study enrolled couples with singleton pregnancies and known paternity. All participants signed informed consent and the local ethics committee approved the study. Peripheral blood was collected in EDTA tubes (mother) and in FTA paper (father). Maternal plasma DNA was extracted by using NucliSens EasyMAG. Fetal gender was determined by qPCR targeting DYS-14 in maternal plasma and it was also confirmed after the delivery. From all included volunteers, the first consecutive 20 mothers bearing male fetuses and 10 mothers bearing female fetuses were selected for the Y-STR analysis. The median gestational age was 12 weeks (range 12-36). All DNA samples were subjected to PCR amplification by PowerPlex Y23, ampFLSTR Yfiler, and two in-house multiplexes, which together accounts for 27 different Y-STR. The PCR products were detected with 3500 Genetic Analyzer and they were analyzed using GeneMapper-IDX. Fetuses' haplotypes (Yfiler format) were compared to other 5328 Brazilian haplotypes available on Y-chromosome haplotypes reference database (YHRD). As a result, between 22 and 27 loci were successfully amplified from maternal plasma in all 20 cases of male fetuses. None of the women bearing female fetuses had a falsely amplified Y-STR haplotype. The haplotype detected in maternal plasma completely matched the alleged father haplotype in 16 out of the 20 cases. Four cases showed single mismatches and they did not configure exclusions; 1 case showed a mutation in the DYS 458 locus due to the loss of one repeat unit and 3 cases showed one DYS 385I/II locus dropout. All mismatches were confirmed after the delivery. Seventeen fetuses' haplotypes were not found in YHRD and one of them had a mutation, which corresponded to the paternity probability of 99.9812% and 95.7028%, respectively

  11. Analysis of premature centromere division (PCD) of the X chromosome in Alzheimer patients through the cell cycle.

    Science.gov (United States)

    Spremo-Potparevic, Biljana; Zivkovic, Lada; Djelic, Ninoslav; Bajic, Vladan

    2004-05-01

    Cytogenetic analysis of the X chromosome in phytohaemagglutinin stimulated peripheral blood lymphocytes was evaluated in 12 sporadic Alzheimer disease (AD) patients and in 11 healthy subjects. For chromosome analysis two methods were used: (1) standard analysis of G-banded metaphase chromosomes and; (2) fluorescent in situ hybridization (FISH) for the detection of the X chromosome centromeric region in interphase nuclei. Cytogenetic analysis revealed that the X chromosome expresses premature centromere division (PCD) in AD females in 10.53% of metaphase cells and in 15.22% of interphase nuclei. In AD men the percentages were 3.98 and 6.06%, respectively. X chromosome PCD in the female control group showed a percentage of 7.46% in metaphase cells and 9.35% in interphase nuclei and in male controls the percentages were 2.84% in metaphases and 5.54% in interphase nuclei. The results of FISH analysis showed that PCD could occur much earlier than metaphase of mitosis, i.e. in interphase of the cell cycle, immediately after replication. The FISH method can be used for PCD verification in all phases of the cell cycle in various disorders including AD.

  12. Local Component Analysis for Nonparametric Bayes Classifier

    CERN Document Server

    Khademi, Mahmoud; safayani, Meharn

    2010-01-01

    The decision boundaries of Bayes classifier are optimal because they lead to maximum probability of correct decision. It means if we knew the prior probabilities and the class-conditional densities, we could design a classifier which gives the lowest probability of error. However, in classification based on nonparametric density estimation methods such as Parzen windows, the decision regions depend on the choice of parameters such as window width. Moreover, these methods suffer from curse of dimensionality of the feature space and small sample size problem which severely restricts their practical applications. In this paper, we address these problems by introducing a novel dimension reduction and classification method based on local component analysis. In this method, by adopting an iterative cross-validation algorithm, we simultaneously estimate the optimal transformation matrices (for dimension reduction) and classifier parameters based on local information. The proposed method can classify the data with co...

  13. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    Science.gov (United States)

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  14. Localization of the homolog of a mouse craniofacial mutant to human chromosome 18q11 and evaluation of linkage to human CLP and CPO

    Energy Technology Data Exchange (ETDEWEB)

    Griffith, A.J.; Burgess, D.L.; Kohrman, D.C.; Yu, J. [Univ. of Michigan, Ann Arbor, MI (United States)] [and others

    1996-06-15

    The transgene-induced mutation 9257 and the spontaneous mutation twirler cause craniofacial and inner ear malformations and are located on mouse chromosome 18 near the ataxia locus ax. To map the human homolog of 9257, a probe from the transgene insertion site was used to screen a human genomic library. Analysis of a cross-hybridizing human clone identified a 3-kb conserved sequence block that does not appear to contain protein coding sequence. Analysis of somatic cell hybrid panels assigned the human locus to 18q11. The polymorphic microsatellite markers D18S1001 and D18S1002 were isolated from the human locus and mapped by linkage analysis using the CEPH pedigrees. The 9257 locus maps close to the centromeres of human chromosome 18q and mouse chromosome 18 at the proximal end of a conserved linkage group. To evaluate the role of this locus in human craniofacial disorders, linkage to D18S1002 was tested in 11 families with autosomal dominant nonsyndromic cleft lip and palate and 3 families with autosomal dominant cleft palate only. Obligatory recombinants were observed in 8 of the families, and negative lod scores from the other families indicated that these disorders are not linked to the chromosome 18 loci. 23 refs., 4 figs., 2 tabs.

  15. Cri-Du-Chat Syndrome: Clinical Profile and Chromosomal Microarray Analysis in Six Patients

    Directory of Open Access Journals (Sweden)

    Layla Damasceno Espirito Santo

    2016-01-01

    Full Text Available Cri-du-chat syndrome is a chromosomal disorder caused by a deletion of the short arm of chromosome 5. The disease severity, levels of intellectual and developmental delay, and patient prognosis have been related to the size and position of the deletion. Aiming to establish genotype-phenotype correlations, we applied array-CGH to evaluate six patients carrying cytogenetically detected deletions of the short arm of chromosome 5 who were followed at a genetics community service. The patients’ cytogenetic and clinical profiles were reevaluated. A database review was performed to predict additional genes and regulatory elements responsible for the characteristic phenotypic and behavioral traits of this disorder. Array-CGH analysis allowed for delineation of the terminal deletions, which ranged in size from approximately 11.2 Mb to 28.6 Mb, with breakpoints from 5p15.2 to 5p13. An additional dup(8(p23 (3.5 Mb, considered to be a benign copy number variation, was also observed in one patient. The correlation coefficient value (ρ=0.13 calculated indicated the presence of a weak relationship between developmental delay and deletion size. Genetic background, family history, epigenetic factors, quantitative trait locus polymorphisms, and environmental factors may also affect patient phenotype and must be taken into account in genotype-phenotype correlations.

  16. Genetic counseling for a prenatal diagnosis of structural chromosomal abnormality with high-resolution analysis using a single nucleotide polymorphism microarray

    Directory of Open Access Journals (Sweden)

    Akiko Takashima

    2016-08-01

    Full Text Available A 41-year old pregnant woman underwent amniocentesis to conduct a conventional karyotyping analysis; the analysis reported an abnormal karyotype: 46,XY,add(9(p24. Chromosomal microarray analysis (CMA is utilized in prenatal diagnoses. A single nucleotide polymorphism microarray revealed a male fetus with balanced chromosomal translocations on 9p and balanced chromosomal rearrangements, but another chromosomal abnormality was detected. The fetus had microduplication. The child was born as a phenotypically normal male. CMA is a simple and informative procedure for prenatal genetic diagnosis. CMA is the detection of chromosomal variants of unknown clinical significance; therefore, genetic counseling is important during prenatal genetic testing.

  17. Use of an intron length polymorphism to localize the tropoelastin gene to mouse Chromosome 5 in a region of linkage conservation with human Chromosome 7

    Energy Technology Data Exchange (ETDEWEB)

    Wydner, K.S.; Passmore, H.C. [Rutgers Univ., Piscataway, NJ (United States); Sechler, J.L.; Boyd, C.D. [UMDNJ-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)

    1994-09-01

    The complete coding sequence for mouse tropoelastin was obtained from overlapping reverse transcriptase polymerase chain reaction (PCR) amplimers. These cDNA fragments were derived from mouse tropoelastin mRNA using PCR oligomers complementary to conserved domains within rat tropoelastin mRNA. A comparison of coding domains of mouse and rat tropoelastin mRNA revealed a greater than 93% homology at the nucleotide level and over 96% similarity in the predicted amino acid sequence. PCR primers complementary to regions of the mouse tropoelastin mRNA were used to define a novel intron length polymorphism (ILP) within intron 8 of the mouse tropoelastin gene (Eln). This ILP proved to be informative in an intraspecific backcross in which genomic DNA samples from 75 backcross mice were used to map the tropoelastin gene to a position in the distal half of mouse chromosome 5. The linkage and genetic distances between Eln and the closest molecular markers used in this study are centromere-D5Mit95, D5Mit96-6.7 cM-Gus, Eln-4.0 cM-Zp3-telomere.

  18. Chromosome evolution in tiger beetles: Karyotypes and localization of 18S rDNA loci in Neotropical Megacephalini (Coleoptera, Cicindelidae

    Directory of Open Access Journals (Sweden)

    Sónia J.R. Proença

    2005-12-01

    Full Text Available Four Neotropical tiger beetle species, three from the genus Megacephala and one from the genus Oxycheila, currently assigned to the tribe Megacephalini were examined cytogenetically. All three Megacephala species showed simple sex chromosome systems of the X0/XX type but different numbers of autosomal pairs (15 in M. cruciata, 14 in M. sobrina and 12 in M. rutilans, while Oxycheila tristis was inferred to have a multiple sex chromosome system with four X chromosomes (2n = 24 + X1X2X3X4Y/X1X1X2X2X3X3X4X4. Fluorescence in situ hybridization (FISH using a PCR-amplified 18S rDNA fragment as a probe revealed the presence of rDNA clusters located exclusively on the autosomes in all the Megacephala species (five clusters in M. cruciata, eight in M. sobrina and three in M. rutilans, indicating variability in the number of clusters and the presence of structural polymorphisms. The same methodology showed that O. tristis had six rDNA clusters, apparently also located on the autosomes. Although our data also show cytogenetic variability within the genus Megacephala, our findings support the most accepted hypothesis for chromosome evolution in the family Cicindelidae. The description of multiple sex chromosomes in O. tristis along with phylogenetic analyses and larval morphological characters may be assumed as an additional evidence for the exclusion of the genus Oxycheila and related taxa from the tribe Megacephalini.

  19. Analysis of chromosome 22 deletions in neurofibromatosis type 2-related tumors

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, R.K.; Frazer, K.A.; Jackler, R.K.; Lanser, M.J.; Pitts, L.H.; Cox, D.R. (Univ. of California, San Francisco, CA (United States))

    1992-09-01

    The neurofibromatosis type 2 (NF2) gene has been hypothesized to be a recessive tumor suppressor, with mutations at the same locus on chromosome 22 that lead to NF2 also leading to sporadic tumors of the types seen in NF2. Flanking markers for this gene have previously been defined as D22S1 centromeric and D22S28 telomeric. Identification of subregions of this interval that are consistently rearranged in the NF2-related tumors would aid in better defining the disease locus. To this end, the authors have compared tumor and constitutional DNAs, isolated from 39 unrelated patients with sporadic and NF2-associated acoustic neuromas, meningiomas, schwannomas, and ependymomas, at eight polymorphic loci on chromosome 22. Two of the tumors studied revealed loss-of-heterozygosity patterns, which is consistent with the presence of chromosome 22 terminal deletions. By using additional polymorphic markers, the terminal deletion breakpoint found in one of the tumors, an acoustic neuroma from an NF2 patient, was mapped within the previously defined NF2 region. The breakpoint occurred between the haplotyped markers D22S41/D22S46 and D22S56. This finding redefines the proximal flanking marker and localizes the NF2 gene between markers D22S41/D22S46 and D22S28. In addition, the authors identified a sporadic acoustic neuroma that reveals a loss-of-heterozygosity pattern consistent with mitotic recombination or deletion and reduplication, which are mechanisms not previously seen in studies of these tumors. This finding, while inconsistent with models of tumorigenesis that invoke single deletions and their gene-dosage effects, lends further support to the recessive tumor-suppressor model. 33 refs., 2 figs., 1 tab.

  20. Undetected sex chromosome aneuploidy by chromosomal microarray.

    Science.gov (United States)

    Markus-Bustani, Keren; Yaron, Yuval; Goldstein, Myriam; Orr-Urtreger, Avi; Ben-Shachar, Shay

    2012-11-01

    We report on a case of a female fetus found to be mosaic for Turner syndrome (45,X) and trisomy X (47,XXX). Chromosomal microarray analysis (CMA) failed to detect the aneuploidy because of a normal average dosage of the X chromosome. This case represents an unusual instance in which CMA may not detect chromosomal aberrations. Such a possibility should be taken into consideration in similar cases where CMA is used in a clinical setting.

  1. Identification of novel RFLPs in the vicinity of CpG islands in Xq28: application to the analysis of the pattern of X chromosome inactivation.

    Science.gov (United States)

    Maestrini, E; Rivella, S; Tribioli, C; Rocchi, M; Camerino, G; Santachiara-Benerecetti, S; Parolini, O; Notarangelo, L D; Toniolo, D

    1992-01-01

    Probes for CpG islands were cloned from the distal long arm of the human X chromosome; three of them were found to be polymorphic. A HindIII RFLP was identified by the probe 2-25 (DXS606), and it was mapped to the Xq27-Xq28 boundary. Probes 2-19 (DXS605) and 2-55 (DXS707), which identify EcoRI and MspI polymorphisms, respectively, have been mapped to the distal part of Xq28, in the G6PD-RCP/GCP gene region. Probe 2-19 has been further localized about 16 kb from the 3' end of the G6PD gene. The new RFLPs may be useful for the precise mapping of the many disease genes localized in this part of the human X chromosome. Probe 2-19 is highly informative, and it has been studied in greater detail. Using the methylation-sensitive rare-cutter enzyme EagI in conjunction with the polymorphic EcoRI site, we were able to demonstrate that the RFLP may be used both to study randomness of X chromosome inactivation and for carrier detection in X-linked syndromes where nonrandom X inactivation occurs. It is conceivable that the combined use of 2-19 and of the probes described so far (pSPT-PGK and M27 beta) will make analysis of X inactivation feasible in virtually every female.

  2. Identification of novel RFLPs in the vicinity of CpG islands in Xq28: Application to the analysis of the pattern of X chromosome inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Camerino, G.; Santachiara-Benerecetti, S. (Univ. di Pavia (Italy)); Rocchi, M. (Univ. di Bari (Italy)); Parolini, O.; Notarangelo, L.D. (Univ. di Brecscia (Italy)); Maestrini, E.; Rivella, S.; Tribioli, C.; Toniolo, D.

    1992-01-01

    Probes of CpG islands were cloned from the distal long arm of the human X chromosome; three of them were found to be polymorphic. A HindIII RFLP was identified by the probe 2-25 (DXS606), and it was mapped to the Xq27-Xq28 boundary. Probes 2-19 (DXS605) and 2-55 (DXS707), which identify EcoRI and MspI polymorphisms, respectively, have been mapped to the distal part of Xq28, in the G6PD-RCP/GCP gene region. Probe 2-19 has been further localized about 16 kb from the 3{prime} end of the G6PD gene. The new RFLPs may be useful for the precise mapping of the many disease genes localized in this part of the human X chromosome. Using the methylation-sensitive rare-cutter enzyme EagI in conjunction with the polymorphic EcoRI site, the authors were able to demonstrate that the RFLP may be used both to study randomness of X chromosome inactivation and for carrier detection in X-linked syndromes where nonrandom X inactivation occurs. It is conceivable that the combined use of 2-19 and of the probes described so far (pSPT-PGK and M27{beta}) will make analysis of X inactivation feasible in virtually every female.

  3. Comparative analysis of clastogen-induced chromosome aberrations observed with light microscopy and by means of atomic force microscopy.

    Science.gov (United States)

    Koleva, Vanya Petrova; Dragoeva, Asya Pencheva; Andreeva, Andreana Ivanova; Burova, Marina Todorova; Georgiev, Sevdalin; Enchev, Dobromir Dimitrov

    2013-04-30

    Different types of chromosome aberration were observed in mouse bone-marrow cells after treatment with 4-bromo-N,N-diethyl-5,5-dimethyl-2,5-dihydro-1,2-oxaphosphol-2-amine 2-oxide (Br-oxaphosphole, Br-oxph) in a previous study. The aim of the present study is to perform a comparative analysis of these chromosomal damages observed with light microscopy (LM) and by means of atomic force microscopy (AFM). The kinds of aberrations scored by LM were substantially corrected by images at the ultrastructural level. The AFM analysis excluded 29.0% of gaps and 33.3% of fusion-type aberrations. On the other hand, AFM revealed the presence of aberrations that were not visible under the LM. This indicates that only AFM images would provide precise information about the real nature of chromosomal damages. The results of our study revealed that the 'real gaps' represented about 50% of all the gaps visible under LM. Excluded 'false gaps' were detected via AFM as breaks or decondensed chromosome regions. These results would support the statement that gaps must be included when testing genotoxicity. The ultrastructural analysis also confirmed the validity of using LM in the mouse bone-marrow chromosome aberration test, as a tool for detecting genotoxicity of chemicals in routine studies. When there is a need for precise evaluation of chromosome damage, only AFM images can provide information on specific genotoxic effects.

  4. Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens type A.

    Directory of Open Access Journals (Sweden)

    Päivi Lahti

    Full Text Available Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmental samples. Different tolerance to food processing conditions by the plasmid-borne and chromosomal cpe-carrying strains has been reported, but the reservoirs and contamination routes of enterotoxin-producing C. perfringens remain unknown. A comparative genomic hybridization (CGH analysis with a DNA microarray based on three C. perfringens type A genomes was conducted to shed light on the epidemiology of C. perfringens food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains by comparing chromosomal and plasmid-borne cpe-positive and cpe-negative C. perfringens isolates from human, animal, environmental, and food samples. The chromosomal and plasmid-borne cpe-positive C. perfringens genotypes formed two distinct clusters. Variable genes were involved with myo-inositol, ethanolamine and cellobiose metabolism, suggesting a new epidemiological model for C. perfringens food poisonings. The CGH results were complemented with growth studies, which demonstrated different myo-inositol, ethanolamine, and cellobiose metabolism between the chromosomal and plasmid-borne cpe-carrying strains. These findings support a ubiquitous occurrence of the plasmid-borne cpe-positive strains and their adaptation to the mammalian intestine, whereas the chromosomal cpe-positive strains appear to have a narrow niche in environments containing degrading plant material. Thus the epidemiology of the food poisonings caused by two populations appears different, the plasmid-borne cpe-positive strains probably contaminating foods via humans and the chromosomal strains being connected to plant material.

  5. Analysis of Y chromosome microdeletions and CFTR gene mutations as genetic markers of infertility in Serbian men

    Directory of Open Access Journals (Sweden)

    Dinić Jelena

    2007-01-01

    Full Text Available Background/Aim. Impaired fertility of a male partner is the main cause of infertility in up to one half of all infertile couples. At the genetic level, male infertility can be caused by chromosome aberrations or gene mutations. The presence and types of Y chromosome microdeletions and cystic fybrosis transmembrane conductance regulator (CFTR gene mutations as genetic cause of male infertility was tested in Serbian men. The aim of this study was to analyze CFTR gene mutations and Y chromosome microdelations as potential causes of male infertility in Serbian patients, as well as to test the hypothesis that CFTR mutations in infertile men are predominantly located in the several last exons of the gene. Methods. This study has encompassed 33 men with oligo- or azoospermia. The screening for Y chromosome microdeletions in the azoospermia factor (AZF region was performed by multiplex PCR analysis. The screening of the CFTR gene was performed by denaturing gradient gel electrophoresis (DGGE method. Results. Deletions on Y chromosome were detected in four patients, predominantly in AZFc region (four of total six deletions. Mutations in the CFTR gene were detected on eight out of 66 analyzed chromosomes of infertile men. The most common mutation was F508del (six of total eight mutations. Conclusion. This study confirmed that both Y chromosome microdeletions and CFTR gene mutations played important role in etiology of male infertility in Serbian infertile men. Genetic testing for Y chromosome microdeletions and CFTR gene mutations has been introduced in routine diagnostics and offered to couples undergoing assisted reproduction techniques. Considering that both the type of Y chromosome microdeletion and the type of CFTR mutation have a prognostic value, it is recommended that AZF and CFTR genotyping should not only be performed in patients with reduced sperm quality before undergoing assisted reproduction, but also for the purpose of preimplantation and

  6. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    Science.gov (United States)

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding.

  7. Enhancement of Local Climate Analysis Tool

    Science.gov (United States)

    Horsfall, F. M.; Timofeyeva, M. M.; Dutton, J.

    2012-12-01

    The National Oceanographic and Atmospheric Administration (NOAA) National Weather Service (NWS) will enhance its Local Climate Analysis Tool (LCAT) to incorporate specific capabilities to meet the needs of various users including energy, health, and other communities. LCAT is an online interactive tool that provides quick and easy access to climate data and allows users to conduct analyses at the local level such as time series analysis, trend analysis, compositing, correlation and regression techniques, with others to be incorporated as needed. LCAT uses principles of Artificial Intelligence in connecting human and computer perceptions on application of data and scientific techniques in multiprocessing simultaneous users' tasks. Future development includes expanding the type of data currently imported by LCAT (historical data at stations and climate divisions) to gridded reanalysis and General Circulation Model (GCM) data, which are available on global grids and thus will allow for climate studies to be conducted at international locations. We will describe ongoing activities to incorporate NOAA Climate Forecast System (CFS) reanalysis data (CFSR), NOAA model output data, including output from the National Multi Model Ensemble Prediction System (NMME) and longer term projection models, and plans to integrate LCAT into the Earth System Grid Federation (ESGF) and its protocols for accessing model output and observational data to ensure there is no redundancy in development of tools that facilitate scientific advancements and use of climate model information in applications. Validation and inter-comparison of forecast models will be included as part of the enhancement to LCAT. To ensure sustained development, we will investigate options for open sourcing LCAT development, in particular, through the University Corporation for Atmospheric Research (UCAR).

  8. Cytogenetic analysis of the Amazon stingless bee Melipona seminigra merrillae reveals different chromosome number for the genus

    Directory of Open Access Journals (Sweden)

    Izaura Bezerra Francini

    2011-10-01

    Full Text Available Cytogenetic analysis of the Amazon stingless bee Melipona seminigra merrillae, by conventional Giemsa staining and C-banding, revealed a different chromosome number for Melipona: 2n = 22 for females and diploid drones while the haploid drones present n = 11. There is no evidence of B chromosomes. This result contrasts with previous studies, in which the chromosome number of 19 Melipona species was determined as 2n = 18 for females and n = 9 for haploid males. Based on cytogenetic information available for other Melipona species, we propose that M. s. merrillae has a more derived diploid number. This indicates that chromosome number is not a conservative characteristic within the genus as previously thought. Cytogenetic data for stingless bees are scarce, especially in Amazon region. Additional studies will be very important in order to promote Melipona karyoevolution discussion and consequently a taxonomy review.

  9. Independent clonal origin of multiple uterine leiomyomas that was determined by X chromosome inactivation and microsatellite analysis

    DEFF Research Database (Denmark)

    Canevari, Renata A; Pontes, Anaglória; Rosa, Fabíola E;

    2005-01-01

    OBJECTIVE: In an attempt to clarify the clonality and genetic relationships that are involved in the tumorigenesis of uterine leiomyomas, we used a total of 43 multiple leiomyomas from 14 patients and analyzed the allelic status with 15 microsatellite markers and X chromosome inactivation analysis....... STUDY DESIGN: We have used a set of 15 microsatellite polymorphism markers mapped on 3q, 7p, 11, and 15q by automated analysis. The X chromosome inactivation was evaluated by the methylation status of the X-linked androgen receptor gene. RESULTS: Loss of heterozygosity analysis showed a different...... pattern in 7 of the 8 cases with allelic loss for at least 1 of 15 microsatellite markers that were analyzed. A similar loss of heterozygosity findings at 7p22-15 was detected in 3 samples from the same patient. X chromosome inactivation analysis demonstrated the same inactivated allele in all tumors...

  10. An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

    Science.gov (United States)

    Kayser, Manfred; Krawczak, Michael; Excoffier, Laurent; Dieltjes, Patrick; Corach, Daniel; Pascali, Vincente; Gehrig, Christian; Bernini, Luigi F.; Jespersen, Jørgen; Bakker, Egbert; Roewer, Lutz; de Knijff, Peter

    2001-01-01

    The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were .86–.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, ΦST statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure. PMID:11254455

  11. [CHL15--a new gene controlling the replication of chromosomes in saccharomycetes yeast: cloning, physical mapping, sequencing, and sequence analysis].

    Science.gov (United States)

    Kuprina, N Iu; Krol', E S; Koriabin, M Iu; Shestopalov, B V; Bliskovskiĭ, V V; Bannikov, V M; Gizatullin, R Z; Kirillov, A V; Kravtsov, V Iu; Zakhar'ev, V M

    1993-01-01

    We have analyzed the CHL15 gene, earlier identified in a screen for yeast mutants with increased loss of chromosome III and artificial circular and linear chromosomes in mitosis. Mutations in the CHL15 gene lead to a 100-fold increase in the rate of chromosome III loss per cell division and a 200-fold increase in the rate of marker homozygosis on this chromosome by mitotic recombination. Analysis of segregation of artificial circular minichromosome and artificially generated nonessential marker chromosome fragment indicated that sister chromatid loss (1:0 segregation) is a main reason of chromosome destabilization in the chl15-1 mutant. A genomic clone of CHL15 was isolated and used to map its physical position on chromosome XVI. Nucleotide sequence analysis of CHL15 revealed a 2.8-kb open reading frame with a 105-kD predicted protein sequence. At the N-terminal region of the protein sequences potentially able to form DNA-binding domains defined as zinc-fingers were found. The C-terminal region of the predicted protein displayed a similarity to sequence of regulatory proteins known as the helix-loop-helix (HLH) proteins. Data on partial deletion analysis suggest that the HLH domain is essential for the function of the CHL15 gene product. Analysis of the upstream untranslated region of CHL15 revealed the presence of the hexamer element, ACGCGT (an MluI restriction site) controlling both the periodic expression and coordinate regulation of the DNA synthesis genes in budding yeast. Deletion in the RAD52 gene, the product of which is involved in double-strand break/recombination repair and replication, leads to a considerable decrease in the growth rate of the chl15 mutant. We suggest that CHL15 is a new DNA synthesis gene in the yeast Saccharomyces cerevisiae.

  12. Proteomic analysis of human metaphase chromosomes reveals Topoisomerase II alpha as an Aurora B substrate

    DEFF Research Database (Denmark)

    Morrison, Ciaran; Henzing, Alexander J; Jensen, Ole Nørregaard;

    2002-01-01

    The essential Aurora B kinase is a chromosomal passenger protein that is required for mitotic chromosome alignment and segregation. Aurora B function is dependent on the chromosome passenger, INCENP. INCENP, in turn, requires sister chromatid cohesion for its appropriate behaviour. Relatively few...

  13. Analysis of the terminus region of the Caulobacter crescentus chromosome and identification of the dif site

    DEFF Research Database (Denmark)

    Jensen, Rasmus Bugge

    2006-01-01

    The terminus region of the Caulobacter crescentus chromosome and the dif chromosome dimer resolution site were characterized. The Caulobacter genome contains skewed sequences that abruptly switch strands at dif and may have roles in chromosome maintenance and segregation. Absence of dif or the Xer...

  14. Chromosomal localization of NDPK gene in Zhikong scallop Chlamys farreri using BAC-FISH%栉孔扇贝NDPK基因的BAC-FISH定位研究

    Institute of Scientific and Technical Information of China (English)

    黄超; 郇聘; 张晓军; 相建海

    2012-01-01

    栉孔扇贝(Chlamysfarreri)是我国北部沿海一个非常重要的养殖种类。核苷二磷酸激酶(NDPK)是一类广泛存在、高度保守,在细胞能量和信息传递中具有重要作用的酶。作者利用BAC-FISH技术将两个包含栉孔扇贝NDPK基因的BAC克隆定位到染色体同一位置上,该结果验证了物理图谱相关contig组装的可靠性,同时NDPK基因的染色体定位将对深入研究该基因的结构、功能以及应用于生产实践提供理论支撑。本研究结果将对栉孔扇贝染色体的深入研究以及染色体鉴别、图谱整合等工作提供重要参考。%Zhikong scallop(Chlamys farreri) is one of the most economically important aquaculture species in China. Using the technology of BAC-FISH, we localized the BAC clones containing NDPK gene in a pair of ho- mologous chromosomes. This result proved the reliability of the contig assembling of the C. farreri physical map, at the same time, the localization of NDPK gene in chromosome provided further support for research of structures, functions and the application of the gene. This research is the practice of localizing genes of low copies. The result will provide reference to further research and characterization of C farreri chromosomes, and will facilitate the integration of the physical map, linkage map and cytogenetics map of this species.

  15. Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.

    Science.gov (United States)

    Zilina, Olga; Teek, Rita; Tammur, Pille; Kuuse, Kati; Yakoreva, Maria; Vaidla, Eve; Mölter-Väär, Triin; Reimand, Tiia; Kurg, Ants; Ounap, Katrin

    2014-03-01

    Chromosomal microarray analysis (CMA) is now established as the first-tier cytogenetic diagnostic test for fast and accurate detection of chromosomal abnormalities in patients with developmental delay/intellectual disability (DD/ID), multiple congenital anomalies (MCA), and autism spectrum disorders (ASD). We present our experience with using CMA for postnatal and prenatal diagnosis in Estonian patients during 2009-2012. Since 2011, CMA is on the official service list of the Estonian Health Insurance Fund and is performed as the first-tier cytogenetic test for patients with DD/ID, MCA or ASD. A total of 1191 patients were analyzed, including postnatal (1072 [90%] patients and 59 [5%] family members) and prenatal referrals (60 [5%] fetuses). Abnormal results were reported in 298 (25%) patients, with a total of 351 findings (1-3 per individual): 147 (42%) deletions, 106 (30%) duplications, 89 (25%) long contiguous stretches of homozygosity (LCSH) events (>5 Mb), and nine (3%) aneuploidies. Of all findings, 143 (41%) were defined as pathogenic or likely pathogenic; for another 143 findings (41%), most of which were LCSH, the clinical significance remained unknown, while 61 (18%) reported findings can now be reclassified as benign or likely benign. Clinically relevant findings were detected in 126 (11%) patients. However, the proportion of variants of unknown clinical significance was quite high (41% of all findings). It seems that our ability to detect chromosomal abnormalities has far outpaced our ability to understand their role in disease. Thus, the interpretation of CMA findings remains a rather difficult task requiring a close collaboration between clinicians and cytogeneticists.

  16. Chromosomal localization of silkworm (Bombyx mori) sericin gene 1 and chymotrypsin inhibitor 13 using fluorescence in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    Yutaka; BANNO; Hiroshi; FUJII

    2008-01-01

    The chromosomal locations of two single-copy genes, Ser-1 and CI-13, in silkworm (Bombyx mori) were detected at the molecular cytogenetics level by fluorescence in situ hybridization in the study. The results showed that Ser-1 is located near the distal end of the 11th linkage group, relatively at the 12.5±1.4 position in pachytene; and that CI-13 has been mapped near the distal end of the 2nd linkage group, relatively at the 8.2±1.2 position in pachytene. Furthermore, their location model map-FISH map on silkworm chromosome was drawn. The FISH technique and its application to silkworm are also discussed in this paper.

  17. Chromosomal localization of silkworm (Bombyx mori) sericin gene 1 and chymotrypsin inhibitor 13 using fluorescence in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    SONG FangZhou; CHANG PingAn; ZHANG PingBo; YI FaPing; MA YongPing; LU Cheng; Yutaka BANNO; Hiroshi FUJII

    2008-01-01

    The chromosomal locations of two single-copy genes, Ser-1 and C1-13, in silkworm (Bombyx mori)were detected at the molecular cytogenetics level by fluorescence in situ hybridization in the study. The resuits showed that Ser-1 is located near the distal end of the 11th linkage group, relatively st the 12.5±1.4position in pachytene; and that C1-13 has been mapped near the distal end of the 2nd linkage group,relatively at the 8.2±1.2 position in pachytene. Furthermore, their location model map-FISH map on silkworm chromosome was drawn. The FISH technique and its application to silkworm are also discussed in this paper.

  18. Bacterial chromosome segregation.

    Science.gov (United States)

    Possoz, Christophe; Junier, Ivan; Espeli, Olivier

    2012-01-01

    Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with model organisms: Escherichia coli, Bacillus subtilis, Caulobacter crescentus and Vibrio cholerae. We describe the global positionning of the nucleoid in the cell and the specific localization and dynamics of different chromosomal loci, kinetic and biophysic aspects of chromosome segregation are presented. Finally, a presentation of the key proteins involved in the chromosome segregation is made.

  19. Rat phenol-preferring sulfotransferase genes (Stp and Stp2): Localization to mouse chromosomes 7 and 17

    Energy Technology Data Exchange (ETDEWEB)

    Khan, A.S.; Taylor, B.R.; Ringer, D.P. [Oklahoma Medical Research Foundation, Oklahoma City, OK (United States)] [and others

    1995-03-20

    The phenol-preferring sulfotransferases aryl sulfo-transferase IV and N-hydroxyarylamine sulfotransferase catalyze sulfate conjugation of N-hydroxy-2-acetylaminofluorene, a metabolite capable of causing hepatocarcinogenesis in rats. We utilized published cDNA sequences of these sulfotransferases to type the progeny of two multilocus crosses and determined that the genes, aryl sulfotransferase (Stp) and N-hydroxyarylamine sulfotransferase (Stp2), map to positions on mouse chromosomes 7 and 17. 19 refs., 1 fig.

  20. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

    Directory of Open Access Journals (Sweden)

    Zhihao Ding

    2014-11-01

    Full Text Available Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.

  1. Characterization of a new aberration of the human Y chromosome by banding methods and DNA restriction endonuclease analysis.

    Science.gov (United States)

    Schmid, M; Gall, H; Schempp, W; Weber, L; Schmidtke, J

    1981-01-01

    Comparative cytogenetic analyses were performed with ten different banding methods on a previously undescribed, inherited structural aberration of a Y chromosome, and the results compared with those of normal Y chromosomes occurring in the same family. The value of the individual staining techniques in investigations of Y chromosomal aberrations is emphasized. The aberrant Y chromosome analyzed can be formally derived from an isodicentric Y chromosome for the short arm with a very terminal long-arm breakpoint, in which the centromere, an entire short arm, and the proximal region on one long arm was lost. This interpretation was confirmed by determining the amount of the two Y-specific DNA sequences (2.1 and 3.4 kb in length) by means of Hae III restriction endonuclease analysis. The karyotype-phenotype correlations in the men with this aberrant Y chromosome, especially the fertility dysfunctions (oligoasthenoteratozoospermia, cryptozoospermia), are discussed. The possibility of the existence of fertility factors involved in the control of spermatogenesis within the quinacrine-bright heterochromatic region of the Y long arm is presented.

  2. mBAND Analysis of Late Chromosome Aberrations in Human Lymphocytes Induced by Gamma Rays and Fe Ions

    Science.gov (United States)

    Sunagawa, Mayumi; Zhang, Ye; Yeshitla, Samrawit; Kadhim, Munira; Wilson, Bobby; Wu, Honglu

    2014-01-01

    Chromosomal translocations and inversions are considered stable, and cells containing these types of chromosome aberrations can survive multiple cell divisions. An efficient method to detect an inversion is multi-color banding fluorescent in situ hybridization (mBAND) which allows identification of both inter- and intrachromosome aberrations simultaneously. Post irradiation, chromosome aberrations may also arise after multiple cell divisions as a result of genomic instability. To investigate the stable or late-arising chromosome aberrations induced after radiation exposure, we exposed human lymphocytes to gamma rays and Fe ions ex vivo, and cultured the cells for multiple generations. Chromosome aberrations were analyzed in cells collected at first mitosis and at several time intervals during the culture period post irradiation. With gamma irradiation, about half of the damages observed at first mitosis remained after 7 day- and 14 day- culture, suggesting the transmissibility of damages to the surviving progeny. Detailed analysis of chromosome break ends participating in exchanges revealed a greater fraction of break ends involved in intrachromosome aberrations in the 7- and 14-day samples in comparison to the fraction at first mitosis. In particular, simple inversions were found at 7 and 14 days, but not at the first mitosis, suggesting that some of the aberrations might be formed days post irradiation. In contrast, at the doses that produced similar frequencies of gamma-induced chromosome aberrations as observed at first mitosis, a significantly lower yield of aberrations remained at the same population doublings after Fe ion exposure. At these equitoxic doses, more complex type aberrations were observed for Fe ions, indicating that Fe ion-induced initial chromosome damages are more severe and may lead to cell death. Comparison between low and high doses of Fe ion irradiation in the induction of late damages will also be discussed.

  3. Chromosome segregation analysis in human embryos obtained from couples involving male carriers of reciprocal or Robertsonian translocation.

    Directory of Open Access Journals (Sweden)

    Ahmet Yilmaz

    Full Text Available The objective of this study was to investigate the frequency and type of chromosome segregation patterns in cleavage stage embryos obtained from male carriers of Robertsonian (ROB and reciprocal (REC translocations undergoing preimplantation genetic diagnosis (PGD at our reproductive center. We used FISH to analyze chromosome segregation in 308 day 3 cleavage stage embryos obtained from 26 patients. The percentage of embryos consistent with normal or balanced segregation (55.1% vs. 27.1% and clinical pregnancy (62.5% vs. 19.2% rates were higher in ROB than the REC translocation carriers. Involvement of non-acrocentric chromosome(s or terminal breakpoint(s in reciprocal translocations was associated with an increase in the percent of embryos consistent with adjacent 1 but with a decrease in 3∶1 segregation. Similar results were obtained in the analysis of nontransferred embryos donated for research. 3∶1 segregation was the most frequent segregation type in both day 3 (31% and spare (35% embryos obtained from carriers of t(11;22(q23;q11, the only non-random REC with the same breakpoint reported in a large number of unrelated families mainly identified by the birth of a child with derivative chromosome 22. These results suggest that chromosome segregation patterns in day 3 and nontransferred embryos obtained from male translocation carriers vary with the type of translocation and involvement of acrocentric chromosome(s or terminal breakpoint(s. These results should be helpful in estimating reproductive success in translocation carriers undergoing PGD.

  4. The human glia maturation factor-gamma gene: genomic structure and mutation analysis in gliomas with chromosome 19q loss.

    Science.gov (United States)

    Peters, N; Smith, J S; Tachibana, I; Lee, H K; Pohl, U; Portier, B P; Louis, D N; Jenkins, R B

    1999-09-01

    Human glia maturation factor-gamma (hGMF-gamma) is a recently identified gene that may be involved in glial differentiation, neural regeneration, and inhibition of tumor cell proliferation. The gene maps to the long arm of chromosome 19 at band q13.2, a region that is frequently deleted in human malignant gliomas and is thus suspected to harbor a glioma tumor suppressor gene. Given the putative role of hGMF-gamma in cell differentiation and proliferation and its localization to chromosome 19q13, this gene is an interesting candidate for the chromosome 19q glioma tumor suppressor gene. To evaluate this possibility, we determined the genomic structure of human hGMF-gamma and performed mutation screening in a series of 41 gliomas with and without allelic loss of chromosome 19q. Mutations were not detected, which suggests that hGMF-gamma is not the chromosome 19q glioma suppressor gene. However, the elucidation of the genomic structure of hGMF-gamma may prove useful in future investigations of hGMF-gamma in the normal adult and developing human nervous system.

  5. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species.

    Science.gov (United States)

    Wang, Xueying; Walton, Jay R; Parshad, Rana D; Storey, Katie; Boggess, May

    2014-06-01

    The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we analyze the dynamical system model of the TYC strategy, with the aim of studying the viability of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped after some time? Can the invasive species recover? To answer that question, we perform a rigorous bifurcation analysis and study the basin of attraction of the recovery state and the extinction state in both the full model and a certain reduced model. In particular, we find a theoretical condition for the eradication strategy to work. Additionally, the consideration of an Allee effect and the possibility of a Turing instability are also studied in this work. Our results show that: (1) with the inclusion of an Allee effect, the number of the invasive females is not required to be very low when the introduction of the sex-reversed trojan females is stopped, and the remaining Trojan Y-Chromosome population is sufficient to induce extinction of the invasive females; (2) incorporating diffusive spatial spread does not produce a Turing instability, which would have suggested that the TYC eradication strategy might be only partially effective, leaving a patchy distribution of the invasive species.

  6. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species

    KAUST Repository

    Wang, Xueying

    2013-05-24

    The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we analyze the dynamical system model of the TYC strategy, with the aim of studying the viability of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped after some time? Can the invasive species recover? To answer that question, we perform a rigorous bifurcation analysis and study the basin of attraction of the recovery state and the extinction state in both the full model and a certain reduced model. In particular, we find a theoretical condition for the eradication strategy to work. Additionally, the consideration of an Allee effect and the possibility of a Turing instability are also studied in this work. Our results show that: (1) with the inclusion of an Allee effect, the number of the invasive females is not required to be very low when the introduction of the sex-reversed trojan females is stopped, and the remaining Trojan Y-Chromosome population is sufficient to induce extinction of the invasive females; (2) incorporating diffusive spatial spread does not produce a Turing instability, which would have suggested that the TYC eradication strategy might be only partially effective, leaving a patchy distribution of the invasive species. © 2013 Springer-Verlag Berlin Heidelberg.

  7. [Analysis of chromosome composition in interspecific embryonic stem hybrid cells of mice].

    Science.gov (United States)

    Pristiazhniuk, I E; Matveeva, N M; Grafodatskiĭ, A S; Serdiukova, N A; Serov, O L

    2010-01-01

    Chromosome complements of twenty hybrid clones obtained by fusion of Mus musculus embryonic stem cells (ESC) and M. caroli splenocytes were studied. Using of double-color in situ hybridization with chromosome- and species-specific probes we were able to detect the parental origin for each chromosome in hybrid cells. Based on parental chromosome ratio, all 20 hybrid clones were separated in some different groups: from the group containing practically tetraploid M. musculus genome with single M. caroli chromosomes to hybrids with dominance of M. caroli chromosome homologues. In 8 hybrid cells clones we observed prevalence of chromosomes originated from ESC in ratio from 5:1 to 3:1. Another hybrid cells clones have either equal (1:1, 1:2) ratio of M. musculus to M. caroli chromosomes or with the prevalence of ESC- (2:1) or splenocyte- (1:2) originated parental chromosome homologues. In 3 hybrid cells clones, we observed preferable segregation of ESC-originated pluripotent chromosomes. This phenomenon was found for the first time and it possibly indicates compensation of the epigenetic differences between parental chromosomes of ESC- and splenocyte-origination.

  8. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

    Directory of Open Access Journals (Sweden)

    Bruggmann Rémy

    2007-05-01

    Full Text Available Abstract Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL. To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions

  9. Chromosome Mapping, Expression and Polymorphism Analysis of CRABP1 Gene in Pigs

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shuan-ping; TANG Zhong-lin; ZHOU Rong; QU Chang-qing; ZHENG Jian-wei; LI Kui

    2014-01-01

    Cellular retinoic acid-binding protein 1 (CRABP1) is a well-conserved member of cytosolic lipid-binding protein family. It is an important modulator of retinoic acid signaling. Long serial analysis of gene expression (LongSAGE) analysis suggested that CRABP1 gene was differentially expressed during prenatal skeletal muscle development in porcine. Here, we obtained the full-length coding region sequence and genomic sequence of the porcine CRABP1 gene and analyzed its genomic structures. Subsequently, we examined CRABP1 chromosome assignment using INRA-University of Minnesota 7 000 porcine radiation hybrid panel (IMpRH) and explored its tissue distribution in adult Tongcheng pigs and dynamical expression proifles in prenatal skeletal muscle (33, 65 and 90 days post coitus, dpc) from Landrace (lean-type) (described as L33, L65 and L90) and Tongcheng pigs (obese-type) (described as T33, T65 and T90). The CRABP1 gene was mapped to chromosome 7q11-q23 and closely linked to the microsatellite marker SWR1928. Quantitative real-time PCR showed that CRABP1 mRNA was highly expressed in lung and stomach, moderately expressed in placenta and uterus, and weakly expressed in other tissues. Moreover, CRABP1 gene was down-regulated during prenatal skeletal muscle development in both Landrace and Tongcheng pigs and it was expressed much higher in T33 than L33. Two single-nucleotide polymorphisms (SNPs) were detected by sequencing and mass spectrometry methods, allele frequency analysis indicated that g. 281 (G>A) and g. 2992 (G>A) were deviated from Hardy-Weinberg equilibrium in the Landrace and DLY (Duroc×(Landrace×Yorkshire)) pig breeds.

  10. High-Throughput Live-Cell Microscopy Analysis of Association Between Chromosome Domains and the Nucleolus in S. cerevisiae.

    Science.gov (United States)

    Wang, Renjie; Normand, Christophe; Gadal, Olivier

    2016-01-01

    Spatial organization of the genome has important impacts on all aspects of chromosome biology, including transcription, replication, and DNA repair. Frequent interactions of some chromosome domains with specific nuclear compartments, such as the nucleolus, are now well documented using genome-scale methods. However, direct measurement of distance and interaction frequency between loci requires microscopic observation of specific genomic domains and the nucleolus, followed by image analysis to allow quantification. The fluorescent repressor operator system (FROS) is an invaluable method to fluorescently tag DNA sequences and investigate chromosome position and dynamics in living cells. This chapter describes a combination of methods to define motion and region of confinement of a locus relative to the nucleolus in cell's nucleus, from fluorescence acquisition to automated image analysis using two dedicated pipelines.

  11. Chromosome region-specific libraries for human genome analysis. Final progress report, 1 March 1991--28 February 1994

    Energy Technology Data Exchange (ETDEWEB)

    Kao, F.T.

    1994-04-01

    The objectives of this grant proposal include (1) development of a chromosome microdissection and PCR-mediated microcloning technology, (2) application of this microtechnology to the construction of region-specific libraries for human genome analysis. During this grant period, the authors have successfully developed this microtechnology and have applied it to the construction of microdissection libraries for the following chromosome regions: a whole chromosome 21 (21E), 2 region-specific libraries for the long arm of chromosome 2, 2q35-q37 (2Q1) and 2q33-q35 (2Q2), and 4 region-specific libraries for the entire short arm of chromosome 2, 2p23-p25 (2P1), 2p21-p23 (2P2), 2p14-p16 (wP3) and 2p11-p13 (2P4). In addition, 20--40 unique sequence microclones have been isolated and characterized for genomic studies. These region-specific libraries and the single-copy microclones from the library have been used as valuable resources for (1) isolating microsatellite probes in linkage analysis to further refine the disease locus; (2) isolating corresponding clones with large inserts, e.g. YAC, BAC, P1, cosmid and phage, to facilitate construction of contigs for high resolution physical mapping; and (3) isolating region-specific cDNA clones for use as candidate genes. These libraries are being deposited in the American Type Culture Collection (ATCC) for general distribution.

  12. Vibrio chromosomes share common history

    Directory of Open Access Journals (Sweden)

    Gevers Dirk

    2010-05-01

    Full Text Available Abstract Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history. Conclusions Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA for one chromosome to be applied equally to both chromosomes.

  13. Marker chromosomes.

    Science.gov (United States)

    Rao, Kiran Prabhaker; Belogolovkin, Victoria

    2013-04-01

    Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

  14. Exploration of Shape Variation Using Localized Components Analysis

    OpenAIRE

    Alcantara, Dan A; Carmichael, Owen; Harcourt-Smith, Will; Sterner, Kirstin; Frost, Stephen R.; Dutton, Rebecca; Thompson, Paul; Delson, Eric; Amenta, Nina

    2009-01-01

    Localized Components Analysis (LoCA) is a new method for describing surface shape variation in an ensemble of objects using a linear subspace of spatially localized shape components. In contrast to earlier methods, LoCA optimizes explicitly for localized components and allows a flexible trade-off between localized and concise representations, and the formulation of locality is flexible enough to incorporate properties such as symmetry. This paper demonstrates that LoCA can provide intuitive p...

  15. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases.

    Directory of Open Access Journals (Sweden)

    Xinyan Lu

    Full Text Available BACKGROUND: Array Comparative Genomic Hybridization (a-CGH is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA. METHODS AND FINDINGS: CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5% of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872 with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524 abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS: This large set of clinical results demonstrates the significantly improved sensitivity

  16. Genomic organization and chromosomal localization of the human and mouse genes encoding the alpha receptor component for ciliary neurotrophic factor.

    Science.gov (United States)

    Valenzuela, D M; Rojas, E; Le Beau, M M; Espinosa, R; Brannan, C I; McClain, J; Masiakowski, P; Ip, N Y; Copeland, N G; Jenkins, N A

    1995-01-01

    Ciliary neurotrophic factor (CNTF) has recently been found to share receptor components with, and to be structurally related to, a family of broadly acting cytokines, including interleukin-6, leukemia inhibitory factor, and oncostatin M. However, the CNTF receptor complex also includes a CNTF-specific component known as CNTF receptor alpha (CNTFR alpha). Here we describe the molecular cloning of the human and mouse genes encoding CNTFR. We report that the human and mouse genes have an identical intron-exon structure that correlates well with the domain structure of CNTFR alpha. That is, the signal peptide and the immunoglobulin-like domain are each encoded by single exons, the cytokine receptor-like domain is distributed among 4 exons, and the C-terminal glycosyl phosphatidylinositol recognition domain is encoded by the final coding exon. The position of the introns within the cytokine receptor-like domain corresponds to those found in other members of the cytokine receptor superfamily. Confirming a recent study using radiation hybrids, we have also mapped the human CNTFR gene to chromosome band 9p13 and the mouse gene to a syntenic region of chromosome 4.

  17. Cloning of the VASP (Vasodilator-Stimulated Phosphoprotein) genes in human and mouse: Structure, sequence, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Zimmer, M.; Fischer, L.; Hauser, W. [Medizinische Universitaetsklinik, Wuerzburg (Germany)] [and others

    1996-09-01

    The genes encoding the vasodilator-stimulated phosphoprotein (VASP) in human and mouse were isolated, and major parts were sequenced. In both species the gene is composed of 13 exons with conserved exon-intron positions. The mouse VASP cDNA sequence was deduced from the genomic sequence. The predicted amino acid sequence is 89% identical to the human protein. The high nucleotide sequence homology extends not only over the coding regions but also into the 3{prime}-UTRs, indicating a possible function in mRNA targeting or regulation of translation. Prominent 5{prime} CpG islands including multiple SP1 sites indicate a housekeeping function of VASP. Using cosmid DNA as a probe for fluorescence in situ hybridization, the human VASP gene was assigned to chromosome 19q13.2-q13.3, an extended region with homology to mouse chromosome 7. A sequence overlap of the VASP 5{prime}-region with the telomeric end of a cosmid contig physically links the VASP gene with ERCC1. VASP is located about 92 kb distal to ERCC1 and about 300 kb proximal to the myotonic dystrophy protein kinase gene. 43 refs., 6 figs.

  18. Co-Localization of Somatic and Meiotic Double Strand Breaks Near the Myc Oncogene on Mouse Chromosome 15

    Science.gov (United States)

    Ng, Siemon H.; Maas, Sarah A.; Petkov, Petko M.; Mills, Kevin D.; Paigen, Kenneth

    2010-01-01

    Both somatic and meiotic recombinations involve the repair of DNA double strand breaks (DSBs) that occur at preferred locations in the genome. Improper repair of DSBs during either mitosis or meiosis can lead to mutations, chromosomal aberration such as translocations, cancer and/or cell death. Currently, no model exists that explains the locations of either spontaneous somatic DSBs or programmed meiotic DSBs or relates them to each other. One common class of tumorigenic translocations arising from DSBs is chromosomal rearrangements near the Myc oncogene. Myc translocations have been associated with Burkitt lymphoma in humans, plasmacytoma in mice and immunocytoma in rats. Comparing the locations of somatic and meiotic DSBs near the mouse Myc oncogene, we demonstrated that the placement of these DSBs is not random and that both events clustered in the same short discrete region of the genome. Our work shows that both somatic and meiotic DSBs tend to occur in proximity to each other within the Myc region, suggesting that they share common originating features. It is likely that some regions of the genome are more susceptible to both somatic and meiotic DSBs, and the locations of meiotic hotspots may be an indicator of genomic regions more susceptible to DNA damage. PMID:19603522

  19. Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4.

    Science.gov (United States)

    Silva, K M; Bastiaansen, J W M; Knol, E F; Merks, J W M; Lopes, P S; Guimarães, S E F; van Arendonk, J A M

    2011-06-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.

  20. A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data

    OpenAIRE

    Emmert-Streib, Frank; de Matos Simoes, Ricardo; Tripathi, Shailesh; Glazko, Galina V.; Dehmer, Matthias

    2012-01-01

    In this paper, we present a Bayesian approach to estimate a chromosome and a disorder network from the Online Mendelian Inheritance in Man (OMIM) database. In contrast to other approaches, we obtain statistic rather than deterministic networks enabling a parametric control in the uncertainty of the underlying disorder-disease gene associations contained in the OMIM, on which the networks are based. From a structural investigation of the chromosome network, we identify three chromosome subgrou...

  1. High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis

    DEFF Research Database (Denmark)

    Bosch, Elena; Calafell, Francesc; Rosser, Zoë H;

    2003-01-01

    settlers from Iceland, who may have been assimilated 500 years ago, and the Danish-Norwegian colonists of the eighteenth century. Insufficient differentiation between modern Icelandic and Danish Y chromosomes means that a choice between these cannot be made on the basis of diversity analysis. However...

  2. Clinical utility of chromosomal microarray analysis of DNA from buccal cells: detection of mosaicism in three patients.

    Science.gov (United States)

    Sdano, Mallory R; Vanzo, Rena J; Martin, Megan M; Baldwin, Erin E; South, Sarah T; Rope, Alan F; Allen, William P; Kearney, Hutton

    2014-12-01

    Mosaic chromosomal abnormalities are relatively common. However, mosaicism may be missed due to multiple factors including failure to recognize clinical indications and order appropriate testing, technical limitations of diagnostic assays, or sampling tissue (s) in which mosaicism is either not present, or present at very low levels. Blood leukocytes have long been the "gold standard" sample for cytogenetic analysis; however, the culturing process for routine chromosome analysis can complicate detection of mosaicism since the normal cell line may have a growth advantage in culture, or may not be present in the cells that produce metaphases (the lymphocytes). Buccal cells are becoming increasingly utilized for clinical analyses and are proving to have many advantages. Buccal swabs allow for simple and noninvasive DNA collection. When coupled with a chromosomal microarray that contains single nucleotide polymorphic probes, analysis of buccal cells can maximize a clinician's opportunity to detect cytogenetic mosaicism. We present three cases of improved diagnosis of mosaic aberrations using buccal specimens for chromosomal microarray analysis. In each case, the aberration was either undetectable in blood or present at such a low level it likely could have gone undetected. These cases highlight the limitations of certain laboratory methodologies for identifying mosaicism. We also present practice implications for genetic counselors, including clinic workflow changes and counseling approaches based on increasing use of buccal samples.

  3. Chromosome painting reveals asynaptic full alignment of homologs and HIM-8-dependent remodeling of X chromosome territories during Caenorhabditis elegans meiosis.

    Directory of Open Access Journals (Sweden)

    Kentaro Nabeshima

    2011-08-01

    Full Text Available During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs with mobile patches of the nuclear envelope (NE-spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners.

  4. Amplification, analysis and chromosome mapping of novel homeobox-containing and homeobox-flanking sequences in rice

    Institute of Scientific and Technical Information of China (English)

    刘国振; 严长杰; 翟文学; 何平; 杨江; 李小兵; 朱立煌

    1999-01-01

    Homeobox genes, widely distributed among animal and plant kingdoms, play an important role in developmental process. Several homeobox conserved fragments were amplified by PCR and the flanking regions were also obtained by an LM-PCR procedure. Sequencing and Southern analysis showed that they belong to a homeobox gene family of rice. Six homeobox-containing fragments were mapped on the molecular linkage map of rice. They were located on chromosomes 3, 4 and 7 respectively. It is noteworthy that there are 4 homeobox fragments located on rice chromosome 3 and the result is also consistent with the comparative genomics between rice and maize.

  5. Clastogenic effects of known and suspect spindle poisons studied by chromosome analysis in mouse bone marrow cells.

    Science.gov (United States)

    Xu, W; Adler, I D

    1990-07-01

    The present study was performed within the project 'Genomic Mutations' (sponsored by the Commission of the European Communities) in order to gather all possible experimental information on 10 chemicals selected on the basis of their possible capacity to induce aneuploidy. An analysis of chromosomal aberrations was carried out in bone marrow cells of mice with the first five chemicals: colchicine (COL), econazole (EZ), chloralhydrate (CH), hydroquinone (HQ) and diazepam (DIAZ). The experiments were performed in parallel to micronucleus tests with the objective to distinguish a positive micronucleus response due to chromosomal breakage from that obtained by lagging chromosomes. The results of the micronucleus tests will be reported elsewhere. COL, CH, EZ and DIAZ showed no clastogenic effects in mouse bone marrow cells after single intraperitoneal injection. Polyploid cells were significantly more frequent after COL treatment. HQ showed a dose-dependent induction of chromosomal aberrations at 6 and 24 h after treatment. After 24 h, cells with multiple aberrations up to complete chromosome fragmentation were frequently observed. They indicate that a small fraction of the cell population, probably related to a specific stage of the cell cycle, was particularly sensitive to HQ. A sex difference in clastogenic response to HQ was not observed. It is concluded that of the five chemicals tested only HQ was clastogenic in mouse bone marrow cells under the present experimental conditions.

  6. Chromosomal instability in meningiomas.

    Science.gov (United States)

    van Tilborg, Angela A G; Al Allak, Bushra; Velthuizen, Sandra C J M; de Vries, Annie; Kros, Johan M; Avezaat, Cees J J; de Klein, Annelies; Beverloo, H Berna; Zwarthoff, Ellen C

    2005-04-01

    Approximately 60% of sporadic meningiomas are caused by inactivation of the NF2 tumor suppressor gene on chromosome 22. No causative gene is known for the remaining 40%. Cytogenetic analysis shows that meningiomas caused by inactivation of the NF2 gene can be divided into tumors that show monosomy 22 as the sole abnormality and tumors with a more complex karyotype. Meningiomas not caused by the NF2 gene usually have a diploid karyotype. Here we report that, besides the clonal chromosomal aberrations, the chromosome numbers in many meningiomas varied from one metaphase spread to the other, a feature that is indicative of chromosomal instability. Unexpectedly and regardless of genotype, a subgroup of tumors was observed with an average number of 44.9 chromosomes and little variation in the number of chromosomes per metaphase spread. In addition, a second subgroup was recognized with a hyperdiploid number of chromosomes (average 48.5) and considerable variation in numbers per metaphase. However, this numerical instability resulted in a clonal karyotype with chromosomal gains and losses in addition to loss of chromosome 22 only in meningiomas caused by inactivation of the NF2 gene. In cultured cells of all tumor groups, bi- and multinucleated cells were seen, as well as anaphase bridges, residual chromatid strings, multiple spindle poles, and unseparated chromatids, suggesting defects in the mitotic apparatus or kinetochore. Thus, we conclude that even a benign and slow-growing tumor like a meningioma displays chromosomal instability.

  7. High resolution chromosome analysis and fluorescence in situ hybridization in patients referred for Prader-Willi or Angelman syndrome

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-08

    Laboratory testing is helpful in the evaluation of patients suspected to have either Prader-Willi syndrome (PWS) or Angelman syndrome (AS) because most of the patients have recognizable cytogenetic deletions of 15q11q13. Maternal uniparental disomy of chromosome 15, identified by molecular genetic techniques, is found in about 20 to 25% of PWS patients. Paternal uniparental disomy of chromosome 15 is seen in 2 to 3% of AS patients. Thus, PWS and AS represent the first examples in humans of genetic imprinting or the differential expression of genetic information depending on the parental origin. Herein, I report our experience with FISH and high resolution chromosome analysis in patients referred to confirm or rule out PWS or AS. 10 refs., 1 tab.

  8. Local Data Libraries for Quantitative Political Analysis.

    Science.gov (United States)

    Tanenbaum, Eric

    1979-01-01

    Considers several systems automating local departmental-based data facilities. Describes design and implementation of a simple system. Concludes by reflecting on changes needed in the system. (Author/CK)

  9. Analysis of the sex-chromosome constitution of digynic triploid mouse embryos.

    Science.gov (United States)

    Speirs, S; Kaufman, M H

    1989-01-01

    LT/Sv strain mice regularly ovulate up to 50% of their eggs as primary oocytes, which are fertilisable and give rise to digynic triploid embryos. A similar number of eggs are ovulated as secondary oocytes and, following fertilisation, give rise to normal diploid embryos. Pregnant LT/Sv females were autopsied at about midday on day 10 of gestation, when normal diploid embryos would be expected to possess between 25 and 30 pairs of somites. While a few of the triploid embryos either consisted of disorganised embryonic masses or were resorbing, most were at readily recognisable embryonic stages. Just over half of the embryos recovered were "unturned," while the remainder had "turned" and possessed between 15 and 25 pairs of somites. The triploids were usually readily recognised, owing to their small size and because they often displayed neural tube and cardiac defects. All of the embryos recovered were analysed cytogenetically by G-banding to establish their ploidy and sex-chromosome constitution. The XY:XX sex ratio of the 105 diploid embryos recovered, all of which had "turned," was 1.06:1, while the overall XXY:XXX sex ratio of the 120 triploids was 1:1. Analysis of only the developmentally most advanced triploid embryos (i.e., the 49 that had "turned") revealed that the XXY:XXX sex ratio in this group was 1.13:1, which was not significantly different from the expected ratio of 1:1. The crown-rump lengths of the XY and XX "turned" embryos were almost identical, as were those of the XXY and XXX "turned" embryos, although the triploids were significantly smaller than the diploids. No obvious effect of sex-chromosome constitution on developmental potential was therefore observed in this study in relation to either the digynic triploid or the control diploid embryos.

  10. Chromosomal localization of heat shock protein 70 (HSP70) gene in Zhikong scallop Chlamys farreri using BAC-FISH%栉孔扇贝热休克蛋白70(HSP70)基因的BAC-FISH定位

    Institute of Scientific and Technical Information of China (English)

    郇聘; 张晓军; 李富花; 张洋; 赵翠; 刘保忠; 相建海

    2009-01-01

    Zhikong scallop (Chlamys farreri) is one of key species in the marine aquaculture of China. Till present, the disease control is the main issue and many subjects were focused on disease- resistance and stress-related genes. Heat shock protein 70 (HSP70) shows diverse functions in the anti-stress reaction and pathogen-resistance reaction. However, the studies on HSP70 in C. farreri were mainly on a sequence analysis and expression profile, there is no result about the gene localization of HSP70. In this study, with the support of a BAC DNA library of C. farreri, a HSP70-eontaining BAC clone, CFB 123C08, was mapped to the long arms of a pair of homologous chromosomes of C. farreri using BAC-FISH. This study would facilitate further studies on the HSP70 of C. farreri. And as the first attempt of chromosomal mapping of low-copy genes in C. farreri, this study would promote the researches on the chromosome identification of C farreri.%利用BAC-FISH技术,将包含HSP70基因的BAC克隆定位到栉孔扇贝的一对同源染色体的长臂上.HSP70基因的染色体定位将对深入研究该基因的结构及功能并将其应用于生产实践提供基础支持.同时,本研究是首次对栉孔扇贝低拷贝基因进行染色体定位的实践,其结果将为栉孔扇贝的染色体的深入研究以及染色体鉴别等工作提供必要的参考.

  11. Molecular cytogenetic analysis and clinical manifestations of a case with de novo mosaic ring chromosome 7

    Directory of Open Access Journals (Sweden)

    Fang Jye-Siung

    2011-02-01

    Full Text Available Abstract Aim Clinical and molecular cytogenetic investigations of a newborn girl exhibiting facial dysmorphism with developmental delay. Methods Phenotypic evaluation was first applied to examine the proband's developmental status. Computed tomography and colour transcranial Doppler were used then to investigate her brain structure and function. Subsequently, chromosomal abnormalities were examined by karyotyping and fluorescent in situ hybridization was performed to investigate size of fragments lost at the two distal ends of the ring chromosome 7. In addition, multicolour banding was applied to rule out structural rearrangement occurs in between the ring chromosome 7. Results The proband was born with mosaic supernumerary ring chromosome 7, without a normal karyotype detected in the peripheral blood lymphocytes. The distal arm of chromosome 7p (at least 255 kb from the telomere was part of an extra ring chromosome 7. In addition, the distal arm of 7q, at least 8 kb from the telomere, was missing. There was no other chromosomal rearrangement detected by multicolour banding. Interpretation This is the 19th reported case of complete ring chromosome 7 mosaicism and the first survived case with mosaic supernumerary ring 7 without a normal karyotype detected in the peripheral lymphocytes.

  12. A System To Generate Chromosomal Mutations in Lactococcus lactis Which Allows Fast Analysis of Targeted Genes

    NARCIS (Netherlands)

    Law, Jean; Buist, Girbe; Haandrikman, Alfred; Kok, Jan; Venema, Gerhardus; Leenhouts, Kees

    1995-01-01

    A system for generating chromosomal insertions in lactococci is described. It is based on the conditional replication of lactococcal pWV01-derived Ori+ RepA- vector pORI19, containing lacZα and the multiple cloning site of pUC19. Chromosomal AluI fragments of Lactococcus lactis were cloned in pORI19

  13. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    DEFF Research Database (Denmark)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DY...

  14. The gene for diffuse palmoplantar keratoderma of the type found in northern Sweden is localized to chromosome 12q11-q13

    Energy Technology Data Exchange (ETDEWEB)

    Lind, L.; Holmgren, G.; Lundstroem, A. [Umea Univ. (Sweden)

    1994-09-01

    Hereditary palmoplantar keratoderma (PPK) consists of a heterogeneous group of skin disorders characterized by hyperkeratosis (thickening of the uppermost layer of the epidermis, the stratum corneum), primarily of the palms and soles. Autosomal dominant diffuse PPK has been considered to exist in two types that are clinically similar but microscopically distinguishable: epidermolytic PPK and non-epidermolytic PPK. Recently, though, the existence of a purely hyperkeratotic PPK has been questioned. However, autosomal dominant diffuse non-epidermolytic PPK is a frequent disorder in Northern Sweden with a reported prevalence of 0.3-0.55% among school children. This Swedish variant of PPK does not show any sign of epidermolytic hyprekeratosis but instead the patients exhibit frequent dermatophyte infections, a complication rarely seen in epidermolytic PPK. We have examined two Swedish families with PPK and localized the causative genetic defect to a 14 cM interval on chromosome 12q11-q13, a region known to contain the keratin type II gene cluster as well as the retionic acid receptor {gamma} gene. The PPK variant investigated here is thus both clinically and genetically different from epidermolytic palmoplantar keratoderma which recently has been shown to result from mutations on chromosome 17q in the gene for the type I keratin 9.

  15. Chromosome oscillations in mitosis

    Science.gov (United States)

    Campas, Otger

    2008-03-01

    Successful cell division necessitates a tight regulation of chromosome movement via the activity of molecular motors. Many of the key players at the origin of the forces generating the motion have been identified, but their spatial and temporal organization remains elusive. In animal cells, chromosomes periodically switch between phases of movement towards and away from the pole. This characteristic oscillatory behaviour cannot be explained by the current models of chromosome positioning and congression. We perform a self-contained theoretical analysis in which the motion of mono-oriented chromosomes results from the competition between the activity of the kinetochore and chromokinesin motors on the chromosome arms. Our analysis, consistent with the available experimental data, proposes that the interplay between the aster-like morphology of the spindle and the collective kinetics of molecular motors is at the origin of chromosome oscillations, positioning and congression. It provides a natural explanation for the so-called chromosome directional instability and for the mechanism by which chromosomes sense their position in space. In addition, we estimate the in vivo velocity of chromokinesins at vanishing load and propose new experiments to assess the mechanism at the origin of chromosome movement in cell division.

  16. Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae)

    Indian Academy of Sciences (India)

    Gléia Cristina Laverde Ricci; Alice Maria De Souza-Kaneshima; Mariana Ferrari Felismino; Andrea Beatriz Mendes-Bonato; Maria Suely Pagliarini; Cacilda Borges Do Valle

    2011-08-01

    A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented $2n = 18$; 27 accessions, $2n = 36$; and 2 accessions, $2n = 45$ chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.

  17. Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae).

    Science.gov (United States)

    Ricci, Gléia Cristina Laverde; De Souza-Kaneshima, Alice Maria; Felismino, Mariana Ferrari; Mendes-Bonato, Andrea Beatriz; Pagliarini, Maria Suely; Do Valle, Cacilda Borges

    2011-08-01

    A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented 2n = 18; 27 accessions, 2n = 36; and 2 accessions, 2n = 45 chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.

  18. "Chromosome": a knowledge-based system for the chromosome classification.

    Science.gov (United States)

    Ramstein, G; Bernadet, M

    1993-01-01

    Chromosome, a knowledge-based analysis system has been designed for the classification of human chromosomes. Its aim is to perform an optimal classification by driving a tool box containing the procedures of image processing, pattern recognition and classification. This paper presents the general architecture of Chromosome, based on a multiagent system generator. The image processing tool box is described from the met aphasic enhancement to the fine classification. Emphasis is then put on the knowledge base intended for the chromosome recognition. The global classification process is also presented, showing how Chromosome proceeds to classify a given chromosome. Finally, we discuss further extensions of the system for the karyotype building.

  19. Rapid cloning and bioinformatic analysis of spinach Y chromosome-specific EST sequences

    Indian Academy of Sciences (India)

    Chuan-Liang Deng; Wei-Li Zhang; Ying Cao; Shao-Jing Wang; Shu-Fen Li; Wu-Jun Gao; Long-Dou Lu

    2015-12-01

    The genome of spinach single chromosome complement is about 1000 Mbp, which is the model material to study the molecular mechanisms of plant sex differentiation. The cytological study showed that the biggest spinach chromosome (chromosome 1) was taken as spinach sex chromosome. It had three alleles of sex-related , m and . Many researchers have been trying to clone the sex-determining genes and investigated the molecular mechanism of spinach sex differentiation. However, there are no successful cloned reports about these genes. A new technology combining chromosome microdissection with hybridization-specific amplification (HSA) was adopted. The spinach Y chromosome degenerate oligonucleotide primed-PCR (DOP-PCR) products were hybridized with cDNA of the male spinach flowers in florescence. The female spinach genome was taken as blocker and cDNA library specifically expressed in Y chromosome was constructed. Moreover, expressed sequence tag (EST) sequences in cDNA library were cloned, sequenced and bioinformatics was analysed. There were 63 valid EST sequences obtained in this study. The fragment size was between 53 and 486 bp. BLASTn homologous alignment indicated that 12 EST sequences had homologous sequences of nucleic acids, the rest were new sequences. BLASTx homologous alignment indicated that 16 EST sequences had homologous protein-encoding nucleic acid sequence. The spinach Y chromosome-specific EST sequences laid the foundation for cloning the functional genes, specifically expressed in spinach Y chromosome. Meanwhile, the establishment of the technology system in the research provided a reference for rapid cloning of other biological sex chromosome-specific EST sequences.

  20. Construction and characterization of genomic libraries from specific human chromosomes.

    Science.gov (United States)

    Krumlauf, R; Jeanpierre, M; Young, B D

    1982-05-01

    Highly purified fractions of human chromosomes 21 and 22 were isolated from a suspension of metaphase chromosomes stained with ethidium bromide by using a fluorescence-activated cell sorter (FACS II). Two recombinant DNA libraries, representing chromosomes 21 and 22, were constructed by complete digestion of DNA from these fractions with EcoRI and insertion into the vector lambda gtWES lambda B. Twenty clones selected at random from the chromosome 22 library hybridized to EcoRI-digested human DNA, and five of these clones hybridized to single bands identical in size to the phage inserts. These five single-copy sequences and a clone coding for an 8S RNA isolated by screening the chromosome 22 library for expressed sequences were characterized in detail. Hybridization of all six clones to a panel of sorted chromosomes and hybrid cell lines confirmed the assignment of the sequences to chromosome 22. The sequences were localized to regions of chromosome 22 by hybridization to translocated chromosomes sorted from a cell line having a balanced translocation t(17;22)(p13;q11) and to hybrid cell lines containing the various portions of another translocation t(X;22)(q13;q112). Five clones reside on the long arm of chromosome 22 between q112 and pter, while one clone and an 18S rRNA gene isolated from the chromosome 22 library reside pter and g112. The construction of chromosome-specific libraries by this method has the advantage of being direct and applicable to nearly all human chromosomes and will be important in molecular analysis of human genetic diseases.

  1. Analysis of Chromosomal Aberrations after Low and High Dose Rate Gamma Irradiation in ATM or NBS Suppressed Human Fibroblast Cells

    Science.gov (United States)

    Hada, M.; Huff, J. L.; Patel, Z.; Pluth, J. M.; George, K. A.; Cucinotta, F. A.

    2009-01-01

    A detailed understanding of the biological effects of heavy nuclei is needed for space radiation protection and for cancer therapy. High-LET radiation produces more complex DNA lesions that may be non-repairable or that may require additional processing steps compared to endogenous DSBs, increasing the possibility of misrepair. Interplay between radiation sensitivity, dose, and radiation quality has not been studied extensively. Previously we studied chromosome aberrations induced by low- and high- LET radiation in several cell lines deficient in ATM (ataxia telangactasia mutated; product of the gene that is mutated in ataxia telangiectasia patients) or NBS (nibrin; product of the gene mutated in the Nijmegen breakage syndrome), and gliomablastoma cells that are proficient or lacking in DNA-dependent protein kinase (DNA-PK) activity. We found that the yields of both simple and complex chromosomal aberrations were significantly increased in the DSB repair defective cells compared to normal cells. The increased aberrations observed for the ATM and NBS defective lines was due to a significantly larger quadratic dose-response term compared to normal fibroblasts for both simple and complex aberrations, while the linear dose-response term was significantly higher in NBS cells only for simple exchanges. These results point to the importance of the functions of ATM and NBS in chromatin modifications that function to facilitate correct DSB repair and minimize aberration formation. To further understand the sensitivity differences that were observed in ATM and NBS deficient cells, in this study, chromosomal aberration analysis was performed in normal lung fibroblast cells treated with KU-55933, a specific ATM kinase inhibitor, or Mirin, an MRN complex inhibitor involved in activation of ATM. We are also testing siRNA knockdown of these proteins. Normal and ATM or NBS suppressed cells were irradiated with gamma-rays and chromosomes were collected with a premature chromosome

  2. Validation of QuickScan dicentric chromosome analysis for high throughput radiation biological dosimetry.

    Science.gov (United States)

    Flegal, F N; Devantier, Y; Marro, L; Wilkins, R C

    2012-02-01

    Currently, the dicentric chromosome assay (DCA) is used to estimate radiation doses to individuals following accidental radiological and nuclear overexposures when traditional dosimetry methods are not available. While being an exceptionally sensitive method for estimating doses by radiation, conventional DCA is time-intensive and requires highly trained expertise for analysis. For this reason, in a mass casualty situation, triage-quality conventional DCA struggles to provide dose estimations in a timely manner for triage purposes. In Canada, a new scoring technique, termed DCA QuickScan, has been devised to increase the throughput of this assay. DCA QuickScan uses traditional DCA sample preparation methods while adapting a rapid scoring approach. In this study, both conventional and QuickScan methods of scoring the DCA assay were compared for accuracy and sensitivity. Dose response curves were completed on four different donors based on the analysis of 1,000 metaphases or 200 events at eight to nine dose points by eight different scorers across two laboratories. Statistical analysis was performed on the data to compare the two methods within and across the laboratories and to test their respective sensitivities for dose estimation. This study demonstrated that QuickScan is statistically similar to conventional DCA analysis and is capable of producing dose estimates as low as 0.1 Gy but up to six times faster. Therefore, DCA QuickScan analysis can be used as a sensitive and accurate method for scoring samples for radiological biodosimetry in mass casualty situations or where faster dose assessment is required.

  3. Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations.

    Science.gov (United States)

    Toscanini, Ulises; Brisighelli, Francesca; Moreno, Fabián; Pantoja-Astudillo, Jaime A; Morales, Eugenia Aguirre; Bustos, Patricio; Pardo-Seco, Jacobo; Salas, Antonio

    2016-03-01

    We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation. Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity, and also the highest matching probability of the five Chilean samples, probably reflecting its more marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of the country to 9-10% in the South and 13% in the North, which is in good agreement with the distribution of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed the very low among variation observed in Chilean populations. The present project provides the first Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is also the first reference database for Y-chromosome forensic casework of the country.

  4. Multifractal Analysis of Local Entropies for Gibbs Measures

    NARCIS (Netherlands)

    Takens, Floris; Verbitski, Evgeni

    1998-01-01

    Recently a complete multifractal analysis of local dimensions, entropies and Lyapunov exponents of conformal expanding maps and surface Axion A diffeomorphisms for Gibbs measures was performed. The main goal of this was primarily the analysis of the local (pointwise) dimensions. This is an extremely

  5. The human serotonin N-acetyltransferase (EC 2.3.1.87) gene (AANAT): Structure, chromosomal localization, and tissue expression

    Energy Technology Data Exchange (ETDEWEB)

    Coon, S.L.; Bernard, M.; Roseboom, P.H. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1996-05-15

    Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AA-NAT, HGMW-approved symbol AANAT;EC 2.3.1.87) is the penultimate enzyme in melatonin synthesis and controls the night/day rhythm in melatonin production in the vertebrate pineal gland. We have found that the human AA-NAT gene spans {approx}2.5 kb, contains four exons, and is located at chromosome 17q25. The open reading frame encodes a 23.2-kDa protein that is {approx}80% identical to sheep and rat AA-NAT. The AA-NAT transcript ({approx}1 kb) is highly abundant in the pineal gland and is expressed at lower levels in the retina and in the Y79 retinoblastoma cell line. AA-NAT mRNA is also detectable at low levels in several brain regions and the pituitary gland, but not in several peripheral tissues examined. Brain and pituitary AA-NAT could modulate serotonin-dependent aspects of human behavior and pituitary function. 31 refs., 5 figs.

  6. Chromosomal Analysis of Couples with Repeated Spontaneous Abortions in Northeastern Iran

    Directory of Open Access Journals (Sweden)

    Saeedeh Ghazaey

    2015-04-01

    Full Text Available Background: Cytogenetic study of reproductive wastage is an important aspect in determining the genetic background of early embryogenesis. Approximately 15 to 20% of all pregnancies in humans are terminated as recurrent spontaneous abortions (RSAs. The aim of this study was to detect chromosome abnormalities in couples with RSAs and to compare our results with those reported previously. Materials and Methods: In this retrospective study, the pattern of chromosomal aberrations was evaluated during a six-year period from 2005 to 2011. The population under study was 728 couples who attended genetic counseling services for their RSAs at Pardis Clinical and Genetics Laboratory, Mashhad, Iran. Results: In this study, about 11.7% of couples were carriers of chromosomal aberrations. The majority of abnormalities were found in couples with history of abortion, without stillbirth or livebirth. Balanced reciprocal translocations, Robertsonian translocations, inversions and sex chromosome aneuploidy were seen in these cases. Balanced reciprocal translocations were the most frequent chromosomal anomalies (62.7% detected in current study. Conclusion: These findings suggest that chromosomal abnormalities can be one of the important causes of RSAs. In addition, cytogenetic study of families who experienced RSAs may prevent unnecessary treatment if RSA are caused by chromosomal abnormalities. The results of cytogenetic studies of RSA cases will provide a standard protocol for the genetic counselors in order to follow up and to help these families.

  7. A chromosomal analysis of four species of Chilean Chrysomelinae (Coleoptera, Chrysomelidae

    Directory of Open Access Journals (Sweden)

    Eduard Petitpierre

    2012-10-01

    Full Text Available Four species of Chilean leaf beetles in the subfamily Chrysomelinae have been cytogenetically analyzed, Blaptea elguetai Petitpierre, 2011, Henicotherus porteri Bréthes, 1929 and Jolivetia obscura (Philippi, 1864 show 2n = 28 chromosomes and a 13 + Xyp male meioformula, and Pataya nitida (Philippi, 1864 has the highest number of 2n = 38 chromosomes. The karyotype of H. porteri is made of mostly small meta/submetacentric chromosomes, and that of Jolivetia obscura displays striking procentric blocks of heterochromatin at pachytene autosomic bivalents using conventional staining. These findings are discussed in relation to previous cytogenetic data and current taxonomy of the subfamily.

  8. Likelihood Analysis of the Local Group Acceleration

    CERN Document Server

    Schmoldt, I M; Teodoro, L; Efstathiou, G P; Frenk, C S; Keeble, O; Maddox, S J; Oliver, S; Rowan-Robinson, M; Saunders, W J; Sutherland, W; Tadros, H; White, S D M

    1999-01-01

    We compute the acceleration on the Local Group using 11206 IRAS galaxies from the recently completed all-sky PSCz redshift survey. Measuring the acceleration vector in redshift space generates systematic uncertainties due to the redshift space distortions in the density field. We therefore assign galaxies to their real space positions by adopting a non-parametric model for the velocity field that solely relies on the linear gravitational instability and linear biasing hypotheses. Remaining systematic contributions to the measured acceleration vector are corrected for by using PSCz mock catalogues from N-body experiments. The resulting acceleration vector points approx. 15 degrees away from the CMB dipole apex, with a remarkable alignment between small and large scale contributions. A considerable fraction of the measured acceleration is generated within 40 h-1 Mpc with a non-negligible contribution from scales between 90 and 140 h-1 Mpc after which the acceleration amplitude seems to have converged. The local...

  9. Chromosomal location of the genes encoding complement components C5 and factor H in the mouse

    DEFF Research Database (Denmark)

    D'Eustachio, P; Kristensen, Torsten; Wetsel, R A;

    1986-01-01

    to chromosome 1 or chromosome 3. Following the inheritance of DNA restriction fragment-length polymorphisms revealed by the probes in recombinant inbred mouse strains allowed the factor H-associated fragments to be mapped to Sas-1 on chromosome 1, and the C5-associated fragments to be mapped to Hc. Analysis......Complementary DNA probes corresponding to the factor H and C5 polypeptides have been used to determine the chromosomal localizations of these two complement components. Both probes revealed complex and polymorphic arrays of DNA fragments in Southern blot analysis of mouse genomic DNA. Following...

  10. Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation

    Directory of Open Access Journals (Sweden)

    James E. Haber

    2013-06-01

    Full Text Available Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA. We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.

  11. Forensic analysis of polymorphism and regional stratification of Y-chromosomal microsatellites in Belarus.

    Science.gov (United States)

    Rebała, Krzysztof; Tsybovsky, Iosif S; Bogacheva, Anna V; Kotova, Svetlana A; Mikulich, Alexei I; Szczerkowska, Zofia

    2011-01-01

    Nine loci defining minimal haplotypes and four other Y-chromosomal short tandem repeats (Y-STRs) DYS437, DYS438, DYS439 and GATA H4.1 were analysed in 414 unrelated males residing in four regions of Belarus. Haplotypes of 328 males were further extended by 7 additional Y-STRs: DYS388, DYS426, DYS448, DYS456, DYS458, DYS460 and DYS635. The 13-locus haplotype diversity was 0.9978 and discrimination capacity was 78.7%, indicating presence of identical haplotypes among unrelated males. Seven additional Y-STRs enabled almost complete discrimination of undifferentiated 13-locus haplotypes, increasing haplotype diversity to 0.9998 and discrimination capacity to 97.9%. Analysis of molecular variance of minimal haplotypes excluded the use of a Y-STR database for Belarusians residing in northeastern Poland as representative for the Belarusian population in forensic practice, and revealed regional stratification within the country. However, four additional markers (DYS437, DYS438, DYS439 and GATA H4.1) were shown to eliminate the observed geographical substructure among Belarusian males. The results imply that in case of minimal and PowerPlex Y haplotypes, a separate frequency database should be used for northern Belarus to estimate Y-STR profile frequencies in forensic casework. In case of Yfiler haplotypes, regional stratification within Belarus may be neglected.

  12. Sequence analysis of 21 genes located in the Kartagener syndrome linkage region on chromosome 15q.

    Science.gov (United States)

    Geremek, Maciej; Schoenmaker, Frederieke; Zietkiewicz, Ewa; Pogorzelski, Andrzej; Diehl, Scott; Wijmenga, Cisca; Witt, Michal

    2008-06-01

    Primary ciliary dyskinesia (PCD) is a rare genetic disorder, which shows extensive genetic heterogeneity and is mostly inherited in an autosomal recessive fashion. There are four genes with a proven pathogenetic role in PCD. DNAH5 and DNAI1 are involved in 28 and 10% of PCD cases, respectively, while two other genes, DNAH11 and TXNDC3, have been identified as causal in one PCD family each. We have previously identified a 3.5 cM (2.82 Mb) region on chromosome 15q linked to Kartagener syndrome (KS), a subtype of PCD characterized by the randomization of body organ positioning. We have now refined the KS candidate region to a 1.8 Mb segment containing 18 known genes. The coding regions of these genes and three neighboring genes were subjected to sequence analysis in seven KS probands, and we were able to identify 60 single nucleotide sequence variants, 35 of which resided in mRNA coding sequences. However, none of the variations alone could explain the occurrence of the disease in these patients.

  13. Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan.

    Science.gov (United States)

    Achakzai, Niaz M; Rahman, Z; Shahzad, M S; Daud, S; Zar, M S; Israr, M; Husnain, T; Willuweit, Sascha; Roewer, Lutz

    2012-07-01

    Afghanistan is a landlocked country in the heart of Asia and since the dawn of humankind Afghanistan has faced centuries of turmoil, strife, conflict, warfare, distress, social unrest, difficult climate, harsh terrain and due to its unique geostrategic position in Eurasia which has historically attracted commerce and conflict. It is an important stop along the Silk Road, connecting the far eastern civilizations to the western world. A 5000-year history of constant invasion. Afghanistan has been repeatedly invaded and conquered by rulers and super powers, neighboring interference in this conflict-tattered land for centuries yet rarely leading to the conquest of this rugged and challenging terrain nation. Afghans are not only shepherds, farmers and nomads but also intense fighters and fierce warriors. Currently very limited genetic studies have been performed in Afghan populations. 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 125 unrelated Pashtun (in hindi: Pathan) males residing in the Kandahar region of Southern Afghanistan. A total of 92 unique haplotypes were observed. The predominant haplotype reached a frequency of 9.6%. The haplotype diversity was 0.987 and the discrimination capacity 73.6%. Analysis of molecular variance (AMOVA) reveals a considerable regional stratification within the country as well as between different Pashtun (Pathan) groups from Afghanistan, Pakistan and India.

  14. Chromosomal and Genetic Analysis of a Human Lung Adenocarcinoma Cell Line OM

    Institute of Scientific and Technical Information of China (English)

    Yong-Wu Li; Lin Bai; Lyu-Xia Dai; Xu He; Xian-Ping Zhou

    2016-01-01

    Background: Lung cancer has become the leading cause of death in many regions.Carcinogenesis is caused by the stepwise accumulation of genetic and chromosomal changes.The aim of this study was to investigate the chromosome and gene alterations in the human lung adenocarcinoma cell line OM.Methods: We used Giemsa banding and multiplex fluorescence in situ hybridization focusing on the human lung adenocarcinoma cell line OM to analyze its chromosome alterations.In addition, the gains and losses in the specific chromosome regions were identified by comparative genomic hybridization (CGH) and the amplifications of cancer-related genes were also detected by polymerase chain reaction (PCR).Results: We identified a large number of chromosomal numerical alterations on all chromosomes except chromosome X and 19.Chromosome 10 is the most frequently involved in translocations with six different interchromosomal translocations.CGH revealed the gains on chromosome regions of 3q25.3-28, 5p13, 12q22-23.24, and the losses on 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p 13.31-13.33 and 17p 13.1-13.3.And PCR showed the amplification of genes: Membrane metalloendopeptidase (MME), sucrase-isomaltase (SI), butyrylcholinesterase (BCHE), and kininogen (KNG).Conclusions: The lung adenocarcinoma cell line OM exhibited multiple complex karyotypes, and chromosome 10 was frequently involved in chromosomal translocation, which may play key roles in tumorigenesis.We speculated that the oncogenes may be located at 3q25.3-28, 5p13, 12q22-23.24, while tumor suppressor genes may exist in 3p25-26, 6p25, 6q26-27, 7q34-36, 8p22-23, 9p21-24, 10q25-26.3, 12p 13.31-13.33, and 17p 13.1-13.3.Moreover, at least four genes (MME, SI, BCHE, and KNG) may be involved in the human lung adenocarcinoma cell line OM.

  15. Exploration of shape variation using localized components analysis.

    Science.gov (United States)

    Alcantara, Dan A; Carmichael, Owen; Harcourt-Smith, Will; Sterner, Kirstin; Frost, Stephen R; Dutton, Rebecca; Thompson, Paul; Delson, Eric; Amenta, Nina

    2009-08-01

    Localized Components Analysis (LoCA) is a new method for describing surface shape variation in an ensemble of objects using a linear subspace of spatially localized shape components. In contrast to earlier methods, LoCA optimizes explicitly for localized components and allows a flexible trade-off between localized and concise representations, and the formulation of locality is flexible enough to incorporate properties such as symmetry. This paper demonstrates that LoCA can provide intuitive presentations of shape differences associated with sex, disease state, and species in a broad range of biomedical specimens, including human brain regions and monkey crania.

  16. Evidence for the absence of intron H of the histidine-rich glycoprotein (HRG) gene: Genetic mapping and in situ localization of HRG to chromosome 3q28-q29

    Energy Technology Data Exchange (ETDEWEB)

    Hennis, B.C.; Poort, E.W. van der; Kluft, C.; Frants, R.R.; Bakker, E.; Vossen, R.H.A.M.; Blonden, L.A.; Khan, P.M. (Leiden Univ. (Netherlands)); Cox, S.; Spurr, N.K. (Imperial Cancer Research Fund, London (United Kingdom))

    1994-01-01

    Histidine-rich glycoprotein (HRG) belongs to the cystatin superfamily and appears to be a potential risk factor for thrombosis. An increased prevalence of elevated HRG plasma levels in patients with venous thrombosis and families with thrombophilia has been reported. It is interesting to note that the genes of four different members of the cystatin superfamily are located on the distal section of the long arm of chromosome 3: Stefin A (STF1) on 3q21, Kininogen (KNG) on 3q26-qter, [alpha]-2-HS-glycoprotein (AHSG) on 3q27-q28, and HRG on 3q21-qter. To further investigate the evolutionary relationship between HRG and members of the cystatin superfamily, the authors isolated a cosmid that was used to refine the chromosomal localization of HRG by in situ hybridization. In addition, they used a dinucleotide repeat polymorphism to localize HRG on the linkage map of chromosome 3q. 10 refs., 2 figs.

  17. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations

    Science.gov (United States)

    Dulik, Matthew C.; Owings, Amanda C.; Gaieski, Jill B.; Vilar, Miguel G.; Andre, Alestine; Lennie, Crystal; Mackenzie, Mary Adele; Kritsch, Ingrid; Snowshoe, Sharon; Wright, Ruth; Martin, James; Gibson, Nancy; Andrews, Thomas D.; Schurr, Theodore G.; Adhikarla, Syama; Adler, Christina J.; Balanovska, Elena; Balanovsky, Oleg; Bertranpetit, Jaume; Clarke, Andrew C.; Comas, David; Cooper, Alan; Der Sarkissian, Clio S. I.; GaneshPrasad, ArunKumar; Haak, Wolfgang; Haber, Marc; Hobbs, Angela; Javed, Asif; Jin, Li; Kaplan, Matthew E.; Li, Shilin; Martínez-Cruz, Begoña; Matisoo-Smith, Elizabeth A.; Melé, Marta; Merchant, Nirav C.; Mitchell, R. John; Parida, Laxmi; Pitchappan, Ramasamy; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Santos, Fabrício R.; Soodyall, Himla; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Tyler-Smith, Chris; Santhakumari, Arun Varatharajan; Vieira, Pedro Paulo; Wells, R. Spencer; Zalloua, Pierre A.; Ziegle, Janet S.

    2012-01-01

    For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich’in, and Tłįchǫ populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįchǫ being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized. PMID:22586127

  18. Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services.

    Science.gov (United States)

    Roberts, Jennifer L; Hovanes, Karine; Dasouki, Majed; Manzardo, Ann M; Butler, Merlin G

    2014-02-01

    Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.

  19. AN ANALYSIS OF MARKETING CHANNELS OF LOCAL FOOD IN SCOTLAND

    OpenAIRE

    Revoredo-Giha, Cesar; Watts, D.; Leat, Philip M.K.

    2010-01-01

    Local food and its possibilities for addressing sustainable regional growth, food availability, accessibility and affordability has received considerable attention in the discussion on and development of the National Food Policy in Scotland. In terms of methodology, the paper continues the analysis of the local food database for Scotland constructed in Watts et al (2010) by exploring the marketing outlets used by the local food enterprises. This subject is important because it may provide inf...

  20. Molecular and chromosomal analysis of ribosomal cistrons in two cartilaginous fish, Taeniura lymma and Raja montagui (Chondrichthyes, Batoidea).

    Science.gov (United States)

    Rocco, L; Costagliola, D; Fiorillo, M; Tinti, F; Stingo, V

    2005-03-01

    We used silver nitrate staining, CMA3 and FISH to study the chromosomal localization of both the major ribosomal genes and the nucleolar organizer regions as well as that of the minor ribosomal genes (5S rDNA) in two species of Batoidea, Taeniura lymma (Dasyatidae) and Raja montagui (Rajidae). In both species, all the metaphases examined showed the presence of multiple NOR-bearing sites, while the gene for 5S rRNA proved to be localized on two chromosome pairs. Furthermore, one of the two 5S rDNA sites in T. lymma was shown to be co-localized with the major ribosomal cluster. The presence of multiple nucleolar organizer regions in the two species might be interpreted as being the result of intraspecific polymorphisms, or as a phenomenon of the amplified transposition of mobile elements of the genome. We also determined the nucleotide sequence of the 5S rRNA gene, consisting of 564 bp in R. montagui and 612 bp in T. lymma. We also found TATA-like and (TGC)n trinucleotides, (CA)n dinucleotides and (GTGA)n tetranucleotides, which probably influence gene regulation.

  1. Examination of X chromosome markers in Rett syndrome: Exclusion mapping with a novel variation on multilocus linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ellison, K.A.; Fill, C.P. (Baylor College of Medicine, Houston, TX (United States)); Terwililger, J.; Percy, A.K.; Zobhbi, H. (Columbia University, NY (United States)); DeGennaro, L.J.; Ott, J. (University of Massachusetts Medical School, Worcester (United States)); Anvret, M.; Martin-Gallardo, A. (National Institutes of Health, Bethesda, MD (United States))

    1992-02-01

    Rett syndrome is a neurologic disorder characterized by early normal development followed by regression, acquired deceleration of head growth, autism, ataxia, and sterotypic hand movements. The exclusive occurrence of the syndrome in females and the occurrence of a few familial cases with inheritance through maternal lines suggest that this disorder is most likely secondary to a mutation on the X chromosome. To address this hypothesis and to identify candidate regions for the Rett syndrome gene locus, genotypic analysis was performed in two families with maternally related affected half-sisters by using 63 DNA markers from the X chromosome. Nineteen of the loci studied were chosen for multipoint linkage analysis because they have been previously genetically mapped using a large number of meioses from reference families. Using the exclusion criterion of a lod score less than [minus]2, the authors were able to exclude the region between the Duchenne muscular dystrophy locus and the DXS456 locus. This region extends from Xp21.2 to Xq21-q23. The use of the multipoint linkage analysis approach outlined in this study should allow the exclusion of additional regions of the X chromosome as new markers are analyzed.

  2. Haplotype analysis of DNA microsatellites tightly linked to the locus of Usher syndrome type I on chromosome 11q

    Energy Technology Data Exchange (ETDEWEB)

    Korostishevsky, M.; Kalinsky, H.; Seroussi, E. [Sackler Faculty of Medicine, Ramat-Aviv (Israel)] [and other

    1994-09-01

    Usher syndrome type I (USHI), an autosomal recessive disorder associated with congenital sensorineural deafness and progressive visual loss, is closely linked to the D11S533 locus. The availability of 7 other polymorphic markers within few centimorgans spanning the disease locus allowed us to identify a unique and single haplotype among all carriers of USHI gene in the Samaritan kindred. Occurrence of recombination in this small chromosomal interval is rare, hindering the detection of the mitotic recombination events needed for analysis by traditional linkage methods. Attempts to order the eight loci by linkage disequilibrium models proved to be problematic. However, our haplotype analysis implied that recombinations which had arisen in past generations may be utilized in fine mapping of the USHI gene and in resolving the conflicting linkage maps previously obtained for this region. We have developed a simple algorithm for predicting the order of the microsatellites on the basis of haplotype resemblance. The following chromosomal map in which the USHI gene is closest to D11S533 (location score of 31.0 by multipoint analysis) is suggested: D11S916, GARP, D11S527, D11S533, OMP, D11S906, D11S911, D11S937. Physical mapping efforts are currently directed to verify and to detail the map of this chromosomal region.

  3. Hierarchical radial and polar organisation of chromosomes in human sperm.

    Science.gov (United States)

    Millan, N M; Lau, P; Hann, M; Ioannou, D; Hoffman, D; Barrionuevo, M; Maxson, W; Ory, S; Tempest, H G

    2012-10-01

    It is well established that chromosomes occupy distinct positions within the interphase nuclei, conferring a potential functional implication to the genome. In addition, alterations in the nuclear organisation patterns have been associated with disease phenotypes (e.g. cancer or laminopathies). The human sperm is the smallest cell in the body with specific DNA packaging and the mission of delivering the paternal genome to the oocyte during fertilisation. Studies of nuclear organisation in the sperm have postulated nonrandom chromosome position and have proposed a chromocentre model with the centromeres facing toward the interior and the telomeres toward the periphery of the nucleus. Most studies have assessed the nuclear address in the sperm longitudinally predominantly using centromeric or telomeric probes and to a lesser extent with whole chromosome paints. To date, studies investigating the radial organisation of human sperm have been limited. The purpose of this study was to utilise whole chromosome paints for six clinically important chromosomes (18, 19, 21, 22, X, and Y) to investigate nuclear address by assessing their radial and longitudinal nuclear organisation. A total of 10,800 sperm were analysed in nine normozoospermic individuals. The results have shown nonrandom chromosome position for all chromosomes using both methods of analysis. We present novel radial and polar analysis of chromosome territory localization within the human sperm nucleus. Specifically, a hierarchical organisation was observed radially with chromosomes organised from the interior to the periphery (chromosomes 22, 21, Y, X, 19, and 18 respectively) and polar organisation from the sperm head to tail (chromosomes X, 19, Y, 22, 21, and 18, respectively). We provide evidence of defined nuclear organisation in the human sperm and discuss the function of organisation and potential possible clinical ramifications of these results in regards to male infertility and early human development.

  4. Chromosomal Microarray Analysis of Consecutive Individuals with Autism Spectrum Disorders Using an Ultra-High Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Karen S. Ho

    2016-12-01

    Full Text Available Copy number variants (CNVs detected by chromosomal microarray analysis (CMA significantly contribute to understanding the etiology of autism spectrum disorder (ASD and other related conditions. In recognition of the value of CMA testing and its impact on medical management, CMA is in medical guidelines as a first-tier test in the evaluation of children with these disorders. As CMA becomes adopted into routine care for these patients, it becomes increasingly important to report these clinical findings. This study summarizes the results of over 4 years of CMA testing by a CLIA-certified clinical testing laboratory. Using a 2.8 million probe microarray optimized for the detection of CNVs associated with neurodevelopmental disorders, we report an overall CNV detection rate of 28.1% in 10,351 consecutive patients, which rises to nearly 33% in cases without ASD, with only developmental delay/intellectual disability (DD/ID and/or multiple congenital anomalies (MCA. The overall detection rate for individuals with ASD is also significant at 24.4%. The detection rate and pathogenic yield of CMA vary significantly with the indications for testing, age, and gender, as well as the specialty of the ordering doctor. We note discrete differences in the most common recurrent CNVs found in individuals with or without a diagnosis of ASD.

  5. Basic functional analysis of six unknown open reading frames from Saccharomyces cerevisiae: four from chromosome VII and two from chromosome XV.

    Science.gov (United States)

    Pearson, Bruce M; Schweizer, Michael

    2002-01-30

    Six open reading frames (ORFs) of unknown function from Saccharomyces cerevisiae from the left arms of chromosomes VII and XV were disrupted by the short-flanking homology method in the diploid strains FY1679 and CENPK2. In each case, the entire ORF, with the exception of the first nucleotide of the start codon, was eliminated and replaced by the kanMX4 cassette. Correct integration of the disrupting marker was checked by colony PCR of the geneticin (G418)-resistant transformants. Sporulation followed by tetrad dissection of the diploids revealed that none of the ORFs encoded a product essential for the viability of either yeast strain. The neutral effect of these disruptions extended to mating and sporulation, since it was possible to create homozygous diploid disruptants that were capable of sporulation. Basic phenotypic analysis was carried out on all strains by growing them on three different media at three different temperatures and revealed no significant differences between disruptants and the parental strains. A cognate clone and a kanMX4 disruption cassette were created for five of the six ORFs by gap repair with specific long-flanking homology cassettes. For experimental reasons, the cognate clone and disruption cassette corresponding to the sixth ORF (YGL161w) had to be created by PCR.

  6. [Analysis of fragments of intergenome spacers of human body observed in chromosomes containing no nuclear organization].

    Science.gov (United States)

    Kupriyanova, N S; Nechvolodov, K K; Korsunenko, A V

    2014-01-01

    Tandem repetitions of rDNA provide so-called nuclear organizations (NOR). On the other hand, rDNA-structures are observed in some NOR chromosomes. It was demonstrated that, in addition to ribosome biogenesis, nucleoli provided a number of functions: cell cycle regulation, stress-induced response, transcription regulation, which often induced cell cascades. The mechanisms of the induction of rDNA segments in NOR chromosomes are obscure and require further research. About 1/3 repetitions are associated with nucleoli and SINE/Alu repetitions, homogeneous repetition, and tandem repetition. Perhaps, relative position of nucleoli and chromosomes may facilitate/prevent interaction of chromosomes with rDNA clusters. The variability of two larger repetitions in the central part of rMGS, LR1, and LR2 similar by -90% and separated by several hundred pairs of bases from each other was studied in our previous works. This work was devoted to the search for the LR1-LR2 segments in other chromosomes, characterization of their terminal tips at rupture points and genome areas of incorporation of the LR1-LR2 segments.

  7. Fast-FISH Detection and Semi-Automated Image Analysis of Numerical Chromosome Aberrations in Hematological Malignancies

    Directory of Open Access Journals (Sweden)

    Arif Esa

    1998-01-01

    Full Text Available A new fluorescence in situ hybridization (FISH technique called Fast-FISH in combination with semi-automated image analysis was applied to detect numerical aberrations of chromosomes 8 and 12 in interphase nuclei of peripheral blood lymphocytes and bone marrow cells from patients with acute myelogenous leukemia (AML and chronic lymphocytic leukemia (CLL. Commercially available α-satellite DNA probes specific for the centromere regions of chromosome 8 and chromosome 12, respectively, were used. After application of the Fast-FISH protocol, the microscopic images of the fluorescence-labelled cell nuclei were recorded by the true color CCD camera Kappa CF 15 MC and evaluated quantitatively by computer analysis on a PC. These results were compared to results obtained from the same type of specimens using the same analysis system but with a standard FISH protocol. In addition, automated spot counting after both FISH techniques was compared to visual spot counting after standard FISH. A total number of about 3,000 cell nuclei was evaluated. For quantitative brightness parameters, a good correlation between standard FISH labelling and Fast-FISH was found. Automated spot counting after Fast-FISH coincided within a few percent to automated and visual spot counting after standard FISH. The examples shown indicate the reliability and reproducibility of Fast-FISH and its potential for automatized interphase cell diagnostics of numerical chromosome aberrations. Since the Fast-FISH technique requires a hybridization time as low as 1/20 of established standard FISH techniques, omitting most of the time consuming working steps in the protocol, it may contribute considerably to clinical diagnostics. This may especially be interesting in cases where an accurate result is required within a few hours.

  8. A genome-wide association analysis of chromosomal aberrations and Hirschsprung disease.

    Science.gov (United States)

    Bae, Joon Seol; Koh, InSong; Cheong, Hyun Sub; Seo, Jeong-Meen; Kim, Dae-Yeon; Oh, Jung-Tak; Kim, Hyun-Young; Jung, Kyuwhan; Sul, Jae Hoon; Park, Woong-Yang; Kim, Jeong-Hyun; Shin, Hyoung Doo

    2016-11-01

    Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR.

  9. Demographic estimates from Y chromosome microsatellite polymorphisms: Analysis of a worldwide sample

    Directory of Open Access Journals (Sweden)

    Macpherson J

    2004-08-01

    Full Text Available Abstract Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

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

    Science.gov (United States)

    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.

  11. Localization of X chromosome short arm markers relative to synovial sarcoma- and renal adenocarcinoma-associated translocation breakpoints

    NARCIS (Netherlands)

    Sinke, R J; de Leeuw, B; Janssen, H A; Weghuis, D O; Suijkerbuijk, R F; Meloni, A M; Gilgenkrantz, S; Berger, W; Ropers, H H; Sandberg, A A

    1993-01-01

    A series of thirteen different DNA markers was mapped relative to papillary renal cell carcinoma- and synovial sarcoma-associated translocation breakpoints in Xp11.2 using a panel of tumor-derived somatic cell hybrids in conjunction with Southern blot analysis. Our results indicate that the two tran

  12. Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer

    DEFF Research Database (Denmark)

    Roylance, Rebecca; Endesfelder, David; Gorman, Patricia

    2011-01-01

    methods, such as centromeric FISH, aimed at determining the variation around the modal number of two or more chromosomes within individual tumor nuclei. Here, we document the frequency of tumor CIN by dual centromeric FISH analysis in a retrospective primary breast cancer cohort of 246 patients...... with survival outcome. Results: There was increased CIN and clonal eterogeneity in ER-negative compared with ER-positive breast cancer. Consistent with a negative impact of CIN on cellular fitness, extreme CIN in ER-negative breast cancer was an independent variable associated with improved long-term survival......Background: Chromosomal instability (CIN) is thought to be associated with poor prognosis in solid tumors; however, evidence from preclinical and mouse tumor models suggest that CIN may paradoxically enhance or impair cancer cell fitness. Breast cancer prognostic expression signature sets, which...

  13. Chromosome Mapping of 18S Ribosomal RNA Genes in Eleven Hypostomus Species (Siluriformes, Loricariidae): Diversity Analysis of the Sites.

    Science.gov (United States)

    Rubert, Marceléia; da Rosa, Renata; Zawadzki, Claudio H; Mariotto, Sandra; Moreira-Filho, Orlando; Giuliano-Caetano, Lucia

    2016-08-01

    We investigated the chromosomal distribution of 18S ribosomal DNA (rDNA) in different populations of 11 species of Hypostomus collected in important Brazilian basins, namely South Atlantic, Upper Paraná, and Paraguay applying the fluorescence in situ hybridization (FISH). Hypostomus cochliodon, Hypostomus commersoni, Hypostomus hermanni, Hypostomus regani, Hypostomus albopunctatus, Hypostomus paulinus, Hypostomus aff. paulinus, Hypostomus iheringii, and Hypostomus mutucae presented multiple 18S rDNA sites while Hypostomus strigaticeps and Hypostomus nigromaculatus exhibited a single pair of chromosomes with 18S rDNA sites. The studied species presented variations in the number and position of these sites. The results accomplished were similar to those obtained by the analysis of AgNORs, revealing the same interspecific variability. Each species exhibited distinctive patterns of AgNOR and 18S rDNA distribution, which can be considered cytogenetic markers in each species of the genus and help improve the discussions on the phylogeny of the group.

  14. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes

    Directory of Open Access Journals (Sweden)

    Austen B. McGuire

    2016-05-01

    Full Text Available Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G negative euchromatic (light bands and G-positive heterochromatic (dark bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  15. Morphometric Analysis of Recognized Genes for Autism Spectrum Disorders and Obesity in Relationship to the Distribution of Protein-Coding Genes on Human Chromosomes.

    Science.gov (United States)

    McGuire, Austen B; Rafi, Syed K; Manzardo, Ann M; Butler, Merlin G

    2016-05-05

    Mammalian chromosomes are comprised of complex chromatin architecture with the specific assembly and configuration of each chromosome influencing gene expression and function in yet undefined ways by varying degrees of heterochromatinization that result in Giemsa (G) negative euchromatic (light) bands and G-positive heterochromatic (dark) bands. We carried out morphometric measurements of high-resolution chromosome ideograms for the first time to characterize the total euchromatic and heterochromatic chromosome band length, distribution and localization of 20,145 known protein-coding genes, 790 recognized autism spectrum disorder (ASD) genes and 365 obesity genes. The individual lengths of G-negative euchromatin and G-positive heterochromatin chromosome bands were measured in millimeters and recorded from scaled and stacked digital images of 850-band high-resolution ideograms supplied by the International Society of Chromosome Nomenclature (ISCN) 2013. Our overall measurements followed established banding patterns based on chromosome size. G-negative euchromatic band regions contained 60% of protein-coding genes while the remaining 40% were distributed across the four heterochromatic dark band sub-types. ASD genes were disproportionately overrepresented in the darker heterochromatic sub-bands, while the obesity gene distribution pattern did not significantly differ from protein-coding genes. Our study supports recent trends implicating genes located in heterochromatin regions playing a role in biological processes including neurodevelopment and function, specifically genes associated with ASD.

  16. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    OpenAIRE

    Purps, J.; Siegert, S.; Willuweit, S.; Nagy, M.; C. Alves; Salazar, R.; Angustia, S.M.T.; Santos,L.H.; Anslinger, K.; Bayer, B.; Ayub, Q.; Wei, W; Xue, Y.; Tyler-Smith, C; Bafalluy, M.B.

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different\\ud populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci\\ud (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439,\\ud DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643)\\ud and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic\\ud spectra of...

  17. Localization of the human achaete-scute homolog gene (ASCL 1) distal to phenylalanine hydroxylase (PAH) and proximal to tumor rejection antigen (TRA 1) on chromosome 12q22-q23

    Energy Technology Data Exchange (ETDEWEB)

    Renault, B.; Kucherlapati, R.; Krauter, K. [Albert Einstein College of Medicine, Bronx, NY (United States); Lieman, J.; Ward, D. [Yale Univ. School of Medicine, New Haven, CT (United States)

    1995-11-01

    ASCL1, the human achaete-scute homolog, is a helix-loop-helix transcription factor that was previously assigned to chromosome 12 using a rodent-human somatic hybrid panel. We now placed this gene on a yeast artificial chromosome contig encompassing position 119 cM of the Genethon genetic map between the two genes phenylalanine hydroxylase (PAH) and tumor rejection antigen 1 (TRA1). We also localized ASCL1 in the 12q22-q23 cytogenetic interval by using fluorescence in situ hybridization. 13 refs., 2 figs.

  18. Identification and Preliminary Analysis of Several Centromere-associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Although the centromeres of some plants have been investigated previously, our knowledge of the wheat centromere is still very limited. To understand the structure and function of the wheat centromere, we used two centromeric repeats (RCS1 and CCS1-5ab) to obtain some centromere-associated bacterial artificial chromosome (BAC) clones in 32 RCS1-related BAC clones that had been screened out from a diploid wheat (Triticum boeoticum Boiss.; 2n=2x=14) BAC library. Southern hybridization results indicated that, of the 32 candidates,there were 28 RCS1-positive clones. Based on gel blot patterns, the frequency of RCS1 was approximately one copy every 69.4 kb in these 28 RCS1-positive BAC clones. More bands were detected when the same filter was probed with CCS1-5ab. Furthermore, the CCS1 bands covered all the bands detected by RCS1, which suggests that some CCS1 repeats were distributed together with RCS1. The frequency of CCS1 families was once every 35.8 kb, nearly twice that of RCS1. Fluorescence in situ hybridization (FISH) analysis indicated that the five BAC clones containing RCS1 and CCS1 sequences all detected signals at the centromeric regions in hexaploid wheat, but the signal intensities on the A-genome chromosomes were stronger than those on the B- and/or D-genome chromosomes. The FISH analysis among nine Triticeae cereals indicated that there were A-genomespecific (or rich) sequences dispersing on chromosome arms in the BAC clone TbBAC5. In addition, at the interphase cells, the centromeres of diploid species usually clustered at one pole and formed a ring-like allocation in the period before metaphase.

  19. 染色体核型异常患者全基因组芯片扫描结果分析%Analysis on the results of chromosomal microarray in patients with chromosome abnormality

    Institute of Scientific and Technical Information of China (English)

    姚如恩; 傅启华; 余永国

    2014-01-01

    目的:利用全基因组芯片扫描技术对染色体核型检测结果异常的患者样本进行重复检测分析,验证并确认患者染色体的具体核型。方法利用基因分型芯片技术对9例临床表型皆为智力落后合并多发畸形,且核型结果异常的样本进行检测分析,比较两种技术之间结果相符程度,通过芯片平台结果来验证染色体核型技术的准确性,同时分析其临床适用性。结果染色体核型结果和全基因组芯片分析技术的结果完全符合的为2例Turner综合征患者,均为嵌合型;3例染色体核型结果阳性患者,全基因组芯片分析结果为阴性,其中2例为随体增加,1例为染色体内倒位;4例涉及染色体片段大小不同的缺失和复制的患者,核型结果和全基因组芯片结果差异较大,并且核型检测结果与患者实际核型相差较大。结论染色体核型技术在用于以往认定的适应症如智力落后、多发畸形的检测中,检测的准确性相对全基因组芯片技术较低,在明确定位染色体缺失和复制大小及位置的能力上有明显的不足,但对于检测染色体平衡性结构性变化的作用不能被芯片所取代。%Objective To analyze the results of patients with chromosome abnormality by chromosomal microarray, and validate and depict patient′s karyotype.Methods Genotyping array was applied to assess in 9 patients with hypophrenia and deformity.The samples with karyotype analysis abnormality were determined.Comparison between karyotyping and microarray analysis was considered to validate the clinical utility of chromosomal microarray analysis. Results Two Turner syndrome patients had completely concordant results from karyotype analysis and chromosomal microarray.Three patients showed abnormal karyotyping results (2 patients with excess trabant and 1 patients with chromosomal inversion) were detected negative with chromosomal microarray

  20. Face Recognition Using Double Sparse Local Fisher Discriminant Analysis

    Directory of Open Access Journals (Sweden)

    Zhan Wang

    2015-01-01

    Full Text Available Local Fisher discriminant analysis (LFDA was proposed for dealing with the multimodal problem. It not only combines the idea of locality preserving projections (LPP for preserving the local structure of the high-dimensional data but also combines the idea of Fisher discriminant analysis (FDA for obtaining the discriminant power. However, LFDA also suffers from the undersampled problem as well as many dimensionality reduction methods. Meanwhile, the projection matrix is not sparse. In this paper, we propose double sparse local Fisher discriminant analysis (DSLFDA for face recognition. The proposed method firstly constructs a sparse and data-adaptive graph with nonnegative constraint. Then, DSLFDA reformulates the objective function as a regression-type optimization problem. The undersampled problem is avoided naturally and the sparse solution can be obtained by adding the regression-type problem to a l1 penalty. Experiments on Yale, ORL, and CMU PIE face databases are implemented to demonstrate the effectiveness of the proposed method.

  1. A high-resolution interval map of the q21 region of the human X chromosome

    Energy Technology Data Exchange (ETDEWEB)

    Philippe, C.; Monaco, A.P. [ICRF Laboratories, Oxford (United Kingdom)] [and others; Arnould, C. [Laboratoire de Genetique Humaine, Vandoeuvre-les-Nancy (France)] [and others

    1995-06-10

    In a previous study, we have developed a panel of chromosomal rearrangements for the physical mapping of the q13-q21 region of the human X chromosome. Here, we report the physical localization of 36 additional polymorphic markers by polymerase chain reaction analysis. The high density of chromosomal breakpoints in Xq21 allows us to map 58 DNA loci in 22 intervals. As a result, this segment of the X chromosome is saturated with approximately three sequence tagged sites per megabase of DNA, which will facilitate the construction of a YAC contig of this region. 26 refs., 1 fig., 1 tab.

  2. Analysis of local subassembly accident in KALIMER

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Young Min; Jeong, Kwan Seong; Hahn, Do Hee

    2000-10-01

    Subassembly Accidents (S-A) in the Liquid Metal Reactor (LMR) may cause extensive clad and fuel melting and are thus regarded as a potential whole core accident initiator. The possibility of S-A occurrence must be very low frequency by the design features, and reactor must have specific instrumentation to interrupt the S-A sequences by causing a reactor shutdown. The evaluation of the relevant initiators, the event sequences which follow them, and their detection are the essence of the safety issue. Particularly, the phenomena of flow blockage caused by foreign materials and/or the debris from the failed fuel pin have been researched world-widely. The foreign strategies for dealing with the S-A and the associated safety issues with experimental and theoretical R and D results are reviewed. This report aims at obtaining information to reasonably evaluate the thermal-hydraulic effect of S-A for a wire-wrapped LMR fuel pin bundle. The mechanism of blockage formation and growth within a pin bundle and at the subassembly entrance is reviewed in the phenomenological aspect. Knowledge about the recent LMR subassembly design and operation procedure to prevent flow blockage will be reflected for KALIMER design later. The blockage analysis method including computer codes and related analytical models are reviewed. Especially SABRE4 code is discussed in detail. Preliminary analyses of flow blockage within a 271-pin driver subassembly have been performed using the SABRE4 computer code. As a result no sodium boiling occurred for the central 24-subchannel blockage as well as 6-subchannel blockage.

  3. Modeling Chromosomes

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Learning about chromosomes is standard fare in biology classrooms today. However, students may find it difficult to understand the relationships among the "genome", "chromosomes", "genes", a "gene locus", and "alleles". In the simple activity described in this article, which follows the 5E approach…

  4. Mutation screening and association analysis of six candidate genes for autism on chromosome 7q

    DEFF Research Database (Denmark)

    Bonora, Elena; Lamb, Janine A; Barnby, Gabrielle;

    2005-01-01

    Genetic studies have provided evidence for an autism susceptibility locus (AUTS1) on chromosome 7q. Screening for mutations in six genes mapping to 7q, CUTL1, SRPK2, SYPL, LAMB1, NRCAM and PTPRZ1 in 48 unrelated individuals with autism led to the identification of several new coding variants...

  5. Cytogenetic Mapping of Disease Resistance Genes and Analysis of Their Distribution Features on Chromosomes in Maize

    Institute of Scientific and Technical Information of China (English)

    LiLi-jia; SongYun-chun

    2003-01-01

    Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Htl, Htnl and Ht2, Helminthosporium maydis Nisik resistance genes Rhml and Rhm2,maize dwarf mosaic virus resistance gene Mdml, wheat streak mosaic virus resistance gene Wsml, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2. 1 of tomato, and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i. e. , chromosomesl, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3. 25) except for genes Rhml, Rhm2, Mdml and Wsml which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.

  6. Analysis of the Ambient Particulate Matter-induced Chromosomal Aberrations Using an In Vitro System.

    Science.gov (United States)

    Miousse, Isabelle R; Koturbash, Igor; Chalbot, Marie-Cécile; Hauer-Jensen, Martin; Kavouras, Ilias; Pathak, Rupak

    2016-12-21

    Exposure to particulate matter (PM) is a major world health concern, which may damage various cellular components, including the nuclear genetic material. To assess the impact of PM on nuclear genetic integrity, structural chromosomal aberrations are scored in the metaphase spreads of mouse RAW264.7 macrophage cells. PM is collected from ambient air with a high volume total suspended particles sampler. The collected material is solubilized and filtered to retain the water-soluble, fine portion. The particles are characterized for chemical composition by nuclear magnetic resonance (NMR) spectroscopy. Different concentrations of particle suspension are added onto an in vitro culture of RAW264.7 mouse macrophages for a total exposure time of 72 hr, along with untreated control cells. At the end of exposure, the culture is treated with colcemid to arrest cells in metaphase. Cells are then harvested, treated with hypotonic solution, fixed in acetomethanol, dropped onto glass slides and finally stained with Giemsa solution. Slides are examined to assess the structural chromosomal aberrations (CAs) in metaphase spreads at 1,000X magnification using a bright-field microscope. 50 to 100 metaphase spread are scored for each treatment group. This technique is adapted for the detection of structural chromosomal aberrations (CAs), such as chromatid-type breaks, chromatid-type exchanges, acentric fragments, dicentric and ring chromosomes, double minutes, endoreduplication, and Robertsonian translocations in vitro after exposure to PM. It is a powerful method to associate a well-established cytogenetic endpoint to epigenetic alterations.

  7. Karyotype analysis of Lilium longiflorum and Lilium rubellum by chromosome banding and fluorescence in situ hybridisation

    NARCIS (Netherlands)

    Lim, K.B.; Wennekes, J.; Jong, de J.H.S.G.M.; Jacobsen, E.; Tuyl, van J.M.

    2001-01-01

    Detailed karyotypes of Lilium longiflorum and L. rubellum were constructed on the basis of chromosome arm lengths, C-banding, AgNO3 staining, and PI-DAPI banding, together with fluorescence in situ hybridisation (FISH) with the 5S and 45S rDNA sequences as probes. The C-banding patterns that were ob

  8. Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca.

    Science.gov (United States)

    Hallinan, Nathaniel M; Lindberg, David R

    2011-01-01

    The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda.

  9. Array comparative genomic hybridization analysis of small supernumerary marker chromosomes in human infertility.

    Science.gov (United States)

    Guediche, N; Tosca, L; Kara Terki, A; Bas, C; Lecerf, L; Young, J; Briand-Suleau, A; Tou, B; Bouligand, J; Brisset, S; Misrahi, M; Guiochon-Mantel, A; Goossens, M; Tachdjian, G

    2012-01-01

    Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by conventional banding cytogenetics. This study describes four patients with sSMC in relation with infertility. Patient 1 had primary infertility. His brother, fertile, carried the same sSMC (patient 2). Patient 3 presented polycystic ovary syndrome and patient 4 primary ovarian insufficiency. Cytogenetic studies, array comparative genomic hybridization (CGH) and sperm analyses were compared with cases previously reported. sSMC corresponded to the 15q11.2 region (patients 1 and 2), the centromeric chromosome 15 region (patient 3) and the 21p11.2 region (patient 4). Array CGH showed 3.6-Mb gain for patients 1 and 2 and 0.266-Mb gain for patient 4. Sperm fluorescent in-situ hybridization analyses found ratios of 0.37 and 0.30 of sperm nuclei with sSMC(15) for patients 1 and 2, respectively (P < 0.001). An increase of sperm nuclei with disomy X, Y and 18 was noted for patient 1 compared with control and patient 2 (P < 0.001). Among the genes mapped in the unbalanced chromosomal regions, POTE B and BAGE are related to the testis and ovary, respectively. The implication of sSMC in infertility could be due to duplication, but also to mechanical effects perturbing meiosis.

  10. Selective chromosome analysis in couples with two or more miscarriages : case-control study

    NARCIS (Netherlands)

    Franssen, MTM; Korevaar, JC; Leschot, NJ; Bossuyt, PMM; Knegt, AC; Gerssen-Schoorl, KBJ; Wouters, CH; Hansson, KBM; Hochstenbach, R; Madan, K; van der Veen, F; Goddijn, M

    2005-01-01

    Objective To identify additional factors, such as maternal age or factors related to previous reproductive outcome or family history, and the corresponding probability of carrying a chromosome abnormality in couples with two or more miscarriages. Design Nested case-control study. Setting Six centres

  11. Population Genetics of a Parasitic Chromosome : Theoretical Analysis of PSR in Subdivided Populations

    NARCIS (Netherlands)

    Werren, John H.; Beukeboom, Leo W.; Wu, Chung-I

    1993-01-01

    An assemblage of non-Mendelian sex ratio elements occurs in natural populations of the parasitoid wasp Nasonia vitripennis. These include Maternal Sex Ratio (MSR), a cytoplasmic element that causes nearly all-female families, and Paternal Sex Ratio (PSR), a B chromosome that causes all-male families

  12. Population Genetics of a Parasitic Chromosome : Experimental Analysis of PSR in Subdivided Populations

    NARCIS (Netherlands)

    Beukeboom, Leo W.; Werren, John H.; Charlesworth, B.

    1992-01-01

    Nasonia vitripennis is a parasitoid wasp that harbors several non-Mendelian sex-ratio distorters. These include MSR (Maternal Sex Ratio), a cytoplasmic element that causes nearly all-female families, and PSR (Paternal Sex Ratio), a supernumerary chromosome that causes all-male families. As in other

  13. Mutation screening and association analysis of six candidate genes for autism on chromosome 7q

    DEFF Research Database (Denmark)

    Bonora, E.; Lamb, J.A.; Barnby, G.;

    2005-01-01

    Genetic studies have provided evidence for an autism susceptibility locus (AUTS1) on chromosome 7q. Screening for mutations in six genes mapping to 7q, CUTL1, SRPK2, SYPL, LAMB1, NRCAM and PTPRZ1 in 48 unrelated individuals with autism led to the identification of several new coding variants in t...

  14. A meta-analysis of local adaptation in plants.

    Directory of Open Access Journals (Sweden)

    Roosa Leimu

    Full Text Available Local adaptation is of fundamental importance in evolutionary, population, conservation, and global-change biology. The generality of local adaptation in plants and whether and how it is influenced by specific species, population and habitat characteristics have, however, not been quantitatively reviewed. Therefore, we examined published data on the outcomes of reciprocal transplant experiments using two approaches. We conducted a meta-analysis to compare the performance of local and foreign plants at all transplant sites. In addition, we analysed frequencies of pairs of plant origin to examine whether local plants perform better than foreign plants at both compared transplant sites. In both approaches, we also examined the effects of population size, and of the habitat and species characteristics that are predicted to affect local adaptation. We show that, overall, local plants performed significantly better than foreign plants at their site of origin: this was found to be the case in 71.0% of the studied sites. However, local plants performed better than foreign plants at both sites of a pair-wise comparison (strict definition of local adaption only in 45.3% of the 1032 compared population pairs. Furthermore, we found local adaptation much more common for large plant populations (>1000 flowering individuals than for small populations (<1000 flowering individuals for which local adaptation was very rare. The degree of local adaptation was independent of plant life history, spatial or temporal habitat heterogeneity, and geographic scale. Our results suggest that local adaptation is less common in plant populations than generally assumed. Moreover, our findings reinforce the fundamental importance of population size for evolutionary theory. The clear role of population size for the ability to evolve local adaptation raises considerable doubt on the ability of small plant populations to cope with changing environments.

  15. Numerous transitions of sex chromosomes in Diptera.

    Science.gov (United States)

    Vicoso, Beatriz; Bachtrog, Doris

    2015-04-01

    Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.

  16. cDNA cloning, tissue distribution, and chromosomal localization of Ocp2, a gene encoding a putative transcription-associated factor predominantly expressed in the auditory organs

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hong; Thalmann, I.; Thalmann, R. [Washington Univ., St. Louis, MO (United States)] [and others

    1995-06-10

    We report the cloning of the Ocp2 gene encoding OCP-II from a guinea pig organ-of-Corti cDNA library. The predicted open reading frame encodes a protein of 163 amino acids with an estimated molecular mass of 18.6 kDa. A homology search revealed that Ocp2 shares significant sequence similarity with p15, a sub-unit of transcription factor SIII that regulates the activity of the RNA polymerase II elongation complex. The Ocp2 messenger RNA is expressed abundantly in the cochlea while not significantly in any other tissues examined, including brain, eye, heart, intestine, kidney, liver, lung, thigh muscle, and testis, demonstrating that the expression of this gene may be restricted to auditory organs. A polyclonal antiserum was raised against the N-terminal region of OCP-II. Immunohistochemical staining of paraffin-embedded sections of the cochlea showed that OCP-II is localized abundantly in nonsensory cells in the organ of Corti; in addition, it was also detected, at a lower concentration, in vestibular sensory organs, as well as auditory and vestibular brain stem nuclei. The Ocp2 gene was mapped to mouse chromosome 4 as well as 11. Our results suggest that OCP-II may be involved in transcription regulation for the development or maintenance of specialized functions of the inner ear. 40 refs., 5 figs.

  17. Molecular cloning of the cDNA and chromosomal localization of the gene for a putative seven-transmembrane segment (7-TMS) receptor isolated from human spleen

    Energy Technology Data Exchange (ETDEWEB)

    Federsppiel, B.; Melhado, I.G.; Delaney, A.; Clark-Lewis, I. (Univ. of British Columbia, Vancouver (Canada)); Duncan, A.M.V. (Queens Univ., Kinston, Ontario (Canada)); Jirik, F.R. (Hospital for Sick Children, Toronto, Ontario (Canada))

    1993-06-01

    A family of proinflammatory cytokines sharing several structural features has been described and includes, for example, interleukin-8, monocyte chemoattractant protein-1, and melanocyte growth stimulatory activity. Recently, the receptors for interleukin-8 have been isolated and found to belong to the seven-transmembrane domain class of G protein-coupled receptors. As other members of this cytokine family likely interact with similar receptors, the polymerase chain reaction was employed to isolate related receptors from human peripheral blood adherent cells. Degenerate oligonucleotide primers based on the rabbit interleukin-8 receptor sequence were used. The corresponding full-length cDNA was isolated from a human spleen cDNA library. The predicted protein sequence of this clone, designated pBE1.3, was 93% identical to that of a cDNA isolated from bovine locus coeruleus, which apparently encodes a neuropeptide Y receptor, and also shows similarity with the interleukin-8 receptor and the human cytomegalovirus US28 sequences. The gene, designated D2S201E, was localized to human chromosome 2q21. By Northern blotting, transcripts hybridizing to this cDNA were present in a variety of tissues and cells, including those of hemopoietic origin. 32 refs., 5 figs.

  18. Characterization of the human and rat phospholemman (PLM) cDNAs and localization of the human PLM gene to chromosome 19q13.1.

    Science.gov (United States)

    Chen, L S; Lo, C F; Numann, R; Cuddy, M

    1997-05-01

    Previous reports have demonstrated that the phospholemman (PLM), a 72-residue plasma-membrane protein enriched in skeletal muscle and heart, is a major substrate phosphorylated in response to insulin and adrenergic stimulation. Here we describe the isolation and characterization of human and rat PLM cDNA from the heart. Both PLM proteins share significant nucleotide and amino acid sequence and structural similarities with the previously published canine PLM and, to a lesser degree, with Na+/K(+)-ATPase gamma subunit, Mat-8 protein, and CHIF protein. Despite the functional diversity, all these proteins are quite small and possess a single transmembrane domain. Human PLM appears to be a unique gene localized on chromosome 19q13.1. The PLM mRNA is widely distributed in human tissues, with the highest expression in skeletal muscle and heart, suggesting a functional role in muscle contraction. Like canine PLM, both human and rat PLM induce a hyperpolarization-activated chloride current when expressed in Xenopus oocytes. The high degree of sequence and functional conservation among the mammalian PLM proteins indicates that this gene is conserved throughout evolution.

  19. The gene for calcium-modulating cyclophilin ligand (CAMLG) is located on human Chromosome 5q23 and a syntenic region of mouse chromosome 13

    Energy Technology Data Exchange (ETDEWEB)

    Bram, R.J.; Valentine, V.; Shapiro, D.N. [St. Jude Children`s Research Hospital, Memphis, TN (United States)]|[Univ. of Tennessee, Memphis, TN (United States)] [and others

    1996-01-15

    The CAMLG gene encodes a novel cyclophilin B-binding protein called calcium-modulating cyclophilin ligand, which appears to be involved in the regulation of calcium signaling in T lymphocytes and other cells. The murine homolog, Caml, was localized by interspecific backcross analysis in the middle of chromosome 13. By fluorescence in situ hybridization, this gene was localized to human chromosome 5 in a region (q23) known to be syntenic to mouse chromosome 13. These results provide further evidence supporting the extensive homology between human chromosome 5q and mouse chromosome 13. In addition, the results will provide a basis for further evaluation of cytogenetic anomalies that may contribute to inherited defects in calcium signaling or immune system function. 15 refs., 2 figs.

  20. Cytogenetic Mapping of Disease Resistance Genes and Analysis of Their Distribution Features on Chromosomes in Maize

    Institute of Scientific and Technical Information of China (English)

    Li Li-jia; Song Yun-chun

    2003-01-01

    Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Ht1, Htn1 and Ht2, Helminthosporium maydis Nisik resistance genes Rhm1 and Rhm2, maize dwarf mosaic virus resistance gene Mdm1, wheat streak mosaic virus resistance gene Wsm1, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2.1 of tomato,and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i.e., chromosomes1, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3.25) except for genes Rhm1, Rhm2, Mdm1 and Wsm1 which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.

  1. A Habermasian Analysis of Local Renewable Energy Deliberations

    Science.gov (United States)

    Fast, Stewart

    2013-01-01

    This study pursues a Habermasian analysis of citizen discussions and of the local public sphere to shed light on renewable energy futures in rural east-central Canada. Using data from group discussions, it pursues an investigation of utterances, validity claims and of discourses. The analysis is supplemented by participant observation of publicly…

  2. Bloom syndrome and maternal uniparental disomy for chromosome 15

    Energy Technology Data Exchange (ETDEWEB)

    Woodage, T.; Prasad, M.; Trent, R.J.; Smith, A. (Children' s Hospital, Camperdown, New South Wales (New Zealand)); Dixon, J.W.; Romain, D.R.; Columbano-Green, L.M.; Selby, R.E. (Wellington Hospital (New Zealand)); Graham, D. (Waikato Hospital, Hamilton (New Zealand)); Rogan, P.K. (Pennsylvania State Univ., Hershey, PA (United States)) (and others)

    1994-07-01

    Bloom syndrome (BS) is an autosomal recessive disorder characterized by increases in the frequency of sister-chromatid exchange and in the incidence of malignancy. Chromosome-transfer studies have shown the BS locus to map to chromosome 15q. This report describes a subject with features of both BS and Prader-Willi syndrome (PWS). Molecular analysis showed maternal uniparental disomy for chromosome 15. Meiotic recombination between the two disomic chromosomes 15 has resulted in heterodisomy for proximal 15q and isodisomy for distal 15q. In this individual BS is probably due to homozygosity for a gene that is telomeric to D15S95 (15q25), rather than to genetic imprinting, the mechanism responsible for the development of PWS. This report represents the first application of disomy analysis to the regional localization of a disease gene. This strategy promises to be useful in the genetic mapping of other uncommon autosomal recessive conditions. 37 refs., 3 figs., 2 tabs.

  3. Polymorphism analysis of microsatellites and construction of linkage map in part regions of four chromosomes in chicken

    Institute of Scientific and Technical Information of China (English)

    WANG Shouzhi; LI Hui; LI Ning; GAO Yu; DU Zhiqiang; GU Zhiliang; WANG Qigui; LI Zhihui; WANG Ying

    2007-01-01

    Based on chicken' consensus map issued in 2000, 17 microsatellites near 4 candidate genes such as IGF2, OBR, GDFS and APOA1 in 4 chromosomes (chromosome 5, 7, 8 and 24) were chosen for polymorphism analysis and construction of linkage map. Combining the technique of PCR and the fluorescent semi-automated detection, genome scanning was performed for 440 chickens, which was derived from China Agricultural University chicken resource families within three generations. The individuals of this resource families were genotyped. The results showed that the number of alleles ranged from 4 to 14; heterozygosity (H) of markers was between 0.3116 and 0.9148. Polymorphic information content (PIC) varied from 0.2672 to 0.8679. Microsatellites along with above-mentioned 4 candidate genes doing as general markers were used to construct linkage map. The spans of 4 linkage maps constructed in the part region of chromosome 5, 7, 8 and 24 were 263.5, 79.9, 206.2 and 104.2 cM, respectively. The order of markers was consistent with that of counterpart of reported consensus map. However, The spans of linkage map were larger than that of consensus map. The constructed linkage maps laid the foundation for mapping quantitative trait loci (QTL) responsible for economically important traits in chicken.

  4. Genetic Alterations in Pesticide Exposed Bolivian Farmers: An evaluation by analysis of chromosomal aberrations and the comet assay

    Directory of Open Access Journals (Sweden)

    Erik Jørs

    2007-01-01

    Full Text Available Background: Pesticides are of concern in Bolivia because of increasing use. Frequent intoxications have been demonstrated due to use of very toxic pesticides, insufficient control of distribution and sale and little knowledge among farmers of protective measures and hygienic procedures.Method: Questionnaires were applied and blood tests taken from 81 volunteers from La Paz County, of whom 48 were pesticide exposed farmers and 33 non-exposed controls. Sixty males and 21 females participated with a mean age of 37.3 years (range 17–76. Data of exposure and possible genetic damage were collected and evaluated by well known statistical methods, controlling for relevant confounders. To measure genetic damage chromosomal aberrations and the comet assay analysis were performed.Results: Pesticide exposed farmers had a higher degree of genetic damage compared to the control group. The number of chromosomal aberrations increased with the intensity of pesticide exposure. Females had a lower number of chromosomal aberrations than males, and people living at altitudes above 2500 metres seemed to exhibit more DNA damage measured by the comet assay.Conclusions: Bolivian farmers showed signs of genotoxic damage, probably related to exposure to pesticides. Due to the potentially negative long term health effects of genetic damage on reproduction and the development of cancer, preventive measures are recommended. Effective control with imports and sales, banning of the most toxic pesticides, education and information are possible measures, which could help preventing the negative effects of pesticides on human health and the environment.

  5. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis.

    Directory of Open Access Journals (Sweden)

    Viviana Kozina

    Full Text Available BACKGROUND: Y-chromosomal microdeletions (YCMD are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. PRINCIPAL FINDINGS: The widely established "EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004" were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. SIGNIFICANCE: With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.

  6. Antenatal screening combined with chromosome analysis to prevent fetus birth with chromosome disease%产前筛查并染色体分析预防染色体病胎儿出生

    Institute of Scientific and Technical Information of China (English)

    王宏; 陈武斌

    2011-01-01

    目的 对产前筛查和染色体分析预防染色体病胎儿出生的工作进行回顾性的总结,为今后减少出生缺陷提供指导.方法 通过对优生咨询、血清筛查检出的高风险孕妇和超声筛查怀疑胎儿有染色体病的孕妇进行胎儿染色体分析,核型严重异常者终止妊娠.结果 ①优生咨询筛查出的高风险孕妇中接受染色体分析者372例,染色体异常检出率为4.57%(17/372),终止妊娠5例;②血清筛查孕妇共32 848例,高风险2 085例,筛查阳性率6.35%;染色体分析740例,染色体异常检出率为4.59%(34/740),终止妊娠18例;③超声筛查异常进行染色体分析177例,异常检出率为19.77%(35/177),终止妊娠32例;④染色体分析共1 289例,异常检出率为6.67%(86/1 289),数目异常50例全部终止妊娠,结构异常36例中有5例终止妊娠,终止妊娠率为4.27%(55/1 289).结论 优生咨询、血清筛查、超声筛查组成的筛查体系结合染色体分析可提高染色体病的检出率,超声筛查的检出率最高;每位孕妇都应接受系统的产前筛查,高危孕妇应接受染色体分析,最大限度地避免染色体病胎儿出生.%Objective To retrospectively analyze the results of antenatal screening and chromosome analysis on the prevalence of fetus birth with chromosome disease so as to provide guidance for reducing birth defects in the future. Methods Fetal chromosomal analysis was done for high-risk pregnant women screened by eugenic consulation and serum screening and for those whose fetus were suspected to have chromosomal abnormalities detected by ultrasonography. Termination of pregnancy ( TOP ) was given to severe abnormal karyotype. Results Among the high-risk pregnant women screened by eugenic consulation, 372 cases received chromosome analysis, and the detection rate of chromosomal abnormality was 4. 57% ( 17/372 ). Five cases accepted TOP. There were 2 085 cases with high risk among 32 848 pregnant women receiving serum

  7. Genomic structure, chromosomal localization and expression profile of a novel melanoma differentiation associated (mda-7) gene with cancer specific growth suppressing and apoptosis inducing properties.

    Energy Technology Data Exchange (ETDEWEB)

    Huang, E. Y.; Madireddi, M. T.; Gopalkrishnan, R. V.; Leszczyniecka, M.; Su, Z. Z.; Lebedeva, I. V.; Kang, D. C.; Jian, H.; Lin, J. J.; Alexandre, D.; Chen, Y.; Vozhilla, N.; Mei, M. X.; Christiansen, K. A.; Sivo, F.; Goldstein, N. I.; Chada, S.; Huberman, E.; Pestka, S.; Fisher, P. B.; Biochip Technology Center; Columbia Univ.; Introgen Therapeutics Inc.; UMDNJ-Robert Wood Johnson Medical School

    2001-10-25

    Abnormalities in cellular differentiation are frequent occurrences in human cancers. Treatment of human melanoma cells with recombinant fibroblast interferon (IFN-beta) and the protein kinase C activator mezerein (MEZ) results in an irreversible loss in growth potential, suppression of tumorigenic properties and induction of terminal cell differentiation. Subtraction hybridization identified melanoma differentiation associated gene-7 (mda-7), as a gene induced during these physiological changes in human melanoma cells. Ectopic expression of mda-7 by means of a replication defective adenovirus results in growth suppression and induction of apoptosis in a broad spectrum of additional cancers, including melanoma, glioblastoma multiforme, osteosarcoma and carcinomas of the breast, cervix, colon, lung, nasopharynx and prostate. In contrast, no apparent harmful effects occur when mda-7 is expressed in normal epithelial or fibroblast cells. Human clones of mda-7 were isolated and its organization resolved in terms of intron/exon structure and chromosomal localization. Hu-mda-7 encompasses seven exons and six introns and encodes a protein with a predicted size of 23.8 kDa, consisting of 206 amino acids. Hu-mda-7 mRNA is stably expressed in the thymus, spleen and peripheral blood leukocytes. De novo mda-7 mRNA expression is also detected in human melanocytes and expression is inducible in cells of melanocyte/melanoma lineage and in certain normal and cancer cell types following treatment with a combination of IFN-beta plus MEZ. Mda-7 expression is also induced during megakaryocyte differentiation induced in human hematopoietic cells by treatment with TPA (12-O-tetradecanoyl phorbol-13-acetate). In contrast, de novo expression of mda-7 is not detected nor is it inducible by IFN-beta+MEZ in a spectrum of additional normal and cancer cells. No correlation was observed between induction of mda-7 mRNA expression and growth suppression following treatment with IFN-beta+MEZ and

  8. Chromosome studies of European cyprinid fishes: cross-species painting reveals natural allotetraploid origin of a Carassius female with 206 chromosomes.

    Science.gov (United States)

    Knytl, M; Kalous, L; Symonová, R; Rylková, K; Ráb, P

    2013-01-01

    A single female with 206 chromosomes and another 26 females with 156 chromosomes identified as Prussian carp, Carassius gibelio, and 5 individuals with 100 chromosomes identified as crucian carp, C. carassius, were sampled during field survey in one locality in the upper Elbe River. To identify the origin of females with high chromosome numbers, comparative karyotype analysis, GISH, with whole C. carassius DNA as probe and phylogenetic positions of sampled individuals revealed by cytochrome b mitochondrial marker were performed. GISH showed consistently bright labeling of 50 chromosomal elements out of 206, corresponding to the haploid chromosome number of C. carassius. The position of these females with high chromosome numbers in a reconstructed phylogenetic tree was within the clade of C. gibelio, documenting its affiliation to C. gibelio mitochondrial, i.e. maternal lineage. Our findings indicated that the mother of the female with high chromosome numbers was a gynogenetically reproducing 156-chromosome C. gibelio female and the father a bisexually reproducing C. carassius male. We, therefore, hypothesized that the C. gibelio × C. carassius allopolyploid female with 206 chromosomes arose by a mechanism of sperm genome addition to an unreduced egg of the mother.

  9. Experimental Researches on Carcinogenesis or Tumorigenicity of MDCK Canine Kidney Cell(CKC) Lines and Analysis of Their Chromosome Karyotypes

    Institute of Scientific and Technical Information of China (English)

    ZHANG De-li; FANG Fu-de; LI Liu-jin; XIA Geng-tian; HE Xu-yu; GAO Bu-xian; BAI Xiao-hong; HUANG Gao-sheng; LIU Shang-gao; YAN Long-fei

    2002-01-01

    The chromosomal number variations & structural aberrations of the MDCK cell line, primary feline or canine kidney cell(FKC or CKC) and Hela cell line were investigated and their karyotypes of conventional chromosome bands were analyzed. The carcinogenesis or tumorigenicity testing of these cell lines in about 232 nude mice and for colony formation in soft agarose and for haemagglutination under different concentration of plant lectins of these cells were carried out. Under the prerequisite that the incidence of cancer or tumor in negative-control nude mice inoculated subcutaneously with primary feline or canine kidney cell cultures purified in vitro at passage 3 was 0 (0/22) and 0 (0/10), respectively. The incidence of the progressively-growing malignant tumor(MT) in positive-control nude mice inoculated subcutaneously with Hela cell cultures of KB, X, or NM20/X strain was 10/10, 25/25 and 5/51, respectively. The results showed that the incidence of tumor in nude mice with tetrapioid YA strain of MDCK cell during 20 - 45 passages, with hypodiploid JB strain of MDCK cell on passage 25, with di-and hypoploid JC strain of MDCK cell during 2 - 15passages or with hypoploid M strain of MDCK cell during 9 - 27 passages was 28/58, 1/5, 4/18 and 0/31,respectively. The chromosomal analysis results showed that the ratio of difference in the rate of modal chromosome number between high (mcs + n) and lowest (mcs)passages was not more than 5 % - 15 % and the structure aberrations was generally 0 - 3%. These results proved that the genetic characteristics of chromosomal number of cell lines determines their tumorigenicity, but it is species-specific. MDCK line has tumorigenicity no matter what its chromosome karyotype is, at least it has very low tumorigenicity even when its modal chromosome number is hypoploid. The repeatedly frozen, thawed and split controls of tumorigenicity-positive cell lines(X strain of Hela, M strain of BHK-21, JA strain of Vero, YA strain of MDCK) have

  10. [Sex chromosomes and meiosis].

    Science.gov (United States)

    Guichaoua, M-R; Geoffroy-Siraudin, C; Tassistro, V; Ghalamoun-Slaimi, R; Perrin, J; Metzler-Guillemain, C

    2009-01-01

    Sex chromosome behaviour fundamentally differs between male and female meiosis. In oocyte, X chromosomes synapse giving a XX bivalent which is not recognizable in their morphology and behaviour from autosomal bivalents. In human male, X and Y chromosomes differ from one another in their morphology and their genetic content, leading to a limited pairing and preventing genetic recombination, excepted in homologous region PAR1. During pachytene stage of the first meiotic prophase, X and Y chromosomes undergo a progressive condensation and form a transcriptionally silenced peripheral XY body. The condensation of the XY bivalent during pachytene stage led us to describe four pachytene substages and to localize the pachytene checkpoint between substages 2 and 3. We also defined the pachytene index (PI=P1+P2/P1+P2+P3+P4) which is always less than 0.50 in normal meiosis. XY body undergoes decondensation at diplotene stage, but transcriptional inactivation of the two sex chromosomes or Meiotic Sex Chromosome Inactivation (MSCI) persists through to the end of spermatogenesis. Sex chromosome inactivation involves several proteins, some of them were now identified. Two isoforms of the HP1 protein, HP1beta and HP1gamma, are involved in the facultative heterochromatinization of the XY body, but the initiation of this process involves the phosphorylation of the protein H2AX by the kinase ATR whose recruitment depends on BRCA1. Extensive researches on the inactivation of the sex chromosomes during male meiosis will allow to a better understanding of some male infertilities.

  11. The Staurotypus turtles and aves share the same origin of sex chromosomes but evolved different types of heterogametic sex determination.

    Science.gov (United States)

    Kawagoshi, Taiki; Uno, Yoshinobu; Nishida, Chizuko; Matsuda, Yoichi

    2014-01-01

    Reptiles have a wide diversity of sex-determining mechanisms and types of sex chromosomes. Turtles exhibit temperature-dependent sex determination and genotypic sex determination, with male heterogametic (XX/XY) and female heterogametic (ZZ/ZW) sex chromosomes. Identification of sex chromosomes in many turtle species and their comparative genomic analysis are of great significance to understand the evolutionary processes of sex determination and sex chromosome differentiation in Testudines. The Mexican giant musk turtle (Staurotypus triporcatus, Kinosternidae, Testudines) and the giant musk turtle (Staurotypus salvinii) have heteromorphic XY sex chromosomes with a low degree of morphological differentiation; however, their origin and linkage group are still unknown. Cross-species chromosome painting with chromosome-specific DNA from Chinese soft-shelled turtle (Pelodiscus sinensis) revealed that the X and Y chromosomes of S. triporcatus have homology with P. sinensis chromosome 6, which corresponds to the chicken Z chromosome. We cloned cDNA fragments of S. triporcatus homologs of 16 chicken Z-linked genes and mapped them to S. triporcatus and S. salvinii chromosomes using fluorescence in situ hybridization. Sixteen genes were localized to the X and Y long arms in the same order in both species. The orders were also almost the same as those of the ostrich (Struthio camelus) Z chromosome, which retains the primitive state of the avian ancestral Z chromosome. These results strongly suggest that the X and Y chromosomes of Staurotypus turtles are at a very early stage of sex chromosome differentiation, and that these chromosomes and the avian ZW chromosomes share the same origin. Nonetheless, the turtles and birds acquired different systems of heterogametic sex determination during their evolution.

  12. The Staurotypus turtles and aves share the same origin of sex chromosomes but evolved different types of heterogametic sex determination.

    Directory of Open Access Journals (Sweden)

    Taiki Kawagoshi

    Full Text Available Reptiles have a wide diversity of sex-determining mechanisms and types of sex chromosomes. Turtles exhibit temperature-dependent sex determination and genotypic sex determination, with male heterogametic (XX/XY and female heterogametic (ZZ/ZW sex chromosomes. Identification of sex chromosomes in many turtle species and their comparative genomic analysis are of great significance to understand the evolutionary processes of sex determination and sex chromosome differentiation in Testudines. The Mexican giant musk turtle (Staurotypus triporcatus, Kinosternidae, Testudines and the giant musk turtle (Staurotypus salvinii have heteromorphic XY sex chromosomes with a low degree of morphological differentiation; however, their origin and linkage group are still unknown. Cross-species chromosome painting with chromosome-specific DNA from Chinese soft-shelled turtle (Pelodiscus sinensis revealed that the X and Y chromosomes of S. triporcatus have homology with P. sinensis chromosome 6, which corresponds to the chicken Z chromosome. We cloned cDNA fragments of S. triporcatus homologs of 16 chicken Z-linked genes and mapped them to S. triporcatus and S. salvinii chromosomes using fluorescence in situ hybridization. Sixteen genes were localized to the X and Y long arms in the same order in both species. The orders were also almost the same as those of the ostrich (Struthio camelus Z chromosome, which retains the primitive state of the avian ancestral Z chromosome. These results strongly suggest that the X and Y chromosomes of Staurotypus turtles are at a very early stage of sex chromosome differentiation, and that these chromosomes and the avian ZW chromosomes share the same origin. Nonetheless, the turtles and birds acquired different systems of heterogametic sex determination during their evolution.

  13. FINANCIAL SIDE ANALYSIS OF LOCAL AUTONOMY IN ROMANIA

    Directory of Open Access Journals (Sweden)

    ICHIM CRISTINEL

    2012-05-01

    Full Text Available Financial side of local autonomy expresses the capacity of local communities to have their own revenue and expenditure budget, distinct from that of the state in which revenues can cover expenses incurred to meet their requirements. The analysis of financial autonomy of administrative-territorial units in Romania is an interesting but complex approach given that some factors are actually difficult to predict and quantify.The purpose of this paper is to clarify the meaning of financial side of local autonomy and analyze this in Romania based on indicators established in recent years for measuring the position of administrative-territorial units in relation to central government.

  14. Distribution of the sex chromosome during mouse spermatogenesis in testis tissue sections.

    Science.gov (United States)

    Otaka, Kosuke; Hiradate, Yuuki; Kobayashi, Norio; Shirakata, Yoshiki; Tanemura, Kentaro

    2015-01-01

    During mammalian spermatogenesis, spermatogenic cells undergo mitotic division and are subsequently divided into haploid spermatids by meiotic division, but the dynamics of sex chromosomes during spermatogenesis are unclear in vivo. To gain insight into the distribution of sex chromosomes in the testis, we examined the localization of sex chromosomes before and after meiosis in mouse testis sections. Here, we developed a method of fluorescence in situ hybridization (FISH) using specific probes for the X and Y chromosomes to obtain their positional information in histological testis sections. FISH analysis revealed the sex chromosomal position during spermatogenesis in each stage of seminiferous epithelia and in each spermatogenic cell. In the spermatogonia and leptotene spermatocytes, sex chromosomes were distantly positioned in the cell. In the zygotene and pachytene spermatocytes at prophase I, X and Y chromosomes had a random distribution. After meiosis, the X and Y spermatids were random in every seminiferous epithelium. We also detected aneuploidy of sex chromosomes in spermatogenic cells using our developed FISH analysis. Our results provide further insight into the distribution of sex chromosomes during spermatogenesis, which could help to elucidate a specific difference between X and Y spermatids and sex chromosome-specific behavior.

  15. System-wide immunohistochemical analysis of protein co-localization.

    Directory of Open Access Journals (Sweden)

    Minjung Kim

    Full Text Available The analysis of co-localized protein expression in a tissue section is often conducted with immunofluorescence histochemical staining which is typically visualized in localized regions. On the other hand, chromogenic immunohistochemical staining, in general, is not suitable for the detection of protein co-localization. Here, we developed a new protocol, based on chromogenic immunohistochemical stain, for system-wide detection of protein co-localization and differential expression.In combination with a removable chromogenic stain, an efficient antibody stripping method was developed to enable sequential immunostaining with different primary antibodies regardless of antibody's host species. Sections were scanned after each staining, and the images were superimposed together for the detection of protein co-localization and differential expression. As a proof of principle, differential expression and co-localization of glutamic acid decarboxylase67 (GAD67 and parvalbumin proteins was examined in mouse cortex.All parvalbumin-containing neurons express GAD67 protein, and GAD67-positive neurons that do not express parvalbumin were readily visualized from thousands of other neurons across mouse cortex. The method provided a global view of protein co-localization as well as differential expression across an entire tissue section. Repeated use of the same section could combine assessments of co-localization and differential expression of multiple proteins.

  16. Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings.

    Science.gov (United States)

    Martinez-Cruz, Begoña; Ioana, Mihai; Calafell, Francesc; Arauna, Lara R; Sanz, Paula; Ionescu, Ramona; Boengiu, Sandu; Kalaydjieva, Luba; Pamjav, Horolma; Makukh, Halyna; Plantinga, Theo; van der Meer, Jos W M; Comas, David; Netea, Mihai G

    2012-01-01

    Vlad III The Impaler, also known as Dracula, descended from the dynasty of Basarab, the first rulers of independent Wallachia, in present Romania. Whether this dynasty is of Cuman (an admixed Turkic people that reached Wallachia from the East in the 11(th) century) or of local Romanian (Vlach) origin is debated among historians. Earlier studies have demonstrated the value of investigating the Y chromosome of men bearing a historical name, in order to identify their genetic origin. We sampled 29 Romanian men carrying the surname Basarab, in addition to four Romanian populations (from counties Dolj, N = 38; Mehedinti, N = 11; Cluj, N = 50; and Brasov, N = 50), and compared the data with the surrounding populations. We typed 131 SNPs and 19 STRs in the non-recombinant part of the Y-chromosome in all the individuals. We computed a PCA to situate the Basarab individuals in the context of Romania and its neighboring populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name. All haplogroups are common in Romania and other Central and Eastern European populations. In a PCA, the Basarab group clusters within other Romanian populations. We found several clusters of Basarab individuals having a common ancestor within the period of the last 600 years. The diversity of haplogroups found shows that not all individuals carrying the surname Basarab can be direct biological descendants of the Basarab dynasty. The absence of Eastern Asian lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of the Basarab dynasty, although it cannot be positively ruled out. It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

  17. Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings.

    Directory of Open Access Journals (Sweden)

    Begoña Martinez-Cruz

    Full Text Available Vlad III The Impaler, also known as Dracula, descended from the dynasty of Basarab, the first rulers of independent Wallachia, in present Romania. Whether this dynasty is of Cuman (an admixed Turkic people that reached Wallachia from the East in the 11(th century or of local Romanian (Vlach origin is debated among historians. Earlier studies have demonstrated the value of investigating the Y chromosome of men bearing a historical name, in order to identify their genetic origin. We sampled 29 Romanian men carrying the surname Basarab, in addition to four Romanian populations (from counties Dolj, N = 38; Mehedinti, N = 11; Cluj, N = 50; and Brasov, N = 50, and compared the data with the surrounding populations. We typed 131 SNPs and 19 STRs in the non-recombinant part of the Y-chromosome in all the individuals. We computed a PCA to situate the Basarab individuals in the context of Romania and its neighboring populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name. All haplogroups are common in Romania and other Central and Eastern European populations. In a PCA, the Basarab group clusters within other Romanian populations. We found several clusters of Basarab individuals having a common ancestor within the period of the last 600 years. The diversity of haplogroups found shows that not all individuals carrying the surname Basarab can be direct biological descendants of the Basarab dynasty. The absence of Eastern Asian lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of the Basarab dynasty, although it cannot be positively ruled out. It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

  18. Linkage analysis of 19 French breast cancer families, with five chromosome 17q markers.

    OpenAIRE

    Mazoyer, S; Lalle, P.; Narod, S. A.; Bignon, Y J; Courjal, F; Jamot, B.; Dutrillaux, B.; Stoppa-Lyonnett, D; Sobol, H

    1993-01-01

    Nineteen French breast and breast-ovarian cancer families were tested for linkage with five chromosome 17q markers. The five breast-ovarian cancer families as a group give positive evidence for linkage, whereas the 14 breast cancer-only families do not. Heterogeneity of linkage of breast and breast-ovarian cancers is significant in France and supports the existence of more than one susceptibility gene.

  19. [Analysis of DNA and chromosome damage by the methods of molecular cytogenetics].

    Science.gov (United States)

    Arutiunian, R M; Oganesian, G G

    2011-01-01

    The main hybrid techniques of molecular cytogenetics are described. Methodological aspects of combination of fluorescence in situ hybridization (FISH) with the comet assay and micronuclei (MN) test are discussed along with results of their application to evaluate and locate DNA and chromosome damage in the genome. The experience of the authors with the application of FISH in combination with the comet assay and MN test are reported.

  20. A phylogenetic analysis using multidirectional chromosome painting of three species (Uroderma magnirostrum, U. bilobatum and Artibeus obscurus) of subfamily Stenodermatinae (Chiroptera-Phyllostomidae).

    Science.gov (United States)

    Pieczarka, J C; Gomes, A J B; Nagamachi, C Y; Rocha, D C C; Rissino, J D; O'Brien, P C M; Yang, F; Ferguson-Smith, M A

    2013-07-01

    The species of genera Uroderma and Artibeus are medium-sized bats belonging to the family Phyllostomidae and subfamily Stenodermatinae (Mammalia, Chiroptera) from South America. They have a wide distribution in the Neotropical region, with two currently recognized species in Uroderma and approximately 20 species in Artibeus. These two genera have different rates of chromosome evolution, with Artibeus probably having retained the ancestral karyotype for the subfamily. We used whole chromosome paint probe sets from Carollia brevicauda and Phyllostomus hastatus on Uroderma magnirostrum, Uroderma bilobatum, and Artibeus obscurus. With the aim of testing the previous phylogenies of these bats using cytogenetics, we compared these results with published painting maps on Phyllostomidae. The genome-wide comparative maps based on chromosome painting and chromosome banding reveal the chromosome forms that characterize each taxonomic level within the Phyllostomidae and show the chromosome evolution of this family. Based on this, we are able to suggest an ancestral karyotype for Phyllostomidae. Our cladistic analysis is an independent confirmation using multidirectional chromosome painting of the previous Phyllostomidae phylogenies.

  1. Detection and analysis of chromosomal arsenic resistance in Pseudomonas fluorescens strain MSP3.

    Science.gov (United States)

    Prithivirajsingh, S; Mishra, S K; Mahadevan, A

    2001-02-09

    Pseudomonas fluorescens MSP3 isolated from sea water was resistant to arsenate. This bacterium harbored no plasmids, indicating that arsenic resistance was chromosomally encoded. The chromosomal DNA from MSP3 when transformed onto Escherichia coli DH5alpha using pBluescript exhibited resistance to sodium arsenate and sodium arsenite. Three clones MSA1, MSA2, and MSI3 containing the ars genes were obtained and further subcloning resulted in three fragments of size 2.2, 2.6, and 2.1 kb for pMSA11, pMSA12, and pMSI13, respectively, which contained the genes arsRBC of the arsenic operon. An efflux mechanism of detoxification was observed which was ATP dependent. The resistance mechanism was encoded from a single operon which consisted of an arsenite inducible repressor that regulates the expression of arsenate reductase (ars C) and inner membrane associated arsenite export system encoded by ars B. The chromosomal operon was cloned, sequenced, and found to consist of three cistrons, named as ars R, ars B, and ars C. Southern hybridization and mating experiments confirmed the functioning of the ars genes in the operon, thereby conferring increased resistance to sodium arsenate and sodium arsenite.

  2. Molecular cloning and analysis of breakpoints on ring chromosome 17 in a patient with autism.

    Science.gov (United States)

    Vazna, Alzbeta; Havlovicova, Marketa; Sedlacek, Zdenek

    2008-01-15

    The breakpoint junction on a ring chromosome 17 in a girl with autism, mental retardation, mild dysmorphism and neurofibromatosis was identified and analysed at the nucleotide level. The extent of the deleted segments was about 1.9 Mb on 17p and about 1.0 Mb on 17q. The structure of the junction between the 17p and 17q arms, especially the lack of significant homology between the juxtaposed genomic regions and the presence of short microhomology at the junction site, indicated non-homologous end joining as the most likely mechanism leading to the rearrangement. In addition to the 17p-17q junction itself, a de novo 1 kb deletion in a distance of 400 bp from the junction was identified, which arose most likely as a part of the rearrangement. The defect directly inactivated 3 genes, and the deleted terminal chromosome segments harboured 27 and 14 protein-coding genes from 17p and 17q, respectively. Several of the genes affected by the rearrangement are candidates for the symptoms observed in the patient. Additional rearrangements similar to the 1 kb deletion observed in our patient may remain undetected but can participate in the phenotype of patients with chromosomal aberrations. They can also be the reason for repeated failures to clone breakpoint junctions in other patients described in the literature.

  3. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data

    Directory of Open Access Journals (Sweden)

    Baudis Michael

    2007-12-01

    Full Text Available Abstract Background Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. Methods Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed. Results With large variation in overall genomic instability, recurring genomic gains and losses were prominent. Most entities showed frequent gains involving 8q2, while gains on 20q, 1q, 3q, 5p, 7q and 17q were frequent in different entities. Loss "hot spots" included 3p, 4q, 13q, 17p and 18q among others. Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca. and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites. Conclusion Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. Focus on the respective regions should aid in target gene detection and pathway deduction.

  4. An analysis of meiotic impairment and of sex chromosome associations throughout meiosis in XYY mice.

    Science.gov (United States)

    Mahadevaiah, S K; Evans, E P; Burgoyne, P S

    2000-01-01

    The existing XYY meiotic data for mice present a very heterogeneous picture with respect to the relative frequencies of different sex chromosome associations, both at pachytene and diakinesis/metaphase I. Furthermore, where both pachytene and diakinesis/MI data are available for the same males, the frequencies of the different configurations at the two stages are very different. In the present paper we utilise "XYY" and "XY/XYY" mosaic mice with cytologically distinguishable Y chromosomes to investigate the factors responsible for this heterogeneity between different males and between the two meiotic stages. It is concluded (1) that the initial pattern of synapsis is driven by the relatedness of the three pseudoautosomal regions (PARs); (2) that the order and extent of PAR synapsis within radial trivalents are also affected by PAR relatedness and that this leads to chiasmata being preferentially formed between closely related PARs; (3) that trivalents with a single chiasma resolve into a bivalent + univalent by the diakinesis stage; (4) that although many spermatocytes with asynapsed sex chromosomes are eliminated between pachytene and diakinesis, those that survive this phase of elimination progress to the first meiotic metaphase (MI) and accumulate in large numbers, leading to an over-representation of those with univalents as compared to radial trivalents; and (5) that the arrested MI cells are eventually eliminated, so that very few "XYY" cells contribute products to MII.

  5. Generation and Analysis of Transposon Ac/Ds-Induced Chromosomal Rearrangements in Rice Plants.

    Science.gov (United States)

    Xuan, Yuan Hu; Peterson, Thomas; Han, Chang-Deok

    2016-01-01

    Closely-located transposable elements (TEs) have been known to induce chromosomal breakage and rearrangements via alternative transposition. To study genome rearrangements in rice, an Ac/Ds system has been employed. This system comprises an immobile Ac element expressed under the control of CaMV 35S promoter, and a modified Ds element. A starter line carried Ac and a single copy of Ds at the OsRLG5 (Oryza sativa receptor-like gene 5). To enhance the transpositional activity, seed-derived calli were cultured and regenerated into plants. Among 270 lines regenerated from the starter, one line was selected that contained a pair of inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like gene 5). The selected line was again subjected to tissue culture to obtain a regenerant population. Among 300 regenerated plants, 107 (36 %) contained chromosomal rearrangements including deletions, duplications, and inversions of various sizes. From 34 plants, transposition mechanisms leading to such genomic rearrangements were analyzed. The rearrangements were induced by sister chromatid transposition (SCT), homologous recombination (HR), and single chromatid transposition (SLCT). Among them, 22 events (65 %) were found to be transmitted to the next generation. These results demonstrate a great potential of tissue culture regeneration and the Ac/Ds system in understanding alternative transposition mechanisms and in developing chromosome engineering in plants.

  6. A time stamp comparative analysis of frequent chromosomal abnormalities in Romanian patients.

    Science.gov (United States)

    Suciu, Nicolae; Plaiasu, Vasilica

    2014-01-01

    Chromosome abnormalities represent the leading cause in many human genetic disorders. Gain or loss of genetic material can disrupt the normal expression of genes important in fetal development and result in abnormal phenotypes. Approximately 60% of first-trimester spontaneous abortions exhibit karyotype abnormalities. The majority of these abnormalities consist of numerical chromosomal changes, such as autosomal trisomy, monosomy X and polyploidy. In our current study, 411 cases were analyzed over a period of 5 years, which reflected the incidence of cytogenetic abnormalities in Romania. Down syndrome showed the highest frequency at 79%. At 2.6% structural chromosome abnormality syndromes and Turner syndrome followed suit. Next were the Edwards and Patau syndromes with an incidence of 1.2%. Klinefelter, Cri du chat and Wolf-Hirschhorn syndromes all had an incidence of 0.7%. Finally, the lowest frequencies were shown by Williams at 0.4% and only one case of Beckwith-Wiedemann syndrome with abnormal karyotype. The average maternal age at childbirth was 31.15 years (SD = 6.96) and the average paternal age was 33.41 years (SD = 7.17).

  7. Chromosome analysis of five Brazilian species of poison frogs (Anura: Dendrobatidae)

    Indian Academy of Sciences (India)

    Paula Camargo Rodrigues; Odair Aguiar; Flávia Serpieri; Albertina Pimentel Lima; Masao Uetanebaro; Shirlei Maria Recco-Pimentel

    2011-04-01

    Dendrobatid frogs have undergone an extensive systematic reorganization based on recent molecular findings. The present work describes karyotypes of the Brazilian species Adelphobates castaneoticus, A. quinquevittatus, Ameerega picta, A. galactonotus and Dendrobates tinctorius which were compared to each other and with previously described related species. All karyotypes consisted of $2n = 18$ chromosomes, except for A. picta which had $2n = 24$. The karyotypes of the Adelphobates and D. tinctorius species were highly similar to each other and to the other $2n = 18$ previously studied species, revealing conserved karyotypic characteristics in both genera. In recent phylogenetic studies, all Adelphobates species were grouped in a clade separated from the Dendrobates species. Thus, we hypothesized that their common karyotypic traits may have a distinct origin by chromosome rearrangements and mutations. In A. picta, with $2n = 24$, chromosome features of pairs from 1 to 8 are shared with other previously karyotyped species within this genus. Hence, the A. picta data reinforced that the C-banding pattern and the NOR location are species-specific traits in the genus Ameerega. Moreover, the Ameerega monophyletism proposed by previous phylogenetic studies indicates that the karyotypic differences among species in this genus result from a long divergence time.

  8. Localization of the outer membrane protein OmpA2 in Caulobacter crescentus depends on the position of the gene in the chromosome.

    Science.gov (United States)

    Ginez, Luis David; Osorio, Aurora; Poggio, Sebastian

    2014-08-01

    The outer membrane of Gram-negative bacteria is an essential structure involved in nutrient uptake, protection against harmful substances, and cell growth. Different proteins keep the outer membrane from blebbing out by simultaneously interacting with it and with the cell wall. These proteins have been mainly studied in enterobacteria, where OmpA and the Braun and Pal lipoproteins stabilize the outer membrane. Some degree of functional redundancy exists between these proteins, since none of them is essential but the absence of two of them results in a severe phenotype. Caulobacter crescentus has a different strategy to maintain its outer membrane, since it lacks the Braun lipoprotein and Pal is essential. In this work, we characterized OmpA2, an OmpA-like protein, in this bacterium. Our results showed that this protein is required for normal stalk growth and that it plays a minor role in the stability of the outer membrane. An OmpA2 fluorescent fusion protein showed that the concentration of this protein decreases from the stalk to the new pole. This localization pattern is important for its function, and it depends on the position of the gene locus in the chromosome and, as a consequence, in the cell. This result suggests that little diffusion occurs from the moment that the gene is transcribed until the mature protein attaches to the cell wall in the periplasm. This mechanism reveals the integration of different levels of information from protein function down to genome arrangement that allows the cell to self-organize.

  9. Affected kindred analysis of human X chromosome exomes to identify novel X-linked intellectual disability genes.

    Directory of Open Access Journals (Sweden)

    Tejasvi S Niranjan

    Full Text Available X-linked Intellectual Disability (XLID is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.

  10. Affected kindred analysis of human X chromosome exomes to identify novel X-linked intellectual disability genes.

    Science.gov (United States)

    Niranjan, Tejasvi S; Skinner, Cindy; May, Melanie; Turner, Tychele; Rose, Rebecca; Stevenson, Roger; Schwartz, Charles E; Wang, Tao

    2015-01-01

    X-linked Intellectual Disability (XLID) is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome) in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families) using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.

  11. NOR sites detected by Ag-dAPI staining of an unusual autosome chromosome of Bradysia hygida (Diptera:Sciaridae) colocalize with C-banded heterochromatic region.

    Science.gov (United States)

    Gaspar, Vanessa Pinatto; Borges, Alex Rodrigues; Fernandez, Maria Aparecida

    2002-01-01

    The study of chromosomes in insects is a good tool in mitotic process analysis, zoographic localization and evolution investigation. Among them, the Sciaridae offers a karyotype with a small number of chromosomes, where the heterochromatin and nucleolar organizer region, NOR, are easily analyzed in metaphase chromosomes obtained from cerebral ganglia squashes. In this work, the heterochromatic regions on Bradysia hygida mitotic chromosomes, revealed by C-banding, were identified as centromeric blocks on A and C chromosomes and as dark interstitial region in B and X chromosomes. By Ag-DAPI staining, active nucleolus organizer region, NOR, was revealed associated to the constitutive heterochromatin in the end of the C autosome chromosome. The C-band regions and the unusual ribosomal site localization are discussed.

  12. Flow karyotyping and sorting of human chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Gray, J.W.; Lucas, J.; Peters, D.; Pinkel, D.; Trask, B.; van den Engh, G.; Van Dilla, M.A.

    1986-07-16

    Flow cytometry and sorting are becoming increasingly useful as tools for chromosome classfication and for the detection of numerical and structural chromosome aberrations. Chromosomes of a single type can be purified with these tools to facilitate gene mapping or production of chromosome specific recombinant DNA libraries. For analysis of chromosomes with flow cytometry, the chromosomes are extracted from mitotic cells, stained with one or more fluorescent dyes and classified one-by-one according to their dye content(s). Thus, the flow approach is fundamentally different than conventional karyotyping where chromosomes are classified within the context of a metaphase spread. Flow sorting allows purification of chromosomes that can be distinguished flow cytometrically. The authors describe the basic principles of flow cytometric chromosome classification i.e. flow karyotyping, and chromosome sorting and describe several applications. 30 refs., 8 figs.

  13. Global and Local Sensitivity Analysis Methods for a Physical System

    Science.gov (United States)

    Morio, Jerome

    2011-01-01

    Sensitivity analysis is the study of how the different input variations of a mathematical model influence the variability of its output. In this paper, we review the principle of global and local sensitivity analyses of a complex black-box system. A simulated case of application is given at the end of this paper to compare both approaches.…

  14. mBAND Analysis of Early and Late Damages in the Chromosome of Human Lymphocytes after Exposures to Gamma Rays and Fe Ions

    Science.gov (United States)

    Sunagawa, Mayumi; Zhang, Ye; Yeshitla, Samrawit; Kadhim, Munira; Wilson, Bobby; Wu, Honglu

    2013-01-01

    Stable type chromosome aberrations that survive multiple generations of cell division include translocation and inversions. An efficient method to detect an inversion is multi-color banding fluorescent in situ hybridization (mBAND) which allows identification of both inter- and intrachromosome aberrations simultaneously. Post irradiation, chromosome aberrations may also arise after multiple cell divisions as a result of genomic instability. To investigate the stable or late-arising chromosome aberrations induced after radiation exposure, we exposed human lymphocytes to gamma rays and Fe ions ex vivo, and cultured the cells for multiple generations. Chromosome aberrations were analyzed in cells collected at first mitosis and at several time intervals during the culture period post irradiation. With gamma irradiation, about half of the damages observed at first mitosis remained after 7 day- and 14 day- culture, suggesting the transmissibility of damages to the surviving progeny. At the doses that produced similar frequencies of gamma-induced chromosome aberrations as observed at first mitosis, a significantly lower yield of aberrations remained at the same population doublings after Fe ion exposure. At these equitoxic doses, more complex type aberrations were observed for Fe ions, indicating that Fe ion-induced initial chromosome damages are more severe and may lead to cell death. Detailed analysis of breaks participating in total chromosome exchanges within the first cell cycle post irradiation revealed a common hotspot located in the 3p21 region, which is a known fragile site corresponding to the band 6 in the mBand analysis. The breakpoint distribution in chromosomes collected at 7 days, but not at 14 days, post irradiation appeared similar to the distribution in cells collected within the first cell cycle post irradiation. The breakpoint distribution for human lymphocytes after radiation exposure was different from the previously published distribution for human

  15. Cloning of cDNA and genomic DNA encoding human type XVIII collagen and localization of the [alpha]1 (XVIII) collagen gene to mouse chromosome 10 and human chromosome 21

    Energy Technology Data Exchange (ETDEWEB)

    Oh, S.P.; Warman, M.L.; Timmons, S.; Olsen, B.R.; Knoll, J.H.M. (Harvard Medical School, Boston, MA (United States)); Seldin, M.F. (Duke Univ. Medical Center, Durham, NC (United States)); Cheng, Sou-De (Children' s Hospital/Harvard Medical School, Boston, MA (United States))

    1994-02-01

    Types XV and XVIII collagen belong to a unique and novel subclass of the collagen superfamily for which the authors have proposed the name the MULTIPLEXIN family. Members of this class contain polypeptides with multiple triple-helical domains separated and flanked by non-triple-helical regions. In this paper, they report the isolation of human cDNAs and genomic DNAs encoding the [alpha]1 (XVIII) collagen chain. Utilizing a genomic clone as probe, they have mapped the COL18A1 gene to chromosome 21q22.3 by fluorescence in situ hybridization. In addition, using an interspecific backcross panel, they have shown that the murine Col18a1 locus is on chromosome 10, close to the loci for Col6a1 and Col6a2. 16 refs., 5 figs.

  16. Identification of Chromosome Abnormalities in Subtelomeric Regions by Microarray Analysis: A Study of 5,380 Cases

    Science.gov (United States)

    Shao, Lina; Shaw, Chad A.; Lu, Xin-Yan; Sahoo, Trilochan; Bacino, Carlos A.; Lalani, Seema R.; Stankiewicz, Pawel; Yatsenko, Svetlana A.; Li, Yinfeng; Neill, Sarah; Pursley, Amber N.; Chinault, A. Craig; Patel, Ankita; Beaudet, Arthur L.; Lupski, James R.; Cheung, Sau W.

    2009-01-01

    Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances. PMID

  17. Analysis of two novel cDNAs from the Smith-Magenis syndrome region on chromosome 17

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Z.Y.; Lee, C.C.; Jiralerspong, S. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Smith-Magenis syndrome (SMS) is a clinically recognizable multiple congenital anomaly/mental retardation syndrome associated with deletion of chromosome 17p11.2. To date, only one gene encoding snRNA U3 has been mapped to this region. Here we report the identification of two novel genes, designated 463 and B9, which have been mapped to the SMS region. A full-length cDNA corresponding to each of these genes has been cloned and sequenced. Deletion analysis has been conducted on somatic cell hybrids retaining the del(17)(p11.2) chromosome from each of 15 SMS patients by PCR of sequence tagged sites for the cDNAs and confirmed by Southern analysis. The gene 463 is deleted in 15/15 patients analyzed to date, whereas the gene B9 is deleted in 10/15 of the patients analyzed. Fluorescence in situ hybridization is used to analyze additional SMS patients for hemizygosity at these loci. A physical map of the region is being constructed to determine the relative location of these cDNAs within 17p11.2. Our studies to date, thus, suggest that although both genes 463 and B9 are located within 17p11.2, gene 463 is more likely to be associated with SMS. Complete and exhaustive definition of the critical interval is required to demonstrate the role and importance of gene 463 in SMS.

  18. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

    DEFF Research Database (Denmark)

    Pereira, Rui; Pereira, Vania; Gomes, Iva;

    2012-01-01

    , given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X......-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian...

  19. Characterization of some Indian Himalayan Capsicums through floral morphology and EMA-based chromosome analysis.

    Science.gov (United States)

    Jha, Timir Baran; Saha, Partha Sarathi

    2017-03-01

    The North Eastern Himalayan (NEH) regions of India are considered as one of the major repositories of the "Capsicum annuum complex" which comprises of three cultivated species namely C. annuum, C. frutescens, and C. chinense. The interspecific delimitation within this large complex is ill-defined due to poorly developed crossing barriers and lack of discontinuous morphological characters. The present study elucidates the relationship among nine different cultivars of three Capsicum species on the basis of floral morphology and karyological parameters for the first time. Different floral characteristics such as margins and constrictions of calyx, type of pedicel, flower size, and color were found to have paramount importance in the species delimitation within the studied members of "C. annuum complex." The present karyomorphometric study explicitly revealed differences between the observed chromosomal data such as karyotype formulae, ordering of satellite bearing chromosome pairs and total diploid chromatin length which aid in resolving interspecific relationship among the studied cultivars of Capsicum. The present analyses unambiguously distinguished all cultivars of C. annuum from the members of C. frutescens and C. chinense and also proposed that among the five cultivars of C. annuum, Ghee lanka was comparatively distant from the other four cultivars on the basis of their karyomorphological characteristics. For the first time karyotype of hottest Indian chili is included in this paper. Comprehensive knowledge on floral morphology and karyotypes of some Himalayan Capsicums not only help to conserve genetic diversity but also help capsicum breeders for their basic and applied research.

  20. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    Science.gov (United States)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cíntia; Salazar, Renato; Angustia, Sheila M.T.; Santos, Lorna H.; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martínez-Jarreta, Begoña; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bäßler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstätter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F.; Domingues, Patricia M.; Chamoun, Wafaa Takash; Coble, Michael D.; Hill, Carolyn R.; Corach, Daniel; Caputo, Mariela; D’Amato, Maria E.; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H.D.; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E.; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rüdiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E.; García, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; Andari, Ansar El; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martín, Pablo; Luque, Gracia M.; Alonso, Antonio; Miranda, Luís Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Neto, Rodrigo S. Moura; Nogueira, Tatiana L.S.; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Núñez, Carolina; Pancorbo, Marian Martínez de; Olofsson, Jill K.; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cárdenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L.; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U.; Guevara, Evelyn; Salvador, Jazelyn; Ungria, Maria Corazon De; Rodriguez, Jae Joseph Russell; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M.; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; Calvit, Lina Solis de; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H.; Gwynne, Gareth M.; Jobling, Mark A.; Whittle, Martin R.; Sumita, Denilce R.; Wolańska-Nowak, Paulina; Yong, Rita Y.Y.; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. PMID:24854874

  1. A simple and rapid fluorescence in situ hybridization microwave protocol for reliable dicentric chromosome analysis.

    Science.gov (United States)

    Cartwright, Ian M; Genet, Matthew D; Kato, Takamitsu A

    2013-03-01

    Fluorescence in situhybridization (FISH) is an extremely effective and sensitive approach to analyzing chromosome aberrations. Until recently, this procedure has taken multiple days to complete. The introduction of telomeric and centromeric peptide nucleic acid (PNA) probes has reduced the procedure's duration to several hours, but the protocols still call for a high temperature (80-90°C) step followed by 1-3 h of hybridization. The newest method to speed up the FISH protocol is the use of a microwave to shorten the heating element to less than a minute; however this protocol still calls for a 1-h hybridization period. We have utilized PNA centromere/telomere probes in conjunction with a microwave oven to show telomere and centromere staining in as little as 30 s. We have optimized the hybridization conditions to increase the sensitivity and effectiveness of the new protocol and can effectively stain chromosomes in 2 min and 30 s of incubation. We have found that our new approach to FISH produces extremely clear and distinct signals. Radiation-induced dicentric formation in mouse and human fibroblast cells was analyzed by two individual scorers and the observed dicentrics matched very well.

  2. Analysis of Unstable Chromosome Aberrations for Partial Body Exposures with Gamma Rays

    Energy Technology Data Exchange (ETDEWEB)

    Syaifudin, Mukh [Center for Technology of Radiation Safety and Metrology, National Nuclear Energy Agency, Jakarta (Indonesia); Yun, Hyun Jin; Kim, Eun Ju; Kang, Chang Mo [Laboratory of Cytogenetics and Tissue Regeneration, Korea Institute of Radiological and Medical Sciences, Seoul (Korea, Republic of)

    2009-04-15

    Scoring of unstable chromosome aberrations (dicentrics, rings and fragments) in circulating lymphocytes are the most extensively studied biological means for estimating individual exposure to ionizing radiation. The effects of radiation, however, can be significantly different when only portions of the body or an individual organ system are irradiated, such as might occur during the use of radiation for medical treatment, where some problems can arise especially to quantify the fraction of body irradiated. After partial-body exposure, peripheral blood samples contain a mixture of exposed and unexposed lymphocytes, which render the interpretation of the overall aberration frequencies more difficult. In this experiment, peripheral blood samples from four volunteers (two Indonesian and two Korean) were irradiated with 2.0 Gy of gamma rays for simulation of partial-body exposure by mixing irradiated and non-irradiated blood from the same volunteers in proportions of 10-100%. Dose estimates are crucial for risk assessment as well as for clinical planning of treatment of highly exposed victims. The results presented in this experiment concluded that the scoring of chromosome aberration is reliable methodology for investigating exposure to ionizing irradiation, such as partial-body ones. This study constitutes a preliminary step in our process of defining the possibilities of cytological technique for biological dosimetry expertise. Because of the limitations of a number of cases, no clear conclusion could be reached.

  3. Local bifurcation analysis of a four-dimensional hyperchaotic system

    Institute of Scientific and Technical Information of China (English)

    Wu Wen-Juan; Chen Zeng-Qiang; Yuan Zhu-Zhi

    2008-01-01

    Local bifurcation phenomena in a four-dimensional continuous hyperchaotic system, which has rich and complex dynamical behaviours, are analysed. The local bifurcations of the system are investigated by utilizing the bifurcation theory and the centre manifold theorem, and thus the conditions of the existence of pitchfork bifurcation and Hopf bifurcation are derived in detail. Numerical simulations are presented to verify the theoretical analysis, and they show some interesting dynamics, including stable periodic orbits emerging from the new fixed points generated by pitchfork bifurcation, coexistence of a stable limit cycle and a chaotic attractor, as well as chaos within quite a wide parameter region.

  4. Adaptive Local Image Registration: Analysis on Filter Size

    OpenAIRE

    Vishnukumar S; M.Wilscy

    2012-01-01

    Adaptive Local Image Registration is a Local Image Registration based on an Adaptive Filtering frame work. A filter of appropriate size convolves with reference image and gives the pixel values corresponding to the distorted image and the filter is updated in each stage of the convolution. When the filter converges to the system model, it provides the registered image. The filter size plays an important role in this method. The analysis on the filter size is done using Peak Signal-to-Noise Ra...

  5. The analysis of mutant alleles of different strength reveals multiple functions of topoisomerase 2 in regulation of Drosophila chromosome structure.

    Science.gov (United States)

    Mengoli, Valentina; Bucciarelli, Elisabetta; Lattao, Ramona; Piergentili, Roberto; Gatti, Maurizio; Bonaccorsi, Silvia

    2014-10-01

    Topoisomerase II is a major component of mitotic chromosomes but its role in the assembly and structural maintenance of chromosomes is rather controversial, as different chromosomal phenotypes have been observed in various organisms and in different studies on the same organism. In contrast to vertebrates that harbor two partially redundant Topo II isoforms, Drosophila and yeasts have a single Topo II enzyme. In addition, fly chromosomes, unlike those of yeast, are morphologically comparable to vertebrate chromosomes. Thus, Drosophila is a highly suitable system to address the role of Topo II in the assembly and structural maintenance of chromosomes. Here we show that modulation of Top2 function in living flies by means of mutant alleles of different strength and in vivo RNAi results in multiple cytological phenotypes. In weak Top2 mutants, meiotic chromosomes of males exhibit strong morphological abnormalities and dramatic segregation defects, while mitotic chromosomes of larval brain cells are not affected. In mutants of moderate strength, mitotic chromosome organization is normal, but anaphases display frequent chromatin bridges that result in chromosome breaks and rearrangements involving specific regions of the Y chromosome and 3L heterochromatin. Severe Top2 depletion resulted in many aneuploid and polyploid mitotic metaphases with poorly condensed heterochromatin and broken chromosomes. Finally, in the almost complete absence of Top2, mitosis in larval brains was virtually suppressed and in the rare mitotic figures observed chromosome morphology was disrupted. These results indicate that different residual levels of Top2 in mutant cells can result in different chromosomal phenotypes, and that the effect of a strong Top2 depletion can mask the effects of milder Top2 reductions. Thus, our results suggest that the previously observed discrepancies in the chromosomal phenotypes elicited by Topo II downregulation in vertebrates might depend on slight differences

  6. The analysis of mutant alleles of different strength reveals multiple functions of topoisomerase 2 in regulation of Drosophila chromosome structure.

    Directory of Open Access Journals (Sweden)

    Valentina Mengoli

    2014-10-01

    Full Text Available Topoisomerase II is a major component of mitotic chromosomes but its role in the assembly and structural maintenance of chromosomes is rather controversial, as different chromosomal phenotypes have been observed in various organisms and in different studies on the same organism. In contrast to vertebrates that harbor two partially redundant Topo II isoforms, Drosophila and yeasts have a single Topo II enzyme. In addition, fly chromosomes, unlike those of yeast, are morphologically comparable to vertebrate chromosomes. Thus, Drosophila is a highly suitable system to address the role of Topo II in the assembly and structural maintenance of chromosomes. Here we show that modulation of Top2 function in living flies by means of mutant alleles of different strength and in vivo RNAi results in multiple cytological phenotypes. In weak Top2 mutants, meiotic chromosomes of males exhibit strong morphological abnormalities and dramatic segregation defects, while mitotic chromosomes of larval brain cells are not affected. In mutants of moderate strength, mitotic chromosome organization is normal, but anaphases display frequent chromatin bridges that result in chromosome breaks and rearrangements involving specific regions of the Y chromosome and 3L heterochromatin. Severe Top2 depletion resulted in many aneuploid and polyploid mitotic metaphases with poorly condensed heterochromatin and broken chromosomes. Finally, in the almost complete absence of Top2, mitosis in larval brains was virtually suppressed and in the rare mitotic figures observed chromosome morphology was disrupted. These results indicate that different residual levels of Top2 in mutant cells can result in different chromosomal phenotypes, and that the effect of a strong Top2 depletion can mask the effects of milder Top2 reductions. Thus, our results suggest that the previously observed discrepancies in the chromosomal phenotypes elicited by Topo II downregulation in vertebrates might depend on

  7. Synthetic chromosomes.

    Science.gov (United States)

    Schindler, Daniel; Waldminghaus, Torsten

    2015-11-01

    What a living organism looks like and how it works and what are its components-all this is encoded on DNA, the genetic blueprint. Consequently, the way to change an organism is to change its genetic information. Since the first pieces of recombinant DNA have been used to transform cells in the 1970s, this approach has been enormously extended. Bigger and bigger parts of the genetic information have been exchanged or added over the years. Now we are at a point where the construction of entire chromosomes becomes a reachable goal and first examples appear. This development leads to fundamental new questions, for example, about what is possible and desirable to build or what construction rules one needs to follow when building synthetic chromosomes. Here we review the recent progress in the field, discuss current challenges and speculate on the appearance of future synthetic chromosomes.

  8. 羊水细胞染色体分析在产前的应用%Amniotic fluid cel chromosome analysis in prenatal application

    Institute of Scientific and Technical Information of China (English)

    王亚群; 童克婷

    2013-01-01

    Objective Study amniotic fluid cel chromosome usefulness in clinical prenatal diagnosis and in the diagnosis of chromosomal disorders. Methods Puncture indications of second trimester amniotic fluid cel culture and chromosome analysis detected abnormal karyotype types and statistics. Results 474 cases were successfuly cultured amniotic fluid detection of abnormal karyotype 22 cases, autosomal abnormal number of 15 cases, the sex chromosome abnormalities, six cases of chromosome structural abnormalities, abnormal detection rate of 4.64%, chromosome polymorphismThe karyotype 22 cases. A conclusion Second trimester amniotic fluid chromosome chromosome-risk pregnant woman is an important means of prenatal diagnosis.%  目的研究羊水细胞染色体检查在临床产前诊断中的实用性和在染色体疾病诊断中的意义.方法对孕中期有穿刺指征的孕妇羊水细胞培养并进行染色体分析,检出异常核型及类型并统计.结果在成功培养的474例羊水中,检出异常核型22例,其中常染色体数目异常15例,性染色体数目异常1例,染色体结构异常6例,异常检出率为4.64%,染色体多态性核型22例.结论孕中期对染色体高危孕妇进行羊水染色体检查是产前诊断的重要手段.

  9. Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-10-01

    Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

  10. Construction and analysis of tree models for chromosomal classification of diffuse large B-cell lymphomas

    Institute of Scientific and Technical Information of China (English)

    Hui-Yong Jiang; Zhong-Xi Huang; Xue-Feng Zhang; Richard Desper; Tong Zhao

    2007-01-01

    AIM: To construct tree models for classification of diffuse large B-cell lymphomas (DLBCL) by chromosome copy numbers, to compare them with cDNA microarray classification, and to explore models of multi-gene, multi-step and multi-pathway processes of DLBCL tumorigenesis.METHODS: Maximum-weight branching and distance based models were constructed based on the comparative genomic hybridization (CGH) data of 123 DLBCL samples using the established methods and software of Desper et al. A maximum likelihood tree model was also used to analyze the data. By comparing with the results reported in literature, values of tree models in the classification of DLBCL were elucidated.RESULTS: Both the branching and the distance-based trees classified DLBCL into three groups. We combined the classification methods of the two models and classified DLBCL into three categories according to their characteristics. The first group was marked by +Xq, +Xp, -17p and +13q; the second group by +3q, +18q and +18p; and the third group was marked by -6q and +6p. This chromosomal classification was consistent with cDNA classification. It indicated that -6q and +3q were two main events in the tumorigenesis of lymphoma.CONCLUSION: Tree models of lymphoma established from CGH data can be used in the classification of DLBCL. These models can suggest multi-gene, multi-step and multi-pathway processes of tumorigenesis.Two pathways, -6q preceding +6q and +3q preceding +18q, may be important in understanding tumorigenesis of DLBCL. The pathway, -6q preceding +6q, may have a close relationship with the tumorigenesis of non-GCB DLBCL.

  11. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization.

    Science.gov (United States)

    Coluccia, E; Deidda, F; Cannas, R; Lobina, C; Cuccu, D; Deiana, A M; Salvadori, S

    2015-09-01

    A comparative cytogenetic analysis, using both conventional staining techniques and fluorescence in situ hybridization, of six Indo-Pacific moray eels from three different genera (Gymnothorax fimbriatus, Gymnothorax flavimarginatus, Gymnothorax javanicus, Gymnothorax undulatus, Echidna nebulosa and Gymnomuraena zebra), was carried out to investigate the chromosomal differentiation in the family Muraenidae. Four species displayed a diploid chromosome number 2n = 42, which is common among the Muraenidae. Two other species, G. javanicus and G. flavimarginatus, were characterized by different chromosome numbers (2n = 40 and 2n = 36). For most species, a large amount of constitutive heterochromatin was detected in the chromosomes, with species-specific C-banding patterns that enabled pairing of the homologous chromosomes. In all species, the major ribosomal genes were localized in the guanine-cytosine-rich region of one chromosome pair, but in different chromosomal locations. The (TTAGGG)n telomeric sequences were mapped onto chromosomal ends in all muraenid species studied. The comparison of the results derived from this study with those available in the literature confirms a substantial conservation of the diploid chromosome number in the Muraenidae and supports the hypothesis that rearrangements have occurred that have diversified their karyotypes. Furthermore, the finding of two species with different diploid chromosome numbers suggests that additional chromosomal rearrangements, such as Robertsonian fusions, have occurred in the karyotype evolution of the Muraenidae.

  12. Chromosomal localization of mitochondrial transcription factor A (TCF6), single-stranded DNA-binding protein (SSBP), and endonuclease G (ENDOG), three human housekeeping genes involving in mitochondrial biogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Tiranti, V.; Rossi, G.; DiDonato, S. [Istituto Nazionale Neurologico, Carlo Besta (Italy)] [and others

    1995-01-20

    By using a PCR-based screening of a somatic cell hybrid panel and FISH, we have assigned the loci of mitochondrial single-stranded DNA-binding protein (SSBP), mitochondrial transcription factor A (TCF6), and mitochondrial endonuclease G (ENDOG) genes to human chromosomes 7q34, 10q21, and 9q34.1, respectively. The products of these three genes are involved in fundamental aspects of mitochondrial biogenesis, such as replication and transcription of the mitochondrial genome. The chromosomal localization of these genes is important to testing whether the corresponding proteins may play a role in the etiopathogenesis of human disorders associated with qualitative or quantitative abnormalities of mitochondrial DNA. 20 refs., 1 fig., 2 tabs.

  13. Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L.

    Science.gov (United States)

    Wang, Kai; Guo, Wangzhen; Zhang, Tianzhen

    2007-09-01

    Fluorescence in situ hybridization (FISH), using bacterial artificial chromosome (BAC) clone as probe, is a reliable cytological technique for chromosome identification. It has been used in many plants, especially in those containing numerous small chromosomes. We previously developed eight chromosome-specific BAC clones from tetraploid cotton, which were used as excellent cytological markers for chromosomes identification. Here, we isolated the other chromosome-specific BAC clones to make a complete set for the identification of all 26 chromosome-pairs by this technology in tetraploid cotton (Gossypium hirsutum L.). This set of BAC markers was demonstrated to be useful to assign each chromosome to a genetic linkage group unambiguously. In addition, these BAC clones also served as convenient and reliable landmarks for establishing physical linkage with unknown targeted sequences. Moreover, one BAC containing an EST, with high sequence similarity to a G. hirsutum ethylene-responsive element-binding factor was located physically on the long arm of chromosome A7 with the help of a chromosome-A7-specific BAC FISH marker. Comparative analysis of physical marker positions in the chromosomes by BAC-FISH and genetic linkage maps demonstrated that most of the 26 BAC clones were localized close to or at the ends of their respective chromosomes, and indicated that the recombination active regions of cotton chromosomes are primarily located in the distal regions. This technology also enables us to make associations between chromosomes and their genetic linkage groups and re-assign each chromosome according to the corresponding genetic linkage group. This BAC clones and BAC-FISH technology will be useful for us to evaluate grossly the degree to which a linkage map provides adequate coverage for developing a saturated genetic map, and provides a powerful resource for cotton genomic researches.

  14. M-BAND Study of Radiation-Induced Chromosome Aberrations in Human Epithelial Cells: Radiation Quality and Dose Rate Effects

    Science.gov (United States)

    Hada, Megumi; Cucinotta, Francis; Wu, Honglu

    2009-01-01

    The advantage of the multicolor banding in situ hybridization (mBAND) technique is its ability to identify both inter- (translocation to unpainted chromosomes) and intra- (inversions and deletions within a single painted chromosome) chromosome aberrations simultaneously. To study the detailed rearrangement of low- and high-LET radiation induced chromosome aberrations in human epithelial cells (CH184B5F5/M10) in vitro, we performed a series of experiments with Cs-137 gamma rays of both low and high dose rates, neutrons of low dose rate and 600 MeV/u Fe ions of high dose rate, with chromosome 3 painted with multi-binding colors. We also compared the chromosome aberrations in both 2- and 3-dimensional cell cultures. Results of these experiments revealed the highest chromosome aberration frequencies after low dose rate neutron exposures. However, detailed analysis of the radiation induced inversions revealed that all three radiation types induced a low incidence of simple inversions. Most of the inversions in gamma-ray irradiated samples were accompanied by other types of intra-chromosomal aberrations but few inversions were accompanied by inter-chromosomal aberrations. In contrast, neutrons and Fe ions induced a significant fraction of inversions that involved complex rearrangements of both inter- and intrachromosomal exchanges. The location of the breaks involved in chromosome exchanges was analyzed along the painted chromosome. The breakpoint distribution was found to be randomly localized on chromosome 3 after neutron or Fe ion exposure, whereas non-random distribution with clustering breakpoints was observed after -ray exposure. Our comparison of chromosome aberration yields between 2- and 3-dimensional cell cultures indicated a significant difference for gamma exposures, but not for Fe ion exposures. These experimental results indicated that the track structure of the radiation and the cellular/chromosome structure can both affect radiation-induced chromosome

  15. Morphological images analysis and chromosomic aberrations classification based on fuzzy logic; Analise morfologica de imagens e classificacao de aberracoes cromossomicas por meio de logica fuzzy

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Leonardo Peres

    2011-07-01

    This work has implemented a methodology for automation of images analysis of chromosomes of human cells irradiated at IEA-R1 nuclear reactor (located at IPEN, Sao Paulo, Brazil), and therefore subject to morphological aberrations. This methodology intends to be a tool for helping cytogeneticists on identification, characterization and classification of chromosomal metaphasic analysis. The methodology development has included the creation of a software application based on artificial intelligence techniques using Fuzzy Logic combined with image processing techniques. The developed application was named CHRIMAN and is composed of modules that contain the methodological steps which are important requirements in order to achieve an automated analysis. The first step is the standardization of the bi-dimensional digital image acquisition procedure through coupling a simple digital camera to the ocular of the conventional metaphasic analysis microscope. Second step is related to the image treatment achieved through digital filters application; storing and organization of information obtained both from image content itself, and from selected extracted features, for further use on pattern recognition algorithms. The third step consists on characterizing, counting and classification of stored digital images and extracted features information. The accuracy in the recognition of chromosome images is 93.9%. This classification is based on classical standards obtained at Buckton [1973], and enables support to geneticist on chromosomic analysis procedure, decreasing analysis time, and creating conditions to include this method on a broader evaluation system on human cell damage due to ionizing radiation exposure. (author)

  16. Structural organization of the inactive X chromosome in the mouse.

    Science.gov (United States)

    Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job

    2016-07-28

    X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions,remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes indifferent neural progenitor clones are associated with the presence of different TAD

  17. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2

    Science.gov (United States)

    2012-01-01

    Background Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa), may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05) and type 2 diabetes (P = 0.00578). Through the estimation of variance of genetic component (heritability) for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479) between genetic contributions of human and pig to obesity traits. Furthermore, we noted that human chromosome 2 (syntenic to pig chromosomes 3 and 15) was most important in explaining the phenotypic variance for obesity. Conclusions Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B. PMID:23253381

  18. An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2

    Directory of Open Access Journals (Sweden)

    Kim Jaemin

    2012-12-01

    Full Text Available Abstract Background Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa, may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05 and type 2 diabetes (P = 0.00578. Through the estimation of variance of genetic component (heritability for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479 between genetic contributions of human and pig to obesity traits. Furthermore, we noted that human chromosome 2 (syntenic to pig chromosomes 3 and 15 was most important in explaining the phenotypic variance for obesity. Conclusions Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B.

  19. Localization of the cellular retinoic acid binding protein (CRABP) gene relative to the acute promyelocytic leukemia-associated breakpoint on human chromosome 15

    NARCIS (Netherlands)

    A.H.M. Geurts van Kessel (Ad); H. de Leeuw (H.); E.J. Dekker (E.); J.M. Rijks (Jolianne); N. Spurr (N.); A.M. Ledbetter (Andrew M.); E. Kootwijk (E.); M.J. Vaessen (Marie-Josée)

    1991-01-01

    textabstractA human genomic fragment comprising the cellular retinoic acid binding protein (CRABP) gene was isolated. By using a panel of somatic cell hybrids, this gene could be assigned to human chromosome 15. Subsequently, a possible involvement of the CRABP gene in translocation (15;17) (q22;q11

  20. SOE-LRed: a simple and time-efficient method to localize genes with point mutations onto the Escherichia coli chromosome

    Science.gov (United States)

    Benson, Ryan W.; Cafarelli, Tiziana M.; Godoy, Veronica G.

    2011-01-01

    We report a powerful method to replace wild type genes on the chromosome of Escherichia coli. Employing a unique form of PCR, we generate easily constructible gene fusions bearing single point mutations. Used in conjunction with homologous recombination, this method eliminates cloning procedures previously used for this purpose. PMID:21185880

  1. Local classification: Locally weighted-partial least squares-discriminant analysis (LW-PLS-DA).

    Science.gov (United States)

    Bevilacqua, Marta; Marini, Federico

    2014-08-01

    The possibility of devising a simple, flexible and accurate non-linear classification method, by extending the locally weighted partial least squares (LW-PLS) approach to the cases where the algorithm is used in a discriminant way (partial least squares discriminant analysis, PLS-DA), is presented. In particular, to assess which category an unknown sample belongs to, the proposed algorithm operates by identifying which training objects are most similar to the one to be predicted and building a PLS-DA model using these calibration samples only. Moreover, the influence of the selected training samples on the local model can be further modulated by adopting a not uniform distance-based weighting scheme which allows the farthest calibration objects to have less impact than the closest ones. The performances of the proposed locally weighted-partial least squares-discriminant analysis (LW-PLS-DA) algorithm have been tested on three simulated data sets characterized by a varying degree of non-linearity: in all cases, a classification accuracy higher than 99% on external validation samples was achieved. Moreover, when also applied to a real data set (classification of rice varieties), characterized by a high extent of non-linearity, the proposed method provided an average correct classification rate of about 93% on the test set. By the preliminary results, showed in this paper, the performances of the proposed LW-PLS-DA approach have proved to be comparable and in some cases better than those obtained by other non-linear methods (k nearest neighbors, kernel-PLS-DA and, in the case of rice, counterpropagation neural networks).

  2. Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16.

    Science.gov (United States)

    Goidts, Violaine; Szamalek, Justyna M; de Jong, Pieter J; Cooper, David N; Chuzhanova, Nadia; Hameister, Horst; Kehrer-Sawatzki, Hildegard

    2005-09-01

    Analyses of chromosomal rearrangements that have occurred during the evolution of the hominoids can reveal much about the mutational mechanisms underlying primate chromosome evolution. We characterized the breakpoints of the pericentric inversion of chimpanzee chromosome 18 (PTR XVI), which is homologous to human chromosome 16 (HSA 16). A conserved 23-kb inverted repeat composed of satellites, LINE and Alu elements was identified near the breakpoints and could have mediated the inversion by bringing the chromosomal arms into close proximity with each other, thereby facilitating intrachromosomal recombination. The exact positions of the breakpoints may then have been determined by local DNA sequence homologies between the inversion breakpoints, including a 22-base pair direct repeat. The similarly located pericentric inversion of gorilla (GGO) chromosome XVI, was studied by FISH and PCR analysis. The p- and q-arm breakpoints of the inversions in PTR XVI and GGO XVI were found to occur at slightly different locations, consistent with their independent origin. Further, FISH studies of the homologous chromosomal regions in macaque and orangutan revealed that the region represented by HSA BAC RP11-696P19, which spans the inversion breakpoint on HSA 16q11-12, was derived from the ancestral primate chromosome homologous to HSA 1. After the divergence of orangutan from the other great apes approximately 12 million years ago (Mya), a duplication of the corresponding region occurred followed by its interchromosomal transposition to the ancestral chromosome 16q. Thus, the most parsimonious interpretation is that the gorilla and chimpanzee homologs exhibit similar but nonidentical derived pericentric inversions, whereas HSA 16 represents the ancestral form among hominoids.

  3. A data skimming service for locally resident analysis data

    Science.gov (United States)

    Cranshaw, J.; Gardner, R. W.; Gieraltowski, J.; Malon, D.; Mambelli, M.; May, E.

    2008-07-01

    A Data Skimming Service (DSS) is a site-level service for rapid event filtering and selection from locally resident datasets based on metadata queries to associated 'tag' databases. In US ATLAS, we expect most if not all of the AOD-based datasets to be replicated to each of the five Tier 2 regional facilities in the US Tier 1 'cloud' coordinated by Brookhaven National Laboratory. Entire datasets will consist of on the order of several terabytes of data, and providing easy, quick access to skimmed subsets of these data will be vital to physics working groups. Typically, physicists will be interested in portions of the complete datasets, selected according to event-level attributes (number of jets, missing Et, etc) and content (specific analysis objects for subsequent processing). In this paper we describe methods used to classify data (metadata tag generation) and to store these results in a local database. Next we discuss a general framework which includes methods for accessing this information, defining skims, specifying event output content, accessing locally available storage through a variety of interfaces (SRM, dCache/dccp, gridftp), accessing remote storage elements as specified, and user job submission tools through local or grid schedulers. The advantages of the DSS are the ability to quickly 'browse' datasets and design skims, for example, pre-adjusting cuts to get to a desired skim level with minimal use of compute resources, and to encode these analysis operations in a database for re-analysis and archival purposes. Additionally the framework has provisions to operate autonomously in the event that external, central resources are not available, and to provide, as a reduced package, a minimal skimming service tailored to the needs of small Tier 3 centres or individual users.

  4. A data skimming service for locally resident analysis data

    Energy Technology Data Exchange (ETDEWEB)

    Cranshaw, J; Gieraltowski, J; Malon, D; May, E [Argonne National Laboratory, Argonne, IL 60439 (United States); Gardner, R W; Mambelli, M [Enrico Fermi Institute, University of Chicago, Chicago, IL 60637 (United States)], E-mail: marco@hep.uchciago.edu

    2008-07-15

    A Data Skimming Service (DSS) is a site-level service for rapid event filtering and selection from locally resident datasets based on metadata queries to associated 'tag' databases. In US ATLAS, we expect most if not all of the AOD-based datasets to be replicated to each of the five Tier 2 regional facilities in the US Tier 1 'cloud' coordinated by Brookhaven National Laboratory. Entire datasets will consist of on the order of several terabytes of data, and providing easy, quick access to skimmed subsets of these data will be vital to physics working groups. Typically, physicists will be interested in portions of the complete datasets, selected according to event-level attributes (number of jets, missing Et, etc) and content (specific analysis objects for subsequent processing). In this paper we describe methods used to classify data (metadata tag generation) and to store these results in a local database. Next we discuss a general framework which includes methods for accessing this information, defining skims, specifying event output content, accessing locally available storage through a variety of interfaces (SRM, dCache/dccp, gridftp), accessing remote storage elements as specified, and user job submission tools through local or grid schedulers. The advantages of the DSS are the ability to quickly 'browse' datasets and design skims, for example, pre-adjusting cuts to get to a desired skim level with minimal use of compute resources, and to encode these analysis operations in a database for re-analysis and archival purposes. Additionally the framework has provisions to operate autonomously in the event that external, central resources are not available, and to provide, as a reduced package, a minimal skimming service tailored to the needs of small Tier 3 centres or individual users.

  5. Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.

    Directory of Open Access Journals (Sweden)

    Szabolcs Szelinger

    Full Text Available In females, X chromosome inactivation (XCI is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.

  6. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.

    Directory of Open Access Journals (Sweden)

    Yingying Zhang

    2009-03-01

    Full Text Available Differential DNA methylation is an essential epigenetic signal for gene regulation, development, and disease processes. We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types. A total of 28,626 subclones were sequenced at high accuracy using (long-read Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG sites. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, both for amplicons and individual subclones, which represent single alleles from individual cells. Within CpG-rich sequences, DNA methylation was found to be anti-correlated with CpG dinucleotide density and GC content, and methylated CpGs are more likely to be flanked by AT-rich sequences. We observed over-representation of CpG sites in distances of 9, 18, and 27 bps in highly methylated amplicons. However, DNA sequence alone is not sufficient to predict an amplicon's DNA methylation status, since 43% of all amplicons are differentially methylated between the cell types studied here. DNA methylation in promoter regions is strongly correlated with the absence of gene expression and low levels of activating epigenetic marks like H3K4 methylation and H3K9 and K14 acetylation. Utilizing the single base pair and single allele resolution of our data, we found that i amplicons from different parts of a CpG island frequently differ in their DNA methylation level, ii methylation levels of individual cells in one tissue are very similar, and iii methylation patterns follow a relaxed site-specific distribution. Furthermore, iv we identified three cases of allele-specific DNA methylation on chromosome 21. Our data shed new light on the nature of methylation patterns in human cells, the sequence dependence of DNA methylation, and its function as epigenetic signal in gene

  7. SRY mutation analysis by next generation (deep sequencing in a cohort of chromosomal Disorders of Sex Development (DSD patients with a mosaic karyotype

    Directory of Open Access Journals (Sweden)

    Hersmus Remko

    2012-11-01

    Full Text Available Abstract Background The presence of the Y-chromosome or Y chromosome-derived material is seen in 4-60% of Turner syndrome patients (Chromosomal Disorders of Sex Development (DSD. DSD patients with specific Y-chromosomal material in their karyotype, the GonadoBlastoma on the Y-chromosome (GBY region, have an increased risk of developing type II germ cell tumors/cancer (GCC, most likely related to TSPY. The Sex determining Region on the Y gene (SRY is located on the short arm of the Y-chromosome and is the crucial switch that initiates testis determination and subsequent male development. Mutations in this gene are responsible for sex reversal in approximately 10-15% of 46,XY pure gonadal dysgenesis (46,XY DSD cases. The majority of the mutations described are located in the central HMG domain, which is involved in the binding and bending of the DNA and harbors two nuclear localization signals. SRY mutations have also been found in a small number of patients with a 45,X/46,XY karyotype and might play a role in the maldevelopment of the gonads. Methods To thoroughly investigate the presence of possible SRY gene mutations in mosaic DSD patients, we performed next generation (deep sequencing on the genomic DNA of fourteen independent patients (twelve 45,X/46,XY, one 45,X/46,XX/46,XY, and one 46,XX/46,XY. Results and conclusions The results demonstrate that aberrations in SRY are rare in mosaic DSD patients and therefore do not play a significant role in the etiology of the disease.

  8. ANALYSIS ON GENETIC POLYMORPHISM OF 6 STR LOCI ON CHROMOSOME 12 IN CHINESE HAN POPULATION

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.

  9. Loss of Heterozygosity Analysis on the Long Arm of Chromosome 7 in Gastric Carcinoma

    Institute of Scientific and Technical Information of China (English)

    JinlianLi; ShijuanMai; BingjianFeng; QishengFeng; LixiHuang; XingiuanYu; ZhizhongPan; YouqingZhon; JianchuanXia

    2004-01-01

    OBJECTIVE In order to define the common deleted region related to primary gastric carcinomas in Chinese, the frequency of loss of heterozygosit (LOH) on human chromosome 7q and its clinical significance were investigated. METHODS A set of 9 microsatellite markers on 7q with an average genetic distance of 10cM were used to identify LOH by multi-PCR amplification of matched tumor and non-tumor DNAs from 70 patients with primary gastric carcinoma. The PCR products were separated by electrophoresis in polyacrylamide gels and analysed for LOH by using Genescan and Genotyper software. RESULTS The total frequency of LOH at any locus on 7q was 34.3% (24/70) in the tumors. Compared to non-tumor DNA, LOH at D7S486 and D7S798 loci were higher, 24.0%(12/50) and 19.2%(5/26), respectively. The total frequency of LOH on 7q was markedly higher with an increase in the clinical stage (P<0.05). The frequency of LOH at D7S486 in cases with lymph node metastasis was significanty higher than in cases without lymph node metastasis, P=0.015. CONCLUSION The higher incidence of LOH at D7S486 and D7S798 inprimary gastric carcinoma compared to normal tissue suggests that the potential tumor suppressor genes (TSGs) involved in the progression of gastric carcinoma might be nearby these 2 loci.

  10. Why Chromosome Palindromes?

    Directory of Open Access Journals (Sweden)

    Esther Betrán

    2012-01-01

    Full Text Available We look at sex-limited chromosome (Y or W evolution with particular emphasis on the importance of palindromes. Y chromosome palindromes consist of inverted duplicates that allow for local recombination in an otherwise nonrecombining chromosome. Since palindromes enable intrachromosomal gene conversion that can help eliminate deleterious mutations, they are often highlighted as mechanisms to protect against Y degeneration. However, the adaptive significance of recombination resides in its ability to decouple the evolutionary fates of linked mutations, leading to both a decrease in degeneration rate and an increase in adaptation rate. Our paper emphasizes the latter, that palindromes may exist to accelerate adaptation by increasing the potential targets and fixation rates of incoming beneficial mutations. This hypothesis helps reconcile two enigmatic features of the “palindromes as protectors” view: (1 genes that are not located in palindromes have been retained under purifying selection for tens of millions of years, and (2 under models that only consider deleterious mutations, gene conversion benefits duplicate gene maintenance but not initial fixation. We conclude by looking at ways to test the hypothesis that palindromes enhance the rate of adaptive evolution of Y-linked genes and whether this effect can be extended to palindromes on other chromosomes.

  11. Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1

    Directory of Open Access Journals (Sweden)

    Wang Pu

    2010-10-01

    Full Text Available Abstract The Epstein-Barr Virus (EBV Nuclear Antigen 1 (EBNA1 protein is required for the establishment of EBV latent infection in proliferating B-lymphocytes. EBNA1 is a multifunctional DNA-binding protein that stimulates DNA replication at the viral origin of plasmid replication (OriP, regulates transcription of viral and cellular genes, and tethers the viral episome to the cellular chromosome. EBNA1 also provides a survival function to B-lymphocytes, potentially through its ability to alter cellular gene expression. To better understand these various functions of EBNA1, we performed a genome-wide analysis of the viral and cellular DNA sites associated with EBNA1 protein in a latently infected Burkitt lymphoma B-cell line. Chromatin-immunoprecipitation (ChIP combined with massively parallel deep-sequencing (ChIP-Seq was used to identify cellular sites bound by EBNA1. Sites identified by ChIP-Seq were validated by conventional real-time PCR, and ChIP-Seq provided quantitative, high-resolution detection of the known EBNA1 binding sites on the EBV genome at OriP and Qp. We identified at least one cluster of unusually high-affinity EBNA1 binding sites on chromosome 11, between the divergent FAM55 D and FAM55B genes. A consensus for all cellular EBNA1 binding sites is distinct from those derived from the known viral binding sites, suggesting that some of these sites are indirectly bound by EBNA1. EBNA1 also bound close to the transcriptional start sites of a large number of cellular genes, including HDAC3, CDC7, and MAP3K1, which we show are positively regulated by EBNA1. EBNA1 binding sites were enriched in some repetitive elements, especially LINE 1 retrotransposons, and had weak correlations with histone modifications and ORC binding. We conclude that EBNA1 can interact with a large number of cellular genes and chromosomal loci in latently infected cells, but that these sites are likely to represent a complex ensemble of direct and indirect EBNA

  12. A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables

    DEFF Research Database (Denmark)

    Endesfelder, David; McGranahan, Nicholas; Birkbak, Nicolai Juul;

    2011-01-01

    . In a breast cancer meta-analysis of 2423 patients we examine the relationship between clinicopathological parameters and two distinct chromosomal instability gene expression signatures in order to address whether younger age at diagnosis is associated with increased tumour genome instability. We find that CIN......, assessed by the two independently derived CIN expression signatures, is significantly associated with increased tumour size, ER negative or HER2 positive disease, higher tumour grade and younger age at diagnosis in ER negative breast cancer. These data support the hypothesis that chromosomal instability...

  13. An improved solution of local window parameters setting for local singularity analysis based on Excel VBA batch processing technology

    Science.gov (United States)

    Zhang, Daojun; Cheng, Qiuming; Agterberg, Frits; Chen, Zhijun

    2016-03-01

    In this paper Excel VBA is used for batch calculation in Local Singularity Analysis (LSA), which is for the information extracting from different kinds of geoscience data. Capabilities and advantages of a new module called Batch Tool for Local Singularity Index Mapping (BTLSIM) are: (1) batch production of series of local singularity maps with different settings of local window size, shape and orientation parameters; (2) local parameter optimization based on statistical tests; and (3) provision of extra output layers describing how spatial changes induced by parameter optimization are related to spatial structure of the original input layers.

  14. Biological dosimetry of ionizing radiation by chromosomal aberration analysis; Dosimetria biologica de las radiaciones ionizantes mediante el analisis de aberraciones cromosomicas

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Castano, S.; Silva, A.; Navlet, J.

    1990-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y ={alpha} + {beta}{sub 1}D + {beta}{sub 2}D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs.

  15. Chromosomal localization and molecular marker development of the lipopolysaccharide and beta-1,3-glucan binding protein gene in the Zhikong scallop Chlamys farreri (Jones et Preston (Pectinoida, Pectinidae

    Directory of Open Access Journals (Sweden)

    Pin Huan

    2010-01-01

    Full Text Available Zhikong scallop Chlamys farreri (Jones et Preston is an economically important species in China. Understanding its immune system would be of great help in controlling diseases. In the present study, an important immunity-related gene, the Lipopolysaccharide and Beta-1,3-glucan Binding Protein (LGBP gene, was located on C. farreri chromosomes by mapping several lgbp-containing BAC clones through fluorescence in situ hybridization (FISH. Through the localization of various BAC clones, it was shown that only one locus of this gene existed in the genome of C. farreri, and that this was located on the long arm of a pair of homologous chromosomes. Molecular markers, consisting of eight single nucleotide polymorphism (SNPs markers and one insertion-deletion (indel, were developed from the LGBP gene. Indel marker testing in an F1 family revealed slightly distorted segregation (p = 0.0472. These markers can be used to map the LGBP gene to the linkage map and assign the linkage group to the corresponding chromosome. Segregation distortion of the indel marker indicated genes with deleterious alleles might exist in the surrounding region of the LGBP gene.

  16. Chromosome analysis of 427 cases with primary amenorrhea%原发性闭经427例患者染色体核型分析

    Institute of Scientific and Technical Information of China (English)

    彭琳; 王楠; 邓东锐; 左伟; 程琛; 党静; 郝海燕; 周媛; 蒋敏; 凌霞珍

    2012-01-01

    目的 对原发性闭经患者进行细胞遗传学分析,探讨原发性闭经与染色体异常的关系,用以指导临床诊断及处理.方法 对427例原发性闭经患者进行外周血淋巴细胞培养、染色体制备及核型分析.结果 427例原发性闭经患者中共检出染色体异常核型118例,异常检出率为27.6℅﹙118∕427﹚.性染色体异常中,X染色体数目异常59例、结构异常25例、嵌合体24例,其中有单纯X染色体与常染色体平衡易位1例,合并X的部分缺失2例.常染色体结构异常10例,包括染色体倒位﹙4例﹚、平衡易位﹙4例﹚以及染色体大小异常﹙2例﹚,涉及到第6、7、9、14、15、16、22号常染色体.结论 结合临床表现、影像学检查以及染色体核型检查,可以为原发性闭经患者寻找病因提供理论依据,同时有利于处理措施的制定.%Objective To carry out chromosome analysis of patients with primary amenorrhea and investigate the relationship between primary amenorrhea and chromosome abnormalities, so as to guide clinical diagnosis and treatment. Methods Peripheral blood lymphocyte culture, chromosome preparation and karyotype analysis were done to 427 cases of patients with primary amenorrhea. Results There were 118 cases of abnormal chromosome karyotype with primary amenorrhea, and the anomaly detection rate was 27. 6% ( 118/427 ). In cases with sex chromosome abnormalities, there were 59 patients with numerical abnormalities of X chromosome, 25 patients with X chromosome structural abnormality, and 24 cases of mosaicism. Among them, there was one case of simple reciprocal translocation between X chromosome and autosome, and two cases of consolidation with terminal deletion of X chromosome. There were cases of autosomal structural abnormalities, including chromosomal inversion ( 4 cases ), balanced translocation ( 4 cases ) and abnormal chromosome size ( 2 cases ). Autosomal abnormalities happened on the sixth, seventh, ninth

  17. Enhanced HTS hit selection via a local hit rate analysis.

    Science.gov (United States)

    Posner, Bruce A; Xi, Hualin; Mills, James E J

    2009-10-01

    The postprocessing of high-throughput screening (HTS) results is complicated by the occurrence of false positives (inactive compounds misidentified as active by the primary screen) and false negatives (active compounds misidentified as inactive by the primary screen). An activity cutoff is frequently used to select "active" compounds from HTS data; however, this approach is insensitive to both false positives and false negatives. An alternative method that can minimize the occurrence of these artifacts will increase the efficiency of hit selection and therefore lead discovery. In this work, rather than merely using the activity of a given compound, we look at the presence and absence of activity among all compounds in its "chemical space neighborhood" to give a degree of confidence in its activity. We demonstrate that this local hit rate (LHR) analysis method outperforms hit selection based on ranking by primary screen activity values across ten diverse high throughput screens, spanning both cell-based and biochemical assay formats of varying biology and robustness. On average, the local hit rate analysis method was approximately 2.3-fold and approximately 1.3-fold more effective in identifying active compounds and active chemical series, respectively, than selection based on primary activity alone. Moreover, when applied to finding false negatives, this method was 2.3-fold better than ranking by primary activity alone. In most cases, novel hit series were identified that would have otherwise been missed. Additional uses of and observations regarding this HTS analysis approach are also discussed.

  18. Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people.

    Science.gov (United States)

    Ansari Pour, Naser; Plaster, Christopher A; Bradman, Neil

    2013-04-01

    The expansion of the Bantu-speaking people (EBSP) during the past 3000-5000 years is an event of great importance in the history of humanity. Anthropology, archaeology, linguistics and, in recent decades, genetics have been used to elucidate some of the events and processes involved. Although it is generally accepted that the EBSP has its origin in the so-called Bantu Homeland situated in the area of the border between Nigeria and the Grassfields of Cameroon, and that it followed both western and eastern routes, much less is known about the number and dates of those expansions, if more than one. Mitochondrial, Y-chromosome and autosomal DNA analyses have been carried out in attempts to understand the demographic events that have taken place. There is an increasing evidence that the expansion was a more complex process than originally thought and that neither a single demographic event nor an early split between western and eastern groups occurred. In this study, we analysed unique event polymorphism and short tandem repeat variation in non-recombining Y-chromosome haplogroups contained within the E1b1a haplogroup, which is exclusive to individuals of recent African ancestry, in a large, geographically widely distributed, set of sub-Saharan Africans (groups=43, n=2757), all of whom, except one Nilo-Saharan-speaking group, spoke a Niger-Congo language and most a Bantu tongue. Analysis of diversity and rough estimates of times to the most recent common ancestors of haplogroups provide evidence of multiple expansions along eastern and western routes and a late, exclusively eastern route, expansion.

  19. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions.

    Science.gov (United States)

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

    2016-10-01

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

  20. New Lesions Detected by Single Nucleotide Polymorphism Array–Based Chromosomal Analysis Have Important Clinical Impact in Acute Myeloid Leukemia

    Science.gov (United States)

    Tiu, Ramon V.; Gondek, Lukasz P.; O'Keefe, Christine L.; Huh, Jungwon; Sekeres, Mikkael A.; Elson, Paul; McDevitt, Michael A.; Wang, Xiao Fei; Levis, Mark J.; Karp, Judith E.; Advani, Anjali S.; Maciejewski, Jaroslaw P.

    2009-01-01

    Purpose Cytogenetics is the primary outcome predictor in acute myeloid leukemia (AML). Metaphase cytogenetics (MC) detects an abnormal karyotype in only half of patients with AML, however. Single nucleotide polymorphism arrays (SNP-A) can detect acquired somatic uniparental disomy (UPD) and other cryptic defects, even in samples deemed normal by MC. We hypothesized that SNP-A will improve detection of chromosomal defects in AML and that this would enhance the prognostic value of MC. Patients and Methods We performed 250K and 6.0 SNP-A analyses on 140 patients with primary (p) and secondary (s) AML and correlated the results with clinical outcomes and Flt-3/nucleophosmin (NPM-1) status. Results SNP-A is more sensitive than MC in detecting unbalanced lesions (pAML, 65% v 39%, P = .002; and sAML, 78% v 51%, P = .003). Acquired somatic UPD, not detectable by MC, was common in our AML cohort (29% in pAML and 35% in sAML). Patients with SNP-A lesions including acquired somatic UPD exhibited worse overall survival (OS) and event-free survival (EFS) in pAML with normal MC and in pAML/sAML with abnormal MC. SNP-A improved the predictive value of Flt-3 internal tandem duplication/NPM-1 status, with inferior survival seen in patients with additional SNP-A defects. Multivariate analyses confirmed the independent predictive value of SNP-A defects for OS (hazard ratio [HR] = 2.52; 95% CI, 1.29 to 5.22; P = .006) and EFS (HR = 1.72; 95% CI, 1.12 to 3.48; P = .04). Conclusion SNP-A analysis allows enhanced detection of chromosomal abnormalities and provides important prognostic impact in AML. PMID:19770377

  1. A potential novel spontaneous preterm birth gene, AR, identified by linkage and association analysis of X chromosomal markers.

    Directory of Open Access Journals (Sweden)

    Minna K Karjalainen

    Full Text Available Preterm birth is the major cause of neonatal mortality and morbidity. In many cases, it has severe life-long consequences for the health and neurological development of the newborn child. More than 50% of all preterm births are spontaneous, and currently there is no effective prevention. Several studies suggest that genetic factors play a role in spontaneous preterm birth (SPTB. However, its genetic background is insufficiently characterized. The aim of the present study was to perform a linkage analysis of X chromosomal markers in SPTB in large northern Finnish families with recurrent SPTBs. We found a significant linkage signal (HLOD = 3.72 on chromosome locus Xq13.1 when the studied phenotype was being born preterm. There were no significant linkage signals when the studied phenotype was giving preterm deliveries. Two functional candidate genes, those encoding the androgen receptor (AR and the interleukin-2 receptor gamma subunit (IL2RG, located near this locus were analyzed as candidates for SPTB in subsequent case-control association analyses. Nine single-nucleotide polymorphisms (SNPs within these genes and an AR exon-1 CAG repeat, which was previously demonstrated to be functionally significant, were analyzed in mothers with preterm delivery (n = 272 and their offspring (n = 269, and in mothers with exclusively term deliveries (n = 201 and their offspring (n = 199, all originating from northern Finland. A replication study population consisting of individuals born preterm (n = 111 and term (n = 197 from southern Finland was also analyzed. Long AR CAG repeats (≥ 26 were overrepresented and short repeats (≤ 19 underrepresented in individuals born preterm compared to those born at term. Thus, our linkage and association results emphasize the role of the fetal genome in genetic predisposition to SPTB and implicate AR as a potential novel fetal susceptibility gene for SPTB.

  2. Human Y chromosome microdeletion analysis by PCR multiplex protocols identifying only clinically relevant AZF microdeletions.

    Science.gov (United States)

    Vogt, Peter H; Bender, Ulrike

    2013-01-01

    PCR multiplex assays are the method of choice for quickly revealing genomic microdeletions in the large repetitive genomic sequence blocks on the long arm of the human Y chromosome. They harbor the Azoospermia Factor (AZF) genes, which cause male infertility when functionally disrupted. These protein encoding Y genes are expressed exclusively or predominantly during male germ cell development, i.e., at different phases of human spermatogenesis. They are located in three distinct genomic sequence regions designated AZFa, AZFb, and AZFc, respectively. Complete deletion of an AZF region, also called "classical" AZF microdeletion, is always associated with male infertility and a distinct testicular pathology. Partial AZF deletions including single AZF Y genes can cause the same testicular pathology as the corresponding complete deletion (e.g., DDX3Y gene deletions in AZFa), or might not be associated with male infertility at all (e.g., some BPY2, CDY1, DAZ gene deletions in AZFc). We therefore propose that a PCR multiplex assay aimed to reduce only those AZF microdeletions causing a specific testicular pathology-thus relevant for clinical applications. It only includes Sequence Tagged Site (STS) deletion markers inside the exon structures of the Y genes known to be expressed in male germ cells and located in the three AZF regions. They were integrated in a robust standard protocol for four PCR multiplex mixtures which also include the basic principles of quality control according to the strict guidelines of the European Molecular Genetics Quality Network (EMQN: http://www.emqn.org). In case all Y genes of one AZF region are deleted the molecular extension of this AZF microdeletion is diagnosed to be yes or no comparable to that of the "classical" AZF microdeletion by an additional PCR multiplex assay analyzing the putative AZF breakpoint borderlines.

  3. Performance analysis of sensor self-localization algorithms

    DEFF Research Database (Denmark)

    Hansen, Martin Bøgsted; Rasmussen, Jakob Gulddahl

    reservation concerning this approach: The computational problem of solving the complex nonlinear optimization problem seems at first glance to be enormous. We suggest in the present paper to reduce the computational burden by a simple coordinatewise greedy algorithm, which is nothing else than the successful...... iterative conditional modes (ICM) algorithm from spatial statistics and image analysis. The advantages are that it is 1) distributed, 2) simple and 3) easy to implement. A theoretical lower bound on the average mean square error (AMSE) for all localization estimators in multihop sensor networks is presented...

  4. Behavior of meiotic chromosomes in Pinus wallichiana, P. strobus and their hybrid and nrDNA localization in pollen mother cells of the hybrid by using FISH.

    Science.gov (United States)

    Deng, Hui-Sheng; Zhang, Da-Ming; Fu, Cheng-Xin; Hong, De-Yuan

    2008-03-01

    The complete process of meiosis was investigated in Pinus wallichiana, P. strobus and their artificial hybrid (F1) using microsporocytes. It is revealed that there were slightly lower chiasma frequency, lower ring bivalent frequency, lower meiotic index and distinctly higher frequency of aberrance (chromosomal bridges, fragments or micronuclei) in pollen mother cells (PMCs) of the hybrid (F1) than those of the parental species, which showed a certain degree of differentiation between homologous chromosomes of the two parents. However, relatively higher frequency of ring bivalents and higher meiotic index in all the three entities indicate the great stability of genomes of parental species, and the differentiation of genomes between the two parents must have been slight. Total nineteen signal loci of 18S rDNA were observed in nine bivalents of the hybrid (F1), among which one bivalent bears two loci, while the others have only one. It is suggested that distinct differentiation at genetic level existed in homologous chromosomes of the two parental species, whereas only slight differentiation at karyotypic and genomic levels take place between the parent species.

  5. Behavior of Meiotic Chromosomes in Pinus wallichiana, P. strobus and Their Hybrid and nrDNA Localization in Pollen Mother Cells of the Hybrid by Using FISH

    Institute of Scientific and Technical Information of China (English)

    Hui-Sheng Deng; Da-Ming Zhang; Cheng-Xin Fu; De-Yuan Hong

    2008-01-01

    The complete process of meiosis was investigated in Pinus wallichiana, P. strobus and their artificial hybrid (F1) using microsporocytes. It is revealed that there were slightly lower chiasma frequency, lower ring bivalent frequency, lower meiotic Index and distinctly higher frequency of aberrance (chromosomal bridges, fragments or micronuclei) in pollen mother cells (PMCs) of the hybrid (F1) than those of the parental species, which showed a certain degree of differentiation between homologous chromosomes of the two parents. However, relatively higher frequency of ring bivalents and higher meiotic index in all the three entities indicate the great stability of genomes of parental species, and the differentiation of genomes between the two parents must have been slight. Total nineteen signal loci of 18S rDNA were observed in nine bivalents of the hybrid (F1), among which one bivalent bears two loci, while the others have only one. It is suggested that distinct differentiation at genetic level existed in homologous chromosomes of the two parental species, whereas only slight differentiation at karyotypic and genomic levels take place between the parent species.

  6. Retrospective analysis of fetal sex chromosome abnormalities%胎儿性染色体异常的回顾性分析

    Institute of Scientific and Technical Information of China (English)

    欧德明; 董兴盛; 江陵; 陆林苑; 王德刚

    2015-01-01

    Objective To investigate the incidence of fetal sex chromosomal abnormalities, the distribution of various sex chromosome abnormal karyotypes and the outcomes of pregnancy, in order to provide more evidences for genetic counseling. Methods The cytogenetic analysis results of 8 864 pregnant women underwent prenatal diagnosis in Zhongshan Fraternity Hospital Prenatal Diagnosis Centre during 2009~2013 were retrospectively analyzed. The results of fetal sex chromosome abnormalities and pregnancy outcomes were summarized. Results Among the 57 cases(0. 64 %) with sex chromosomal abnormalities, there were 53 cases were chromosome number abnormalities(0. 60 %), 37 cases were simple type, 16 cases were mosaicism, in which 29 cases were Turner syndrome, 4 cases were XYY syndrome, 11 cases were XXX syndrome,9 cases were XXY syndrome, and 4 cases were chromosomal structural abnormalities ( 0. 05 %) . Conclusion Invasive prenatal diagnosis has an important role for determining fetal sex chromosome abnormalities, and serological screening and B-ultrasound has an important value for fetal sex chromosome abnormalities. The pregnancy outcome and ethical issues related guidelines of fetal sex chromosomal abnormalities need to be developed.%目的 探讨胎儿性染色体异常的发生率、常见分布情况及妊娠结局,为遗传咨询提供更多信息. 方法 回顾性分析2009~2013年中山市博爱医院产前诊断中心8 864 例孕妇产前诊断的染色体检验结果,总结性染色体异常发生情况及妊娠结局. 结果 共检出性染色体异常胎儿57例(0. 64 %). 性染色体异常中,染色体数目异常53例(0. 60%),单纯型37例,嵌合型16例,其中Turner综合征29例,XYY综合征4例,XXX综合征11例,XXY综合征9例;性染色体结构异常4例( 0. 05 %). 结论 介入性产前诊断对确定胎儿性染色体异常具有重要作用. 性染色体异常胎儿的妊娠结局及伦理问题需要国家层面制定相关指南.

  7. Chromosome analysis in the Kruger National Park: Mitotic and meiotic studies in the African elephant loxodonta africana

    Directory of Open Access Journals (Sweden)

    C. Wallace

    1978-09-01

    Full Text Available The present report is published because of the paucity of publication on the mitotic chromosomes of the African elephant Loxodonta africana, and because it is the fisrt study in which the meiotic chromosomes of the species are described.

  8. Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome

    Directory of Open Access Journals (Sweden)

    Wen Ying

    2010-07-01

    Full Text Available Abstract Background The chromosome of Streptomyces has been shown to be unstable, frequently undergoing gross chromosomal rearrangements. However, the mechanisms underlying this phenomenon remain unclear, with previous studies focused on two chromosomal ends as targets for rearrangements. Here we investigated chromosomal instability of Streptomyces avermitilis, an important producer of avermectins, and characterized four gross chromosomal rearrangement events, including a major deletion in the central region. The present findings provide a valuable contribution to the mechanistic study of genetic instability in Streptomyces. Results Thirty randomly-selected "bald" mutants derived from the wild-type strain all contained gross chromosomal rearrangements of various types. One of the bald mutants, SA1-8, had the same linear chromosomal structure as the high avermectin-producing mutant 76-9. Chromosomes of both strains displayed at least three independent chromosomal rearrangements, including chromosomal arm replacement to form new 88-kb terminal inverted repeats (TIRs, and two major deletions. One of the deletions eliminated the 36-kb central region of the chromosome, but surprisingly did not affect viability of the cells. The other deletion (74-kb was internal to the right chromosomal arm. The chromosome of another bald mutant, SA1-6, was circularized with deletions at both ends. No obvious homology was found in all fusion sequences. Generational stability analysis showed that the chromosomal structure of SA1-8 and SA1-6 was stable. Conclusions Various chromosomal rearrangements, including chromosomal arm replacement, interstitial deletions and chromosomal circularization, occurred in S. avermitilis by non-homologous recombination. The finding of an inner deletion involving in the central region of S. avermitilis chromosome suggests that the entire Streptomyces chromosome may be the target for rearrangements, which are not limited, as previously

  9. A comparative chromosome analysis of Thai wild boar (Sus scrofa jubatus and relationship to domestic pig (S. s. domestica by conventional staining, G-banding and high-resolution technique

    Directory of Open Access Journals (Sweden)

    Pornnarong Siripiyasing

    2007-01-01

    Full Text Available This research is the first comparative chromosome analysis report of Thai wild boar (Sus scrofa jubatus and its relationship to domestic pig (S. s. domestica by conventional staining, G-banding and high-resolution technique. Blood samples of the Thai wild boar were taken from two males and two females kept in Nakhon Ratchasima Zoo. After standard whole blood lymphocyte culture at 37 oC for 72 hr. in the presence of colchicine, the metaphase spreads were performed on microscopic slides and airdried. Conventional staining, G-banding and high-resolution technique were applied to stain the chromosomes. The results showed that the number of diploid chromosomes of Thai wild boar was 2n (diploid = 38, and the fundamental numbers (NF were 62 in the male and female. The type of autosomes were 12 metacentric, 14 submetacentric, 4 acrocentric and 6 telocentric chromosomes, with X and Y chromosomes being metacentric chromosomes. We found that chromosomes 1, 5, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, X and Y had the same Gbanding and high-resolution technique patterns as those of domestic pig chromosomes. Chromosomes 2, 3, 4, 6, 9 and 15 are similar to those of domestic pig chromosomes. These results show the evolutionary relationship between the Thai wild boar and the domestic pig.

  10. A rapid local singularity analysis algorithm with applications

    Science.gov (United States)

    Chen, Zhijun; Cheng, Qiuming; Agterberg, Frits

    2015-04-01

    The local singularity model developed by Cheng is fast gaining popularity in characterizing mineralization and detecting anomalies of geochemical, geophysical and remote sensing data. However in one of the conventional algorithms involving the moving average values with different scales is time-consuming especially while analyzing a large dataset. Summed area table (SAT), also called as integral image, is a fast algorithm used within the Viola-Jones object detection framework in computer vision area. Historically, the principle of SAT is well-known in the study of multi-dimensional probability distribution functions, namely in computing 2D (or ND) probabilities (area under the probability distribution) from the respective cumulative distribution functions. We introduce SAT and it's variation Rotated Summed Area Table in the isotropic, anisotropic or directional local singularity mapping in this study. Once computed using SAT, any one of the rectangular sum can be computed at any scale or location in constant time. The area for any rectangular region in the image can be computed by using only 4 array accesses in constant time independently of the size of the region; effectively reducing the time complexity from O(n) to O(1). New programs using Python, Julia, matlab and C++ are implemented respectively to satisfy different applications, especially to the big data analysis. Several large geochemical and remote sensing datasets are tested. A wide variety of scale changes (linear spacing or log spacing) for non-iterative or iterative approach are adopted to calculate the singularity index values and compare the results. The results indicate that the local singularity analysis with SAT is more robust and superior to traditional approach in identifying anomalies.

  11. Localization of a new type of X-linked liver glycogenosis to the chromosomal region Xp22 containing the liver {alpha}-subunit of phosphorylase kinase (PHKA2)

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickx, J.; Coucke, P.; Willems, P.J. [Univ. of Antwerp (Belgium)] [and others

    1994-06-01

    The authors describe here a new type of X-linked liver glycogen storage disease. The main symptoms include liver enlargement and growth retardation. The clinical and biochemical abnormalities of this glycogenosis are similar to those of classical X-linked liver glycogenosis due to phosphorylase kinase deficiency (XLG). However, in constrast to patients with XLG, the patients described here have no reduced phosphorylase kinase activity in erythrocytes and leukocytes, and no enzyme deficiency could be found. Linkage analysis of four families with this X-linked type of liver glycogenosis assigned the disease gene to Xp22. Lod scores obtained with the markers DXS987, DXS207, and DXS999 were 3.97, 2.71, and 2.40, respectively, all at 0% recombination. Multipoint linkage analysis localized the disease gene between DXS143 and DXS989 with a maximum lod score of 4.70 at {theta}=0, relative to DXS987. As both the classical XLG gene and the liver {alpha}-subunit of PHK (PHKA2) are also located in Xp22, this variant type of XLG may be allelic to classical XLG, and both diseases may be caused by mutations in PHKA2. Therefore, they propose to classify XLG as XLG type I (the classical type of XLG) and XLG type II (the variant type of XLG). 28 refs., 2 figs., 3 tabs.

  12. Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer.

    Science.gov (United States)

    Liu, Chao; Srihari, Sriganesh; Lal, Samir; Gautier, Benoît; Simpson, Peter T; Khanna, Kum Kum; Ragan, Mark A; Lê Cao, Kim-Anh

    2016-01-01

    The Homologous Recombination (HR) pathway is crucial for the repair of DNA double-strand breaks (DSBs) generated during DNA replication. Defects in HR repair have been linked to the initiation and development of a wide variety of human malignancies, and exploited in chemical, radiological and targeted therapies. In this study, we performed a personalised pathway analysis independently for four large sporadic breast cancer cohorts to investigate the status of HR pathway dysregulation in individual sporadic breast tumours, its association with HR repair deficiency and its impact on tumour characteristics. Specifically, we first manually curated a list of HR genes according to our recent review on this pathway (Liu et al., 2014), and then applied a personalised pathway analysis method named Pathifier (Drier et al., 2013) on the expression levels of the curated genes to obtain an HR score quantifying HR pathway dysregulation in individual tumours. Based on the score, we observed a great diversity in HR dysregulation between and within gene expression-based breast cancer subtypes, and by using two published HR-defect signatures, we found HR pathway dysregulation reflects HR repair deficiency. Furthermore, we identified a novel association between HR pathway dysregulation and chromosomal instability (CIN) in sporadic breast cancer. Although CIN has long been considered as a hallmark of most solid tumours, with recent extensive studies highlighting its importance in tumour evolution and drug resistance, the molecular basis of CIN in sporadic cancers remains poorly understood. Our results imply that HR pathway dysregulation might contribute to CIN in sporadic breast cancer.

  13. High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

    NARCIS (Netherlands)

    Jehee, F.S.; Krepischi-Santos, A.C.; Rocha, K.M.; Cavalcanti, D.P.; Kim, C.A.; Bertola, D.R.; Alonso, L.G.; D'Angelo, C.S.; Mazzeu, J.F.; Froyen, G.; Lugtenberg, D.; Vianna-Morgante, A.M.; Rosenberg, C.; Passos-Bueno, M.R.

    2008-01-01

    We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric

  14. Analysis of complex-type chromosome exchanges in astronauts' lymphocytes after space flight as a biomarker of high-LET exposure

    Science.gov (United States)

    George, Kerry; Wu, Honglu; Willingham, Veronica; Cucinotta, Francis A.

    2002-01-01

    High-LET radiation is more efficient in producing complex-type chromosome exchanges than sparsely ionizing radiation, and this can potentially be used as a biomarker of radiation quality. To investigate if complex chromosome exchanges are induced by the high-LET component of space radiation exposure, damage was assessed in astronauts' blood lymphocytes before and after long duration missions of 3-4 months. The frequency of simple translocations increased significantly for most of the crewmembers studied. However, there were few complex exchanges detected and only one crewmember had a significant increase after flight. It has been suggested that the yield of complex chromosome damage could be underestimated when analyzing metaphase cells collected at one time point after irradiation, and analysis of chemically-induced PCC may be more accurate since problems with complicated cell-cycle delays are avoided. However, in this case the yields of chromosome damage were similar for metaphase and PCC analysis of astronauts' lymphocytes. It appears that the use of complex-type exchanges as biomarker of radiation quality in vivo after low-dose chronic exposure in mixed radiation fields is hampered by statistical uncertainties.

  15. An image analysis method to quantify CFTR subcellular localization.

    Science.gov (United States)

    Pizzo, Lucilla; Fariello, María Inés; Lepanto, Paola; Aguilar, Pablo S; Kierbel, Arlinet

    2014-08-01

    Aberrant protein subcellular localization caused by mutation is a prominent feature of many human diseases. In Cystic Fibrosis (CF), a recessive lethal disorder that results from dysfunction of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), the most common mutation is a deletion of phenylalanine-508 (pF508del). Such mutation produces a misfolded protein that fails to reach the cell surface. To date, over 1900 mutations have been identified in CFTR gene, but only a minority has been analyzed at the protein level. To establish if a particular CFTR variant alters its subcellular distribution, it is necessary to quantitatively determine protein localization in the appropriate cellular context. To date, most quantitative studies on CFTR localization have been based on immunoprecipitation and western blot. In this work, we developed and validated a confocal microscopy-image analysis method to quantitatively examine CFTR at the apical membrane of epithelial cells. Polarized MDCK cells transiently transfected with EGFP-CFTR constructs and stained for an apical marker were used. EGFP-CFTR fluorescence intensity in a region defined by the apical marker was normalized to EGFP-CFTR whole cell fluorescence intensity, rendering "apical CFTR ratio". We obtained an apical CFTR ratio of 0.67 ± 0.05 for wtCFTR and 0.11 ± 0.02 for pF508del. In addition, this image analysis method was able to discriminate intermediate phenotypes: partial rescue of the pF508del by incubation at 27 °C rendered an apical CFTR ratio value of 0.23 ± 0.01. We concluded the method has a good sensitivity and accurately detects milder phenotypes. Improving axial resolution through deconvolution further increased the sensitivity of the system as rendered an apical CFTR ratio of 0.76 ± 0.03 for wild type and 0.05 ± 0.02 for pF508del. The presented procedure is faster and simpler when compared with other available methods and it is therefore suitable as a screening method to identify

  16. Mitotic chromosome condensation in vertebrates

    Energy Technology Data Exchange (ETDEWEB)

    Vagnarelli, Paola, E-mail: P.Vagnarelli@ed.ac.uk

    2012-07-15

    Work from several laboratories over the past 10-15 years has revealed that, within the interphase nucleus, chromosomes are organized into spatially distinct territories [T. Cremer, C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells, Nat. Rev. Genet. 2 (2001) 292-301 and T. Cremer, M. Cremer, S. Dietzel, S. Muller, I. Solovei, S. Fakan, Chromosome territories-a functional nuclear landscape, Curr. Opin. Cell Biol. 18 (2006) 307-316]. The overall compaction level and intranuclear location varies as a function of gene density for both entire chromosomes [J.A. Croft, J.M. Bridger, S. Boyle, P. Perry, P. Teague,W.A. Bickmore, Differences in the localization and morphology of chromosomes in the human nucleus, J. Cell Biol. 145 (1999) 1119-1131] and specific chromosomal regions [N.L. Mahy, P.E. Perry, S. Gilchrist, R.A. Baldock, W.A. Bickmore, Spatial organization of active and inactive genes and noncoding DNA within chromosome territories, J. Cell Biol. 157 (2002) 579-589] (Fig. 1A, A'). In prophase, when cyclin B activity reaches a high threshold, chromosome condensation occurs followed by Nuclear Envelope Breakdown (NEB) [1]. At this point vertebrate chromosomes appear as compact structures harboring an attachment point for the spindle microtubules physically recognizable as a primary constriction where the two sister chromatids are held together. The transition from an unshaped interphase chromosome to the highly structured mitotic chromosome (compare Figs. 1A and B) has fascinated researchers for several decades now; however a definite picture of how this process is achieved and regulated is not yet in our hands and it will require more investigation to comprehend the complete process. From a biochemical point of view a vertebrate mitotic chromosomes is composed of DNA, histone proteins (60%) and non-histone proteins (40%) [6]. I will discuss below what is known to date on the contribution of these two different classes

  17. Genomic insights into hybridization in a localized region of sympatr y between pewee sister species (Contopus sordidulus × C. virens) and their chromosomal patterns of differentiation

    Institute of Scientific and Technical Information of China (English)

    Joseph D Manthey; and Mark B Robbins

    2016-01-01

    Background: The Great Plains of the United States includes a large number of hybrid and contact zones between bird species. The amount of gene lfow between sister species in these zones ranges from very rare hybridization events to widespread and prevalent introgression. Some of these avian systems have been studied extensively, while others have been indeterminate of whether hybridization exists in areas of sympatry. Using genomic-level approaches allows investigation of genomic patterns of hybridization and gene lfow between species—or lack thereof. Methods: We investigated a narrow zone of sympatry in Nebraska, USA between pewee species (Contopus sordidu-lus and C. virens), for which no hybridization has been conifrmed. We used thousands of single nucleotide polymor-phisms to identify potential hybridization and investigate genomic patterns of differentiation between these two species. Results: We found evidence of multiple hybrid individuals in the contact zone. Little genomic variation was ifxed between species, but a large proportion had differentiated allele frequencies between species. There was a positive relationship between genetic differentiation and chromosome size. Conclusions: We provided the ifrst conclusive evidence of hybridization between C. sordidulus and C. virens, in a region where secondary contact likely occurred due to human disturbance and habitat modiifcation. The genomic patterns of differentiation affrm that these species split in the relatively recent past. Finally, the relationship of chro-mosome size and genetic differentiation may have resulted from differential rates of chromosomal recombination in songbirds and genetic differentiation between species largely due to genetic drift (possibly in concert with selection).

  18. New image analysis methods for 3D visualization and assessment of mapping distance for chromosomes in interphase nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Ikizyan, I.; Burde, S.; Leary, J.F. (Univ. of Rochester, NY (United States))

    1993-01-01

    Confocal microscopy (Meridian Instruments, Inc.) images of interphase nuclei with portions or entire chromosomes singley- or doubly-labeled by fluorescence in situ hybridization were analyzed with newly-developed software on an 80486 PC equipped with an autostereoscopic display (Dimension Technologies, Inc.). The computer display is hologram-like with the ability to address points in 3D space using the associated mouse. Software was developed which allowed for reduction of background by a 19 voxel (3x3x3 voxel cube without corner voxels) median filtering algorithm followed by rendering of a 3D surface and skeleton figure of a chromosome. Visualization at multiple viewing angles by animation allows approximate coordinate locations to be obtained with a 3D mouse to guide the process thereby reducing significantly the required calculation times. Two biological applications under development include (1) correct counting of a given chromosome's copy number using centromere/chromosome-specific probes, and (2) visualization of painted chromosomes and subregion-specific probes at different locations on that chromosome for physical mapping. In either application, real-world distances within each confocal plane and between planes are calculable to give physical mapping distances in three dimensions and along the chromosome.

  19. Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19

    Directory of Open Access Journals (Sweden)

    Ferrell Robert E

    2011-01-01

    Full Text Available Abstract Background Abdominal aortic aneurysm (AAA is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM database. Methods Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22 were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies. Results Several SNPs were nominally associated with AAA (p CEBPG, peptidase D (PEPD, and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples. Conclusions Association testing

  20. Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla.

    Science.gov (United States)

    Li, Xiu-Qing; Du, Donglei

    2014-01-01

    C+G content (GC content or G+C content) is known to be correlated with genome/chromosome size in bacteria but the relationship for other kingdoms remains unclear. This study analyzed genome size, chromosome size, and base composition in most of the available sequenced genomes in various kingdoms. Genome size tends to increase during evolution in plants and animals, and the same is likely true for bacteria. The genomic C+G contents were found to vary greatly in microorganisms but were quite similar within each animal or plant subkingdom. In animals and plants, the C+G contents are ranked as follows: monocot plants>mammals>non-mammalian animals>dicot plants. The variation in C+G content between chromosomes within species is greater in animals than in plants. The correlation between average chromosome C+G content and chromosome length was found to be positive in Proteobacteria, Actinobacteria (but not in other analyzed bacterial phyla), Ascomycota fungi, and likely also in some plants; negative in some animals, insignificant in two protist phyla, and likely very weak in Archaea. Clearly, correlations between C+G content and chromosome size can be positive, negative, or not significant depending on the kingdoms/groups or species. Different phyla or species exhibit different patterns of correlation between chromosome-size and C+G content. Most chromosomes within a species have a similar pattern of variation in C+G content but outliers are common. The data presented in this study suggest that the C+G content is under genetic control by both trans- and cis- factors and that the correlation between C+G content and chromosome length can be positive, negative, or not significant in different phyla.

  1. Comprehensive analysis on 486 fetuses with abnormal chromosomal karyotypes%486例异常胎儿染色体核型综合分析

    Institute of Scientific and Technical Information of China (English)

    赵春荣

    2012-01-01

    目的:通过对产前彩超检查出的异常胎儿进行脐血染色体分析,了解胎儿异常与染色体异常的关系.方法:选择2006年1月~2010年1月在临沂市沂水中心医院产前检查的孕妇,行彩超检查出异常胎儿行引产或分娩,引产前或分娩后抽羊水和脐带血行染色体检查,在显微镜下观察染色体的结构和数量.共486例培养成功,记录染色体异常胎儿的发病时间.结果:486例异常胎儿共查出染色体异常65例,39例数目异常,26例结构异常.65例中21-三体占多数,胎儿染色体异常的发生率与孕妇年龄呈正相关.B超显示轻度畸形,染色体检查确认为21-三体.结论:随着孕妇年龄的增长,胎儿异常及胎儿染色体异常发生率逐渐增加.判定胎儿畸形与染色体异常是否有联系时,畸形的数量、类别、严重程度,胎儿能被超声检查出的时间是重要的参考依据.当临床上B超显示轻度畸形应采集脐血检查排除21-三体.%Objective: To understand the relationship between fetal abnormality and chromosomal abnormality by conducting chromosomal analysis of umbilical cord blood in abnormal fetuses found by prenatal ultrasonography. Methods: The pregnant women who received prenatal examination in the hospital from January 2006 to January 2010 were selected, then the abnormal fetuses detected by color ultrasonography underwent induced abortion or delivery, amniotic fluid samples and umbilical cord samples were obtained before induced abortion or after delivery for chromosomal examination, chromosomal structure and number were observed under microscope. A total of 486 cases were cultured successfully, the onset times of fetuses with chromosomal abnormality was recorded. Results; Among 486 abnormal fetuses, 65 fetuses were found with chromosomal abnormality, including 39 fetuses with chromosomal numerical abnormality and 26 fetuses with chromosomal structural abnormality. The fetuses with trisomy 21 were in the

  2. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.

    Science.gov (United States)

    Someswara Rao, Chinta; Viswanadha Raju, S

    2016-03-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship between the H. sapiens and monkey. This similarity will be helpful at theft identification, maternity identification, disease identification, etc.

  3. Compaction bands in porous rocks: localization analysis using breakage mechanics

    Science.gov (United States)

    Das, Arghya; Nguyen, Giang; Einav, Itai

    2010-05-01

    It has been observed in fields and laboratory studies that compaction bands are formed within porous rocks and crushable granular materials (Mollema and Antonellini, 1996; Wong et al., 2001). These localization zones are oriented at high angles to the compressive maximum principal stress direction. Grain crushing and pore collapse are the integral parts of the compaction band formation; the lower porosity and increased tortuosity within such bands tend to reduce their permeability compared to the outer rock mass. Compaction bands may thereafter act as flow barriers, which can hamper the extraction or injection of fluid into the rocks. The study of compaction bands is therefore not only interesting from a geological viewpoint but has great economic importance to the extraction of oil or natural gas in the industry. In this paper, we study the formation of pure compaction bands (i.e. purely perpendicular to the principal stress direction) or shear-enhanced compaction bands (i.e. with angles close to the perpendicular) in high-porosity rocks using both numerical and analytical methods. A model based on the breakage mechanics theory (Einav, 2007a, b) is employed for the present analysis. The main aspect of this theory is that it enables to take into account the effect that changes in grain size distribution has on the constitutive stress-strain behaviour of granular materials at the microscopic level due to grain crushing. This microscopic phenomenon of grain crushing is explicitly linked with a macroscopic internal variable, called Breakage, so that the evolving grain size distribution can be continuously monitored at macro scale during the process of deformation. Through the inclusion of an appropriate parameter the model is also able to capture the effects of pore collapse on the macroscopic response. Its possession of few physically identifiable parameters is another important feature which minimises the effort of their recalibration, since those become less

  4. Sex chromosome diversity in Armenian toad grasshoppers (Orthoptera, Acridoidea, Pamphagidae)

    Science.gov (United States)

    Bugrov, Alexander G.; Jetybayev, Ilyas E.; Karagyan, Gayane H.; Rubtsov, Nicolay B.

    2016-01-01

    Abstract Although previous cytogenetic analysis of Pamphagidae grasshoppers pointed to considerable karyotype uniformity among most of the species in the family, our study of species from Armenia has discovered other, previously unknown karyotypes, differing from the standard for Pamphagidae mainly in having unusual sets of sex chromosomes. Asiotmethis turritus (Fischer von Waldheim, 1833), Paranocaracris rubripes (Fischer von Waldheim, 1846), and Nocaracris cyanipes (Fischer von Waldheim, 1846) were found to have the karyotype 2n♂=16+neo-XY and 2n♀=16+neo-XX, the neo-X chromosome being the result of centromeric fusion of an ancient acrocentric X chromosome and a large acrocentric autosome. The karyotype of Paranothrotes opacus (Brunner von Wattenwyl, 1882) was found to be 2n♂=14+X1X2Y and 2n♀=14+X1X1X2X2., the result of an additional chromosome rearrangement involving translocation of the neo-Y and another large autosome. Furthermore, evolution of the sex chromosomes in these species has involved different variants of heterochromatinization and miniaturization of the neo-Y. The karyotype of Eremopeza festiva (Saussure, 1884), in turn, appeared to have the standard sex determination system described earlier for Pamphagidae grasshoppers, 2n♂=18+X0 and 2n♀=18+XX, but all the chromosomes of this species were found to have small second C-positive arms. Using fluorescent in situ hybridization (FISH) with 18S rDNA and telomeric (TTAGG)n DNA repeats to yield new data on the structural organization of chromosomes in the species studied, we found that for most of them, clusters of repeats homologous to 18S rDNA localize on two, three or four pairs of autosomes and on the X. In Eremopeza festiva, however, FISH with labelled 18S rDNA painted C-positive regions of all autosomes and the X chromosome; clusters of telomeric repeats localized primarily on the ends of the chromosome arms. Overall, we conclude that the different stages of neo-Y degradation revealed in

  5. Rapid Online Analysis of Local Feature Detectors and Their Complementarity

    Directory of Open Access Journals (Sweden)

    Shoaib Ehsan

    2013-08-01

    Full Text Available A vision system that can assess its own performance and take appropriate actions online to maximize its effectiveness would be a step towards achieving the long-cherished goal of imitating humans. This paper proposes a method for performing an online performance analysis of local feature detectors, the primary stage of many practical vision systems. It advocates the spatial distribution of local image features as a good performance indicator and presents a metric that can be calculated rapidly, concurs with human visual assessments and is complementary to existing offline measures such as repeatability. The metric is shown to provide a measure of complementarity for combinations of detectors, correctly reflecting the underlying principles of individual detectors. Qualitative results on well-established datasets for several state-of-the-art detectors are presented based on the proposed measure. Using a hypothesis testing approach and a newly-acquired, larger image database, statistically-significant performance differences are identified. Different detector pairs and triplets are examined quantitatively and the results provide a useful guideline for combining detectors in applications that require a reasonable spatial distribution of image features. A principled framework for combining feature detectors in these applications is also presented. Timing results reveal the potential of the metric for online applications.

  6. Locality-Driven Parallel Static Analysis</